From sl0003 at yahoo.com Mon Jan 4 05:25:29 2010 From: sl0003 at yahoo.com (sl0003 at yahoo.com) Date: Mon, 04 Jan 2010 02:25:29 -0800 (PST) Subject: [Mristudio-users] DTI-Studio and tensor filtering... (Action Required) Message-ID: <195368.68651.qm@web45101.mail.sp1.yahoo.com> Hello susumu mori, This message serves as notification that you will not receive any more courtesy notices from our members for two days. Messages you have sent will remain in a lower priority queue for our member to review at their leisure. Future messages will be more likely to be viewed if you are on our member's priority Guest List. Thank you, sl0003 at yahoo.com About Boxbe This courtesy notice is part of a free service to make email more reliable and useful. Boxbe (http://www.boxbe.com) uses your existing social network and that of your friends to keep your inbox clean and make sure you receive email from people who matter to you. 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Follow instructions in above notice Status: 4.7.0 -------------- next part -------------- >From susumu mori Wed Dec 23 15:56:23 2009 X-Apparently-To: sl0003 at yahoo.com via 68.180.197.85; Wed, 23 Dec 2009 08:33:53 -0800 Return-Path: X-YMailISG: k2dzDKMWLDtuvt4eZglyXPDdSBClli0ZCI.st7LJyaHIegm5vZJf8B4AjrO_Xm_s8WhyUrEcVCSNZXPDL.ltMDnO6aVu7wZRM25yrUeNz4JoGx8pDghGqgnMsPXlZ5_pdH1ugUZGigs9LqEvZ5TvmZNqTDorjheArmS1hu5Plrw5wNHUGcKH5UouRM1VAGeSTrjgFaAaoqfilajzBUmWeObE5JeIc2uPFB2Kw_Hkgusf4hOrM0Z2ALjzZMlpSBg.xHqglxhbx6pOijL7UYR0hLHgSQuaT.Qu8C0689mFEDOXkKyg9UkAqA.Csm0Xo25SjksDxi7TGe7f0DjlP5VcmZirc3rpW6cEu8.cIxWu9KCnTXZTlPgtAp_X5hKmMsMI20axbJwnykIROFg1AKVND1wRZr.yk05GsUkZ8C4k3MaLDOKztpaqUerjVDyVeZKyWWexuK.N X-Originating-IP: [162.129.8.141] Authentication-Results: mta1067.mail.sk1.yahoo.com from=mristudio.org; domainkeys=neutral (no sig); from=mristudio.org; dkim=neutral (no sig) Received: from 127.0.0.1 (EHLO ipex1.johnshopkins.edu) (162.129.8.141) by mta1067.mail.sk1.yahoo.com with SMTP; Wed, 23 Dec 2009 08:33:52 -0800 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AscCAJPUMUuA3OjrjGdsb2JhbACTc4cePwEBAQocrxyFWIgohDMEhWmEfw X-IronPort-AV: E=Sophos;i="4.47,442,1257138000"; d="scan'208";a="280904715" Received: from smtp.mristudio.org (HELO io16.mristudio.org) ([128.220.232.235]) by ipex1.johnshopkins.edu with ESMTP/TLS/DHE-RSA-AES256-SHA; 23 Dec 2009 11:33:50 -0500 Received: from io16.mristudio.org (io16.mristudio.org [127.0.0.1]) by io16.mristudio.org (8.13.8/8.13.8) with ESMTP id nBNFuP6x010449; Wed, 23 Dec 2009 10:56:30 -0500 Received: from jhuin3.jhu.edu (jhuin3.jhu.edu [10.181.31.167]) by io16.mristudio.org (8.13.8/8.13.8) with ESMTP id nBNFuONY010432 for ; Wed, 23 Dec 2009 10:56:24 -0500 Received: from ipex4.johnshopkins.edu (ipex4.johnshopkins.edu [10.181.31.141]) by jhuin3.jhu.edu (Sun Java System Messaging Server 6.1 HotFix 0.02 (built Aug 25 2004)) with ESMTPS id <0KV40021A49Z8D30 at jhuin3.jhu.edu> for mristudio-users at mristudio.org; Wed, 23 Dec 2009 10:56:24 -0500 (EST) Received: from mail-gx0-f222.google.com ([209.85.217.222]) by ipex4.johnshopkins.edu with ESMTP; Wed, 23 Dec 2009 10:56:23 -0500 Received: by gxk22 with SMTP id 22so6919433gxk.18 for ; Wed, 23 Dec 2009 07:56:23 -0800 (PST) Received: by 10.101.129.8 with SMTP id g8mr16460923ann.37.1261583783301; Wed, 23 Dec 2009 07:56:23 -0800 (PST) Date: Wed, 23 Dec 2009 10:56:23 -0500 From: susumu mori In-reply-to: <4B323755.6020906 at puc.cl> To: grojas at computer.org, "DTI Studio, ROI Editor, Landmarker Questions/Support" Message-id: MIME-version: 1.0 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: Ap4BAOfLMUvRVdnekGdsb2JhbACPaoQIhx4/AQEBAQkJDAcTA65eMYU6IYgiAQIDBYQuBIVphUg X-IronPort-AV: E=Sophos;i="4.47,442,1257138000"; d="scan'208";a="314514406" X-Google-Sender-Auth: 3cf0f602e5899706 References: <4B323755.6020906 at puc.cl> Subject: Re: [Mristudio-users] DTI-Studio and tensor filtering... X-BeenThere: mristudio-users at mristudio.org X-Mailman-Version: 2.1.9 Precedence: list Reply-To: "DTI Studio, ROI Editor, Landmarker Questions/Support" List-Id: "DTI Studio, ROI Editor, Landmarker Questions/Support" List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Content-Type: multipart/mixed; boundary="===============6116950329658781138==" Sender: mristudio-users-bounces at mristudio.org Errors-To: mristudio-users-bounces at mristudio.org Content-Length: 2962 From jmcentee at jhmi.edu Wed Jan 6 15:40:48 2010 From: jmcentee at jhmi.edu (Julie McEntee) Date: Wed, 06 Jan 2010 15:40:48 -0500 Subject: [Mristudio-users] adjust gradients during initial AIR? Message-ID: Hi- There is an option at the bottom of the AIR window (in DTI-Studio) to ?Adjust the gradients for the diffusion-weighted images.? When do/should you choose to do this? Also, when do tensor calculations, no longer outputs mean of B0?s (image.b0) and mean of DWI?s (image.iso). Am I missing something? Thanks for your help, Julie Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100106/1e979123/attachment-0001.html From susumu at mri.jhu.edu Wed Jan 6 16:24:13 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 06 Jan 2010 16:24:13 -0500 Subject: [Mristudio-users] adjust gradients during initial AIR? In-Reply-To: References: Message-ID: Hi Julie, Strictly speaking, if you do coregistration and the registration includes rotation, you get more accurate results by rewriting the gradient table based on the rotation angle. If you click this button, it does this small correction. If your study is successful, you usually expect less than 1 degree of rotation in average, while the test-retest reproducibility of typical 5-10 min DTI should be somewhere around 2-5 degree of fiber angle uncertainty. If the subject moves like 5 degree, I would worry about the overall quality of the image rather than check this box and become happy. So, I have a mixed feeling about this button, but yes, it makes your paper more bulletproof. We are working on reporting system, which warns you if there is excessive subject motion or image degradation, but it is still work in progress. The mean of b0 and DWIs (there is a dedicated button for that) should be available independent of tensor calculation. susumu On Wed, Jan 6, 2010 at 3:40 PM, Julie McEntee wrote: > Hi- > > There is an option at the bottom of the AIR window (in DTI-Studio) to > ?Adjust the gradients for the diffusion-weighted images.? When do/should you > choose to do this? > > Also, when do tensor calculations, no longer outputs mean of B0?s > (image.b0) and mean of DWI?s (image.iso). Am I missing something? > > Thanks for your help, > > Julie > > Julie E. McEntee, MA, CCRP > Senior Research Program Coordinator > Department of Psychiatry- Neuroimaging > Johns Hopkins University School of Medicine > 600 N. Wolfe St./Phipps 300 > Baltimore, MD 21287 > Phone: 410-502-0468 > Fax: 410-614-3676 > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100106/46d1ad8f/attachment.html From luca.pamparana at gmail.com Wed Jan 6 23:31:48 2010 From: luca.pamparana at gmail.com (Luca Pamparana) Date: Thu, 07 Jan 2010 04:31:48 +0000 Subject: [Mristudio-users] all positive eigenvectors! In-Reply-To: <4B30F151.80101@sri.utoronto.ca> References: <4B2A73E3.2030603@sri.utoronto.ca> <4B30F151.80101@sri.utoronto.ca> Message-ID: <94ca0b991001062031q72f9e986q5b1f237a754404f8@mail.gmail.com> This could be because of how ANALYZE mgiht be interpreting these values. Could be an issue with coordinate handedness where it is flipping two of the axes. Cheers, Luca On Tue, Dec 22, 2009 at 4:18 PM, Mojdeh wrote: > Thanks Susumu! I looked at the eigenvector file in the DTIstudio and it > indeed has both + and - numbers! The problem is that when I save the > file in the "Analyze" ?format and open it ?in MATLAB ?all the values are > between 0-1! I was thinking this is because the real x-y-z coordinate > values are converted into RGB values, is this right? how can I access > the actual coordinate values in MATLAB? > > Thanks a lot, > Mojdeh > > Mojdeh wrote: >> Hi there, >> >> I have 49 slice DTI image of brain with 2 B0 + ?23 gradient >> directions. I loaded the image and calculated the tensor, >> eigenvectors, ... for the image and then save the results in analyze >> format. However, when I load the eigenvectors into MATLAB and look at >> the x-y-z coordinates of eigenvectors they are all positive numbers >> which doesn't make any sense to me! Does anyone know what might be the >> problem? >> >> Thanks a lot in advance, >> Mojdeh >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From saksena.sona at gmail.com Thu Jan 7 14:48:24 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Thu, 07 Jan 2010 14:48:24 -0500 Subject: [Mristudio-users] fiber tracking Message-ID: <9018fecc1001071148y68116cd1nb9998f0c0d8d13ef@mail.gmail.com> Hello, Please can you tell me steps of performing fiber tracking in brain tumor patients using DTI studio. The DTI data is on 3T GE scanner with gradients applied in 26 directions. How to generate the reconstructed fibres? thanks regards Sona Saksena -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100107/0f1761e9/attachment.html From susumu at mri.jhu.edu Thu Jan 7 15:32:59 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 07 Jan 2010 15:32:59 -0500 Subject: [Mristudio-users] fiber tracking In-Reply-To: <9018fecc1001071148y68116cd1nb9998f0c0d8d13ef@mail.gmail.com> References: <9018fecc1001071148y68116cd1nb9998f0c0d8d13ef@mail.gmail.com> Message-ID: Hi Sona, I suggest you to go through the manual section in www.mristudio.org. There you can find a user's manual for DtiStudio. It gives you the step-by-step procedure for tensor calculation and fiber tracking. On Thu, Jan 7, 2010 at 2:48 PM, Sona Saksena wrote: > Hello, > > Please can you tell me steps of performing fiber tracking in brain tumor > patients using DTI studio. The DTI data is on 3T GE scanner with gradients > applied in 26 directions. How to generate the reconstructed fibres? > > thanks > > regards > > Sona Saksena > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100107/07eaa8a2/attachment.html From saksena.sona at gmail.com Fri Jan 8 10:34:50 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Fri, 08 Jan 2010 10:34:50 -0500 Subject: [Mristudio-users] fiber tracking In-Reply-To: References: <9018fecc1001071148y68116cd1nb9998f0c0d8d13ef@mail.gmail.com> Message-ID: <9018fecc1001080734oaf156c6xe075f3c21019a4a8@mail.gmail.com> Hi, Thanks for your suggestion. There is a option in the fiber tracking parameters "Flip Eigen Vector". Do I have to use this check box? Actually we have applied gradients in 26 directions (GE Scanner, 3Tesla). I am not sure about the sign of all of the components in the gradient table. What shall I do? This is the gradient table. 0: 0.000000, 0.000000, 0.000000 1: 1.000000, 0.000000, 0.000000 2: 0.849000, 0.528000, 0.000000 3: -0.108000, 0.565000, 0.818000 4: 0.884000, -0.345000, -0.315000 5: -0.003000, -0.736000, 0.677000 6: -0.868000, -0.238000, 0.436000 7: 0.799000, 0.370000, 0.475000 8: -0.162000, 0.987000, 0.000000 9: 0.866000, -0.129000, 0.483000 10: -0.212000, -0.936000, 0.281000 11: 0.068000, -0.892000, -0.446000 12: 0.550000, -0.544000, -0.634000 13: -0.435000, -0.422000, 0.795000 14: -0.599000, 0.780000, 0.182000 15: -0.525000, 0.030000, -0.851000 16: -0.600000, -0.688000, 0.409000 17: 0.653000, -0.060000, -0.755000 18: 0.207000, -0.076000, -0.975000 19: -0.413000, -0.699000, -0.584000 20: -0.436000, 0.822000, -0.366000 21: 0.462000, 0.874000, 0.148000 22: -0.503000, 0.488000, -0.713000 23: 0.824000, -0.530000, 0.202000 24: 0.297000, 0.349000, 0.889000 25: -0.040000, 0.318000, -0.947000 Please do suggest? regards sona On Thu, Jan 7, 2010 at 3:32 PM, susumu mori wrote: > Hi Sona, > > I suggest you to go through the manual section in www.mristudio.org. There > you can find a user's manual for DtiStudio. It gives you the step-by-step > procedure for tensor calculation and fiber tracking. > > On Thu, Jan 7, 2010 at 2:48 PM, Sona Saksena wrote: > >> Hello, >> >> Please can you tell me steps of performing fiber tracking in brain tumor >> patients using DTI studio. The DTI data is on 3T GE scanner with gradients >> applied in 26 directions. How to generate the reconstructed fibres? >> >> thanks >> >> regards >> >> Sona Saksena >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -- Sona Saksena Ph. D Scholar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100108/fca7c40c/attachment-0001.html From susumu at mri.jhu.edu Fri Jan 8 12:53:42 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 08 Jan 2010 12:53:42 -0500 Subject: [Mristudio-users] fiber tracking In-Reply-To: <9018fecc1001080734oaf156c6xe075f3c21019a4a8@mail.gmail.com> References: <9018fecc1001071148y68116cd1nb9998f0c0d8d13ef@mail.gmail.com> <9018fecc1001080734oaf156c6xe075f3c21019a4a8@mail.gmail.com> Message-ID: Hi Sona, There is detailed description about the "flip" function in the manual. the truth is, nobody is sure about the sign because scanners can change it dynamically depending on your scan protocol. There is a way to rigorously solve this problem, but it is very difficult and that's why we just empirically solve it by checking all 4 options (no check, x, y, z flipped). Good news is, if the signs are wrong, tracking doesn't make sense. On Fri, Jan 8, 2010 at 10:34 AM, Sona Saksena wrote: > Hi, > > Thanks for your suggestion. There is a option in the fiber tracking > parameters "Flip Eigen Vector". Do I have to use this check box? > > Actually we have applied gradients in 26 directions (GE Scanner, 3Tesla). I > am not sure about the sign of all of the components in the gradient > table. What shall I do? > > This is the gradient table. > > > 0: 0.000000, 0.000000, 0.000000 > > 1: 1.000000, 0.000000, 0.000000 > > 2: 0.849000, 0.528000, 0.000000 > > 3: -0.108000, 0.565000, 0.818000 > > 4: 0.884000, -0.345000, -0.315000 > > 5: -0.003000, -0.736000, 0.677000 > > 6: -0.868000, -0.238000, 0.436000 > > 7: 0.799000, 0.370000, 0.475000 > > 8: -0.162000, 0.987000, 0.000000 > > 9: 0.866000, -0.129000, 0.483000 > > 10: -0.212000, -0.936000, 0.281000 > > 11: 0.068000, -0.892000, -0.446000 > > 12: 0.550000, -0.544000, -0.634000 > > 13: -0.435000, -0.422000, 0.795000 > > 14: -0.599000, 0.780000, 0.182000 > > 15: -0.525000, 0.030000, -0.851000 > > 16: -0.600000, -0.688000, 0.409000 > > 17: 0.653000, -0.060000, -0.755000 > > 18: 0.207000, -0.076000, -0.975000 > > 19: -0.413000, -0.699000, -0.584000 > > 20: -0.436000, 0.822000, -0.366000 > > 21: 0.462000, 0.874000, 0.148000 > > 22: -0.503000, 0.488000, -0.713000 > > 23: 0.824000, -0.530000, 0.202000 > > 24: 0.297000, 0.349000, 0.889000 > > 25: -0.040000, 0.318000, -0.947000 > > > > Please do suggest? > > > > regards > > > > sona > > > > > On Thu, Jan 7, 2010 at 3:32 PM, susumu mori wrote: > >> Hi Sona, >> >> I suggest you to go through the manual section in www.mristudio.org. >> There you can find a user's manual for DtiStudio. It gives you the >> step-by-step procedure for tensor calculation and fiber tracking. >> >> On Thu, Jan 7, 2010 at 2:48 PM, Sona Saksena wrote: >> >>> Hello, >>> >>> Please can you tell me steps of performing fiber tracking in brain tumor >>> patients using DTI studio. The DTI data is on 3T GE scanner with gradients >>> applied in 26 directions. How to generate the reconstructed fibres? >>> >>> thanks >>> >>> regards >>> >>> Sona Saksena >>> >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > > -- > Sona Saksena > Ph. D Scholar > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100108/1bc56a13/attachment.html From rebecca.kozitza at duke.edu Fri Jan 8 15:21:15 2010 From: rebecca.kozitza at duke.edu (Rebecca L Kozitza) Date: Fri, 08 Jan 2010 15:21:15 -0500 Subject: [Mristudio-users] Fornix tractography Message-ID: What is the best method for tracking the fornix (specifically the fimbria) using DTI studio? Thanks, Rebecca -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100108/17afd126/attachment.html From saksena.sona at gmail.com Fri Jan 8 15:47:12 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Fri, 08 Jan 2010 15:47:12 -0500 Subject: [Mristudio-users] fiber tracking In-Reply-To: References: <9018fecc1001071148y68116cd1nb9998f0c0d8d13ef@mail.gmail.com> <9018fecc1001080734oaf156c6xe075f3c21019a4a8@mail.gmail.com> Message-ID: <9018fecc1001081247q671d18byccdb6f0dee6fd29d@mail.gmail.com> Hello, After placing the ROI, the statistics for the mostly recent ROI is shown in the fiber control panel. What is the difference between the statistics after pressing the "Go button" in the "Fiber Statistics" option and the most recent statisitcs in the ROI control panel. What should I take for my final calculations and results. Please do suggest. thanks regards sona On Fri, Jan 8, 2010 at 12:53 PM, susumu mori wrote: > Hi Sona, > > There is detailed description about the "flip" function in the manual. the > truth is, nobody is sure about the sign because scanners can change it > dynamically depending on your scan protocol. > There is a way to rigorously solve this problem, but it is very difficult > and that's why we just empirically solve it by checking all 4 options (no > check, x, y, z flipped). Good news is, if the signs are wrong, tracking > doesn't make sense. > > > On Fri, Jan 8, 2010 at 10:34 AM, Sona Saksena wrote: > >> Hi, >> >> Thanks for your suggestion. There is a option in the fiber tracking >> parameters "Flip Eigen Vector". Do I have to use this check box? >> >> Actually we have applied gradients in 26 directions (GE Scanner, 3Tesla). >> I am not sure about the sign of all of the components in the gradient >> table. What shall I do? >> >> This is the gradient table. >> >> >> 0: 0.000000, 0.000000, 0.000000 >> >> 1: 1.000000, 0.000000, 0.000000 >> >> 2: 0.849000, 0.528000, 0.000000 >> >> 3: -0.108000, 0.565000, 0.818000 >> >> 4: 0.884000, -0.345000, -0.315000 >> >> 5: -0.003000, -0.736000, 0.677000 >> >> 6: -0.868000, -0.238000, 0.436000 >> >> 7: 0.799000, 0.370000, 0.475000 >> >> 8: -0.162000, 0.987000, 0.000000 >> >> 9: 0.866000, -0.129000, 0.483000 >> >> 10: -0.212000, -0.936000, 0.281000 >> >> 11: 0.068000, -0.892000, -0.446000 >> >> 12: 0.550000, -0.544000, -0.634000 >> >> 13: -0.435000, -0.422000, 0.795000 >> >> 14: -0.599000, 0.780000, 0.182000 >> >> 15: -0.525000, 0.030000, -0.851000 >> >> 16: -0.600000, -0.688000, 0.409000 >> >> 17: 0.653000, -0.060000, -0.755000 >> >> 18: 0.207000, -0.076000, -0.975000 >> >> 19: -0.413000, -0.699000, -0.584000 >> >> 20: -0.436000, 0.822000, -0.366000 >> >> 21: 0.462000, 0.874000, 0.148000 >> >> 22: -0.503000, 0.488000, -0.713000 >> >> 23: 0.824000, -0.530000, 0.202000 >> >> 24: 0.297000, 0.349000, 0.889000 >> >> 25: -0.040000, 0.318000, -0.947000 >> >> >> >> Please do suggest? >> >> >> >> regards >> >> >> >> sona >> >> >> >> >> On Thu, Jan 7, 2010 at 3:32 PM, susumu mori wrote: >> >>> Hi Sona, >>> >>> I suggest you to go through the manual section in www.mristudio.org. >>> There you can find a user's manual for DtiStudio. It gives you the >>> step-by-step procedure for tensor calculation and fiber tracking. >>> >>> On Thu, Jan 7, 2010 at 2:48 PM, Sona Saksena wrote: >>> >>>> Hello, >>>> >>>> Please can you tell me steps of performing fiber tracking in brain tumor >>>> patients using DTI studio. The DTI data is on 3T GE scanner with gradients >>>> applied in 26 directions. How to generate the reconstructed fibres? >>>> >>>> thanks >>>> >>>> regards >>>> >>>> Sona Saksena >>>> >>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> >> -- >> Sona Saksena >> Ph. D Scholar >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -- Sona Saksena Ph. D Scholar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100108/b7595950/attachment-0001.html From saksena.sona at gmail.com Mon Jan 11 08:58:51 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Mon, 11 Jan 2010 08:58:51 -0500 Subject: [Mristudio-users] Fwd: fiber tracking In-Reply-To: <9018fecc1001081247q671d18byccdb6f0dee6fd29d@mail.gmail.com> References: <9018fecc1001071148y68116cd1nb9998f0c0d8d13ef@mail.gmail.com> <9018fecc1001080734oaf156c6xe075f3c21019a4a8@mail.gmail.com> <9018fecc1001081247q671d18byccdb6f0dee6fd29d@mail.gmail.com> Message-ID: <9018fecc1001110558y3033535dq379641a016079ec8@mail.gmail.com> ---------- Forwarded message ---------- From: Sona Saksena Date: Fri, Jan 8, 2010 at 3:47 PM Subject: Re: [Mristudio-users] fiber tracking To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < mristudio-users at mristudio.org> Hello, After placing the ROI, the statistics for the mostly recent ROI is shown in the fiber control panel. What is the difference between the statistics after pressing the "Go button" in the "Fiber Statistics" option and the most recent statisitcs in the ROI control panel. What should I take for my final calculations and results. Please do suggest. thanks regards sona On Fri, Jan 8, 2010 at 12:53 PM, susumu mori wrote: > Hi Sona, > > There is detailed description about the "flip" function in the manual. the > truth is, nobody is sure about the sign because scanners can change it > dynamically depending on your scan protocol. > There is a way to rigorously solve this problem, but it is very difficult > and that's why we just empirically solve it by checking all 4 options (no > check, x, y, z flipped). Good news is, if the signs are wrong, tracking > doesn't make sense. > > > On Fri, Jan 8, 2010 at 10:34 AM, Sona Saksena wrote: > >> Hi, >> >> Thanks for your suggestion. There is a option in the fiber tracking >> parameters "Flip Eigen Vector". Do I have to use this check box? >> >> Actually we have applied gradients in 26 directions (GE Scanner, 3Tesla). >> I am not sure about the sign of all of the components in the gradient >> table. What shall I do? >> >> This is the gradient table. >> >> >> 0: 0.000000, 0.000000, 0.000000 >> >> 1: 1.000000, 0.000000, 0.000000 >> >> 2: 0.849000, 0.528000, 0.000000 >> >> 3: -0.108000, 0.565000, 0.818000 >> >> 4: 0.884000, -0.345000, -0.315000 >> >> 5: -0.003000, -0.736000, 0.677000 >> >> 6: -0.868000, -0.238000, 0.436000 >> >> 7: 0.799000, 0.370000, 0.475000 >> >> 8: -0.162000, 0.987000, 0.000000 >> >> 9: 0.866000, -0.129000, 0.483000 >> >> 10: -0.212000, -0.936000, 0.281000 >> >> 11: 0.068000, -0.892000, -0.446000 >> >> 12: 0.550000, -0.544000, -0.634000 >> >> 13: -0.435000, -0.422000, 0.795000 >> >> 14: -0.599000, 0.780000, 0.182000 >> >> 15: -0.525000, 0.030000, -0.851000 >> >> 16: -0.600000, -0.688000, 0.409000 >> >> 17: 0.653000, -0.060000, -0.755000 >> >> 18: 0.207000, -0.076000, -0.975000 >> >> 19: -0.413000, -0.699000, -0.584000 >> >> 20: -0.436000, 0.822000, -0.366000 >> >> 21: 0.462000, 0.874000, 0.148000 >> >> 22: -0.503000, 0.488000, -0.713000 >> >> 23: 0.824000, -0.530000, 0.202000 >> >> 24: 0.297000, 0.349000, 0.889000 >> >> 25: -0.040000, 0.318000, -0.947000 >> >> >> >> Please do suggest? >> >> >> >> regards >> >> >> >> sona >> >> >> >> >> On Thu, Jan 7, 2010 at 3:32 PM, susumu mori wrote: >> >>> Hi Sona, >>> >>> I suggest you to go through the manual section in www.mristudio.org. >>> There you can find a user's manual for DtiStudio. It gives you the >>> step-by-step procedure for tensor calculation and fiber tracking. >>> >>> On Thu, Jan 7, 2010 at 2:48 PM, Sona Saksena wrote: >>> >>>> Hello, >>>> >>>> Please can you tell me steps of performing fiber tracking in brain tumor >>>> patients using DTI studio. The DTI data is on 3T GE scanner with gradients >>>> applied in 26 directions. How to generate the reconstructed fibres? >>>> >>>> thanks >>>> >>>> regards >>>> >>>> Sona Saksena >>>> >>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> >> -- >> Sona Saksena >> Ph. D Scholar >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -- Sona Saksena Ph. D Scholar -- Sona Saksena Ph. D Scholar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100111/34eb3a57/attachment.html From susumu at mri.jhu.edu Mon Jan 11 11:56:07 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 11 Jan 2010 11:56:07 -0500 Subject: [Mristudio-users] fiber tracking In-Reply-To: <9018fecc1001081247q671d18byccdb6f0dee6fd29d@mail.gmail.com> References: <9018fecc1001071148y68116cd1nb9998f0c0d8d13ef@mail.gmail.com> <9018fecc1001080734oaf156c6xe075f3c21019a4a8@mail.gmail.com> <9018fecc1001081247q671d18byccdb6f0dee6fd29d@mail.gmail.com> Message-ID: The statistics in the ROI panel is to measure pixel values inside the ROI. It is just a simple ROI-based quantification. In the fiber panel, you draw ROI to create tract paths. Then the quantification is based on pixel values of the reconstructed fibers. On Fri, Jan 8, 2010 at 3:47 PM, Sona Saksena wrote: > Hello, > > After placing the ROI, the statistics for the mostly recent ROI is shown in > the fiber control panel. What is the difference between the statistics after > pressing the "Go button" in the "Fiber Statistics" option and the most > recent statisitcs in the ROI control panel. What should I take for my final > calculations and results. > > Please do suggest. > > thanks > > regards > > sona > > On Fri, Jan 8, 2010 at 12:53 PM, susumu mori wrote: > >> Hi Sona, >> >> There is detailed description about the "flip" function in the manual. the >> truth is, nobody is sure about the sign because scanners can change it >> dynamically depending on your scan protocol. >> There is a way to rigorously solve this problem, but it is very difficult >> and that's why we just empirically solve it by checking all 4 options (no >> check, x, y, z flipped). Good news is, if the signs are wrong, tracking >> doesn't make sense. >> >> >> On Fri, Jan 8, 2010 at 10:34 AM, Sona Saksena wrote: >> >>> Hi, >>> >>> Thanks for your suggestion. There is a option in the fiber tracking >>> parameters "Flip Eigen Vector". Do I have to use this check box? >>> >>> Actually we have applied gradients in 26 directions (GE Scanner, 3Tesla). >>> I am not sure about the sign of all of the components in the gradient >>> table. What shall I do? >>> >>> This is the gradient table. >>> >>> >>> 0: 0.000000, 0.000000, 0.000000 >>> >>> 1: 1.000000, 0.000000, 0.000000 >>> >>> 2: 0.849000, 0.528000, 0.000000 >>> >>> 3: -0.108000, 0.565000, 0.818000 >>> >>> 4: 0.884000, -0.345000, -0.315000 >>> >>> 5: -0.003000, -0.736000, 0.677000 >>> >>> 6: -0.868000, -0.238000, 0.436000 >>> >>> 7: 0.799000, 0.370000, 0.475000 >>> >>> 8: -0.162000, 0.987000, 0.000000 >>> >>> 9: 0.866000, -0.129000, 0.483000 >>> >>> 10: -0.212000, -0.936000, 0.281000 >>> >>> 11: 0.068000, -0.892000, -0.446000 >>> >>> 12: 0.550000, -0.544000, -0.634000 >>> >>> 13: -0.435000, -0.422000, 0.795000 >>> >>> 14: -0.599000, 0.780000, 0.182000 >>> >>> 15: -0.525000, 0.030000, -0.851000 >>> >>> 16: -0.600000, -0.688000, 0.409000 >>> >>> 17: 0.653000, -0.060000, -0.755000 >>> >>> 18: 0.207000, -0.076000, -0.975000 >>> >>> 19: -0.413000, -0.699000, -0.584000 >>> >>> 20: -0.436000, 0.822000, -0.366000 >>> >>> 21: 0.462000, 0.874000, 0.148000 >>> >>> 22: -0.503000, 0.488000, -0.713000 >>> >>> 23: 0.824000, -0.530000, 0.202000 >>> >>> 24: 0.297000, 0.349000, 0.889000 >>> >>> 25: -0.040000, 0.318000, -0.947000 >>> >>> >>> >>> Please do suggest? >>> >>> >>> >>> regards >>> >>> >>> >>> sona >>> >>> >>> >>> >>> On Thu, Jan 7, 2010 at 3:32 PM, susumu mori wrote: >>> >>>> Hi Sona, >>>> >>>> I suggest you to go through the manual section in www.mristudio.org. >>>> There you can find a user's manual for DtiStudio. It gives you the >>>> step-by-step procedure for tensor calculation and fiber tracking. >>>> >>>> On Thu, Jan 7, 2010 at 2:48 PM, Sona Saksena wrote: >>>> >>>>> Hello, >>>>> >>>>> Please can you tell me steps of performing fiber tracking in brain >>>>> tumor patients using DTI studio. The DTI data is on 3T GE scanner with >>>>> gradients applied in 26 directions. How to generate the reconstructed >>>>> fibres? >>>>> >>>>> thanks >>>>> >>>>> regards >>>>> >>>>> Sona Saksena >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>> >>> >>> -- >>> Sona Saksena >>> Ph. D Scholar >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > > -- > Sona Saksena > Ph. D Scholar > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100111/38425070/attachment-0001.html From hjiang at jhmi.edu Mon Jan 11 12:18:50 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Mon, 11 Jan 2010 12:18:50 -0500 Subject: [Mristudio-users] fiber tracking In-Reply-To: References: <9018fecc1001071148y68116cd1nb9998f0c0d8d13ef@mail.gmail.com> <9018fecc1001080734oaf156c6xe075f3c21019a4a8@mail.gmail.com> <9018fecc1001081247q671d18byccdb6f0dee6fd29d@mail.gmail.com> Message-ID: <145933A2BE9E4F48AE079A201379BF2F1FC4145E29@RAD-EXCH1.win.ad.jhu.edu> as the name suggested: values under "mostly recent ROI" is the results from the ROI you just drew. the values after "Go Button" are of all ROIs (the combination of ROIs you had drawn). ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: Monday, January 11, 2010 11:56 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] fiber tracking The statistics in the ROI panel is to measure pixel values inside the ROI. It is just a simple ROI-based quantification. In the fiber panel, you draw ROI to create tract paths. Then the quantification is based on pixel values of the reconstructed fibers. On Fri, Jan 8, 2010 at 3:47 PM, Sona Saksena > wrote: Hello, After placing the ROI, the statistics for the mostly recent ROI is shown in the fiber control panel. What is the difference between the statistics after pressing the "Go button" in the "Fiber Statistics" option and the most recent statisitcs in the ROI control panel. What should I take for my final calculations and results. Please do suggest. thanks regards sona On Fri, Jan 8, 2010 at 12:53 PM, susumu mori > wrote: Hi Sona, There is detailed description about the "flip" function in the manual. the truth is, nobody is sure about the sign because scanners can change it dynamically depending on your scan protocol. There is a way to rigorously solve this problem, but it is very difficult and that's why we just empirically solve it by checking all 4 options (no check, x, y, z flipped). Good news is, if the signs are wrong, tracking doesn't make sense. On Fri, Jan 8, 2010 at 10:34 AM, Sona Saksena > wrote: Hi, Thanks for your suggestion. There is a option in the fiber tracking parameters "Flip Eigen Vector". Do I have to use this check box? Actually we have applied gradients in 26 directions (GE Scanner, 3Tesla). I am not sure about the sign of all of the components in the gradient table. What shall I do? This is the gradient table. 0: 0.000000, 0.000000, 0.000000 1: 1.000000, 0.000000, 0.000000 2: 0.849000, 0.528000, 0.000000 3: -0.108000, 0.565000, 0.818000 4: 0.884000, -0.345000, -0.315000 5: -0.003000, -0.736000, 0.677000 6: -0.868000, -0.238000, 0.436000 7: 0.799000, 0.370000, 0.475000 8: -0.162000, 0.987000, 0.000000 9: 0.866000, -0.129000, 0.483000 10: -0.212000, -0.936000, 0.281000 11: 0.068000, -0.892000, -0.446000 12: 0.550000, -0.544000, -0.634000 13: -0.435000, -0.422000, 0.795000 14: -0.599000, 0.780000, 0.182000 15: -0.525000, 0.030000, -0.851000 16: -0.600000, -0.688000, 0.409000 17: 0.653000, -0.060000, -0.755000 18: 0.207000, -0.076000, -0.975000 19: -0.413000, -0.699000, -0.584000 20: -0.436000, 0.822000, -0.366000 21: 0.462000, 0.874000, 0.148000 22: -0.503000, 0.488000, -0.713000 23: 0.824000, -0.530000, 0.202000 24: 0.297000, 0.349000, 0.889000 25: -0.040000, 0.318000, -0.947000 Please do suggest? regards sona On Thu, Jan 7, 2010 at 3:32 PM, susumu mori > wrote: Hi Sona, I suggest you to go through the manual section in www.mristudio.org. There you can find a user's manual for DtiStudio. It gives you the step-by-step procedure for tensor calculation and fiber tracking. On Thu, Jan 7, 2010 at 2:48 PM, Sona Saksena > wrote: Hello, Please can you tell me steps of performing fiber tracking in brain tumor patients using DTI studio. The DTI data is on 3T GE scanner with gradients applied in 26 directions. How to generate the reconstructed fibres? thanks regards Sona Saksena _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -- Sona Saksena Ph. D Scholar _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -- Sona Saksena Ph. D Scholar _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Mon Jan 11 21:24:06 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 11 Jan 2010 21:24:06 -0500 Subject: [Mristudio-users] Fornix tractography In-Reply-To: References: Message-ID: Hi Rebecca, The fornix has "Y" shape pathways. The stem part is where the two projections from each hemisphere merges in the ventricle and goes down toward the anterior commissure. The branches veer into lateral regions toward the hippocampus. The stem area is larger (because it is actually two tracts) and easier to reconstruct. With 2.2 - 2.5 mm resolution, sometimes you can't reconstruct the tract in the branching section; it may terminate before it reaches the hippocampus. The best ROIs would be one in the stem section close to the anterior commissure and the other in the lateral hippocampal area. If you get the fiber, you can get the very clean fornix reconstructed. The only problem is that, because these two ROIs are so far away, you may not get any results in a significant portion of the subjects. You need good SNR and resolution to get it reconstructed in almost all subjects. This is because we didn't include fornix in our tractography protocol paper in NeuroImage. It's not 100% reproducible with 2.2-2.5 mm resolution and 5 -10 min scan. You can reconstruct the short stretch of the stem area using CUT operation, which could be a compromise protocol. In this case, one ROI defines the stem close to the anterior commissure and the other right before it branches into two pathways. Susumu On Fri, Jan 8, 2010 at 3:21 PM, Rebecca L Kozitza wrote: > > What is the best method for tracking the fornix (specifically the fimbria) > using DTI studio? > > Thanks, > Rebecca > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100111/711e0590/attachment.html From miguel.burgaleta at uam.es Tue Jan 12 05:56:44 2010 From: miguel.burgaleta at uam.es (Miguel Burgaleta) Date: Tue, 12 Jan 2010 11:56:44 +0100 Subject: [Mristudio-users] Track ACC connexions In-Reply-To: References: Message-ID: <5842CA45-928B-4731-9B75-FC046C417F82@uam.es> Dear all, I would like to use DTIStudio to do tractography of the WM pathways associated to the anterior cingulate cortex. Could you please suggest the best way to do this? Drawing one single medial sagittal ROI for the ACC itself is what I had in mind, but am not sure whether it is correct or not. Any help is highly appreciated. Best, Miguel From saksena.sona at gmail.com Tue Jan 12 11:20:32 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Tue, 12 Jan 2010 11:20:32 -0500 Subject: [Mristudio-users] fiber tracking In-Reply-To: References: <9018fecc1001071148y68116cd1nb9998f0c0d8d13ef@mail.gmail.com> <9018fecc1001080734oaf156c6xe075f3c21019a4a8@mail.gmail.com> <9018fecc1001081247q671d18byccdb6f0dee6fd29d@mail.gmail.com> Message-ID: <9018fecc1001120820t38a424a4hed4b8dcb86984112@mail.gmail.com> Hello, Thanks for the reply. I am facing a problem regarding the reconstruction of fibre tracts. I want to track the CST fibres of a tumor patient, after placing the ROI on the CST at the level of medulla the tracts are generated but they are not exactly the same as shown in publications (reconstructed fibers are not fine and refined). I have taken the following fiber tracking parameters: Start Tracking if FA>0.25 Stop Tracking if FA<0.25 if Tract turning-angle>45 Flip Eigen Vector X, Y, Z components have been checked I am attaching a print screen shot of the image, please suggest some changes. regards sona On Mon, Jan 11, 2010 at 11:56 AM, susumu mori wrote: > The statistics in the ROI panel is to measure pixel values inside the ROI. > It is just a simple ROI-based quantification. > > In the fiber panel, you draw ROI to create tract paths. Then the > quantification is based on pixel values of the reconstructed fibers. > > > On Fri, Jan 8, 2010 at 3:47 PM, Sona Saksena wrote: > >> Hello, >> >> After placing the ROI, the statistics for the mostly recent ROI is shown >> in the fiber control panel. What is the difference between the statistics >> after pressing the "Go button" in the "Fiber Statistics" option and the most >> recent statisitcs in the ROI control panel. What should I take for my final >> calculations and results. >> >> Please do suggest. >> >> thanks >> >> regards >> >> sona >> >> On Fri, Jan 8, 2010 at 12:53 PM, susumu mori wrote: >> >>> Hi Sona, >>> >>> There is detailed description about the "flip" function in the manual. >>> the truth is, nobody is sure about the sign because scanners can change it >>> dynamically depending on your scan protocol. >>> There is a way to rigorously solve this problem, but it is very difficult >>> and that's why we just empirically solve it by checking all 4 options (no >>> check, x, y, z flipped). Good news is, if the signs are wrong, tracking >>> doesn't make sense. >>> >>> >>> On Fri, Jan 8, 2010 at 10:34 AM, Sona Saksena wrote: >>> >>>> Hi, >>>> >>>> Thanks for your suggestion. There is a option in the fiber tracking >>>> parameters "Flip Eigen Vector". Do I have to use this check box? >>>> >>>> Actually we have applied gradients in 26 directions (GE >>>> Scanner, 3Tesla). I am not sure about the sign of all of the components in >>>> the gradient table. What shall I do? >>>> >>>> This is the gradient table. >>>> >>>> >>>> 0: 0.000000, 0.000000, 0.000000 >>>> >>>> 1: 1.000000, 0.000000, 0.000000 >>>> >>>> 2: 0.849000, 0.528000, 0.000000 >>>> >>>> 3: -0.108000, 0.565000, 0.818000 >>>> >>>> 4: 0.884000, -0.345000, -0.315000 >>>> >>>> 5: -0.003000, -0.736000, 0.677000 >>>> >>>> 6: -0.868000, -0.238000, 0.436000 >>>> >>>> 7: 0.799000, 0.370000, 0.475000 >>>> >>>> 8: -0.162000, 0.987000, 0.000000 >>>> >>>> 9: 0.866000, -0.129000, 0.483000 >>>> >>>> 10: -0.212000, -0.936000, 0.281000 >>>> >>>> 11: 0.068000, -0.892000, -0.446000 >>>> >>>> 12: 0.550000, -0.544000, -0.634000 >>>> >>>> 13: -0.435000, -0.422000, 0.795000 >>>> >>>> 14: -0.599000, 0.780000, 0.182000 >>>> >>>> 15: -0.525000, 0.030000, -0.851000 >>>> >>>> 16: -0.600000, -0.688000, 0.409000 >>>> >>>> 17: 0.653000, -0.060000, -0.755000 >>>> >>>> 18: 0.207000, -0.076000, -0.975000 >>>> >>>> 19: -0.413000, -0.699000, -0.584000 >>>> >>>> 20: -0.436000, 0.822000, -0.366000 >>>> >>>> 21: 0.462000, 0.874000, 0.148000 >>>> >>>> 22: -0.503000, 0.488000, -0.713000 >>>> >>>> 23: 0.824000, -0.530000, 0.202000 >>>> >>>> 24: 0.297000, 0.349000, 0.889000 >>>> >>>> 25: -0.040000, 0.318000, -0.947000 >>>> >>>> >>>> >>>> Please do suggest? >>>> >>>> >>>> >>>> regards >>>> >>>> >>>> >>>> sona >>>> >>>> >>>> >>>> >>>> On Thu, Jan 7, 2010 at 3:32 PM, susumu mori wrote: >>>> >>>>> Hi Sona, >>>>> >>>>> I suggest you to go through the manual section in www.mristudio.org. >>>>> There you can find a user's manual for DtiStudio. It gives you the >>>>> step-by-step procedure for tensor calculation and fiber tracking. >>>>> >>>>> On Thu, Jan 7, 2010 at 2:48 PM, Sona Saksena >>>> > wrote: >>>>> >>>>>> Hello, >>>>>> >>>>>> Please can you tell me steps of performing fiber tracking in brain >>>>>> tumor patients using DTI studio. The DTI data is on 3T GE scanner with >>>>>> gradients applied in 26 directions. How to generate the reconstructed >>>>>> fibres? >>>>>> >>>>>> thanks >>>>>> >>>>>> regards >>>>>> >>>>>> Sona Saksena >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Mristudio-users mailing list >>>>>> Mristudio-users at mristudio.org >>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>> Unsubscribe, send a blank email to: >>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>>> >>>> >>>> >>>> -- >>>> Sona Saksena >>>> Ph. D Scholar >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> >> -- >> Sona Saksena >> Ph. D Scholar >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -- Sona Saksena Ph. D Scholar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100112/95903a93/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: CST_RT.TIF Type: image/tiff Size: 543554 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100112/95903a93/attachment-0001.tiff From susumu at mri.jhu.edu Tue Jan 12 13:59:28 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 12 Jan 2010 13:59:28 -0500 Subject: [Mristudio-users] fiber tracking In-Reply-To: <9018fecc1001120820t38a424a4hed4b8dcb86984112@mail.gmail.com> References: <9018fecc1001071148y68116cd1nb9998f0c0d8d13ef@mail.gmail.com> <9018fecc1001080734oaf156c6xe075f3c21019a4a8@mail.gmail.com> <9018fecc1001081247q671d18byccdb6f0dee6fd29d@mail.gmail.com> <9018fecc1001120820t38a424a4hed4b8dcb86984112@mail.gmail.com> Message-ID: It's hard to tell. Usually, it is often difficult to reconstruct the entire CST all the way from the medulla to the motor cortex because it's very long and also penetrate regions with complex fiber structures such as the pons. On Tue, Jan 12, 2010 at 11:20 AM, Sona Saksena wrote: > Hello, > > Thanks for the reply. I am facing a problem regarding the reconstruction of > fibre tracts. I want to track the CST fibres of a tumor patient, after > placing the ROI on the CST at the level of medulla the tracts are generated > but they are not exactly the same as shown in publications (reconstructed > fibers are not fine and refined). > > I have taken the following fiber tracking parameters: > > Start Tracking > if FA>0.25 > > Stop Tracking > if FA<0.25 > if Tract turning-angle>45 > > Flip Eigen Vector > > X, Y, Z components have been checked > > I am attaching a print screen shot of the image, please suggest some > changes. > regards > > sona > On Mon, Jan 11, 2010 at 11:56 AM, susumu mori wrote: > >> The statistics in the ROI panel is to measure pixel values inside the ROI. >> It is just a simple ROI-based quantification. >> >> In the fiber panel, you draw ROI to create tract paths. Then the >> quantification is based on pixel values of the reconstructed fibers. >> >> >> On Fri, Jan 8, 2010 at 3:47 PM, Sona Saksena wrote: >> >>> Hello, >>> >>> After placing the ROI, the statistics for the mostly recent ROI is shown >>> in the fiber control panel. What is the difference between the statistics >>> after pressing the "Go button" in the "Fiber Statistics" option and the most >>> recent statisitcs in the ROI control panel. What should I take for my final >>> calculations and results. >>> >>> Please do suggest. >>> >>> thanks >>> >>> regards >>> >>> sona >>> >>> On Fri, Jan 8, 2010 at 12:53 PM, susumu mori wrote: >>> >>>> Hi Sona, >>>> >>>> There is detailed description about the "flip" function in the manual. >>>> the truth is, nobody is sure about the sign because scanners can change it >>>> dynamically depending on your scan protocol. >>>> There is a way to rigorously solve this problem, but it is very >>>> difficult and that's why we just empirically solve it by checking all 4 >>>> options (no check, x, y, z flipped). Good news is, if the signs are wrong, >>>> tracking doesn't make sense. >>>> >>>> >>>> On Fri, Jan 8, 2010 at 10:34 AM, Sona Saksena wrote: >>>> >>>>> Hi, >>>>> >>>>> Thanks for your suggestion. There is a option in the fiber tracking >>>>> parameters "Flip Eigen Vector". Do I have to use this check box? >>>>> >>>>> Actually we have applied gradients in 26 directions (GE >>>>> Scanner, 3Tesla). I am not sure about the sign of all of the components in >>>>> the gradient table. What shall I do? >>>>> >>>>> This is the gradient table. >>>>> >>>>> >>>>> 0: 0.000000, 0.000000, 0.000000 >>>>> >>>>> 1: 1.000000, 0.000000, 0.000000 >>>>> >>>>> 2: 0.849000, 0.528000, 0.000000 >>>>> >>>>> 3: -0.108000, 0.565000, 0.818000 >>>>> >>>>> 4: 0.884000, -0.345000, -0.315000 >>>>> >>>>> 5: -0.003000, -0.736000, 0.677000 >>>>> >>>>> 6: -0.868000, -0.238000, 0.436000 >>>>> >>>>> 7: 0.799000, 0.370000, 0.475000 >>>>> >>>>> 8: -0.162000, 0.987000, 0.000000 >>>>> >>>>> 9: 0.866000, -0.129000, 0.483000 >>>>> >>>>> 10: -0.212000, -0.936000, 0.281000 >>>>> >>>>> 11: 0.068000, -0.892000, -0.446000 >>>>> >>>>> 12: 0.550000, -0.544000, -0.634000 >>>>> >>>>> 13: -0.435000, -0.422000, 0.795000 >>>>> >>>>> 14: -0.599000, 0.780000, 0.182000 >>>>> >>>>> 15: -0.525000, 0.030000, -0.851000 >>>>> >>>>> 16: -0.600000, -0.688000, 0.409000 >>>>> >>>>> 17: 0.653000, -0.060000, -0.755000 >>>>> >>>>> 18: 0.207000, -0.076000, -0.975000 >>>>> >>>>> 19: -0.413000, -0.699000, -0.584000 >>>>> >>>>> 20: -0.436000, 0.822000, -0.366000 >>>>> >>>>> 21: 0.462000, 0.874000, 0.148000 >>>>> >>>>> 22: -0.503000, 0.488000, -0.713000 >>>>> >>>>> 23: 0.824000, -0.530000, 0.202000 >>>>> >>>>> 24: 0.297000, 0.349000, 0.889000 >>>>> >>>>> 25: -0.040000, 0.318000, -0.947000 >>>>> >>>>> >>>>> >>>>> Please do suggest? >>>>> >>>>> >>>>> >>>>> regards >>>>> >>>>> >>>>> >>>>> sona >>>>> >>>>> >>>>> >>>>> >>>>> On Thu, Jan 7, 2010 at 3:32 PM, susumu mori wrote: >>>>> >>>>>> Hi Sona, >>>>>> >>>>>> I suggest you to go through the manual section in www.mristudio.org. >>>>>> There you can find a user's manual for DtiStudio. It gives you the >>>>>> step-by-step procedure for tensor calculation and fiber tracking. >>>>>> >>>>>> On Thu, Jan 7, 2010 at 2:48 PM, Sona Saksena < >>>>>> saksena.sona at gmail.com> wrote: >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> Please can you tell me steps of performing fiber tracking in brain >>>>>>> tumor patients using DTI studio. The DTI data is on 3T GE scanner with >>>>>>> gradients applied in 26 directions. How to generate the reconstructed >>>>>>> fibres? >>>>>>> >>>>>>> thanks >>>>>>> >>>>>>> regards >>>>>>> >>>>>>> Sona Saksena >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Mristudio-users mailing list >>>>>>> Mristudio-users at mristudio.org >>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>> Unsubscribe, send a blank email to: >>>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Mristudio-users mailing list >>>>>> Mristudio-users at mristudio.org >>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>> Unsubscribe, send a blank email to: >>>>>> Mristudio-users-unsubscribe at mristudio.org >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Sona Saksena >>>>> Ph. D Scholar >>>>> >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>> >>> >>> -- >>> Sona Saksena >>> Ph. D Scholar >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > > -- > Sona Saksena > Ph. D Scholar > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100112/dd76b666/attachment.html From planetta at uic.edu Wed Jan 13 18:55:09 2010 From: planetta at uic.edu (Peggy J. Planetta) Date: Wed, 13 Jan 2010 17:55:09 -0600 Subject: [Mristudio-users] alignlinear. exe error Message-ID: <0d2e06108229333e514c134bceefb8fd.squirrel@webmail.uic.edu> Hi, I am new user of DTI Studio and DiffeoMap, and need help figuring out an error I keep getting. In DiffeoMap I load my template followed by my subject data. Next, I attempt to perform a Linear AIR tranformation, but I get the following error "C:\Diffeomap\alignlinear.exe The parameter is incorrect" followed by "Cannot find air file." Any ideas? Thank you in advance for your assistance, Peggy From xli16 at jhmi.edu Thu Jan 14 09:33:00 2010 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 14 Jan 2010 09:33:00 -0500 Subject: [Mristudio-users] alignlinear. exe error In-Reply-To: <0d2e06108229333e514c134bceefb8fd.squirrel@webmail.uic.edu> References: <0d2e06108229333e514c134bceefb8fd.squirrel@webmail.uic.edu> Message-ID: Hello Peggy, You need several exe files to run AIR transformation. Please check the information at https://www.mristudio.org/wiki/user_manual/landmarker/installation. Xin ----- Original Message ----- From: "Peggy J. Planetta" Date: Wednesday, January 13, 2010 6:55 pm Subject: [Mristudio-users] alignlinear. exe error To: mristudio-users at mristudio.org > Hi, > > I am new user of DTI Studio and DiffeoMap, and need help figuring out > an > error I keep getting. In DiffeoMap I load my template followed by my > subject data. Next, I attempt to perform a Linear AIR tranformation, > but I > get the following error "C:\Diffeomap\alignlinear.exe The parameter > is > incorrect" followed by "Cannot find air file." Any ideas? > > Thank you in advance for your assistance, > Peggy > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From planetta at uic.edu Thu Jan 14 09:39:22 2010 From: planetta at uic.edu (Peggy J. Planetta) Date: Thu, 14 Jan 2010 08:39:22 -0600 Subject: [Mristudio-users] alignlinear. exe error In-Reply-To: References: <0d2e06108229333e514c134bceefb8fd.squirrel@webmail.uic.edu> Message-ID: <02a872b3b127b9ee44dc2f69b3b18927.squirrel@webmail.uic.edu> Hi Xin, I have already done this step (i.e., create the exe files). Any other ideas? Peggy On Thu, January 14, 2010 8:33 am, Xin Li wrote: > Hello Peggy, > > You need several exe files to run AIR transformation. Please check the > information at > https://www.mristudio.org/wiki/user_manual/landmarker/installation. > > > Xin > > > > > ----- Original Message ----- > From: "Peggy J. Planetta" > Date: Wednesday, January 13, 2010 6:55 pm > Subject: [Mristudio-users] alignlinear. exe error > To: mristudio-users at mristudio.org > > >> Hi, >> >> I am new user of DTI Studio and DiffeoMap, and need help figuring out >> an >> error I keep getting. In DiffeoMap I load my template followed by my >> subject data. Next, I attempt to perform a Linear AIR tranformation, >> but I >> get the following error "C:\Diffeomap\alignlinear.exe The parameter >> is >> incorrect" followed by "Cannot find air file." Any ideas? >> >> Thank you in advance for your assistance, >> Peggy >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > ======================== Peggy J. Planetta, Ph.D. Department of Kinesiology and Nutrition University of Illinois at Chicago 1919 West Taylor Street, 650 AHSB (M/C 994) Chicago, IL 60612 P: 312-355-0737 F: 312-413-0319 From xli16 at jhmi.edu Thu Jan 14 09:44:29 2010 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 14 Jan 2010 09:44:29 -0500 Subject: [Mristudio-users] alignlinear. exe error In-Reply-To: <0d2e06108229333e514c134bceefb8fd.squirrel@webmail.uic.edu> References: <0d2e06108229333e514c134bceefb8fd.squirrel@webmail.uic.edu> Message-ID: Hello Peggy, Sorry for my previous reply. After I read your email again, I think you already have alginlinear.exe. It seems that the linear registration failed. You can send me your image data. I will test them in my machine. Xin ----- Original Message ----- From: "Peggy J. Planetta" Date: Wednesday, January 13, 2010 6:55 pm Subject: [Mristudio-users] alignlinear. exe error To: mristudio-users at mristudio.org > Hi, > > I am new user of DTI Studio and DiffeoMap, and need help figuring out > an > error I keep getting. In DiffeoMap I load my template followed by my > subject data. Next, I attempt to perform a Linear AIR tranformation, > but I > get the following error "C:\Diffeomap\alignlinear.exe The parameter > is > incorrect" followed by "Cannot find air file." Any ideas? > > Thank you in advance for your assistance, > Peggy > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Thu Jan 14 09:58:41 2010 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 14 Jan 2010 09:58:41 -0500 Subject: [Mristudio-users] alignlinear. exe error In-Reply-To: <02a872b3b127b9ee44dc2f69b3b18927.squirrel@webmail.uic.edu> References: <0d2e06108229333e514c134bceefb8fd.squirrel@webmail.uic.edu> <02a872b3b127b9ee44dc2f69b3b18927.squirrel@webmail.uic.edu> Message-ID: Hello Peggy, It seems that the registration failed. You may send me your image data. I will test them in my machine. Xin ----- Original Message ----- From: "Peggy J. Planetta" Date: Thursday, January 14, 2010 9:39 am Subject: Re: [Mristudio-users] alignlinear. exe error To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hi Xin, > > I have already done this step (i.e., create the exe files). Any other > ideas? > > Peggy > > > > On Thu, January 14, 2010 8:33 am, Xin Li wrote: > > Hello Peggy, > > > > You need several exe files to run AIR transformation. Please check > the > > information at > > > > > > > > Xin > > > > > > > > > > ----- Original Message ----- > > From: "Peggy J. Planetta" > > Date: Wednesday, January 13, 2010 6:55 pm > > Subject: [Mristudio-users] alignlinear. exe error > > To: mristudio-users at mristudio.org > > > > > >> Hi, > >> > >> I am new user of DTI Studio and DiffeoMap, and need help figuring > out > >> an > >> error I keep getting. In DiffeoMap I load my template followed by > my > >> subject data. Next, I attempt to perform a Linear AIR tranformation, > >> but I > >> get the following error "C:\Diffeomap\alignlinear.exe The parameter > >> is > >> incorrect" followed by "Cannot find air file." Any ideas? > >> > >> Thank you in advance for your assistance, > >> Peggy > >> > >> > >> _______________________________________________ > >> Mristudio-users mailing list > >> Mristudio-users at mristudio.org > >> > >> Unsubscribe, send a blank email to: > >> Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > ======================== > Peggy J. Planetta, Ph.D. > Department of Kinesiology and Nutrition > University of Illinois at Chicago > 1919 West Taylor Street, 650 AHSB (M/C 994) > Chicago, IL 60612 > P: 312-355-0737 > F: 312-413-0319 > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Thu Jan 14 19:25:41 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 14 Jan 2010 19:25:41 -0500 Subject: [Mristudio-users] Track ACC connexions In-Reply-To: <5842CA45-928B-4731-9B75-FC046C417F82@uam.es> References: <5842CA45-928B-4731-9B75-FC046C417F82@uam.es> Message-ID: In general, there are two approaches; 1) You have a region of interest (in your case, the cingular cortex) and you don't have a priori knowledge (or assumption) about which tract is the one you are interested. So, you will use tractography to identify it. In this case, you'd better define the entire ROI (the cingular cortex) and identify the tract of your interest after tractography. Here you need 3D ROI, for which RoiEditor could be easier to use. 2) You use existing knowledge. For example, in your case, the cingulum bundle is the best candidate that is known to be associated with the cingular cortex. Then, your question is now how to reconstruct the cingulum, which can be found in one of our tractography protocol papers (Wakana et al, NeuroImage). Susumu On Tue, Jan 12, 2010 at 5:56 AM, Miguel Burgaleta wrote: > > Dear all, > > I would like to use DTIStudio to do tractography of the WM pathways > associated to the anterior cingulate cortex. Could you please suggest > the best way to do this? Drawing one single medial sagittal ROI for > the ACC itself is what I had in mind, but am not sure whether it is > correct or not. > > Any help is highly appreciated. > > Best, > Miguel > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100114/c26fbfc6/attachment.html From miguel.burgaleta at uam.es Fri Jan 15 08:30:34 2010 From: miguel.burgaleta at uam.es (Miguel Burgaleta) Date: Fri, 15 Jan 2010 14:30:34 +0100 Subject: [Mristudio-users] Track ACC connexions In-Reply-To: References: <5842CA45-928B-4731-9B75-FC046C417F82@uam.es> Message-ID: <8BEADC88-1DFF-46FA-88E1-3760E67B7D20@uam.es> That was very helpful - thanks! Miguel On Jan 15, 2010, at 1:25 AM, susumu mori wrote: > In general, there are two approaches; > > 1) You have a region of interest (in your case, the cingular cortex) > and you don't have a priori knowledge (or assumption) about which > tract is the one you are interested. So, you will use tractography > to identify it. In this case, you'd better define the entire ROI > (the cingular cortex) and identify the tract of your interest after > tractography. Here you need 3D ROI, for which RoiEditor could be > easier to use. > > 2) You use existing knowledge. For example, in your case, the > cingulum bundle is the best candidate that is known to be associated > with the cingular cortex. Then, your question is now how to > reconstruct the cingulum, which can be found in one of our > tractography protocol papers (Wakana et al, NeuroImage). > > Susumu > > On Tue, Jan 12, 2010 at 5:56 AM, Miguel Burgaleta > wrote: > > Dear all, > > I would like to use DTIStudio to do tractography of the WM pathways > associated to the anterior cingulate cortex. Could you please suggest > the best way to do this? Drawing one single medial sagittal ROI for > the ACC itself is what I had in mind, but am not sure whether it is > correct or not. > > Any help is highly appreciated. > > Best, > Miguel > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100115/5ab97fe7/attachment.html From daisondias at terra.com.br Sat Jan 16 13:11:10 2010 From: daisondias at terra.com.br (Dr Daison Nelson Ferreira Dias) Date: Sat, 16 Jan 2010 18:11:10 +0000 Subject: [Mristudio-users] Track ACC connexions Message-ID: <60221.1263665470@terra.com.br> Dear colleagues, I still can not download the DTIStudio. I did my register and I contacted the support but I could not get it. There is a problem with my browser (I use the Internet Explorer 7 in Windows Vista Ultimate). How can I get a copy of the program? Can you send me the program via e-mail? Best, Daison Dr Daison Nelson Ferreira Dias Cremers 32506 Officce Rua Caju, 28, Sala 1006, Petr?polis, Porto Alegre, RS. Cep.: 90690-310 Brasil + 55 51-30192872 || + 55 51-85113345 On Sex 15/01/10 11:30 , Miguel Burgaleta miguel.burgaleta at uam.es sent: That was very helpful - thanks! Miguel On Jan 15, 2010, at 1:25 AM, susumu mori wrote: In general, there are two approaches; 1) You have a region of interest (in your case, the cingular cortex) and you don't have a priori knowledge (or assumption) about which tract is the one you are interested. So, you will use tractography to identify it. In this case, you'd better define the entire ROI (the cingular cortex) and identify the tract of your interest after tractography. Here you need 3D ROI, for which RoiEditor could be easier to use. 2) You use existing knowledge. For example, in your case, the cingulum bundle is the best candidate that is known to be associated with the cingular cortex. Then, your question is now how to reconstruct the cingulum, which can be found in one of our tractography protocol papers (Wakana et al, NeuroImage). Susumu On Tue, Jan 12, 2010 at 5:56 AM, Miguel Burgaleta wrote: Dear all, I would like to use DTIStudio to do tractography of the WM pathways associated to the anterior cingulate cortex. Could you please suggest the best way to do this? Drawing one single medial sagittal ROI for the ACC itself is what I had in mind, but am not sure whether it is correct or not. Any help is highly appreciated. Best, Miguel _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ [1] Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100116/a8ca8827/attachment-0001.html From daisondias at terra.com.br Sat Jan 16 13:13:00 2010 From: daisondias at terra.com.br (Dr Daison Nelson Ferreira Dias) Date: Sat, 16 Jan 2010 18:13:00 +0000 Subject: [Mristudio-users] Track ACC connexions Message-ID: <60250.1263665580@terra.com.br> Dear colleagues, I still can not download the DTIStudio. I did my register and I contacted the support but I could not get it. There is a problem with my browser (I use the Internet Explorer 7 in Windows Vista Ultimate). How can I get a copy of the program? Can you send me the program via e-mail? Best, Daison Dr Daison Nelson Ferreira Dias Cremers 32506 Officce Rua Caju, 28, Sala 1006, Petr?polis, Porto Alegre, RS. Cep.: 90690-310 Brasil + 55 51-30192872 || + 55 51-85113345 On Sex 15/01/10 11:30 , Miguel Burgaleta miguel.burgaleta at uam.es sent: That was very helpful - thanks! Miguel On Jan 15, 2010, at 1:25 AM, susumu mori wrote: In general, there are two approaches; 1) You have a region of interest (in your case, the cingular cortex) and you don't have a priori knowledge (or assumption) about which tract is the one you are interested. So, you will use tractography to identify it. In this case, you'd better define the entire ROI (the cingular cortex) and identify the tract of your interest after tractography. Here you need 3D ROI, for which RoiEditor could be easier to use. 2) You use existing knowledge. For example, in your case, the cingulum bundle is the best candidate that is known to be associated with the cingular cortex. Then, your question is now how to reconstruct the cingulum, which can be found in one of our tractography protocol papers (Wakana et al, NeuroImage). Susumu On Tue, Jan 12, 2010 at 5:56 AM, Miguel Burgaleta wrote: Dear all, I would like to use DTIStudio to do tractography of the WM pathways associated to the anterior cingulate cortex. Could you please suggest the best way to do this? Drawing one single medial sagittal ROI for the ACC itself is what I had in mind, but am not sure whether it is correct or not. Any help is highly appreciated. Best, Miguel _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ [1] Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100116/23f4ff56/attachment.html From hao_y at hsc.pku.edu.cn Sun Jan 17 10:29:08 2010 From: hao_y at hsc.pku.edu.cn (yan hao) Date: Sun, 17 Jan 2010 23:29:08 +0800 Subject: [Mristudio-users] spatial normalization Message-ID: <3EAE6D5F-DB56-4BF2-8846-5F66E416E032@hsc.pku.edu.cn> Hi all, I wonder if I need to do spatial normalization before I do the fiber tracking. I know I can do this in the original space. However some fibers are not easy to define in the original space, so if the images are all in a standard space, I can draw a ROI in a certain slice of the brain. If the spatial normalization is acceptable, could you suggest the way to do the spatial normalization? Any help is highly appreciated. Best, Hao From wmcgarry at gmu.edu Tue Jan 19 02:36:02 2010 From: wmcgarry at gmu.edu (Ryan) Date: Tue, 19 Jan 2010 02:36:02 -0500 Subject: [Mristudio-users] DTI analysis question Message-ID: Hello everyone, I want to confirm that I have the correct order for DTI analysis performed with a Siemens scanner using the Mosaic option, where several sets are collected. After going through the mailing list, I'm still not certain if this order is correct: 1) Load the multiple sets of images 2) Perform auto registration (is this the same as co-registration? if not, how do I do co-registration?) 3) Average the AIRed scans 4) Perform tensor calculations Thank you very much! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100119/f305aca9/attachment.html From xli16 at jhmi.edu Tue Jan 19 09:54:51 2010 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 19 Jan 2010 09:54:51 -0500 Subject: [Mristudio-users] Track ACC connexions In-Reply-To: <60250.1263665580@terra.com.br> References: <60250.1263665580@terra.com.br> Message-ID: Daison, I have uploaded the software to yousendit. You can download it at https://www.yousendit.com/download/VGljT0NaY3lEbUozZUE9PQ Xin ----- Original Message ----- From: Dr Daison Nelson Ferreira Dias Date: Saturday, January 16, 2010 1:13 pm Subject: Re: [Mristudio-users] Track ACC connexions To: mristudio-users at mristudio.org > > > Dear colleagues, > > I still can not download the DTIStudio. I did my register and I > contacted the support but I could not get it. > There is a problem with my browser (I use the Internet Explorer 7 in > Windows Vista Ultimate). > How can I get a copy of the program? Can you send me the program via > e-mail? > Best, > Daison > Dr Daison Nelson Ferreira Dias > Cremers 32506 > Officce > Rua Caju, 28, Sala 1006, Petr?polis, Porto Alegre, RS. Cep.: > 90690-310 > Brasil > + 55 51-30192872 || + 55 51-85113345 > On Sex 15/01/10 11:30 , Miguel Burgaleta miguel.burgaleta at uam.es > sent: > That was very helpful - thanks! > Miguel > On Jan 15, 2010, at 1:25 AM, susumu mori wrote: > In general, there are two approaches; > 1) You have a region of interest (in your case, the cingular cortex) > and you don't have a priori knowledge (or assumption) about which > tract is the one you are interested. So, you will use tractography to > identify it. In this case, you'd better define the entire ROI (the > cingular cortex) and identify the tract of your interest after > tractography. Here you need 3D ROI, for which RoiEditor could be > easier to use. > 2) You use existing knowledge. For example, in your case, the > cingulum bundle is the best candidate that is known to be associated > with the cingular cortex. Then, your question is now how to > reconstruct the cingulum, which can be found in one of our > tractography protocol papers (Wakana et al, NeuroImage). > Susumu > On Tue, Jan 12, 2010 at 5:56 AM, Miguel Burgaleta wrote: > Dear all, > I would like to use DTIStudio to do tractography of the WM pathways > associated to the anterior cingulate cortex. Could you please > suggest > the best way to do this? Drawing one single medial sagittal ROI for > the ACC itself is what I had in mind, but am not sure whether it is > correct or not. > Any help is highly appreciated. > Best, > Miguel > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > [1] > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From saksena.sona at gmail.com Tue Jan 19 10:37:13 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Tue, 19 Jan 2010 10:37:13 -0500 Subject: [Mristudio-users] Track ACC connexions In-Reply-To: References: <60250.1263665580@terra.com.br> Message-ID: <9018fecc1001190737u2749ced9l8c6b8b8b4ac162a@mail.gmail.com> Hello, I would like to use DTIstudio to do fiber tractography of the white matter in brain tumor patients. I have to calculate the FA and ADC values of the reconstructed fibers. Do I have to download other DTIstudio softwares like ROI editor etc for the fiber tractography. Could you please suggest how to do this. Any help is highly appreciated. regards Sona On Tue, Jan 19, 2010 at 9:54 AM, Xin Li wrote: > Daison, > > I have uploaded the software to yousendit. You can download it at > https://www.yousendit.com/download/VGljT0NaY3lEbUozZUE9PQ > > > Xin > > ----- Original Message ----- > From: Dr Daison Nelson Ferreira Dias > Date: Saturday, January 16, 2010 1:13 pm > Subject: Re: [Mristudio-users] Track ACC connexions > To: mristudio-users at mristudio.org > > > > > > > > Dear colleagues, > > > > I still can not download the DTIStudio. I did my register and I > > contacted the support but I could not get it. > > There is a problem with my browser (I use the Internet Explorer 7 in > > Windows Vista Ultimate). > > How can I get a copy of the program? Can you send me the program via > > e-mail? > > Best, > > Daison > > Dr Daison Nelson Ferreira Dias > > Cremers 32506 > > Officce > > Rua Caju, 28, Sala 1006, Petr?polis, Porto Alegre, RS. Cep.: > > 90690-310 > > Brasil > > + 55 51-30192872 || + 55 51-85113345 > > On Sex 15/01/10 11:30 , Miguel Burgaleta miguel.burgaleta at uam.es > > sent: > > That was very helpful - thanks! > > Miguel > > On Jan 15, 2010, at 1:25 AM, susumu mori wrote: > > In general, there are two approaches; > > 1) You have a region of interest (in your case, the cingular cortex) > > and you don't have a priori knowledge (or assumption) about which > > tract is the one you are interested. So, you will use tractography to > > identify it. In this case, you'd better define the entire ROI (the > > cingular cortex) and identify the tract of your interest after > > tractography. Here you need 3D ROI, for which RoiEditor could be > > easier to use. > > 2) You use existing knowledge. For example, in your case, the > > cingulum bundle is the best candidate that is known to be associated > > with the cingular cortex. Then, your question is now how to > > reconstruct the cingulum, which can be found in one of our > > tractography protocol papers (Wakana et al, NeuroImage). > > Susumu > > On Tue, Jan 12, 2010 at 5:56 AM, Miguel Burgaleta wrote: > > Dear all, > > I would like to use DTIStudio to do tractography of the WM pathways > > associated to the anterior cingulate cortex. Could you please > > suggest > > the best way to do this? Drawing one single medial sagittal ROI for > > the ACC itself is what I had in mind, but am not sure whether it is > > correct or not. > > Any help is highly appreciated. > > Best, > > Miguel > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > [1] > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -- Sona Saksena Ph. D Scholar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100119/46749a6f/attachment-0001.html From susumu at mri.jhu.edu Tue Jan 19 20:15:14 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 19 Jan 2010 20:15:14 -0500 Subject: [Mristudio-users] DTI analysis question In-Reply-To: References: Message-ID: The order is correct except for the step #3, which is not necessary. I wonder how you did to average the scan because DtiStudio doesn't offer a function to average scans, I thought. For the tensor fitting with multiple-repetition data, you don't need average the data before the tensor calculation. This is very similar to a simple XY plot linear fitting. Suppose you have 8 measurement points to perform Y=aX+b fitting. If the 8 points are spread along the X axis (say, at X = 1, 3, 5, 7, 9, 11, 13,15), you just perform the fitting. What if the 8 points are at X = 1, 5, 9, 13? This means, at each X value, there are two measurement points. Do you calculate an average value for each X value before the fitting? I think in most case you do the same 8-point fitting in this case too. Likewise, if you have, for example 3 sets of 30-orientation measurements, you don't have to reduce the data to a single 30-orientation before tensor calculation. You can just submit 90-point linear fitting. Hope this is clear. Also for the step #2, Yes, AIR is for co-registration and if you choose Affine, it also does Eddy current correction. On Tue, Jan 19, 2010 at 2:36 AM, Ryan wrote: > Hello everyone, > I want to confirm that I have the correct order for DTI analysis > performed with a Siemens scanner using the Mosaic option, where several sets > are collected. After going through the mailing list, I'm still not certain > if this order is correct: > 1) Load the multiple sets of images > 2) Perform auto registration (is this the same as co-registration? if not, > how do I do co-registration?) > 3) Average the AIRed scans > 4) Perform tensor calculations > > > Thank you very much! > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100119/5e9a362f/attachment.html From lucas_lessa at yahoo.com.br Wed Jan 20 11:47:28 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Wed, 20 Jan 2010 08:47:28 -0800 (PST) Subject: [Mristudio-users] How can I get the angulations? Message-ID: <984438.86012.qm@web110204.mail.gq1.yahoo.com> Hi, I received some exams that I need to process and get the FA in some areas, but the person who gave me the exams didn't give the angulations. Does anyone know how to get this informations inside the DICOM header? The exams were done in a Philips Achieva release 2.1 using 33 directions. Thank you very much. Lucas Lessa. ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100120/24920568/attachment.html From susumu at mri.jhu.edu Wed Jan 20 12:23:42 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 20 Jan 2010 12:23:42 -0500 Subject: [Mristudio-users] How can I get the angulations? In-Reply-To: <984438.86012.qm@web110204.mail.gq1.yahoo.com> References: <984438.86012.qm@web110204.mail.gq1.yahoo.com> Message-ID: Angulation means the angles for oblique plane imaging? If so; > If you are using "non-overplus" gradient table, you don't have to worry about it. > If you are using "overplus" gradient AND DICOM files, you can cut&paste the 33-orientation overplus table in the the "Gradient Table" section and check "Rotate Gradient if Applicable" checkbox. This will automatically read the oblique angle information and recalculate the appropriate gradient table. > If you need the information of the exact place of the angle information in DICOM, Hangyi should know. Susumu On Wed, Jan 20, 2010 at 11:47 AM, Lucas Lessa wrote: > Hi, > > I received some exams that I need to process and get the FA in some areas, > but the person who gave me the exams didn't give the angulations. > Does anyone know how to get this informations inside the DICOM header? > The exams were done in a Philips Achieva release 2.1 using 33 directions. > Thank you very much. > > Lucas Lessa. > > ------------------------------ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10- > Celebridades- > M?sica- > Esportes > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100120/4c78626d/attachment.html From susumu at mri.jhu.edu Wed Jan 20 14:49:36 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 20 Jan 2010 14:49:36 -0500 Subject: [Mristudio-users] spatial normalization In-Reply-To: <3EAE6D5F-DB56-4BF2-8846-5F66E416E032@hsc.pku.edu.cn> References: <3EAE6D5F-DB56-4BF2-8846-5F66E416E032@hsc.pku.edu.cn> Message-ID: This is a good question. > You can perform fiber tracking in the native MRI space. Here "native" means the MRI data as they were acquired. > You can also perform fiber tracking after you standardized the MRI data in the standard coordinate. >> The standardization is either by linear or non-linear transformation. For the linear, you can use rigid (just relocate the brain to a standard position and orientation without changing the shape) or affine (you can adjust the brain size and shape too). >> To perform fiber tracking after the standardization, you have to standardize the tensor file, not FA or vector file. You'd better standardize the tensor file, then create new FA and vector maps from the standardized tensor because standardization of a vector field is difficult. >> After standardization, you can expect ROI drawing could be more reproducible. For example, if you want to identify the anterior limb of internal capsule for fiber tracking, you can create a protocol like, "draw ROI on the internal capsule at coronal slice #50". This kind of protocol is not applicable if we use the native space. >> Also, standardization often involves interpolation to finer resolution (say 2.5 mm native resolution to 1 mm standard coordinates). This has some impact on fiber tracking. I believe the fiber-angle threshold (this prevents sharp turning angle) is effectively reduced. So, you may obtain longer uninterrupted streamlines. Cosmetically, the tracking results may look better with finer resolution. >> Drawback is, because of the extra standardization step that involves interpolation, blurring, tensor re-orientation, and other issues, you may invite some questions and criticisms. In my personal opinion, it is not an issue of one is better than the other. You need to decide the way you do the study and stick to it. I personally support the standardized approach. Susumu 2010/1/17 yan hao > Hi all, > I wonder if I need to do spatial normalization before I do the fiber > tracking. I know I can do this in the original space. However some fibers > are not easy to define in the original space, so if the images are all in a > standard space, I can draw a ROI in a certain slice of the brain.If the > spatial normalization is acceptable, could you suggest the way to do the > spatial normalization?Any help is highly appreciated. > Best,Hao_______________________________________________Mristudio-users > mailing listMristudio-users at mristudio.orghttp:// > lists.mristudio.org/mailman/listinfo/Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100120/86df7d68/attachment.html From vpna at yahoo.com Wed Jan 20 20:18:14 2010 From: vpna at yahoo.com (Vo Phuoc Nhu An) Date: Wed, 20 Jan 2010 17:18:14 -0800 (PST) Subject: [Mristudio-users] How can I get the angulations? In-Reply-To: Message-ID: <968284.63134.qm@web51102.mail.re2.yahoo.com> Dear Susumu, How many seeds are used in DTI Studio Software to do tractography ? Could we change this option in DTI Studio ? Thanks An Vo --- On Wed, 1/20/10, susumu mori wrote: > From: susumu mori > Subject: Re: [Mristudio-users] How can I get the angulations? > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" , "Hangyi Jiang" > Date: Wednesday, January 20, 2010, 12:23 PM > Angulation means the angles for oblique > plane imaging? > > If so; > > > If you are using "non-overplus" gradient > table, you don't have to worry about it. > > If you are using "overplus" gradient AND > DICOM files, you can cut&paste the 33-orientation > overplus table in the the "Gradient Table" section > and check "Rotate Gradient if Applicable" > checkbox. This will automatically read the oblique angle > information and recalculate the appropriate gradient table. > > > If you need the information of the exact place of the > angle information in DICOM, Hangyi should know. > > Susumu > > On Wed, Jan 20, 2010 at 11:47 AM, > Lucas Lessa > wrote: > > > Hi, > > I received some exams that I need to process and get the FA > in some areas, but the person who gave me the exams > didn't give the angulations. > Does anyone know how to get this informations inside the > DICOM header? > > The exams were done in a Philips Achieva release 2.1 using > 33 directions. > Thank you very much. > > Lucas Lessa. > > > > > Veja quais s?o os assuntos do momento > no Yahoo! + Buscados: Top > 10 - Celebridades > - M?sica > - Esportes > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > > > > -----Inline Attachment Follows----- > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From susumu at mri.jhu.edu Wed Jan 20 20:51:20 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 20 Jan 2010 20:51:20 -0500 Subject: [Mristudio-users] How can I get the angulations? In-Reply-To: <968284.63134.qm@web51102.mail.re2.yahoo.com> References: <968284.63134.qm@web51102.mail.re2.yahoo.com> Message-ID: Hi An Vo, There is only one seed in each pixel, which can not be changed. Please note that DtiStudio performs tractography from every pixel in the brain above the specified FA threshold. ROI drawing merely choose those penetrate the ROI and visualize them. If you define a 20-pixel ROI, it is likely that you get more than 100 streamlines. This "inverse" approach has a similar effect to dense and random seeding within a pixel. Susumu On Wed, Jan 20, 2010 at 8:18 PM, Vo Phuoc Nhu An wrote: > Dear Susumu, > > How many seeds are used in DTI Studio Software to do tractography ? > > Could we change this option in DTI Studio ? > > Thanks > An Vo > > > > --- On Wed, 1/20/10, susumu mori wrote: > > > From: susumu mori > > Subject: Re: [Mristudio-users] How can I get the angulations? > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org>, "Hangyi Jiang" > > Date: Wednesday, January 20, 2010, 12:23 PM > > Angulation means the angles for oblique > > plane imaging? > > > > If so; > > > > > If you are using "non-overplus" gradient > > table, you don't have to worry about it. > > > If you are using "overplus" gradient AND > > DICOM files, you can cut&paste the 33-orientation > > overplus table in the the "Gradient Table" section > > and check "Rotate Gradient if Applicable" > > checkbox. This will automatically read the oblique angle > > information and recalculate the appropriate gradient table. > > > > > If you need the information of the exact place of the > > angle information in DICOM, Hangyi should know. > > > > Susumu > > > > On Wed, Jan 20, 2010 at 11:47 AM, > > Lucas Lessa > > wrote: > > > > > > Hi, > > > > I received some exams that I need to process and get the FA > > in some areas, but the person who gave me the exams > > didn't give the angulations. > > Does anyone know how to get this informations inside the > > DICOM header? > > > > The exams were done in a Philips Achieva release 2.1 using > > 33 directions. > > Thank you very much. > > > > Lucas Lessa. > > > > > > > > > > Veja quais s?o os assuntos do momento > > no Yahoo! + Buscados: Top > > 10 - Celebridades > > - M?sica > > - Esportes > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > http://lists.mristudio.org/mailman/listinfo/ > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > > > > > -----Inline Attachment Follows----- > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100120/7499e131/attachment.html From Daniel.Nanz at usz.ch Mon Jan 25 11:34:40 2010 From: Daniel.Nanz at usz.ch (Nanz Daniel Dr.) Date: Mon, 25 Jan 2010 17:34:40 +0100 Subject: [Mristudio-users] Coordinate system for diffusion-gradient directions? Message-ID: <6232CFA90B01CF44BB409B29909CE9E647E2CAA400@DS-00366.usz.ch> Hi I could not find definitions for the coordinate system within which the diffusion directions are to be defined for the input into DTI studio? E.g., on a Philips system, the diffusion direction cosines found in the DICOM header (private and public tags) are independent of slice orientation as well as of patient orientation. Presumably, the direction cosines are given in a magnet-fixed coordinate system. Is this considered and recalculated for tractograpy by DTI studio, based on the information in the DICOM header (slice orientation in patient coordinate system)? Or is the inter-voxel relation of diffusion ellipsoid directions neglected altogether by DTI studio? Or should the directions be re-calculated before feeding the data into DTI studio? If so, into what coordinate system should the directions be transformed? With best regards and thanks Dani Nanz From yj3 at duke.edu Mon Jan 25 11:58:02 2010 From: yj3 at duke.edu (Yi Jiang) Date: Mon, 25 Jan 2010 11:58:02 -0500 Subject: [Mristudio-users] functions for AIR References: <3EAE6D5F-DB56-4BF2-8846-5F66E416E032@hsc.pku.edu.cn> Message-ID: <8E4D96D68F3B4D5DB8BA0D465B2A1016@panpan> Dear All, I am trying to use AIR with DiffeoMap on a 32 bit windows vista. If someone has already built the following functions: makeaheader.exe, alignlinear.exe, align_warp.exe and invert_air.exe Could you please send them to me? Thank you very much! Best, Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100125/4afebd1a/attachment.html From faridisme at gmail.com Mon Jan 25 19:38:32 2010 From: faridisme at gmail.com (mdfarid a r) Date: Tue, 26 Jan 2010 08:38:32 +0800 Subject: [Mristudio-users] Fibertracking dorsal cingulum bundle Message-ID: <7e403aa51001251638k558bea04sd9d1f191fe373281@mail.gmail.com> Dear DTIStudio users, I am interested in investigating the cingulum bundle but am having trouble fibertracking the cingulum bundle. Based on the ColorMap0 and Eigenvector0 values in the region of the dorsal cingulum bundle, I would expect fibertracking to occur in an anterior-posterior manner but it is not the case. 1-ColorMap0.jpeg shows the ColorMap0. At the cingulum bundle region, the 2nd value is the greatest among the 3. (eg: 19,126,27 or 6,136,40) 2-Evector0.jpeg shows the Eigenvector0. At the cingulum bundle region, the 2nd value is the greatest among the 3. (eg: -0.21,0.95,-0.20) 3-fibertrack.jpeg is obtained by fibertracking using the binary image of the left cingulum mask from WMPMII The threshold criteria is restrictive so that not too many fibers obstruct the visualisation of the cingulum (threshold criteria is 0.3 for minimum FA and angle of 50degrees). The resulting fibertrack is still unexpected because it does not traverse in anterior-posterior manner but in the dorsal-ventral manner. Fibertracking at 0.15 minimum FA and angle of 70degrees. results in 4-fibertrack.jpeg. I further select the cingulum bundles by using the ROI AND operation at different coronal slices. At coronal slice 101, I am still able to obtain reasonable fibertrack results. 5-fibertrack.jpeg, the fibertracks lie in the cingulum region that is expected and extends over around14-18 slices from 101 to 114. However, as I try to delineate the cingulum bundle at more anterior coronal slices the cingulum is more horizontal, the fibertracking result delineates in dorsal-ventral manner. In the 6-fibertrack.jpeg, the fibertracks obtained extend over only 7 slices. I do not understand how this is so because the ColorMap0 and the Eigenvector0 seem to indicate that the principle diffusion direction is indeed in the anterior-posterior direction. ----------- Some other information The image I used is a group registered to the JHU-MNI atlas. The images are averaged across many subjects to increase signal to noise ratio. However, when i repeat fibertracking on single subjects, the fibertracking results are still more dorsal-ventral than anterior-posterior. ------------ Pls offer any suggestions. I really need the help. I can offer more additional information on my problem if required. Thank you in advance. I would really appreciate it. Regards, Farid -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100126/c718db28/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: 6-fibertrack.JPG Type: image/jpeg Size: 105629 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100126/c718db28/attachment-0006.jpe -------------- next part -------------- A non-text attachment was scrubbed... Name: 1-ColorMap0.JPG Type: image/jpeg Size: 95558 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100126/c718db28/attachment-0007.jpe -------------- next part -------------- A non-text attachment was scrubbed... Name: 2-Evector0.JPG Type: image/jpeg Size: 153034 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100126/c718db28/attachment-0008.jpe -------------- next part -------------- A non-text attachment was scrubbed... Name: 3-fibertrack.JPG Type: image/jpeg Size: 149511 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100126/c718db28/attachment-0009.jpe -------------- next part -------------- A non-text attachment was scrubbed... Name: 4-fibertrack.JPG Type: image/jpeg Size: 163481 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100126/c718db28/attachment-0010.jpe -------------- next part -------------- A non-text attachment was scrubbed... Name: 5-fibertrack.JPG Type: image/jpeg Size: 116829 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100126/c718db28/attachment-0011.jpe From susumu at mri.jhu.edu Tue Jan 26 11:07:11 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 26 Jan 2010 11:07:11 -0500 Subject: [Mristudio-users] Fibertracking dorsal cingulum bundle In-Reply-To: <7e403aa51001251638k558bea04sd9d1f191fe373281@mail.gmail.com> References: <7e403aa51001251638k558bea04sd9d1f191fe373281@mail.gmail.com> Message-ID: Farid, There are several points I want to make, although at this point, I'm not 100% sure what went wrong; > First of all, your tracking results do look odd. > Second, I'm concerned about the non-conventional orientation of your image. The upper right must be axial and the lower right has to be the coronal. Also, your sagittal is 90 degree rotated. In DtiStudio, the X axis (horizontal) of the upper right and the lower right images are the anatomical right-left, which is assigned red. This part is correct. Then the Y (vertical) of the upper right image and the X axis (horizontal) of the lower left image is the anatomical anterior-posterior, which is assigned green. In your image, these axes have blue color and anatomical superior-inferior. In other words, the definition of the green and blue (anterior-posterior and superior-inferior) are switched. I'm not sure how it happened. If you used our software for image normalization, the consistency of the orientation definition (which is always the Radiology convention) is guaranteed, but if you used another software at some point, it's hard for us to track down the problem. >There is always the issue of +/- definition of gradient tables. Please refer description at " https://www.mristudio.org/wiki/user_manual/DTI_Studio_User_Manual/fiber_tracking" that explains the issue. Before you apply any image transformation, you have to make sure that this +/- issue is correctly addressed. Practically, you need to confirm that you can get correct fiber tracking BEFORE you do any transformation (normalization) of a data; you want to make sure tracking is right in the native space. > Another issue is that you need to transform (normalize) the tensor to create a good population-averaged DTI data. The tensor transformation requires special algorithm for tensor reorientation. MriStudio offers DiffeoMap (formerly known as Landmarker) that provides the state-of-the-art tensor normalization tools ( https://www.mristudio.org/wiki/user_manual/landmarker). In this way, you don't have to worry much of the issues described above. On Mon, Jan 25, 2010 at 7:38 PM, mdfarid a r wrote: > Dear DTIStudio users, > > I am interested in investigating the cingulum bundle but am having trouble > fibertracking the cingulum bundle. > > Based on the ColorMap0 and Eigenvector0 values in the region of the dorsal > cingulum bundle, I would expect fibertracking to occur in an > anterior-posterior manner but it is not the case. > > 1-ColorMap0.jpeg shows the ColorMap0. At the cingulum bundle region, the > 2nd value is the greatest among the 3. (eg: 19,126,27 or 6,136,40) > > 2-Evector0.jpeg shows the Eigenvector0. At the cingulum bundle region, the > 2nd value is the greatest among the 3. (eg: -0.21,0.95,-0.20) > > 3-fibertrack.jpeg is obtained by fibertracking using the binary image of > the left cingulum mask from WMPMII > The threshold criteria is restrictive so that not too many fibers obstruct > the visualisation of the cingulum (threshold criteria is 0.3 for minimum FA > and angle of 50degrees). The resulting fibertrack is still unexpected > because it does not traverse in anterior-posterior manner but in the > dorsal-ventral manner. > > Fibertracking at 0.15 minimum FA and angle of 70degrees. results in > 4-fibertrack.jpeg. I further select the cingulum bundles by using the ROI > AND operation at different coronal slices. > > At coronal slice 101, I am still able to obtain reasonable fibertrack > results. 5-fibertrack.jpeg, the fibertracks lie in the cingulum region that > is expected and extends over around14-18 slices from 101 to 114. > > However, as I try to delineate the cingulum bundle at more anterior coronal > slices the cingulum is more horizontal, the fibertracking result > delineates in dorsal-ventral manner. In the 6-fibertrack.jpeg, the > fibertracks obtained extend over only 7 slices. > > I do not understand how this is so because the ColorMap0 and the > Eigenvector0 seem to indicate that the principle diffusion direction is > indeed in the anterior-posterior direction. > > ----------- > Some other information > The image I used is a group registered to the JHU-MNI atlas. The images are > averaged across many subjects to increase signal to noise ratio. However, > when i repeat fibertracking on single subjects, the fibertracking results > are still more dorsal-ventral than anterior-posterior. > ------------ > > Pls offer any suggestions. I really need the help. I can offer more > additional information on my problem if required. > > Thank you in advance. I would really appreciate it. > Regards, > Farid > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100126/79a4125d/attachment.html From susumu at mri.jhu.edu Tue Jan 26 14:24:03 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 26 Jan 2010 14:24:03 -0500 Subject: [Mristudio-users] Coordinate system for diffusion-gradient directions? In-Reply-To: <6232CFA90B01CF44BB409B29909CE9E647E2CAA400@DS-00366.usz.ch> References: <6232CFA90B01CF44BB409B29909CE9E647E2CAA400@DS-00366.usz.ch> Message-ID: Hi Dani, This issue has been touched upon several times but because it is very important, I want to re-describe it here. > All the users who are using the following conditions do not have to worry anything about gradient coordinate system (magnet frame, patient frame, imaging frame). Based on the patient position and imaging parameters (oblique angles), the gradient table is recalculated within the scanner on-the-fly to assure that gradient table x/y/z correspond to image x/y/z. When [1, 0, 0] is applied, it is along image X axis. All GE scanners with all operating systems Philips scanners with all operating systems except that "Gradient Overplus = on" Siemens scanners after VB15 operating system > The following scanner users have to be worried about gradient coordinates. When oblique plane is used, the gradient table HAS TO BE recalculated because the gradient table is in the magnet x/y/z. Philips scanners when "Gradient Opverplus = on" Siemens scanners before VB15 If you are using DICOM or MOSAIC, you have to check "Rotate gradients if applicable" checkbox beneath the gradient table window. If you are using Philips REC/PAR, please use "DTI_gradient_table _creator" at http://godzilla.kennedykrieger.org/~jfarrell/software_web.htm written by Jonathan Farrel. Susumu On Mon, Jan 25, 2010 at 11:34 AM, Nanz Daniel Dr. wrote: > Hi > > I could not find definitions for the coordinate > system within which the diffusion directions are to > be defined for the input into DTI studio? > > E.g., on a Philips system, the diffusion direction > cosines found in the DICOM header (private and public tags) > are independent of slice orientation as well as of > patient orientation. Presumably, the direction cosines > are given in a magnet-fixed coordinate system. > > Is this considered and recalculated for tractograpy > by DTI studio, based on the information in the DICOM > header (slice orientation in patient coordinate system)? > Or is the inter-voxel relation of diffusion > ellipsoid directions neglected altogether by DTI studio? > > Or should the directions be re-calculated before > feeding the data into DTI studio? If so, into what > coordinate system should the directions be transformed? > > With best regards and thanks > Dani Nanz > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100126/be135197/attachment.html From mithamahesh at gmail.com Wed Jan 27 01:53:50 2010 From: mithamahesh at gmail.com (smitha mahesh) Date: Wed, 27 Jan 2010 12:23:50 +0530 Subject: [Mristudio-users] (no subject) Message-ID: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> Sir, I am working on DTI studio. I am using Seimens mosaic images. When i processed the images using DTI studio, (FA, ADC,....) images i got contains lot of noise. How can i avoid this. Also when i did the fiber tractography the tracts are very short in length. What are your suggestions. -- Smitha K A PhD Student Dept of Imaging Sciences and Technology Sree Chitra Tirunal Institute for Medical Sciences and Technology Trivandrum Kerala. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100127/e0bd4807/attachment.html From faridisme at gmail.com Wed Jan 27 05:21:49 2010 From: faridisme at gmail.com (mdfarid a r) Date: Wed, 27 Jan 2010 18:21:49 +0800 Subject: [Mristudio-users] Fibertracking dorsal cingulum bundle In-Reply-To: References: <7e403aa51001251638k558bea04sd9d1f191fe373281@mail.gmail.com> Message-ID: <7e403aa51001270221o6b810437l76743a55628daf9f@mail.gmail.com> Thank you Dr Mori and Dr Hangyi, Upon ur advice, I investigated the fibertracking and found that at all green regions, fibertracking was in the superior-inferior direction while at the blue regions, fibertracking was in the anterior-posterior direction. I have swapped the y and z columns of the gradient table and now my fibertracks of the cingulum have much better correspondence to the atlas. The consequence also is that, I swapped the green and blue colour around. so that my colormap and eigenvector map does not follow your book. I will try proceeding in this way and see if I experience any other problems with fibertracking. Thanks also for directing me to the page about the "issue of +/- definition of gradient tables". It helped me to understand the significance of the eigenvector directions in x,y,z direction. Regards, Farid On Wed, Jan 27, 2010 at 12:07 AM, susumu mori wrote: > Farid, > > There are several points I want to make, although at this point, I'm not > 100% sure what went wrong; > > > First of all, your tracking results do look odd. > > Second, I'm concerned about the non-conventional orientation of your > image. The upper right must be axial and the lower right has to be the > coronal. Also, your sagittal is 90 degree rotated. In DtiStudio, the X axis > (horizontal) of the upper right and the lower right images are the > anatomical right-left, which is assigned red. This part is correct. Then the > Y (vertical) of the upper right image and the X axis (horizontal) of the > lower left image is the anatomical anterior-posterior, which is assigned > green. In your image, these axes have blue color and anatomical > superior-inferior. In other words, the definition of the green and blue > (anterior-posterior and superior-inferior) are switched. I'm not sure how it > happened. If you used our software for image normalization, the consistency > of the orientation definition (which is always the Radiology convention) is > guaranteed, but if you used another software at some point, it's hard for us > to track down the problem. > >There is always the issue of +/- definition of gradient tables. Please > refer description at " > https://www.mristudio.org/wiki/user_manual/DTI_Studio_User_Manual/fiber_tracking" > that explains the issue. Before you apply any image transformation, you have > to make sure that this +/- issue is correctly addressed. Practically, you > need to confirm that you can get correct fiber tracking BEFORE you do any > transformation (normalization) of a data; you want to make sure tracking is > right in the native space. > > Another issue is that you need to transform (normalize) the tensor to > create a good population-averaged DTI data. The tensor transformation > requires special algorithm for tensor reorientation. > > MriStudio offers DiffeoMap (formerly known as Landmarker) that provides the > state-of-the-art tensor normalization tools ( > https://www.mristudio.org/wiki/user_manual/landmarker). In this way, you > don't have to worry much of the issues described above. > > On Mon, Jan 25, 2010 at 7:38 PM, mdfarid a r wrote: > >> Dear DTIStudio users, >> >> I am interested in investigating the cingulum bundle but am having trouble >> fibertracking the cingulum bundle. >> >> Based on the ColorMap0 and Eigenvector0 values in the region of the dorsal >> cingulum bundle, I would expect fibertracking to occur in an >> anterior-posterior manner but it is not the case. >> >> 1-ColorMap0.jpeg shows the ColorMap0. At the cingulum bundle region, the >> 2nd value is the greatest among the 3. (eg: 19,126,27 or 6,136,40) >> >> 2-Evector0.jpeg shows the Eigenvector0. At the cingulum bundle region, the >> 2nd value is the greatest among the 3. (eg: -0.21,0.95,-0.20) >> >> 3-fibertrack.jpeg is obtained by fibertracking using the binary image of >> the left cingulum mask from WMPMII >> The threshold criteria is restrictive so that not too many fibers obstruct >> the visualisation of the cingulum (threshold criteria is 0.3 for minimum FA >> and angle of 50degrees). The resulting fibertrack is still unexpected >> because it does not traverse in anterior-posterior manner but in the >> dorsal-ventral manner. >> >> Fibertracking at 0.15 minimum FA and angle of 70degrees. results in >> 4-fibertrack.jpeg. I further select the cingulum bundles by using the ROI >> AND operation at different coronal slices. >> >> At coronal slice 101, I am still able to obtain reasonable fibertrack >> results. 5-fibertrack.jpeg, the fibertracks lie in the cingulum region that >> is expected and extends over around14-18 slices from 101 to 114. >> >> However, as I try to delineate the cingulum bundle at more anterior >> coronal slices the cingulum is more horizontal, the fibertracking result >> delineates in dorsal-ventral manner. In the 6-fibertrack.jpeg, the >> fibertracks obtained extend over only 7 slices. >> >> I do not understand how this is so because the ColorMap0 and the >> Eigenvector0 seem to indicate that the principle diffusion direction is >> indeed in the anterior-posterior direction. >> >> ----------- >> Some other information >> The image I used is a group registered to the JHU-MNI atlas. The images >> are averaged across many subjects to increase signal to noise ratio. >> However, when i repeat fibertracking on single subjects, the fibertracking >> results are still more dorsal-ventral than anterior-posterior. >> ------------ >> >> Pls offer any suggestions. I really need the help. I can offer more >> additional information on my problem if required. >> >> Thank you in advance. I would really appreciate it. >> Regards, >> Farid >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100127/6ba9b92f/attachment-0001.html From susumu at mri.jhu.edu Wed Jan 27 08:20:33 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 27 Jan 2010 08:20:33 -0500 Subject: [Mristudio-users] Fibertracking dorsal cingulum bundle In-Reply-To: <7e403aa51001270221o6b810437l76743a55628daf9f@mail.gmail.com> References: <7e403aa51001251638k558bea04sd9d1f191fe373281@mail.gmail.com> <7e403aa51001270221o6b810437l76743a55628daf9f@mail.gmail.com> Message-ID: It seems that you got the matching between the vector orientations and anatomy right. What is not still right (well it is not right or wrong. It's just a convention) is that usually, the first dimension of the data (the x element of your 3D data) is assigned red, second (y) green, and third (z) blue, which usually coincide to right-left, anterior-posterior, and superior-inferior. In your case, the order of the data matrix is right-left / superior-inferior / anterior-posterior. It's just the matter of the order of your 3D matrix. On Wed, Jan 27, 2010 at 5:21 AM, mdfarid a r wrote: > > Thank you Dr Mori and Dr Hangyi, > > Upon ur advice, I investigated the fibertracking and found that at all > green regions, fibertracking was in the superior-inferior direction while at > the blue regions, fibertracking was in the anterior-posterior direction. I > have swapped the y and z columns of the gradient table and now my > fibertracks of the cingulum have much better correspondence to the atlas. > > The consequence also is that, I swapped the green and blue colour around. > so that my colormap and eigenvector map does not follow your book. I will > try proceeding in this way and see if I experience any other problems with > fibertracking. > > Thanks also for directing me to the page about the "issue of +/- definition > of gradient tables". It helped me to understand the significance of the > eigenvector directions in x,y,z direction. > > Regards, > Farid > On Wed, Jan 27, 2010 at 12:07 AM, susumu mori wrote: > >> Farid, >> >> There are several points I want to make, although at this point, I'm not >> 100% sure what went wrong; >> >> > First of all, your tracking results do look odd. >> > Second, I'm concerned about the non-conventional orientation of your >> image. The upper right must be axial and the lower right has to be the >> coronal. Also, your sagittal is 90 degree rotated. In DtiStudio, the X axis >> (horizontal) of the upper right and the lower right images are the >> anatomical right-left, which is assigned red. This part is correct. Then the >> Y (vertical) of the upper right image and the X axis (horizontal) of the >> lower left image is the anatomical anterior-posterior, which is assigned >> green. In your image, these axes have blue color and anatomical >> superior-inferior. In other words, the definition of the green and blue >> (anterior-posterior and superior-inferior) are switched. I'm not sure how it >> happened. If you used our software for image normalization, the consistency >> of the orientation definition (which is always the Radiology convention) is >> guaranteed, but if you used another software at some point, it's hard for us >> to track down the problem. >> >There is always the issue of +/- definition of gradient tables. Please >> refer description at " >> https://www.mristudio.org/wiki/user_manual/DTI_Studio_User_Manual/fiber_tracking" >> that explains the issue. Before you apply any image transformation, you have >> to make sure that this +/- issue is correctly addressed. Practically, you >> need to confirm that you can get correct fiber tracking BEFORE you do any >> transformation (normalization) of a data; you want to make sure tracking is >> right in the native space. >> > Another issue is that you need to transform (normalize) the tensor to >> create a good population-averaged DTI data. The tensor transformation >> requires special algorithm for tensor reorientation. >> >> MriStudio offers DiffeoMap (formerly known as Landmarker) that provides >> the state-of-the-art tensor normalization tools ( >> https://www.mristudio.org/wiki/user_manual/landmarker). In this way, you >> don't have to worry much of the issues described above. >> >> On Mon, Jan 25, 2010 at 7:38 PM, mdfarid a r wrote: >> >>> Dear DTIStudio users, >>> >>> I am interested in investigating the cingulum bundle but am having >>> trouble fibertracking the cingulum bundle. >>> >>> Based on the ColorMap0 and Eigenvector0 values in the region of the >>> dorsal cingulum bundle, I would expect fibertracking to occur in an >>> anterior-posterior manner but it is not the case. >>> >>> 1-ColorMap0.jpeg shows the ColorMap0. At the cingulum bundle region, the >>> 2nd value is the greatest among the 3. (eg: 19,126,27 or 6,136,40) >>> >>> 2-Evector0.jpeg shows the Eigenvector0. At the cingulum bundle region, >>> the 2nd value is the greatest among the 3. (eg: -0.21,0.95,-0.20) >>> >>> 3-fibertrack.jpeg is obtained by fibertracking using the binary image of >>> the left cingulum mask from WMPMII >>> The threshold criteria is restrictive so that not too many fibers >>> obstruct the visualisation of the cingulum (threshold criteria is 0.3 for >>> minimum FA and angle of 50degrees). The resulting fibertrack is still >>> unexpected because it does not traverse in anterior-posterior manner but in >>> the dorsal-ventral manner. >>> >>> Fibertracking at 0.15 minimum FA and angle of 70degrees. results in >>> 4-fibertrack.jpeg. I further select the cingulum bundles by using the ROI >>> AND operation at different coronal slices. >>> >>> At coronal slice 101, I am still able to obtain reasonable fibertrack >>> results. 5-fibertrack.jpeg, the fibertracks lie in the cingulum region that >>> is expected and extends over around14-18 slices from 101 to 114. >>> >>> However, as I try to delineate the cingulum bundle at more anterior >>> coronal slices the cingulum is more horizontal, the fibertracking result >>> delineates in dorsal-ventral manner. In the 6-fibertrack.jpeg, the >>> fibertracks obtained extend over only 7 slices. >>> >>> I do not understand how this is so because the ColorMap0 and the >>> Eigenvector0 seem to indicate that the principle diffusion direction is >>> indeed in the anterior-posterior direction. >>> >>> ----------- >>> Some other information >>> The image I used is a group registered to the JHU-MNI atlas. The images >>> are averaged across many subjects to increase signal to noise ratio. >>> However, when i repeat fibertracking on single subjects, the fibertracking >>> results are still more dorsal-ventral than anterior-posterior. >>> ------------ >>> >>> Pls offer any suggestions. I really need the help. I can offer more >>> additional information on my problem if required. >>> >>> Thank you in advance. I would really appreciate it. >>> Regards, >>> Farid >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100127/35cf8fef/attachment.html From susumu at mri.jhu.edu Wed Jan 27 08:32:53 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 27 Jan 2010 08:32:53 -0500 Subject: [Mristudio-users] (no subject) In-Reply-To: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> Message-ID: This should give you some guidance about SNR: 1.5T: 2.5x2.5x2.5 mm / total 60 DWIs (e.g. 5 repetitions x 12 orientations, 2 repetitions x 30 orientations) should take about 8-9 min with 50-60 slices to cover the entire brain. For example, you can use 96x96 matrix (interpolated to 192x192 or 256x256) for 240x240 mm FOV is a good combination. This gives a decent level of SNR. About 30 DWIs (4 min) (e.g. 2 repetitions x 12 orientation or 1 x 30 orientations) give a bit weak SNR but maybe still usable. Anything lower look noisy. 3.0T 2.2x2.2x2.2mm (e.g. 112x112 matrix (interpolated to 224x224 or 256x256) with 246x246 mm FOV should give a good SNR with 60DWIs (8-9 min). It is also quite usable with 30DWIs (4 min). You maybe able to push the resolution to 2x2x2 (e.g. 112x112 matrix, 224x224 mm FOV) with 60DWIs with a modern head coil. For tracking, please see https://www.mristudio.org/wiki/user_manual/DTI_Studio_User_Manual/fiber_tracking . On Wed, Jan 27, 2010 at 1:53 AM, smitha mahesh wrote: > Sir, > > I am working on DTI studio. I am using Seimens mosaic images. When i > processed the images using DTI studio, (FA, ADC,....) images i got contains > lot of noise. How can i avoid this. Also when i did the fiber tractography > the tracts are very short in length. What are your suggestions. > > > > -- > Smitha K A > PhD Student > Dept of Imaging Sciences and Technology > Sree Chitra Tirunal Institute for Medical Sciences and Technology > Trivandrum > Kerala. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100127/41d176c0/attachment.html From yj3 at duke.edu Fri Jan 29 17:25:53 2010 From: yj3 at duke.edu (Yi Jiang) Date: Fri, 29 Jan 2010 17:25:53 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & command file References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> Message-ID: Hello, dear all, I have two questions and am wondering if someone can help. 1.. I have already had a transformation matrix to map the subject image onto the template image, which was generated by combining AIR rigid, AIR affine, and LDDMM matrix. I want to define some landmarkers on the subject image, and apply the transformation matrix to the landmarkers (to see their corresponding location on the template image). How can I do that? 2.. I would like to use the "load command file" function. I will do AIR linear rigid transformation, AIR linear affine transformation, image format change to byte, automatic intensity correction by histogram, and 2-channel LDDMM. Is it possible to put all these into one command file? If yes, can anyone give me an example file? Thank you very much! Have a nice weekend! Best Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100129/8748249f/attachment-0001.html From susumu at mri.jhu.edu Sat Jan 30 08:29:32 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sat, 30 Jan 2010 08:29:32 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & command file In-Reply-To: References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> Message-ID: Hi Yi, On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: > Hello, dear all, > > > > I have two questions and am wondering if someone can help. > > > > 1. I have already had a transformation matrix to map the subject image > onto the template image, which was generated by combining AIR rigid, AIR > affine, and LDDMM matrix. I want to define some landmarkers on the subject > image, and apply the transformation matrix to the landmarkers (to see their > corresponding location on the template image). How can I do that? > > I think this is exactly what the K and H maps are. I need confirmation from Xin, but in my understanding, these transformation matrices contain vectors at each coordinate, indicating where is the new location. If I'm not mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x Z-dimension. There must be a way to extarct the "Vector" information at the specified coordinate. > > > 1. I would like to use the ?load command file? function. I will do AIR > linear rigid transformation, AIR linear affine transformation, image format > change to byte, automatic intensity correction by histogram, and 2-channel > LDDMM. Is it possible to put all these into one command file? If yes, can > anyone give me an example file? > > I believe the command file is only for the functions within the same box, including byte-integer-float conversion, axial-sagittal-coronal conversion, resampling, etc. They don't include transformation functions. We are working on automation, which will take several months. Meanwhile, I believe it is good idea to use the current way, which forces you to check the result after each step. Transformation sometimes does silly things. Some images may have quality problems. You may want compare different methods (e.g. Mutual Info linear transformation vs AIR, intensity correction methods, contrast of choice). I think it's very important to get a feel about your data and each transformation step. Also, depending on pathology, the transformation strategy may change. Some disease groups have severe intensity changes (e.g. stroke), some have severely enlarged ventricles. You may find the same methods may work for one but not the other. Automation is still a difficult matter for transformation-based analysis. > > > Thank you very much! > > > > Have a nice weekend! > > > > Best > > Yi > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100130/29d70997/attachment.html From yi.jiang at duke.edu Sat Jan 30 13:37:31 2010 From: yi.jiang at duke.edu (Yi Jiang) Date: Sat, 30 Jan 2010 13:37:31 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & commandfile In-Reply-To: References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> Message-ID: <776216510ECF40C4B0E791C68BB67327@YiDell2> Dear Dr Mori, Thank you very much for your quick and detailed answers. 1. One thing I need to note is that the transformation matrix I have is a "final" combined matrix of AIR rigid, AIR affine, and LDDMM K map (so it should be in the raw data format). Can I extract the "vector" information at the specified location in this transformation matrix? And how? 2. I agree that checking the result after each step is necessary. I have manually processed and checked all my data. If there is a way to automate the process by a command file after I have finalized the methods and steps, it will be nice so that it can help avoid any unintended mistake (forget to change a parameter, typo, misclick a button etc) which might happen when I manually process a lot images. So it will be a nice feature, but of course not a must yet. Best, Yi _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Saturday, January 30, 2010 8:30 AM To: Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support; Xin Li; Jiangyang Zhang Subject: Re: [Mristudio-users] apply transformation to landmarkers & commandfile Hi Yi, On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: Hello, dear all, I have two questions and am wondering if someone can help. 1. I have already had a transformation matrix to map the subject image onto the template image, which was generated by combining AIR rigid, AIR affine, and LDDMM matrix. I want to define some landmarkers on the subject image, and apply the transformation matrix to the landmarkers (to see their corresponding location on the template image). How can I do that? I think this is exactly what the K and H maps are. I need confirmation from Xin, but in my understanding, these transformation matrices contain vectors at each coordinate, indicating where is the new location. If I'm not mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x Z-dimension. There must be a way to extarct the "Vector" information at the specified coordinate. 2. I would like to use the "load command file" function. I will do AIR linear rigid transformation, AIR linear affine transformation, image format change to byte, automatic intensity correction by histogram, and 2-channel LDDMM. Is it possible to put all these into one command file? If yes, can anyone give me an example file? I believe the command file is only for the functions within the same box, including byte-integer-float conversion, axial-sagittal-coronal conversion, resampling, etc. They don't include transformation functions. We are working on automation, which will take several months. Meanwhile, I believe it is good idea to use the current way, which forces you to check the result after each step. Transformation sometimes does silly things. Some images may have quality problems. You may want compare different methods (e.g. Mutual Info linear transformation vs AIR, intensity correction methods, contrast of choice). I think it's very important to get a feel about your data and each transformation step. Also, depending on pathology, the transformation strategy may change. Some disease groups have severe intensity changes (e.g. stroke), some have severely enlarged ventricles. You may find the same methods may work for one but not the other. Automation is still a difficult matter for transformation-based analysis. Thank you very much! Have a nice weekend! Best Yi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100130/c9012a9d/attachment-0001.html From xli16 at jhmi.edu Mon Feb 1 10:22:37 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 01 Feb 2010 10:22:37 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & command file In-Reply-To: References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> Message-ID: Hello Yi, As Susumu said, transformation matrices contain vectors at each coordinate, indicating where is the new location. The structure is Vector (x, y, z) x X-dimension x Y-dimension x Z-dimension. You may write matlab code to extract the vector information. Xin ----- Original Message ----- From: susumu mori Date: Saturday, January 30, 2010 8:29 am Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker Questions/Support" , Xin Li , Jiangyang Zhang > Hi Yi, > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: > > > Hello, dear all, > > > > > > > > I have two questions and am wondering if someone can help. > > > > > > > > 1. I have already had a transformation matrix to map the subject > image > > onto the template image, which was generated by combining AIR > rigid, AIR > > affine, and LDDMM matrix. I want to define some landmarkers on > the subject > > image, and apply the transformation matrix to the landmarkers > (to see their > > corresponding location on the template image). How can I do that? > > > > > I think this is exactly what the K and H maps are. I need > confirmation from > Xin, but in my understanding, these transformation matrices contain vectors > at each coordinate, indicating where is the new location. If I'm not > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x Z-dimension. > There must be a way to extarct the "Vector" information at the specified > coordinate. > > > > > > > 1. I would like to use the ?load command file? function. I will > do AIR > > linear rigid transformation, AIR linear affine transformation, > image format > > change to byte, automatic intensity correction by histogram, and > 2-channel > > LDDMM. Is it possible to put all these into one command file? If > yes, can > > anyone give me an example file? > > > > I believe the command file is only for the functions within the > same box, > including byte-integer-float conversion, axial-sagittal-coronal conversion, > resampling, etc. They don't include transformation functions. We are > working > on automation, which will take several months. Meanwhile, I believe > it is > good idea to use the current way, which forces you to check the > result after > each step. Transformation sometimes does silly things. Some images > may have > quality problems. You may want compare different methods (e.g. Mutual > Info > linear transformation vs AIR, intensity correction methods, contrast > of > choice). I think it's very important to get a feel about your data > and each > transformation step. Also, depending on pathology, the transformation > strategy may change. Some disease groups have severe intensity > changes (e.g. > stroke), some have severely enlarged ventricles. You may find the same > methods may work for one but not the other. Automation is still a difficult > matter for transformation-based analysis. > > > > > > > > Thank you very much! > > > > > > > > Have a nice weekend! > > > > > > > > Best > > > > Yi > > > > > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > From saksena.sona at gmail.com Mon Feb 1 11:58:40 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Mon, 01 Feb 2010 11:58:40 -0500 Subject: [Mristudio-users] corpus callsoum segmentation Message-ID: <9018fecc1002010858n57a1f02sf4bbc136f88d889e@mail.gmail.com> Hello, I would like to calculate ADC and FA values in the seven segments of corpus callosum divided according to the Witelson scheme. CAn I do that using DTIstudio software. Please let me know how to divide the corpus callsoum into seven segments using DTIstudio software or suggest any other possible way to do it. Any help will be highly appreciated. thanks regards Sona Saksena -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100201/0739ae86/attachment.html From susumu at mri.jhu.edu Mon Feb 1 16:12:17 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 01 Feb 2010 16:12:17 -0500 Subject: [Mristudio-users] corpus callsoum segmentation In-Reply-To: <9018fecc1002010858n57a1f02sf4bbc136f88d889e@mail.gmail.com> References: <9018fecc1002010858n57a1f02sf4bbc136f88d889e@mail.gmail.com> Message-ID: Hi Sona, This is a question about cross-subject brain registration. Your are basically asking how we can identify the corresponding areas of the CC across multiple subjects. Witelson scheme is one of them, which divide the CC into the seven segments based on pre-defined distance-based criteria. There are two often-counteracting factors in the mapping; reproducibility (reliability) and granularity (the number of segmentation, or the amount of localization information). One extreme of the granularity is the entire CC, in which we get one number for the entire CC (e.g. the size of the mid-sagittal CC). The reliability of the CC definition is high across the subjects because we can unambiguously define the mid-sagittal CC for any subjects, but the localization information is the poorest. If only the genu of the CC is abnormal, such an effect would be diluted by measuring the entire CC at once. Another extreme is the pixel-based analysis, in which we have to make a complete mapping of each pixel between the two subject. If there are 5,000 1x1x1 mm pixels within the mid-sagittal CC, we need to map the all 5,000 pixels to another brain. This is basically the same as making the two CC shapes the identical by image transformation. This has the highest localization information but the reliability is a tough issue. Depending on which transformation algorithm you use, you get different results. This approach has a potential to pin-point a small abnormal region within the CC, but such an effect could be diluted if there is transformation error. Also, each pixel is very noisy and a pixel-based statistics may have poor sensitivity. Often you need to apply a filtering that introduces pixel-averaging for nearby pixels. The Witelson approach is somewhere between these two approaches. It has only 7 very large segments in which 100s of pixels are averaged. Now your question is, if we provide a tool to perform the Witelson segmentation. The short answer is no, but if you take your question as a general brain registration question, the answer is yes. By using DiffeoMap, you can transform one brain to the other. We are using a very advanced diffeomorphic transformation developed by Michael Miller. So you will find the transformation results are of quite high quality. Once you transform one brain to the other, you can do pixel-based analysis. Then you can move the transformed images into RoiEditor, in which you can apply a pre-segmented brain atlas to segment the entire brain up to 176 areas. Currently, the CC is segmented to three areas: genu, body, and splenium. In this atlas, you can create your own segment. For example, you can segment the atlas CC to 7 Witelson segments. Then transform the atlas to each subject (or transform each subject to the atlas) to apply these segments to registered brain. So, I would recommend you to take a look at www.mristudio.org and find what you can do with DiffeoMap and RoiEditor. Susumu On Mon, Feb 1, 2010 at 11:58 AM, Sona Saksena wrote: > Hello, > > I would like to calculate ADC and FA values in the seven segments of corpus > callosum divided according to the Witelson scheme. CAn I do that using > DTIstudio software. Please let me know how to divide the corpus callsoum > into seven segments using DTIstudio software or suggest any other possible > way to do it. > > Any help will be highly appreciated. > > thanks > > regards > > Sona Saksena > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100201/a3886a0a/attachment.html From susumu at mri.jhu.edu Mon Feb 1 17:12:21 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 01 Feb 2010 17:12:21 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & command file In-Reply-To: References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> Message-ID: I talked with Xin and confirmed that the LDDMM-AIR combined transformation matrix has the same format as K/H maps. They are raw files of Vector x X x Y x Z. On Mon, Feb 1, 2010 at 10:22 AM, Xin Li wrote: > Hello Yi, > > As Susumu said, transformation matrices contain vectors at each coordinate, > indicating where is the new location. The structure is Vector (x, y, z) x > X-dimension x Y-dimension x Z-dimension. You may write matlab code to > extract the vector information. > > > Xin > > > > > > ----- Original Message ----- > From: susumu mori > Date: Saturday, January 30, 2010 8:29 am > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command file > To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker > Questions/Support" , Xin Li , > Jiangyang Zhang > > > > Hi Yi, > > > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: > > > > > Hello, dear all, > > > > > > > > > > > > I have two questions and am wondering if someone can help. > > > > > > > > > > > > 1. I have already had a transformation matrix to map the subject > > image > > > onto the template image, which was generated by combining AIR > > rigid, AIR > > > affine, and LDDMM matrix. I want to define some landmarkers on > > the subject > > > image, and apply the transformation matrix to the landmarkers > > (to see their > > > corresponding location on the template image). How can I do that? > > > > > > > > I think this is exactly what the K and H maps are. I need > > confirmation from > > Xin, but in my understanding, these transformation matrices contain > vectors > > at each coordinate, indicating where is the new location. If I'm not > > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x > Z-dimension. > > There must be a way to extarct the "Vector" information at the specified > > coordinate. > > > > > > > > > > > 1. I would like to use the ?load command file? function. I will > > do AIR > > > linear rigid transformation, AIR linear affine transformation, > > image format > > > change to byte, automatic intensity correction by histogram, and > > 2-channel > > > LDDMM. Is it possible to put all these into one command file? If > > yes, can > > > anyone give me an example file? > > > > > > I believe the command file is only for the functions within the > > same box, > > including byte-integer-float conversion, axial-sagittal-coronal > conversion, > > resampling, etc. They don't include transformation functions. We are > > working > > on automation, which will take several months. Meanwhile, I believe > > it is > > good idea to use the current way, which forces you to check the > > result after > > each step. Transformation sometimes does silly things. Some images > > may have > > quality problems. You may want compare different methods (e.g. Mutual > > Info > > linear transformation vs AIR, intensity correction methods, contrast > > of > > choice). I think it's very important to get a feel about your data > > and each > > transformation step. Also, depending on pathology, the transformation > > strategy may change. Some disease groups have severe intensity > > changes (e.g. > > stroke), some have severely enlarged ventricles. You may find the same > > methods may work for one but not the other. Automation is still a > difficult > > matter for transformation-based analysis. > > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > Have a nice weekend! > > > > > > > > > > > > Best > > > > > > Yi > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100201/18d6f402/attachment-0001.html From saksena.sona at gmail.com Wed Feb 3 10:56:26 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Wed, 03 Feb 2010 10:56:26 -0500 Subject: [Mristudio-users] corpus callsoum segmentation In-Reply-To: References: <9018fecc1002010858n57a1f02sf4bbc136f88d889e@mail.gmail.com> Message-ID: <9018fecc1002030756v6b03d0fej1200e9b53a1595af@mail.gmail.com> Hello, I am facing a problem while downloading DiffeoMap-latest-x64.exe and ROIEditor-latest-x64.exe. After running the program, an option comes WinZip Self-Extractor i.e. to unzip all the files by pressing the Unzip button. After unzipping the files the program does not work. Please let me know how to proceed further. Any help is highly appreciated. thanks regards Sona Saksena On Mon, Feb 1, 2010 at 4:12 PM, susumu mori wrote: > Hi Sona, > > This is a question about cross-subject brain registration. Your are > basically asking how we can identify the corresponding areas of the CC > across multiple subjects. Witelson scheme is one of them, which divide the > CC into the seven segments based on pre-defined distance-based criteria. > There are two often-counteracting factors in the mapping; reproducibility > (reliability) and granularity (the number of segmentation, or the amount of > localization information). > > One extreme of the granularity is the entire CC, in which we get one number > for the entire CC (e.g. the size of the mid-sagittal CC). The reliability of > the CC definition is high across the subjects because we can unambiguously > define the mid-sagittal CC for any subjects, but the localization > information is the poorest. If only the genu of the CC is abnormal, such an > effect would be diluted by measuring the entire CC at once. > > Another extreme is the pixel-based analysis, in which we have to make a > complete mapping of each pixel between the two subject. If there are 5,000 > 1x1x1 mm pixels within the mid-sagittal CC, we need to map the all 5,000 > pixels to another brain. This is basically the same as making the two CC > shapes the identical by image transformation. This has the highest > localization information but the reliability is a tough issue. Depending on > which transformation algorithm you use, you get different results. This > approach has a potential to pin-point a small abnormal region within the CC, > but such an effect could be diluted if there is transformation error. Also, > each pixel is very noisy and a pixel-based statistics may have poor > sensitivity. Often you need to apply a filtering that introduces > pixel-averaging for nearby pixels. > > The Witelson approach is somewhere between these two approaches. It has > only 7 very large segments in which 100s of pixels are averaged. > > Now your question is, if we provide a tool to perform the Witelson > segmentation. The short answer is no, but if you take your question as a > general brain registration question, the answer is yes. > > By using DiffeoMap, you can transform one brain to the other. We are using > a very advanced diffeomorphic transformation developed by Michael Miller. So > you will find the transformation results are of quite high quality. Once you > transform one brain to the other, you can do pixel-based analysis. > > Then you can move the transformed images into RoiEditor, in which you can > apply a pre-segmented brain atlas to segment the entire brain up to 176 > areas. Currently, the CC is segmented to three areas: genu, body, and > splenium. In this atlas, you can create your own segment. For example, you > can segment the atlas CC to 7 Witelson segments. Then transform the atlas to > each subject (or transform each subject to the atlas) to apply these > segments to registered brain. > > So, I would recommend you to take a look at www.mristudio.org and find > what you can do with DiffeoMap and RoiEditor. > > Susumu > > On Mon, Feb 1, 2010 at 11:58 AM, Sona Saksena wrote: > >> Hello, >> >> I would like to calculate ADC and FA values in the seven segments of >> corpus callosum divided according to the Witelson scheme. CAn I do that >> using DTIstudio software. Please let me know how to divide the corpus >> callsoum into seven segments using DTIstudio software or suggest any other >> possible way to do it. >> >> Any help will be highly appreciated. >> >> thanks >> >> regards >> >> Sona Saksena >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -- Regards Sona Saksena -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100203/bf5be67b/attachment.html From xli16 at jhmi.edu Wed Feb 3 11:50:37 2010 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 03 Feb 2010 11:50:37 -0500 Subject: [Mristudio-users] corpus callsoum segmentation In-Reply-To: <9018fecc1002030756v6b03d0fej1200e9b53a1595af@mail.gmail.com> References: <9018fecc1002010858n57a1f02sf4bbc136f88d889e@mail.gmail.com> <9018fecc1002030756v6b03d0fej1200e9b53a1595af@mail.gmail.com> Message-ID: Hello Sona, You may need to install runtime components of Visual C++ libraries on your computer. Please take a look at https://www.mristudio.org/wiki/user_manual/landmarker/installation. Vcredist_x86.exe and vcredist_x64.exe are available in the download section. Hope this can solve your problem. Xin ----- Original Message ----- From: Sona Saksena Date: Wednesday, February 3, 2010 10:56 am Subject: Re: [Mristudio-users] corpus callsoum segmentation To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello, > > I am facing a problem while downloading DiffeoMap-latest-x64.exe and > ROIEditor-latest-x64.exe. After running the program, an option comes > WinZip > Self-Extractor i.e. to unzip all the files by pressing the Unzip button. > After unzipping the files the program does not work. Please let me > know how > to proceed further. > > Any help is highly appreciated. > > thanks > > regards > > Sona Saksena > > > > > > > > On Mon, Feb 1, 2010 at 4:12 PM, susumu mori wrote: > > > Hi Sona, > > > > This is a question about cross-subject brain registration. Your are > > basically asking how we can identify the corresponding areas of the > CC > > across multiple subjects. Witelson scheme is one of them, which > divide the > > CC into the seven segments based on pre-defined distance-based criteria. > > There are two often-counteracting factors in the mapping; reproducibility > > (reliability) and granularity (the number of segmentation, or the > amount of > > localization information). > > > > One extreme of the granularity is the entire CC, in which we get > one number > > for the entire CC (e.g. the size of the mid-sagittal CC). The > reliability of > > the CC definition is high across the subjects because we can unambiguously > > define the mid-sagittal CC for any subjects, but the localization > > information is the poorest. If only the genu of the CC is abnormal, > such an > > effect would be diluted by measuring the entire CC at once. > > > > Another extreme is the pixel-based analysis, in which we have to > make a > > complete mapping of each pixel between the two subject. If there > are 5,000 > > 1x1x1 mm pixels within the mid-sagittal CC, we need to map the all > 5,000 > > pixels to another brain. This is basically the same as making the > two CC > > shapes the identical by image transformation. This has the highest > > localization information but the reliability is a tough issue. > Depending on > > which transformation algorithm you use, you get different results. > This > > approach has a potential to pin-point a small abnormal region > within the CC, > > but such an effect could be diluted if there is transformation > error. Also, > > each pixel is very noisy and a pixel-based statistics may have poor > > sensitivity. Often you need to apply a filtering that introduces > > pixel-averaging for nearby pixels. > > > > The Witelson approach is somewhere between these two approaches. It > has > > only 7 very large segments in which 100s of pixels are averaged. > > > > Now your question is, if we provide a tool to perform the Witelson > > segmentation. The short answer is no, but if you take your question > as a > > general brain registration question, the answer is yes. > > > > By using DiffeoMap, you can transform one brain to the other. We > are using > > a very advanced diffeomorphic transformation developed by Michael > Miller. So > > you will find the transformation results are of quite high quality. > Once you > > transform one brain to the other, you can do pixel-based analysis. > > > > Then you can move the transformed images into RoiEditor, in which > you can > > apply a pre-segmented brain atlas to segment the entire brain up to > 176 > > areas. Currently, the CC is segmented to three areas: genu, body, and > > splenium. In this atlas, you can create your own segment. For > example, you > > can segment the atlas CC to 7 Witelson segments. Then transform the > atlas to > > each subject (or transform each subject to the atlas) to apply these > > segments to registered brain. > > > > So, I would recommend you to take a look at www.mristudio.org and find > > what you can do with DiffeoMap and RoiEditor. > > > > Susumu > > > > On Mon, Feb 1, 2010 at 11:58 AM, Sona Saksena wrote: > > > >> Hello, > >> > >> I would like to calculate ADC and FA values in the seven segments > of > >> corpus callosum divided according to the Witelson scheme. CAn I do > that > >> using DTIstudio software. Please let me know how to divide the corpus > >> callsoum into seven segments using DTIstudio software or suggest > any other > >> possible way to do it. > >> > >> Any help will be highly appreciated. > >> > >> thanks > >> > >> regards > >> > >> Sona Saksena > >> > >> > >> _______________________________________________ > >> Mristudio-users mailing list > >> Mristudio-users at mristudio.org > >> > >> Unsubscribe, send a blank email to: > >> Mristudio-users-unsubscribe at mristudio.org > >> > >> > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > -- > Regards > Sona Saksena > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From qianwenshu at gmail.com Mon Feb 8 03:25:09 2010 From: qianwenshu at gmail.com (=?GB2312?B?x67OxMrg?=) Date: Mon, 08 Feb 2010 16:25:09 +0800 Subject: [Mristudio-users] Are calculated resluts influenced by the order of stored images in .REC? Message-ID: <2404f5961002080025p7c8f2cccr8c34fe5a3916136f@mail.gmail.com> Hi, all I have used DTIStudio to calculate tensor index. The former order of stored images in .REC file is "gradient by gradient", every result is OK. The latest two patients' data has been saved as "slice by slice". Though I chose "slice by slice" when input data, the calculated tensor index were all blurry. I wanna know if the resluts will be influenced by the order of stored images in .REC or the blur is just caused by other effects such as movements. Did anyone have the same problem? Thank you! Regards, Wenshu Qian Department of Diagnostic Radiology The University of Hong Kong -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100208/6283c9c3/attachment.html From lucas_lessa at yahoo.com.br Mon Feb 8 04:38:22 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Mon, 08 Feb 2010 01:38:22 -0800 (PST) Subject: [Mristudio-users] How to don't anonymize the processed images Message-ID: <129276.65365.qm@web110208.mail.gq1.yahoo.com> Dear friends and dear Dr. Mori. Good morning. I'd like to know if it's possible to generate FA, ADC, DWI and etc, by the DTI Studio without anonymizing then I always have to edit the header images after I export then to my archive in Osirix, to keep organized and in the same study, and sometimes the images are rotated upside down. Just to save me time I wounder if anybody has a clue. Thank you. Lucas Lessa S?o Paulo - Brazil ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100208/04a0ba25/attachment-0001.html From susumu at mri.jhu.edu Mon Feb 8 08:41:30 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 08 Feb 2010 08:41:30 -0500 Subject: [Mristudio-users] Are calculated resluts influenced by the order of stored images in .REC? In-Reply-To: <2404f5961002080025p7c8f2cccr8c34fe5a3916136f@mail.gmail.com> References: <2404f5961002080025p7c8f2cccr8c34fe5a3916136f@mail.gmail.com> Message-ID: Hi Wenshu, In old days, Philips scanners were saving DTI data in slice-by-slice but I thought the current REC files are gradient-by-gradient order. Anyway, it seems that you can control the way images are saved in a REC file. Please make sure that the locations of the b0 image (either the first or the second from the last) is also correct. Please read the images by Mri3DView first and make sure that the order of the images is the same of your gradient table. If the images are read correctly and the order matches to the gradient table, there is no reason that you can't get the same quality of images. Another possibility is the quality of your data. Please make sure that your subject didn't move. If you acquired multiple REC files, you can create subtracted images to quickly check the subject motion. Susumu On Mon, Feb 8, 2010 at 3:25 AM, ??? wrote: > Hi, all > > I have used DTIStudio to calculate tensor index. The former order of stored > images in .REC file is "gradient by gradient", every result is OK. The > latest two patients' data has been saved as "slice by slice". Though I chose > "slice by slice" when input data, the calculated tensor index were all > blurry. I wanna know if the resluts will be influenced by the order of > stored images in .REC or the blur is just caused by other effects such as > movements. > Did anyone have the same problem? > > Thank you! > > > Regards, > Wenshu Qian > > Department of Diagnostic Radiology > The University of Hong Kong > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100208/786d5b9c/attachment.html From susumu at mri.jhu.edu Mon Feb 8 10:39:06 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 08 Feb 2010 10:39:06 -0500 Subject: [Mristudio-users] How to don't anonymize the processed images In-Reply-To: <129276.65365.qm@web110208.mail.gq1.yahoo.com> References: <129276.65365.qm@web110208.mail.gq1.yahoo.com> Message-ID: We are currently working on linking DtiStudio output to a database. One of the things we are working is to keep the DICOM information in the DtiStudio output. Hangyi, I thought that we are trying DICOM output with the header info retrieved from the original data. Where are we now in this front? Susumu On Mon, Feb 8, 2010 at 4:38 AM, Lucas Lessa wrote: > Dear friends and dear Dr. Mori. > > Good morning. > I'd like to know if it's possible to generate FA, ADC, DWI and etc, by the > DTI Studio without anonymizing then > I always have to edit the header images after I export then to my archive > in Osirix, to keep organized and in the same study, and sometimes the images > are rotated upside down. > Just to save me time I wounder if anybody has a clue. > Thank you. > > Lucas Lessa > S?o Paulo - Brazil > ** > > ------------------------------ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10- > Celebridades- > M?sica- > Esportes > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100208/c85e6165/attachment.html From Jan.Tillema at cchmc.org Mon Feb 8 14:42:25 2010 From: Jan.Tillema at cchmc.org (Jan Tillema) Date: Mon, 08 Feb 2010 14:42:25 -0500 Subject: [Mristudio-users] batch processing Message-ID: <4B7022D1.D7E9.000C.0@cchmc.org> Does anyone have a script or program to have multiple datasets processed in a similar fashion (including a possibility to pre-set parameters for which files are saved etc) or is there such a feature on DTIstudio that I have not been able to find? Thanks Jan Tillema, M.D. Cincinnati, OH -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100208/f1960825/attachment.html From qianwenshu at gmail.com Mon Feb 8 22:55:16 2010 From: qianwenshu at gmail.com (=?GB2312?B?x67OxMrg?=) Date: Tue, 09 Feb 2010 11:55:16 +0800 Subject: [Mristudio-users] Are calculated resluts influenced by the order of stored images in .REC? In-Reply-To: References: <2404f5961002080025p7c8f2cccr8c34fe5a3916136f@mail.gmail.com> Message-ID: <2404f5961002081955v5f21d0e9tf0f0109cf3499139@mail.gmail.com> Dear Prof. Mori, With your suggestion, I have figured this problem out. The order of the images is not the same as the former gradient table, but with b0 images first. Thank you! Regards, Wenshu 2010/2/8 susumu mori > Hi Wenshu, > > In old days, Philips scanners were saving DTI data in slice-by-slice but I > thought the current REC files are gradient-by-gradient order. Anyway, it > seems that you can control the way images are saved in a REC file. Please > make sure that the locations of the b0 image (either the first or the second > from the last) is also correct. > > Please read the images by Mri3DView first and make sure that the order of > the images is the same of your gradient table. If the images are read > correctly and the order matches to the gradient table, there is no reason > that you can't get the same quality of images. > > Another possibility is the quality of your data. Please make sure that your > subject didn't move. If you acquired multiple REC files, you can create > subtracted images to quickly check the subject motion. > > Susumu > > On Mon, Feb 8, 2010 at 3:25 AM, ??? wrote: > >> Hi, all >> >> I have used DTIStudio to calculate tensor index. The former order of >> stored images in .REC file is "gradient by gradient", every result is OK. >> The latest two patients' data has been saved as "slice by slice". Though I >> chose "slice by slice" when input data, the calculated tensor index were all >> blurry. I wanna know if the resluts will be influenced by the order of >> stored images in .REC or the blur is just caused by other effects such as >> movements. >> Did anyone have the same problem? >> >> Thank you! >> >> >> Regards, >> Wenshu Qian >> >> Department of Diagnostic Radiology >> The University of Hong Kong >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100209/8f3ab5f6/attachment.html From susumu at mri.jhu.edu Wed Feb 10 11:01:23 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 10 Feb 2010 11:01:23 -0500 Subject: [Mristudio-users] batch processing In-Reply-To: <4B7022D1.D7E9.000C.0@cchmc.org> References: <4B7022D1.D7E9.000C.0@cchmc.org> Message-ID: Hi Jan, Currently DtiStudio is not supporting batch processing. We are working on it. The key for batch processing is automated quality control reporting. Otherwise, you would not notice of inclusion of data with artifacts due to subject motion, co-registration errors, or scanner problems. We are working on it. Should be out this year. Susumu On Mon, Feb 8, 2010 at 2:42 PM, Jan Tillema wrote: > Does anyone have a script or program to have multiple datasets processed > in a similar fashion (including a possibility to pre-set parameters for > which files are saved etc) or is there such a feature on DTIstudio that I > have not been able to find? > > Thanks > > Jan Tillema, M.D. > Cincinnati, OH > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100210/77659d0c/attachment-0001.html From saksena.sona at gmail.com Thu Feb 11 11:34:42 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Thu, 11 Feb 2010 11:34:42 -0500 Subject: [Mristudio-users] corpus callsoum segmentation In-Reply-To: References: <9018fecc1002010858n57a1f02sf4bbc136f88d889e@mail.gmail.com> <9018fecc1002030756v6b03d0fej1200e9b53a1595af@mail.gmail.com> Message-ID: <9018fecc1002110834q48793385pfa9a346f9fc0b78a@mail.gmail.com> Hello, I am not able to find the downlaod section in the https://www.mristudio.org/wiki/user_manual/landmarker/installation. Please let me know how to download Vcredist_x86.exe and vcredist_x64.exe from the download section. Any help is highly appreciated. thanks On Wed, Feb 3, 2010 at 11:50 AM, Xin Li wrote: > Hello Sona, > > You may need to install runtime components of Visual C++ libraries on your > computer. Please take a look at > https://www.mristudio.org/wiki/user_manual/landmarker/installation. > Vcredist_x86.exe and vcredist_x64.exe are available in the download section. > > Hope this can solve your problem. > > > Xin > > > > > ----- Original Message ----- > From: Sona Saksena > Date: Wednesday, February 3, 2010 10:56 am > Subject: Re: [Mristudio-users] corpus callsoum segmentation > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > > > Hello, > > > > I am facing a problem while downloading DiffeoMap-latest-x64.exe and > > ROIEditor-latest-x64.exe. After running the program, an option comes > > WinZip > > Self-Extractor i.e. to unzip all the files by pressing the Unzip button. > > After unzipping the files the program does not work. Please let me > > know how > > to proceed further. > > > > Any help is highly appreciated. > > > > thanks > > > > regards > > > > Sona Saksena > > > > > > > > > > > > > > > > On Mon, Feb 1, 2010 at 4:12 PM, susumu mori wrote: > > > > > Hi Sona, > > > > > > This is a question about cross-subject brain registration. Your are > > > basically asking how we can identify the corresponding areas of the > > CC > > > across multiple subjects. Witelson scheme is one of them, which > > divide the > > > CC into the seven segments based on pre-defined distance-based > criteria. > > > There are two often-counteracting factors in the mapping; > reproducibility > > > (reliability) and granularity (the number of segmentation, or the > > amount of > > > localization information). > > > > > > One extreme of the granularity is the entire CC, in which we get > > one number > > > for the entire CC (e.g. the size of the mid-sagittal CC). The > > reliability of > > > the CC definition is high across the subjects because we can > unambiguously > > > define the mid-sagittal CC for any subjects, but the localization > > > information is the poorest. If only the genu of the CC is abnormal, > > such an > > > effect would be diluted by measuring the entire CC at once. > > > > > > Another extreme is the pixel-based analysis, in which we have to > > make a > > > complete mapping of each pixel between the two subject. If there > > are 5,000 > > > 1x1x1 mm pixels within the mid-sagittal CC, we need to map the all > > 5,000 > > > pixels to another brain. This is basically the same as making the > > two CC > > > shapes the identical by image transformation. This has the highest > > > localization information but the reliability is a tough issue. > > Depending on > > > which transformation algorithm you use, you get different results. > > This > > > approach has a potential to pin-point a small abnormal region > > within the CC, > > > but such an effect could be diluted if there is transformation > > error. Also, > > > each pixel is very noisy and a pixel-based statistics may have poor > > > sensitivity. Often you need to apply a filtering that introduces > > > pixel-averaging for nearby pixels. > > > > > > The Witelson approach is somewhere between these two approaches. It > > has > > > only 7 very large segments in which 100s of pixels are averaged. > > > > > > Now your question is, if we provide a tool to perform the Witelson > > > segmentation. The short answer is no, but if you take your question > > as a > > > general brain registration question, the answer is yes. > > > > > > By using DiffeoMap, you can transform one brain to the other. We > > are using > > > a very advanced diffeomorphic transformation developed by Michael > > Miller. So > > > you will find the transformation results are of quite high quality. > > Once you > > > transform one brain to the other, you can do pixel-based analysis. > > > > > > Then you can move the transformed images into RoiEditor, in which > > you can > > > apply a pre-segmented brain atlas to segment the entire brain up to > > 176 > > > areas. Currently, the CC is segmented to three areas: genu, body, and > > > splenium. In this atlas, you can create your own segment. For > > example, you > > > can segment the atlas CC to 7 Witelson segments. Then transform the > > atlas to > > > each subject (or transform each subject to the atlas) to apply these > > > segments to registered brain. > > > > > > So, I would recommend you to take a look at www.mristudio.org and > find > > > what you can do with DiffeoMap and RoiEditor. > > > > > > Susumu > > > > > > On Mon, Feb 1, 2010 at 11:58 AM, Sona Saksena < > saksena.sona at gmail.com>wrote: > > > > > >> Hello, > > >> > > >> I would like to calculate ADC and FA values in the seven segments > > of > > >> corpus callosum divided according to the Witelson scheme. CAn I do > > that > > >> using DTIstudio software. Please let me know how to divide the corpus > > >> callsoum into seven segments using DTIstudio software or suggest > > any other > > >> possible way to do it. > > >> > > >> Any help will be highly appreciated. > > >> > > >> thanks > > >> > > >> regards > > >> > > >> Sona Saksena > > >> > > >> > > >> _______________________________________________ > > >> Mristudio-users mailing list > > >> Mristudio-users at mristudio.org > > >> > > >> Unsubscribe, send a blank email to: > > >> Mristudio-users-unsubscribe at mristudio.org > > >> > > >> > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > > > > > -- > > Regards > > Sona Saksena > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -- Regards Sona Saksena -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100211/f6ab9b45/attachment.html From xli16 at jhmi.edu Thu Feb 11 12:20:44 2010 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 11 Feb 2010 12:20:44 -0500 Subject: [Mristudio-users] corpus callsoum segmentation In-Reply-To: <9018fecc1002110834q48793385pfa9a346f9fc0b78a@mail.gmail.com> References: <9018fecc1002010858n57a1f02sf4bbc136f88d889e@mail.gmail.com> <9018fecc1002030756v6b03d0fej1200e9b53a1595af@mail.gmail.com> <9018fecc1002110834q48793385pfa9a346f9fc0b78a@mail.gmail.com> Message-ID: Hello, The dowload section is at https://www.mristudio.org/wiki/installation. You will find vcredist_x86.exe and vcredist_x64.exe there. Xin ----- Original Message ----- From: Sona Saksena Date: Thursday, February 11, 2010 11:34 am Subject: Re: [Mristudio-users] corpus callsoum segmentation To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello, > > I am not able to find the downlaod section in the > Please > let me know how to download Vcredist_x86.exe and vcredist_x64.exe > from the > download section. > > Any help is highly appreciated. > > thanks > > > On Wed, Feb 3, 2010 at 11:50 AM, Xin Li wrote: > > > Hello Sona, > > > > You may need to install runtime components of Visual C++ libraries > on your > > computer. Please take a look at > > > > Vcredist_x86.exe and vcredist_x64.exe are available in the download > section. > > > > Hope this can solve your problem. > > > > > > Xin > > > > > > > > > > ----- Original Message ----- > > From: Sona Saksena > > Date: Wednesday, February 3, 2010 10:56 am > > Subject: Re: [Mristudio-users] corpus callsoum segmentation > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > > mristudio-users at mristudio.org> > > > > > > > Hello, > > > > > > I am facing a problem while downloading DiffeoMap-latest-x64.exe > and > > > ROIEditor-latest-x64.exe. After running the program, an option comes > > > WinZip > > > Self-Extractor i.e. to unzip all the files by pressing the Unzip > button. > > > After unzipping the files the program does not work. Please let > me > > > know how > > > to proceed further. > > > > > > Any help is highly appreciated. > > > > > > thanks > > > > > > regards > > > > > > Sona Saksena > > > > > > > > > > > > > > > > > > > > > > > > On Mon, Feb 1, 2010 at 4:12 PM, susumu mori > wrote: > > > > > > > Hi Sona, > > > > > > > > This is a question about cross-subject brain registration. > Your are > > > > basically asking how we can identify the corresponding areas > of the > > > CC > > > > across multiple subjects. Witelson scheme is one of them, which > > > divide the > > > > CC into the seven segments based on pre-defined distance-based > > criteria. > > > > There are two often-counteracting factors in the mapping; > > reproducibility > > > > (reliability) and granularity (the number of segmentation, or > the > > > amount of > > > > localization information). > > > > > > > > One extreme of the granularity is the entire CC, in which we get > > > one number > > > > for the entire CC (e.g. the size of the mid-sagittal CC). The > > > reliability of > > > > the CC definition is high across the subjects because we can > > unambiguously > > > > define the mid-sagittal CC for any subjects, but the localization > > > > information is the poorest. If only the genu of the CC is abnormal, > > > such an > > > > effect would be diluted by measuring the entire CC at once. > > > > > > > > Another extreme is the pixel-based analysis, in which we have > to > > > make a > > > > complete mapping of each pixel between the two subject. If there > > > are 5,000 > > > > 1x1x1 mm pixels within the mid-sagittal CC, we need to map the > all > > > 5,000 > > > > pixels to another brain. This is basically the same as making > the > > > two CC > > > > shapes the identical by image transformation. This has the highest > > > > localization information but the reliability is a tough issue. > > > Depending on > > > > which transformation algorithm you use, you get different results. > > > This > > > > approach has a potential to pin-point a small abnormal region > > > within the CC, > > > > but such an effect could be diluted if there is transformation > > > error. Also, > > > > each pixel is very noisy and a pixel-based statistics may have > poor > > > > sensitivity. Often you need to apply a filtering that introduces > > > > pixel-averaging for nearby pixels. > > > > > > > > The Witelson approach is somewhere between these two > approaches. It > > > has > > > > only 7 very large segments in which 100s of pixels are averaged. > > > > > > > > Now your question is, if we provide a tool to perform the Witelson > > > > segmentation. The short answer is no, but if you take your question > > > as a > > > > general brain registration question, the answer is yes. > > > > > > > > By using DiffeoMap, you can transform one brain to the other. > We > > > are using > > > > a very advanced diffeomorphic transformation developed by Michael > > > Miller. So > > > > you will find the transformation results are of quite high quality. > > > Once you > > > > transform one brain to the other, you can do pixel-based analysis. > > > > > > > > Then you can move the transformed images into RoiEditor, in which > > > you can > > > > apply a pre-segmented brain atlas to segment the entire brain > up to > > > 176 > > > > areas. Currently, the CC is segmented to three areas: genu, > body, and > > > > splenium. In this atlas, you can create your own segment. For > > > example, you > > > > can segment the atlas CC to 7 Witelson segments. Then > transform the > > > atlas to > > > > each subject (or transform each subject to the atlas) to apply > these > > > > segments to registered brain. > > > > > > > > So, I would recommend you to take a look at www.mristudio.org > and > > find > > > > what you can do with DiffeoMap and RoiEditor. > > > > > > > > Susumu > > > > > > > > On Mon, Feb 1, 2010 at 11:58 AM, Sona Saksena < > > saksena.sona at gmail.com>wrote: > > > > > > > >> Hello, > > > >> > > > >> I would like to calculate ADC and FA values in the seven segments > > > of > > > >> corpus callosum divided according to the Witelson scheme. CAn > I do > > > that > > > >> using DTIstudio software. Please let me know how to divide > the corpus > > > >> callsoum into seven segments using DTIstudio software or suggest > > > any other > > > >> possible way to do it. > > > >> > > > >> Any help will be highly appreciated. > > > >> > > > >> thanks > > > >> > > > >> regards > > > >> > > > >> Sona Saksena > > > >> > > > >> > > > >> _______________________________________________ > > > >> Mristudio-users mailing list > > > >> Mristudio-users at mristudio.org > > > >> > > > >> Unsubscribe, send a blank email to: > > > >> Mristudio-users-unsubscribe at mristudio.org > > > >> > > > >> > > > > > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > > Unsubscribe, send a blank email to: > > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > > > > > > > > > > -- > > > Regards > > > Sona Saksena > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > > > -- > Regards > Sona Saksena > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From rajagov2 at ccf.org Fri Feb 12 12:11:42 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Fri, 12 Feb 2010 12:11:42 -0500 Subject: [Mristudio-users] SS-EPI and SS SE EPI Message-ID: <77A88E90A851594AAEF830450587C39D01EDABEE@CCHSCLEXMB56.cc.ad.cchs.net> Hello All, I couldn't find the answer to the following question by searching the internet, so i thought seeking your help. I would like to know whether single shot spin echo EPI (for DTI studies) will suffer from same susceptibility artifacts (distortions) like single shot EPI. It will be great if someone could tell me the advantages of SS SE-EPI over SS EPI. Thanks in advance. venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100212/0919f68c/attachment-0001.html From susumu at mri.jhu.edu Sun Feb 14 12:33:07 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sun, 14 Feb 2010 12:33:07 -0500 Subject: [Mristudio-users] SS-EPI and SS SE EPI In-Reply-To: <77A88E90A851594AAEF830450587C39D01EDABEE@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D01EDABEE@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Hi Venkateswaran, I believe the amount of the distortion is the same between EPI and SS-EPI. I also believe EPI suffers more from signal drop due to the susceptibility artifacts compared to SS-EPI simply because EPI miss the top-of-the-echo time points for data acquisition. Susumu On Fri, Feb 12, 2010 at 12:11 PM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > Hello All, > > I couldn't find the answer to the following question by searching the > internet, so i thought seeking your help. I would like to know whether > single shot spin echo EPI (for DTI studies) will suffer from same > susceptibility artifacts (distortions) like single shot EPI. It will be > great if someone could tell me the advantages of SS SE-EPI over SS EPI. > > Thanks in advance. > > venkateswaran > > =================================== > > P Please consider the environment before printing this e-mail > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100214/e993f2a2/attachment.html From rajagov2 at ccf.org Mon Feb 15 09:19:18 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Mon, 15 Feb 2010 09:19:18 -0500 Subject: [Mristudio-users] SS-EPI and SS SE EPI References: <77A88E90A851594AAEF830450587C39D01EDABEE@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D01EDABF1@CCHSCLEXMB56.cc.ad.cchs.net> Thanks Dr.Mori, Sorry may be i was not clear is the amount of susceptibility artifacts same for SS spin echo EPI sequence and SS EPI. Thanks again, venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Sun 2/14/2010 12:33 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] SS-EPI and SS SE EPI Hi Venkateswaran, I believe the amount of the distortion is the same between EPI and SS-EPI. I also believe EPI suffers more from signal drop due to the susceptibility artifacts compared to SS-EPI simply because EPI miss the top-of-the-echo time points for data acquisition. Susumu On Fri, Feb 12, 2010 at 12:11 PM, Rajagopalan, Venkateswaran wrote: Hello All, I couldn't find the answer to the following question by searching the internet, so i thought seeking your help. I would like to know whether single shot spin echo EPI (for DTI studies) will suffer from same susceptibility artifacts (distortions) like single shot EPI. It will be great if someone could tell me the advantages of SS SE-EPI over SS EPI. Thanks in advance. venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6227 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100215/c0a7deba/attachment.bin From choisj70 at gmail.com Tue Feb 16 14:21:55 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 16 Feb 2010 14:21:55 -0500 Subject: [Mristudio-users] Question on the Philips Achieva Gradient Scheme Message-ID: This question is for Philips Achieva system users. I am a Philips Achieva system user. I wonder DW gradient schemes that are implemented (6, 15, 32) in Philips Achieva systems are base on Icosahedral scheme or not. In addition, when we use Overplus option how the DW gradient scheme changes. Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100216/d68e01c5/attachment.html From saksena.sona at gmail.com Tue Feb 16 14:23:40 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Tue, 16 Feb 2010 14:23:40 -0500 Subject: [Mristudio-users] Urgent Message-ID: <9018fecc1002161123g6748a71fk54e69a753b1d82f4@mail.gmail.com> Hello, Can we process the spinal cord DTI of a patient using DTIstudio. Please let me know. If not, please suggest the possible reason. Any help is highly appreciated. thnaks regards -- Sona -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100216/615553df/attachment.html From alex.dresner at philips.com Wed Feb 17 07:31:40 2010 From: alex.dresner at philips.com (Dresner, Alex) Date: Wed, 17 Feb 2010 13:31:40 +0100 Subject: [Mristudio-users] DTI Studio in cervical spine In-Reply-To: <9018fecc1002161123g6748a71fk54e69a753b1d82f4@mail.gmail.com> References: <9018fecc1002161123g6748a71fk54e69a753b1d82f4@mail.gmail.com> Message-ID: This journal article uses DTI Studio for cervical spine: http://www.mrijournal.com/article/S0730-725X(09)00141-6/abstract (copied below). Magnetic Resonance Imaging Volume 28, Issue 1, Pages 70-76 (January 2010) Dependence of the fractional anisotropy in cervical spine from the number of diffusion gradients, repeated acquisition and voxel size Received 26 September 2008; received in revised form 15 May 2009; accepted 19 May 2009. published online 06 July 2009. Abstract The aim of this study is to investigate the consequences of using different gradient schemes, number of repeated measurements and voxel size on the fractional anisotropy (FA) value in a diffusion tensor imaging (DTI) sequence on the cervical tract of the spinal cord. Twenty healthy volunteers underwent a total of 86 DTI axial acquisitions performed by using different voxel size and number of diffusion gradient directions (NDGDs). Three different diffusion gradient schemes were applied, named 6, 15 and 32 according to the NDGD. Furthermore, some acquisitions were repeated to investigate the effects of image averaging on FA value. Our results indicate that the FA value in the cervical spinal cord decreases when increasing the NDGD for a fixed spatial resolution, or when identical acquisitions are repeated, thus, increasing the acquisition time. This effect is observed in all subjects without exceptions, and the differences result statistically significant: the average FA obtained from 6, 15 and 32 NDGD is 0.84 (range, 0.82-0.87), 0.75 (range, 0.68-0.80) and 0.70 (range, 0.65-0.77), respectively, for isotropic 8 mm3 voxel size. When varying the spatial resolution in a volume range of 2 to 8 mm3 for a fixed NDGD (6 or 15), the differences in FA values are smaller albeit still statistically significant: the smaller the voxel, the larger the FA. No significant dependence of the FA value from the spatial resolution is observed in the 32 NDGD acquisitions in the studied volume range. In conclusion, our results indicate that the value of the FA in the cervical tract of the spinal cord vary with regularity in intrasubject acquisitions when modifying the NDGD and when repeated acquisitions are used; these observations confirm that the signal-to-noise ratio introduces a systematic error in FA measurements that does not allow simple comparison of quantitative results obtained from separated studies. From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Sona Saksena Sent: Tuesday, February 16, 2010 2:24 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support; susumu mori Subject: [Mristudio-users] Urgent Hello, Can we process the spinal cord DTI of a patient using DTIstudio. Please let me know. If not, please suggest the possible reason. Any help is highly appreciated. thnaks regards -- Sona ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100217/0e24e96c/attachment-0001.html From yj3 at duke.edu Wed Feb 17 08:43:47 2010 From: yj3 at duke.edu (Yi Jiang) Date: Wed, 17 Feb 2010 08:43:47 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & command file References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> Message-ID: <68FC2725584849B0AFA859749CFF3A06@panpan> Hello, Xin, Thank you very much for the information. I have one more question: does the vector indicating new location start from 0 or 1? That is: if my image size is 512x256x256, the vector should be (0-511)x(0-255)x(0-255) or (1-512)x(1-256)x(1-256)? Thank you! Best, Yi ----- Original Message ----- From: "Xin Li" To: "susumu mori" ; "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker Questions/Support" ; "Jiangyang Zhang" Sent: Monday, February 01, 2010 10:22 AM Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file Hello Yi, As Susumu said, transformation matrices contain vectors at each coordinate, indicating where is the new location. The structure is Vector (x, y, z) x X-dimension x Y-dimension x Z-dimension. You may write matlab code to extract the vector information. Xin ----- Original Message ----- From: susumu mori Date: Saturday, January 30, 2010 8:29 am Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker Questions/Support" , Xin Li , Jiangyang Zhang > Hi Yi, > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: > > > Hello, dear all, > > > > > > > > I have two questions and am wondering if someone can help. > > > > > > > > 1. I have already had a transformation matrix to map the subject > image > > onto the template image, which was generated by combining AIR > rigid, AIR > > affine, and LDDMM matrix. I want to define some landmarkers on > the subject > > image, and apply the transformation matrix to the landmarkers > (to see their > > corresponding location on the template image). How can I do that? > > > > > I think this is exactly what the K and H maps are. I need > confirmation from > Xin, but in my understanding, these transformation matrices contain > vectors > at each coordinate, indicating where is the new location. If I'm not > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x > Z-dimension. > There must be a way to extarct the "Vector" information at the specified > coordinate. > > > > > > > 1. I would like to use the ?load command file? function. I will > do AIR > > linear rigid transformation, AIR linear affine transformation, > image format > > change to byte, automatic intensity correction by histogram, and > 2-channel > > LDDMM. Is it possible to put all these into one command file? If > yes, can > > anyone give me an example file? > > > > I believe the command file is only for the functions within the > same box, > including byte-integer-float conversion, axial-sagittal-coronal > conversion, > resampling, etc. They don't include transformation functions. We are > working > on automation, which will take several months. Meanwhile, I believe > it is > good idea to use the current way, which forces you to check the > result after > each step. Transformation sometimes does silly things. Some images > may have > quality problems. You may want compare different methods (e.g. Mutual > Info > linear transformation vs AIR, intensity correction methods, contrast > of > choice). I think it's very important to get a feel about your data > and each > transformation step. Also, depending on pathology, the transformation > strategy may change. Some disease groups have severe intensity > changes (e.g. > stroke), some have severely enlarged ventricles. You may find the same > methods may work for one but not the other. Automation is still a > difficult > matter for transformation-based analysis. > > > > > > > > Thank you very much! > > > > > > > > Have a nice weekend! > > > > > > > > Best > > > > Yi > > > > > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Wed Feb 17 10:01:45 2010 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 17 Feb 2010 10:01:45 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & command file In-Reply-To: <68FC2725584849B0AFA859749CFF3A06@panpan> References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> <68FC2725584849B0AFA859749CFF3A06@panpan> Message-ID: Hello Yi, If your image size is 512x256x256, the vector should be (0-511)x(0-255)x(0-255) Xin ----- Original Message ----- From: Yi Jiang Date: Wednesday, February 17, 2010 8:44 am Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello, Xin, > > Thank you very much for the information. > > I have one more question: does the vector indicating new location > start from > 0 or 1? That is: if my image size is 512x256x256, the vector should > be > (0-511)x(0-255)x(0-255) or (1-512)x(1-256)x(1-256)? > > Thank you! > > Best, > Yi > > > ----- Original Message ----- > From: "Xin Li" > To: "susumu mori" ; "Yi Jiang" ; > "DTI > Studio, ROI Editor, Landmarker Questions/Support" > ; "Jiangyang Zhang" > Sent: Monday, February 01, 2010 10:22 AM > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > > > Hello Yi, > > As Susumu said, transformation matrices contain vectors at each > coordinate, > indicating where is the new location. The structure is Vector (x, y, > z) x > X-dimension x Y-dimension x Z-dimension. You may write matlab code to > > extract the vector information. > > > Xin > > > > > > ----- Original Message ----- > From: susumu mori > Date: Saturday, January 30, 2010 8:29 am > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker > Questions/Support" , Xin Li > , > Jiangyang Zhang > > > > Hi Yi, > > > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: > > > > > Hello, dear all, > > > > > > > > > > > > I have two questions and am wondering if someone can help. > > > > > > > > > > > > 1. I have already had a transformation matrix to map the subject > > image > > > onto the template image, which was generated by combining AIR > > rigid, AIR > > > affine, and LDDMM matrix. I want to define some landmarkers on > > the subject > > > image, and apply the transformation matrix to the landmarkers > > (to see their > > > corresponding location on the template image). How can I do that? > > > > > > > > I think this is exactly what the K and H maps are. I need > > confirmation from > > Xin, but in my understanding, these transformation matrices > contain > > vectors > > at each coordinate, indicating where is the new location. If I'm not > > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x > > Z-dimension. > > There must be a way to extarct the "Vector" information at the specified > > coordinate. > > > > > > > > > > > 1. I would like to use the ?load command file? function. I will > > do AIR > > > linear rigid transformation, AIR linear affine transformation, > > image format > > > change to byte, automatic intensity correction by histogram, > and > > 2-channel > > > LDDMM. Is it possible to put all these into one command file? > If > > yes, can > > > anyone give me an example file? > > > > > > I believe the command file is only for the functions within the > > same box, > > including byte-integer-float conversion, axial-sagittal-coronal > > conversion, > > resampling, etc. They don't include transformation functions. We are > > working > > on automation, which will take several months. Meanwhile, I believe > > it is > > good idea to use the current way, which forces you to check the > > result after > > each step. Transformation sometimes does silly things. Some images > > may have > > quality problems. You may want compare different methods (e.g. Mutual > > Info > > linear transformation vs AIR, intensity correction methods, contrast > > of > > choice). I think it's very important to get a feel about your data > > and each > > transformation step. Also, depending on pathology, the transformation > > strategy may change. Some disease groups have severe intensity > > changes (e.g. > > stroke), some have severely enlarged ventricles. You may find the > same > > methods may work for one but not the other. Automation is still a > > > difficult > > matter for transformation-based analysis. > > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > Have a nice weekend! > > > > > > > > > > > > Best > > > > > > Yi > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From yj3 at duke.edu Wed Feb 17 11:05:27 2010 From: yj3 at duke.edu (Yi Jiang) Date: Wed, 17 Feb 2010 11:05:27 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & command file References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> <68FC2725584849B0AFA859749CFF3A06@panpan> Message-ID: <3DA6F72FDB2B40BF9D193236123F27B7@panpan> Hello Xin, Thank you! I looked at the transformation matrix. Overall it looks reasonable (i.e. I think my reading format of the matrix is correct. I was able to use the vector information to reasonably map land marks I chose). But I found the value of the vector somehow ranges from e.g. (-40~540)x(-30~270)x(-20~280) instead of (0-511)x(0-255)x(0-255) I would expect. What do those out of range (out of (0-511)x(0-255)x(0-255) ) values mean? Best, Yi ----- Original Message ----- From: "Xin Li" To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wednesday, February 17, 2010 10:01 AM Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file Hello Yi, If your image size is 512x256x256, the vector should be (0-511)x(0-255)x(0-255) Xin ----- Original Message ----- From: Yi Jiang Date: Wednesday, February 17, 2010 8:44 am Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello, Xin, > > Thank you very much for the information. > > I have one more question: does the vector indicating new location > start from > 0 or 1? That is: if my image size is 512x256x256, the vector should > be > (0-511)x(0-255)x(0-255) or (1-512)x(1-256)x(1-256)? > > Thank you! > > Best, > Yi > > > ----- Original Message ----- > From: "Xin Li" > To: "susumu mori" ; "Yi Jiang" ; > "DTI > Studio, ROI Editor, Landmarker Questions/Support" > ; "Jiangyang Zhang" > Sent: Monday, February 01, 2010 10:22 AM > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > > > Hello Yi, > > As Susumu said, transformation matrices contain vectors at each > coordinate, > indicating where is the new location. The structure is Vector (x, y, > z) x > X-dimension x Y-dimension x Z-dimension. You may write matlab code to > > extract the vector information. > > > Xin > > > > > > ----- Original Message ----- > From: susumu mori > Date: Saturday, January 30, 2010 8:29 am > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker > Questions/Support" , Xin Li > , > Jiangyang Zhang > > > > Hi Yi, > > > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: > > > > > Hello, dear all, > > > > > > > > > > > > I have two questions and am wondering if someone can help. > > > > > > > > > > > > 1. I have already had a transformation matrix to map the subject > > image > > > onto the template image, which was generated by combining AIR > > rigid, AIR > > > affine, and LDDMM matrix. I want to define some landmarkers on > > the subject > > > image, and apply the transformation matrix to the landmarkers > > (to see their > > > corresponding location on the template image). How can I do that? > > > > > > > > I think this is exactly what the K and H maps are. I need > > confirmation from > > Xin, but in my understanding, these transformation matrices > contain > > vectors > > at each coordinate, indicating where is the new location. If I'm not > > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x > > Z-dimension. > > There must be a way to extarct the "Vector" information at the > specified > > coordinate. > > > > > > > > > > > 1. I would like to use the ?load command file? function. I will > > do AIR > > > linear rigid transformation, AIR linear affine transformation, > > image format > > > change to byte, automatic intensity correction by histogram, > and > > 2-channel > > > LDDMM. Is it possible to put all these into one command file? > If > > yes, can > > > anyone give me an example file? > > > > > > I believe the command file is only for the functions within the > > same box, > > including byte-integer-float conversion, axial-sagittal-coronal > > conversion, > > resampling, etc. They don't include transformation functions. We are > > working > > on automation, which will take several months. Meanwhile, I believe > > it is > > good idea to use the current way, which forces you to check the > > result after > > each step. Transformation sometimes does silly things. Some images > > may have > > quality problems. You may want compare different methods (e.g. Mutual > > Info > > linear transformation vs AIR, intensity correction methods, contrast > > of > > choice). I think it's very important to get a feel about your data > > and each > > transformation step. Also, depending on pathology, the transformation > > strategy may change. Some disease groups have severe intensity > > changes (e.g. > > stroke), some have severely enlarged ventricles. You may find the > same > > methods may work for one but not the other. Automation is still a > > > difficult > > matter for transformation-based analysis. > > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > Have a nice weekend! > > > > > > > > > > > > Best > > > > > > Yi > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Wed Feb 17 11:38:41 2010 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 17 Feb 2010 11:38:41 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & command file In-Reply-To: <3DA6F72FDB2B40BF9D193236123F27B7@panpan> References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> <68FC2725584849B0AFA859749CFF3A06@panpan> <3DA6F72FDB2B40BF9D193236123F27B7@panpan> Message-ID: Hello Yi, How did you get the matrix that you are working on? Is it a lddmm matrix or a combined matrix? Xin ----- Original Message ----- From: Yi Jiang Date: Wednesday, February 17, 2010 11:05 am Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello Xin, > > Thank you! I looked at the transformation matrix. Overall it looks > reasonable (i.e. I think my reading format of the matrix is correct. > I was > able to use the vector information to reasonably map land marks I > chose). > But I found the value of the vector somehow ranges from e.g. > (-40~540)x(-30~270)x(-20~280) instead of (0-511)x(0-255)x(0-255) I > would > expect. What do those out of range (out of (0-511)x(0-255)x(0-255) ) > values > mean? > > Best, > Yi > > > ----- Original Message ----- > From: "Xin Li" > To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker > Questions/Support" > Sent: Wednesday, February 17, 2010 10:01 AM > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > > > Hello Yi, > > If your image size is 512x256x256, the vector should be > (0-511)x(0-255)x(0-255) > > > Xin > > > > > ----- Original Message ----- > From: Yi Jiang > Date: Wednesday, February 17, 2010 8:44 am > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > Hello, Xin, > > > > Thank you very much for the information. > > > > I have one more question: does the vector indicating new location > > start from > > 0 or 1? That is: if my image size is 512x256x256, the vector should > > be > > (0-511)x(0-255)x(0-255) or (1-512)x(1-256)x(1-256)? > > > > Thank you! > > > > Best, > > Yi > > > > > > ----- Original Message ----- > > From: "Xin Li" > > To: "susumu mori" ; "Yi Jiang" ; > > "DTI > > Studio, ROI Editor, Landmarker Questions/Support" > > ; "Jiangyang Zhang" > > Sent: Monday, February 01, 2010 10:22 AM > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > & > > command > > file > > > > > > Hello Yi, > > > > As Susumu said, transformation matrices contain vectors at each > > coordinate, > > indicating where is the new location. The structure is Vector (x, > y, > > z) x > > X-dimension x Y-dimension x Z-dimension. You may write matlab code > to > > > > extract the vector information. > > > > > > Xin > > > > > > > > > > > > ----- Original Message ----- > > From: susumu mori > > Date: Saturday, January 30, 2010 8:29 am > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > & > > command > > file > > To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker > > Questions/Support" , Xin Li > > , > > Jiangyang Zhang > > > > > > > Hi Yi, > > > > > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: > > > > > > > Hello, dear all, > > > > > > > > > > > > > > > > I have two questions and am wondering if someone can help. > > > > > > > > > > > > > > > > 1. I have already had a transformation matrix to map the subject > > > image > > > > onto the template image, which was generated by combining > AIR > > > rigid, AIR > > > > affine, and LDDMM matrix. I want to define some > landmarkers on > > > the subject > > > > image, and apply the transformation matrix to the landmarkers > > > (to see their > > > > corresponding location on the template image). How can I > do that? > > > > > > > > > > > I think this is exactly what the K and H maps are. I need > > > confirmation from > > > Xin, but in my understanding, these transformation matrices > > contain > > > vectors > > > at each coordinate, indicating where is the new location. If > I'm not > > > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x > > > Z-dimension. > > > There must be a way to extarct the "Vector" information at the > > > specified > > > coordinate. > > > > > > > > > > > > > > > 1. I would like to use the ?load command file? function. I > will > > > do AIR > > > > linear rigid transformation, AIR linear affine transformation, > > > image format > > > > change to byte, automatic intensity correction by histogram, > > and > > > 2-channel > > > > LDDMM. Is it possible to put all these into one command file? > > If > > > yes, can > > > > anyone give me an example file? > > > > > > > > I believe the command file is only for the functions within the > > > same box, > > > including byte-integer-float conversion, axial-sagittal-coronal > > > conversion, > > > resampling, etc. They don't include transformation functions. > We are > > > working > > > on automation, which will take several months. Meanwhile, I believe > > > it is > > > good idea to use the current way, which forces you to check the > > > result after > > > each step. Transformation sometimes does silly things. Some images > > > may have > > > quality problems. You may want compare different methods (e.g. > Mutual > > > Info > > > linear transformation vs AIR, intensity correction methods, contrast > > > of > > > choice). I think it's very important to get a feel about your data > > > and each > > > transformation step. Also, depending on pathology, the transformation > > > strategy may change. Some disease groups have severe intensity > > > changes (e.g. > > > stroke), some have severely enlarged ventricles. You may find the > > same > > > methods may work for one but not the other. Automation is still > a > > > > > difficult > > > matter for transformation-based analysis. > > > > > > > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > > > > > Have a nice weekend! > > > > > > > > > > > > > > > > Best > > > > > > > > Yi > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > > Unsubscribe, send a blank email to: > > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From yj3 at duke.edu Wed Feb 17 14:03:49 2010 From: yj3 at duke.edu (Yi Jiang) Date: Wed, 17 Feb 2010 14:03:49 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & command file References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> <68FC2725584849B0AFA859749CFF3A06@panpan> <3DA6F72FDB2B40BF9D193236123F27B7@panpan> Message-ID: <83F95893B34E42E5917605B75970D35F@panpan> Hello Xin, It is a combined matrix. Yi ----- Original Message ----- From: "Xin Li" To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wednesday, February 17, 2010 11:38 AM Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file Hello Yi, How did you get the matrix that you are working on? Is it a lddmm matrix or a combined matrix? Xin ----- Original Message ----- From: Yi Jiang Date: Wednesday, February 17, 2010 11:05 am Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello Xin, > > Thank you! I looked at the transformation matrix. Overall it looks > reasonable (i.e. I think my reading format of the matrix is correct. > I was > able to use the vector information to reasonably map land marks I > chose). > But I found the value of the vector somehow ranges from e.g. > (-40~540)x(-30~270)x(-20~280) instead of (0-511)x(0-255)x(0-255) I > would > expect. What do those out of range (out of (0-511)x(0-255)x(0-255) ) > values > mean? > > Best, > Yi > > > ----- Original Message ----- > From: "Xin Li" > To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker > Questions/Support" > Sent: Wednesday, February 17, 2010 10:01 AM > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > > > Hello Yi, > > If your image size is 512x256x256, the vector should be > (0-511)x(0-255)x(0-255) > > > Xin > > > > > ----- Original Message ----- > From: Yi Jiang > Date: Wednesday, February 17, 2010 8:44 am > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > Hello, Xin, > > > > Thank you very much for the information. > > > > I have one more question: does the vector indicating new location > > start from > > 0 or 1? That is: if my image size is 512x256x256, the vector should > > be > > (0-511)x(0-255)x(0-255) or (1-512)x(1-256)x(1-256)? > > > > Thank you! > > > > Best, > > Yi > > > > > > ----- Original Message ----- > > From: "Xin Li" > > To: "susumu mori" ; "Yi Jiang" ; > > "DTI > > Studio, ROI Editor, Landmarker Questions/Support" > > ; "Jiangyang Zhang" > > Sent: Monday, February 01, 2010 10:22 AM > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > & > > command > > file > > > > > > Hello Yi, > > > > As Susumu said, transformation matrices contain vectors at each > > coordinate, > > indicating where is the new location. The structure is Vector (x, > y, > > z) x > > X-dimension x Y-dimension x Z-dimension. You may write matlab code > to > > > > extract the vector information. > > > > > > Xin > > > > > > > > > > > > ----- Original Message ----- > > From: susumu mori > > Date: Saturday, January 30, 2010 8:29 am > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > & > > command > > file > > To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker > > Questions/Support" , Xin Li > > , > > Jiangyang Zhang > > > > > > > Hi Yi, > > > > > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: > > > > > > > Hello, dear all, > > > > > > > > > > > > > > > > I have two questions and am wondering if someone can help. > > > > > > > > > > > > > > > > 1. I have already had a transformation matrix to map the > subject > > > image > > > > onto the template image, which was generated by combining > AIR > > > rigid, AIR > > > > affine, and LDDMM matrix. I want to define some > landmarkers on > > > the subject > > > > image, and apply the transformation matrix to the landmarkers > > > (to see their > > > > corresponding location on the template image). How can I > do that? > > > > > > > > > > > I think this is exactly what the K and H maps are. I need > > > confirmation from > > > Xin, but in my understanding, these transformation matrices > > contain > > > vectors > > > at each coordinate, indicating where is the new location. If > I'm not > > > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x > > > Z-dimension. > > > There must be a way to extarct the "Vector" information at the > > > specified > > > coordinate. > > > > > > > > > > > > > > > 1. I would like to use the ?load command file? function. I > will > > > do AIR > > > > linear rigid transformation, AIR linear affine transformation, > > > image format > > > > change to byte, automatic intensity correction by histogram, > > and > > > 2-channel > > > > LDDMM. Is it possible to put all these into one command file? > > If > > > yes, can > > > > anyone give me an example file? > > > > > > > > I believe the command file is only for the functions within the > > > same box, > > > including byte-integer-float conversion, axial-sagittal-coronal > > > conversion, > > > resampling, etc. They don't include transformation functions. > We are > > > working > > > on automation, which will take several months. Meanwhile, I believe > > > it is > > > good idea to use the current way, which forces you to check the > > > result after > > > each step. Transformation sometimes does silly things. Some images > > > may have > > > quality problems. You may want compare different methods (e.g. > Mutual > > > Info > > > linear transformation vs AIR, intensity correction methods, > contrast > > > of > > > choice). I think it's very important to get a feel about your data > > > and each > > > transformation step. Also, depending on pathology, the > transformation > > > strategy may change. Some disease groups have severe intensity > > > changes (e.g. > > > stroke), some have severely enlarged ventricles. You may find the > > same > > > methods may work for one but not the other. Automation is still > a > > > > > difficult > > > matter for transformation-based analysis. > > > > > > > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > > > > > Have a nice weekend! > > > > > > > > > > > > > > > > Best > > > > > > > > Yi > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > > Unsubscribe, send a blank email to: > > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Wed Feb 17 14:26:50 2010 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 17 Feb 2010 14:26:50 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & command file In-Reply-To: <83F95893B34E42E5917605B75970D35F@panpan> References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> <68FC2725584849B0AFA859749CFF3A06@panpan> <3DA6F72FDB2B40BF9D193236123F27B7@panpan> <83F95893B34E42E5917605B75970D35F@panpan> Message-ID: Hello Yi, Thank you for your information. I am going to check and give you a reply later. Xin ----- Original Message ----- From: Yi Jiang Date: Wednesday, February 17, 2010 2:04 pm Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello Xin, > > It is a combined matrix. > > Yi > > > ----- Original Message ----- > From: "Xin Li" > To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker > Questions/Support" > Sent: Wednesday, February 17, 2010 11:38 AM > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > > > Hello Yi, > > How did you get the matrix that you are working on? Is it a lddmm > matrix or > a combined matrix? > > > Xin > > > > ----- Original Message ----- > From: Yi Jiang > Date: Wednesday, February 17, 2010 11:05 am > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > Hello Xin, > > > > Thank you! I looked at the transformation matrix. Overall it looks > > reasonable (i.e. I think my reading format of the matrix is correct. > > I was > > able to use the vector information to reasonably map land marks I > > chose). > > But I found the value of the vector somehow ranges from e.g. > > (-40~540)x(-30~270)x(-20~280) instead of (0-511)x(0-255)x(0-255) I > > would > > expect. What do those out of range (out of (0-511)x(0-255)x(0-255) > ) > > values > > mean? > > > > Best, > > Yi > > > > > > ----- Original Message ----- > > From: "Xin Li" > > To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker > > Questions/Support" > > Sent: Wednesday, February 17, 2010 10:01 AM > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > & > > command > > file > > > > > > Hello Yi, > > > > If your image size is 512x256x256, the vector should be > > (0-511)x(0-255)x(0-255) > > > > > > Xin > > > > > > > > > > ----- Original Message ----- > > From: Yi Jiang > > Date: Wednesday, February 17, 2010 8:44 am > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > & > > command > > file > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > > > > > Hello, Xin, > > > > > > Thank you very much for the information. > > > > > > I have one more question: does the vector indicating new location > > > start from > > > 0 or 1? That is: if my image size is 512x256x256, the vector should > > > be > > > (0-511)x(0-255)x(0-255) or (1-512)x(1-256)x(1-256)? > > > > > > Thank you! > > > > > > Best, > > > Yi > > > > > > > > > ----- Original Message ----- > > > From: "Xin Li" > > > To: "susumu mori" ; "Yi Jiang" ; > > > "DTI > > > Studio, ROI Editor, Landmarker Questions/Support" > > > ; "Jiangyang Zhang" > > > Sent: Monday, February 01, 2010 10:22 AM > > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > > & > > > command > > > file > > > > > > > > > Hello Yi, > > > > > > As Susumu said, transformation matrices contain vectors at each > > > coordinate, > > > indicating where is the new location. The structure is Vector (x, > > y, > > > z) x > > > X-dimension x Y-dimension x Z-dimension. You may write matlab code > > to > > > > > > extract the vector information. > > > > > > > > > Xin > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > From: susumu mori > > > Date: Saturday, January 30, 2010 8:29 am > > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > > & > > > command > > > file > > > To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker > > > Questions/Support" , Xin Li > > > , > > > Jiangyang Zhang > > > > > > > > > > Hi Yi, > > > > > > > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: > > > > > > > > > Hello, dear all, > > > > > > > > > > > > > > > > > > > > I have two questions and am wondering if someone can help. > > > > > > > > > > > > > > > > > > > > 1. I have already had a transformation matrix to map > the > > subject > > > > image > > > > > onto the template image, which was generated by combining > > AIR > > > > rigid, AIR > > > > > affine, and LDDMM matrix. I want to define some > > landmarkers on > > > > the subject > > > > > image, and apply the transformation matrix to the landmarkers > > > > (to see their > > > > > corresponding location on the template image). How can > I > > do that? > > > > > > > > > > > > > > I think this is exactly what the K and H maps are. I need > > > > confirmation from > > > > Xin, but in my understanding, these transformation matrices > > > contain > > > > vectors > > > > at each coordinate, indicating where is the new location. If > > I'm not > > > > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension > x > > > > Z-dimension. > > > > There must be a way to extarct the "Vector" information at the > > > > > specified > > > > coordinate. > > > > > > > > > > > > > > > > > > > 1. I would like to use the ?load command file? > function. I > > will > > > > do AIR > > > > > linear rigid transformation, AIR linear affine transformation, > > > > image format > > > > > change to byte, automatic intensity correction by histogram, > > > and > > > > 2-channel > > > > > LDDMM. Is it possible to put all these into one command > file? > > > If > > > > yes, can > > > > > anyone give me an example file? > > > > > > > > > > I believe the command file is only for the functions > within the > > > > same box, > > > > including byte-integer-float conversion, axial-sagittal-coronal > > > > conversion, > > > > resampling, etc. They don't include transformation functions. > > We are > > > > working > > > > on automation, which will take several months. Meanwhile, I > believe > > > > it is > > > > good idea to use the current way, which forces you to check > the > > > > result after > > > > each step. Transformation sometimes does silly things. Some > images > > > > may have > > > > quality problems. You may want compare different methods (e.g. > > Mutual > > > > Info > > > > linear transformation vs AIR, intensity correction methods, > > > contrast > > > > of > > > > choice). I think it's very important to get a feel about > your data > > > > and each > > > > transformation step. Also, depending on pathology, the > > transformation > > > > strategy may change. Some disease groups have severe intensity > > > > changes (e.g. > > > > stroke), some have severely enlarged ventricles. You may > find the > > > same > > > > methods may work for one but not the other. Automation is still > > a > > > > > > > difficult > > > > matter for transformation-based analysis. > > > > > > > > > > > > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > > > > > > > > > Have a nice weekend! > > > > > > > > > > > > > > > > > > > > Best > > > > > > > > > > Yi > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Mristudio-users mailing list > > > > > Mristudio-users at mristudio.org > > > > > > > > > > Unsubscribe, send a blank email to: > > > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > > > > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From saksena.sona at gmail.com Wed Feb 17 16:19:43 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Wed, 17 Feb 2010 16:19:43 -0500 Subject: [Mristudio-users] diffeomap and ROIeditor Message-ID: <9018fecc1002171319x294a3045lf322a3038e1250f2@mail.gmail.com> Hello All, Please let me know what is the purpose of using Diffeomap and ROI editor. Whta is template image and subject image in Diffeomap. Are there any published articles or powerpoint presentation where the methodology of using Diffeomap and ROI editor has been described. thanks regards -- Sona -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100217/975684fe/attachment.html From xli16 at jhmi.edu Wed Feb 17 17:37:29 2010 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 17 Feb 2010 17:37:29 -0500 Subject: [Mristudio-users] diffeomap and ROIeditor In-Reply-To: <9018fecc1002171319x294a3045lf322a3038e1250f2@mail.gmail.com> References: <9018fecc1002171319x294a3045lf322a3038e1250f2@mail.gmail.com> Message-ID: Hello Sona, DiffeoMap is mainly used to do image normalization. ROIEditor can help you generate ROIs. You may check the online manual section at https://www.mristudio.org/wiki/user_manual. Regards, Xin ----- Original Message ----- From: Sona Saksena Date: Wednesday, February 17, 2010 4:19 pm Subject: [Mristudio-users] diffeomap and ROIeditor To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello All, > > Please let me know what is the purpose of using Diffeomap and ROI editor. > Whta is template image and subject image in Diffeomap. > > Are there any published articles or powerpoint presentation where the > methodology of using Diffeomap and ROI editor has been described. > > thanks > > regards > -- > Sona > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Mon Feb 22 12:56:18 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 22 Feb 2010 12:56:18 -0500 Subject: [Mristudio-users] apply transformation to landmarkers & command file In-Reply-To: <83F95893B34E42E5917605B75970D35F@panpan> References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> <68FC2725584849B0AFA859749CFF3A06@panpan> <3DA6F72FDB2B40BF9D193236123F27B7@panpan> <83F95893B34E42E5917605B75970D35F@panpan> Message-ID: Hello Yi, I have asked my colleague about your question. Actually the out of range values are normal. Even in LDDMM, you may find some out-of-range values, and affine will definitely generate more. The out-of-range values do not mean your object in the image will be transformed out-of-range, just some pixels in the background will be moved outside due to mainly affine and, to some degree, LDDMM. If you rotate a square 45 degrees, it will have some part out of the original squre. Regards, Xin ----- Original Message ----- From: Yi Jiang Date: Wednesday, February 17, 2010 2:04 pm Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello Xin, > > It is a combined matrix. > > Yi > > > ----- Original Message ----- > From: "Xin Li" > To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker > Questions/Support" > Sent: Wednesday, February 17, 2010 11:38 AM > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > > > Hello Yi, > > How did you get the matrix that you are working on? Is it a lddmm > matrix or > a combined matrix? > > > Xin > > > > ----- Original Message ----- > From: Yi Jiang > Date: Wednesday, February 17, 2010 11:05 am > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > Hello Xin, > > > > Thank you! I looked at the transformation matrix. Overall it looks > > reasonable (i.e. I think my reading format of the matrix is correct. > > I was > > able to use the vector information to reasonably map land marks I > > chose). > > But I found the value of the vector somehow ranges from e.g. > > (-40~540)x(-30~270)x(-20~280) instead of (0-511)x(0-255)x(0-255) I > > would > > expect. What do those out of range (out of (0-511)x(0-255)x(0-255) > ) > > values > > mean? > > > > Best, > > Yi > > > > > > ----- Original Message ----- > > From: "Xin Li" > > To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker > > Questions/Support" > > Sent: Wednesday, February 17, 2010 10:01 AM > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > & > > command > > file > > > > > > Hello Yi, > > > > If your image size is 512x256x256, the vector should be > > (0-511)x(0-255)x(0-255) > > > > > > Xin > > > > > > > > > > ----- Original Message ----- > > From: Yi Jiang > > Date: Wednesday, February 17, 2010 8:44 am > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > & > > command > > file > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > > > > > Hello, Xin, > > > > > > Thank you very much for the information. > > > > > > I have one more question: does the vector indicating new location > > > start from > > > 0 or 1? That is: if my image size is 512x256x256, the vector should > > > be > > > (0-511)x(0-255)x(0-255) or (1-512)x(1-256)x(1-256)? > > > > > > Thank you! > > > > > > Best, > > > Yi > > > > > > > > > ----- Original Message ----- > > > From: "Xin Li" > > > To: "susumu mori" ; "Yi Jiang" ; > > > "DTI > > > Studio, ROI Editor, Landmarker Questions/Support" > > > ; "Jiangyang Zhang" > > > Sent: Monday, February 01, 2010 10:22 AM > > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > > & > > > command > > > file > > > > > > > > > Hello Yi, > > > > > > As Susumu said, transformation matrices contain vectors at each > > > coordinate, > > > indicating where is the new location. The structure is Vector (x, > > y, > > > z) x > > > X-dimension x Y-dimension x Z-dimension. You may write matlab code > > to > > > > > > extract the vector information. > > > > > > > > > Xin > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > From: susumu mori > > > Date: Saturday, January 30, 2010 8:29 am > > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > > & > > > command > > > file > > > To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker > > > Questions/Support" , Xin Li > > > , > > > Jiangyang Zhang > > > > > > > > > > Hi Yi, > > > > > > > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: > > > > > > > > > Hello, dear all, > > > > > > > > > > > > > > > > > > > > I have two questions and am wondering if someone can help. > > > > > > > > > > > > > > > > > > > > 1. I have already had a transformation matrix to map > the > > subject > > > > image > > > > > onto the template image, which was generated by combining > > AIR > > > > rigid, AIR > > > > > affine, and LDDMM matrix. I want to define some > > landmarkers on > > > > the subject > > > > > image, and apply the transformation matrix to the landmarkers > > > > (to see their > > > > > corresponding location on the template image). How can > I > > do that? > > > > > > > > > > > > > > I think this is exactly what the K and H maps are. I need > > > > confirmation from > > > > Xin, but in my understanding, these transformation matrices > > > contain > > > > vectors > > > > at each coordinate, indicating where is the new location. If > > I'm not > > > > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension > x > > > > Z-dimension. > > > > There must be a way to extarct the "Vector" information at the > > > > > specified > > > > coordinate. > > > > > > > > > > > > > > > > > > > 1. I would like to use the ?load command file? > function. I > > will > > > > do AIR > > > > > linear rigid transformation, AIR linear affine transformation, > > > > image format > > > > > change to byte, automatic intensity correction by histogram, > > > and > > > > 2-channel > > > > > LDDMM. Is it possible to put all these into one command > file? > > > If > > > > yes, can > > > > > anyone give me an example file? > > > > > > > > > > I believe the command file is only for the functions > within the > > > > same box, > > > > including byte-integer-float conversion, axial-sagittal-coronal > > > > conversion, > > > > resampling, etc. They don't include transformation functions. > > We are > > > > working > > > > on automation, which will take several months. Meanwhile, I > believe > > > > it is > > > > good idea to use the current way, which forces you to check > the > > > > result after > > > > each step. Transformation sometimes does silly things. Some > images > > > > may have > > > > quality problems. You may want compare different methods (e.g. > > Mutual > > > > Info > > > > linear transformation vs AIR, intensity correction methods, > > > contrast > > > > of > > > > choice). I think it's very important to get a feel about > your data > > > > and each > > > > transformation step. Also, depending on pathology, the > > transformation > > > > strategy may change. Some disease groups have severe intensity > > > > changes (e.g. > > > > stroke), some have severely enlarged ventricles. You may > find the > > > same > > > > methods may work for one but not the other. Automation is still > > a > > > > > > > difficult > > > > matter for transformation-based analysis. > > > > > > > > > > > > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > > > > > > > > > Have a nice weekend! > > > > > > > > > > > > > > > > > > > > Best > > > > > > > > > > Yi > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Mristudio-users mailing list > > > > > Mristudio-users at mristudio.org > > > > > > > > > > Unsubscribe, send a blank email to: > > > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > > > > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From SyedSalman.Shahid at usq.edu.au Thu Feb 25 02:37:35 2010 From: SyedSalman.Shahid at usq.edu.au (Syed Salman Shahid) Date: Thu, 25 Feb 2010 17:37:35 +1000 Subject: [Mristudio-users] basic information In-Reply-To: References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> <68FC2725584849B0AFA859749CFF3A06@panpan> <3DA6F72FDB2B40BF9D193236123F27B7@panpan> <83F95893B34E42E5917605B75970D35F@panpan> Message-ID: <3318FC529C6A6E448A90CB5AB5B1F56C1F42FCE885@EXCHMB.usq.edu.au> Hi, I would like to use DTI for White matter (anisotropic) conductivity tensor calculation for my project. I was wondering if i am at the correct path. My intention is to use DTI calculated eigen values and import it in FE head model! At this stage i am not sure if this procedure is viable when DTI is involved. BUT most importantly, i was watching the tutorial videos and i came across the major issue i.e. where to get the required data. If you look into the data archives there is a huge amount of data and deciding which one is the required one is impossible. Thank you salman -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li Sent: Thursday, 18 February 2010 5:27 AM To: Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file Hello Yi, Thank you for your information. I am going to check and give you a reply later. Xin ----- Original Message ----- From: Yi Jiang Date: Wednesday, February 17, 2010 2:04 pm Subject: Re: [Mristudio-users] apply transformation to landmarkers & command file To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hello Xin, > > It is a combined matrix. > > Yi > > > ----- Original Message ----- > From: "Xin Li" > To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker > Questions/Support" > Sent: Wednesday, February 17, 2010 11:38 AM > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > > > Hello Yi, > > How did you get the matrix that you are working on? Is it a lddmm > matrix or > a combined matrix? > > > Xin > > > > ----- Original Message ----- > From: Yi Jiang > Date: Wednesday, February 17, 2010 11:05 am > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command > file > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > Hello Xin, > > > > Thank you! I looked at the transformation matrix. Overall it looks > > reasonable (i.e. I think my reading format of the matrix is correct. > > I was > > able to use the vector information to reasonably map land marks I > > chose). > > But I found the value of the vector somehow ranges from e.g. > > (-40~540)x(-30~270)x(-20~280) instead of (0-511)x(0-255)x(0-255) I > > would > > expect. What do those out of range (out of (0-511)x(0-255)x(0-255) > ) > > values > > mean? > > > > Best, > > Yi > > > > > > ----- Original Message ----- > > From: "Xin Li" > > To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker > > Questions/Support" > > Sent: Wednesday, February 17, 2010 10:01 AM > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > & > > command > > file > > > > > > Hello Yi, > > > > If your image size is 512x256x256, the vector should be > > (0-511)x(0-255)x(0-255) > > > > > > Xin > > > > > > > > > > ----- Original Message ----- > > From: Yi Jiang > > Date: Wednesday, February 17, 2010 8:44 am > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > & > > command > > file > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > > > > > Hello, Xin, > > > > > > Thank you very much for the information. > > > > > > I have one more question: does the vector indicating new location > > > start from > > > 0 or 1? That is: if my image size is 512x256x256, the vector should > > > be > > > (0-511)x(0-255)x(0-255) or (1-512)x(1-256)x(1-256)? > > > > > > Thank you! > > > > > > Best, > > > Yi > > > > > > > > > ----- Original Message ----- > > > From: "Xin Li" > > > To: "susumu mori" ; "Yi Jiang" ; > > > "DTI > > > Studio, ROI Editor, Landmarker Questions/Support" > > > ; "Jiangyang Zhang" > > > Sent: Monday, February 01, 2010 10:22 AM > > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > > & > > > command > > > file > > > > > > > > > Hello Yi, > > > > > > As Susumu said, transformation matrices contain vectors at each > > > coordinate, > > > indicating where is the new location. The structure is Vector (x, > > y, > > > z) x > > > X-dimension x Y-dimension x Z-dimension. You may write matlab code > > to > > > > > > extract the vector information. > > > > > > > > > Xin > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > From: susumu mori > > > Date: Saturday, January 30, 2010 8:29 am > > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > > & > > > command > > > file > > > To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker > > > Questions/Support" , Xin Li > > > , > > > Jiangyang Zhang > > > > > > > > > > Hi Yi, > > > > > > > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang wrote: > > > > > > > > > Hello, dear all, > > > > > > > > > > > > > > > > > > > > I have two questions and am wondering if someone can help. > > > > > > > > > > > > > > > > > > > > 1. I have already had a transformation matrix to map > the > > subject > > > > image > > > > > onto the template image, which was generated by combining > > AIR > > > > rigid, AIR > > > > > affine, and LDDMM matrix. I want to define some > > landmarkers on > > > > the subject > > > > > image, and apply the transformation matrix to the landmarkers > > > > (to see their > > > > > corresponding location on the template image). How can > I > > do that? > > > > > > > > > > > > > > I think this is exactly what the K and H maps are. I need > > > > confirmation from > > > > Xin, but in my understanding, these transformation matrices > > > contain > > > > vectors > > > > at each coordinate, indicating where is the new location. If > > I'm not > > > > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension > x > > > > Z-dimension. > > > > There must be a way to extarct the "Vector" information at the > > > > > specified > > > > coordinate. > > > > > > > > > > > > > > > > > > > 1. I would like to use the "load command file" > function. I > > will > > > > do AIR > > > > > linear rigid transformation, AIR linear affine transformation, > > > > image format > > > > > change to byte, automatic intensity correction by histogram, > > > and > > > > 2-channel > > > > > LDDMM. Is it possible to put all these into one command > file? > > > If > > > > yes, can > > > > > anyone give me an example file? > > > > > > > > > > I believe the command file is only for the functions > within the > > > > same box, > > > > including byte-integer-float conversion, axial-sagittal-coronal > > > > conversion, > > > > resampling, etc. They don't include transformation functions. > > We are > > > > working > > > > on automation, which will take several months. Meanwhile, I > believe > > > > it is > > > > good idea to use the current way, which forces you to check > the > > > > result after > > > > each step. Transformation sometimes does silly things. Some > images > > > > may have > > > > quality problems. You may want compare different methods (e.g. > > Mutual > > > > Info > > > > linear transformation vs AIR, intensity correction methods, > > > contrast > > > > of > > > > choice). I think it's very important to get a feel about > your data > > > > and each > > > > transformation step. Also, depending on pathology, the > > transformation > > > > strategy may change. Some disease groups have severe intensity > > > > changes (e.g. > > > > stroke), some have severely enlarged ventricles. You may > find the > > > same > > > > methods may work for one but not the other. Automation is still > > a > > > > > > > difficult > > > > matter for transformation-based analysis. > > > > > > > > > > > > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > > > > > > > > > Have a nice weekend! > > > > > > > > > > > > > > > > > > > > Best > > > > > > > > > > Yi > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Mristudio-users mailing list > > > > > Mristudio-users at mristudio.org > > > > > > > > > > Unsubscribe, send a blank email to: > > > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > > > > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org This email (including any attached files) is confidential and is for the intended recipient(s) only. If you received this email by mistake, please, as a courtesy, tell the sender, then delete this email. The views and opinions are the originator's and do not necessarily reflect those of the University of Southern Queensland. Although all reasonable precautions were taken to ensure that this email contained no viruses at the time it was sent we accept no liability for any losses arising from its receipt. The University of Southern Queensland is a registered provider of education with the Australian Government (CRICOS Institution Code No's. QLD 00244B / NSW 02225M) From susumu at mri.jhu.edu Thu Feb 25 08:14:36 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 25 Feb 2010 08:14:36 -0500 Subject: [Mristudio-users] basic information In-Reply-To: <3318FC529C6A6E448A90CB5AB5B1F56C1F42FCE885@EXCHMB.usq.edu.au> References: <994d85681001262253k7fe2d22axb0458717ffa6f85b@mail.gmail.com> <68FC2725584849B0AFA859749CFF3A06@panpan> <3DA6F72FDB2B40BF9D193236123F27B7@panpan> <83F95893B34E42E5917605B75970D35F@panpan> <3318FC529C6A6E448A90CB5AB5B1F56C1F42FCE885@EXCHMB.usq.edu.au> Message-ID: Hi Salman, please read Clin Neurophysiol. 2004 Mar;115(3):589-95. to see if it is related to your question. For the data used in the totorial, please follow the instruction in https://www.mristudio.org/wiki/Tutorial. Susumu On Thu, Feb 25, 2010 at 2:37 AM, Syed Salman Shahid < SyedSalman.Shahid at usq.edu.au> wrote: > Hi, > > I would like to use DTI for White matter (anisotropic) conductivity tensor > calculation for my project. I was wondering if i am at the correct path. > My intention is to use DTI calculated eigen values and import it in FE head > model! > At this stage i am not sure if this procedure is viable when DTI is > involved. > > BUT most importantly, i was watching the tutorial videos and i came across > the major issue i.e. where to get the required data. If you look into the > data archives there is a huge amount of data and deciding which one is the > required one is impossible. > > Thank you > salman > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li > Sent: Thursday, 18 February 2010 5:27 AM > To: Yi Jiang; DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command file > > Hello Yi, > > Thank you for your information. I am going to check and give you a reply > later. > > > Xin > > > > ----- Original Message ----- > From: Yi Jiang > Date: Wednesday, February 17, 2010 2:04 pm > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > command file > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > > > Hello Xin, > > > > It is a combined matrix. > > > > Yi > > > > > > ----- Original Message ----- > > From: "Xin Li" > > To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker > > Questions/Support" > > Sent: Wednesday, February 17, 2010 11:38 AM > > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > > command > > file > > > > > > Hello Yi, > > > > How did you get the matrix that you are working on? Is it a lddmm > > matrix or > > a combined matrix? > > > > > > Xin > > > > > > > > ----- Original Message ----- > > From: Yi Jiang > > Date: Wednesday, February 17, 2010 11:05 am > > Subject: Re: [Mristudio-users] apply transformation to landmarkers & > > command > > file > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > > > > > Hello Xin, > > > > > > Thank you! I looked at the transformation matrix. Overall it looks > > > reasonable (i.e. I think my reading format of the matrix is correct. > > > I was > > > able to use the vector information to reasonably map land marks I > > > chose). > > > But I found the value of the vector somehow ranges from e.g. > > > (-40~540)x(-30~270)x(-20~280) instead of (0-511)x(0-255)x(0-255) I > > > would > > > expect. What do those out of range (out of (0-511)x(0-255)x(0-255) > > ) > > > values > > > mean? > > > > > > Best, > > > Yi > > > > > > > > > ----- Original Message ----- > > > From: "Xin Li" > > > To: "Yi Jiang" ; "DTI Studio, ROI Editor, Landmarker > > > Questions/Support" > > > Sent: Wednesday, February 17, 2010 10:01 AM > > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > > & > > > command > > > file > > > > > > > > > Hello Yi, > > > > > > If your image size is 512x256x256, the vector should be > > > (0-511)x(0-255)x(0-255) > > > > > > > > > Xin > > > > > > > > > > > > > > > ----- Original Message ----- > > > From: Yi Jiang > > > Date: Wednesday, February 17, 2010 8:44 am > > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > > & > > > command > > > file > > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > > > > > > > > > > > > Hello, Xin, > > > > > > > > Thank you very much for the information. > > > > > > > > I have one more question: does the vector indicating new location > > > > start from > > > > 0 or 1? That is: if my image size is 512x256x256, the vector > should > > > > be > > > > (0-511)x(0-255)x(0-255) or (1-512)x(1-256)x(1-256)? > > > > > > > > Thank you! > > > > > > > > Best, > > > > Yi > > > > > > > > > > > > ----- Original Message ----- > > > > From: "Xin Li" > > > > To: "susumu mori" ; "Yi Jiang" >; > > > > "DTI > > > > Studio, ROI Editor, Landmarker Questions/Support" > > > > ; "Jiangyang Zhang" < > jzhang3 at jhmi.edu> > > > > Sent: Monday, February 01, 2010 10:22 AM > > > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > > > & > > > > command > > > > file > > > > > > > > > > > > Hello Yi, > > > > > > > > As Susumu said, transformation matrices contain vectors at each > > > > coordinate, > > > > indicating where is the new location. The structure is Vector (x, > > > y, > > > > z) x > > > > X-dimension x Y-dimension x Z-dimension. You may write matlab code > > > to > > > > > > > > extract the vector information. > > > > > > > > > > > > Xin > > > > > > > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > > From: susumu mori > > > > Date: Saturday, January 30, 2010 8:29 am > > > > Subject: Re: [Mristudio-users] apply transformation to landmarkers > > > & > > > > command > > > > file > > > > To: Yi Jiang , "DTI Studio, ROI Editor, Landmarker > > > > Questions/Support" , Xin Li > > > > , > > > > Jiangyang Zhang > > > > > > > > > > > > > Hi Yi, > > > > > > > > > > On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang > wrote: > > > > > > > > > > > Hello, dear all, > > > > > > > > > > > > > > > > > > > > > > > > I have two questions and am wondering if someone can help. > > > > > > > > > > > > > > > > > > > > > > > > 1. I have already had a transformation matrix to map > > the > > > subject > > > > > image > > > > > > onto the template image, which was generated by combining > > > AIR > > > > > rigid, AIR > > > > > > affine, and LDDMM matrix. I want to define some > > > landmarkers on > > > > > the subject > > > > > > image, and apply the transformation matrix to the > landmarkers > > > > > (to see their > > > > > > corresponding location on the template image). How can > > I > > > do that? > > > > > > > > > > > > > > > > > I think this is exactly what the K and H maps are. I need > > > > > confirmation from > > > > > Xin, but in my understanding, these transformation matrices > > > > contain > > > > > vectors > > > > > at each coordinate, indicating where is the new location. If > > > I'm not > > > > > mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension > > x > > > > > Z-dimension. > > > > > There must be a way to extarct the "Vector" information at the > > > > > > > specified > > > > > coordinate. > > > > > > > > > > > > > > > > > > > > > > > 1. I would like to use the "load command file" > > function. I > > > will > > > > > do AIR > > > > > > linear rigid transformation, AIR linear affine > transformation, > > > > > image format > > > > > > change to byte, automatic intensity correction by > histogram, > > > > and > > > > > 2-channel > > > > > > LDDMM. Is it possible to put all these into one command > > file? > > > > If > > > > > yes, can > > > > > > anyone give me an example file? > > > > > > > > > > > > I believe the command file is only for the functions > > within the > > > > > same box, > > > > > including byte-integer-float conversion, axial-sagittal-coronal > > > > > conversion, > > > > > resampling, etc. They don't include transformation functions. > > > We are > > > > > working > > > > > on automation, which will take several months. Meanwhile, I > > believe > > > > > it is > > > > > good idea to use the current way, which forces you to check > > the > > > > > result after > > > > > each step. Transformation sometimes does silly things. Some > > images > > > > > may have > > > > > quality problems. You may want compare different methods (e.g. > > > Mutual > > > > > Info > > > > > linear transformation vs AIR, intensity correction methods, > > > > > contrast > > > > > of > > > > > choice). I think it's very important to get a feel about > > your data > > > > > and each > > > > > transformation step. Also, depending on pathology, the > > > transformation > > > > > strategy may change. Some disease groups have severe intensity > > > > > changes (e.g. > > > > > stroke), some have severely enlarged ventricles. You may > > find the > > > > same > > > > > methods may work for one but not the other. Automation is still > > > a > > > > > > > > > difficult > > > > > matter for transformation-based analysis. > > > > > > > > > > > > > > > > > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > > > > > > > > > > > > > Have a nice weekend! > > > > > > > > > > > > > > > > > > > > > > > > Best > > > > > > > > > > > > Yi > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Mristudio-users mailing list > > > > > > Mristudio-users at mristudio.org > > > > > > > > > > > > Unsubscribe, send a blank email to: > > > > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > > Unsubscribe, send a blank email to: > > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > > Unsubscribe, send a blank email to: > > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > This email (including any attached files) is confidential and is for the > intended recipient(s) only. If you received this email by mistake, > please, as a courtesy, tell the sender, then delete this email. > > The views and opinions are the originator's and do not necessarily > reflect those of the University of Southern Queensland. Although all > reasonable precautions were taken to ensure that this email contained no > viruses at the time it was sent we accept no liability for any losses > arising from its receipt. > > The University of Southern Queensland is a registered provider of > education with the Australian Government (CRICOS Institution Code No's. > QLD 00244B / NSW 02225M) > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100225/1c0a0808/attachment-0001.html From d-gitelman at northwestern.edu Sun Feb 28 19:54:36 2010 From: d-gitelman at northwestern.edu (Darren Gitelman) Date: Sun, 28 Feb 2010 18:54:36 -0600 Subject: [Mristudio-users] How to combine DTI data from different runs Message-ID: Hello: Is there a way to combine data across several repeats of a DTI sequence? The reason I ask is that we have a Siemens Trio scanner but are working with another group that has a GE scanner. On the GE scanner the DTI sequence allows NEX > 1 (they are getting 4), which appears to improve their SNR considerably. The Siemens sequences do not allow this, so we are repeating the DTI sequence several times, and want to combine the data across runs. Can this be done within DTIstudio or some other program? Would it be best to do this at the level of the DTI images or the FA maps? Thanks, Darren From susumu at mri.jhu.edu Sun Feb 28 20:30:55 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sun, 28 Feb 2010 20:30:55 -0500 Subject: [Mristudio-users] How to combine DTI data from different runs In-Reply-To: References: Message-ID: Hi Darren, In a previous communication in the mailing list, I explained why we can not use regular k-space averaging for DTI and, therefore, we average data after magnitude calculation (we average images, not k-space data). If anybody remembers which thread it was, I would appreciate it. Anyway, because we first have to calculate image before averaging, there is no point to ask scanners to do the averaging. One downside of the averaging-by-the-scanner is, if the images are mis-registered or there are corrupted images, we can not undo the averaging. I believe that is why Siemens always save all images separately (without creating an "averaged image" even if multiple averaging is specified. Please note the difference between "repeated scans (you submitted the same protocol twice)" and "averaged scans (you specified 2 signal averaging)" when you use Siemens. Either way, all images are saved individually and they are basically the same studies. However, in the former case, the "repeated images" are stored in different directories and Siemens console can not combine them for DTI calculation. With the latter case, the repeated images are stored in the same directory and Siemens console can combine them to calculate one DTI data. Either way, when you use DtiStudio, you need to load all files at once and DtiStudio can combine them to calculate one DTI. Now going back to your question; 1) You can specify the number of signal averaging in Siemens. I'm not sure why you thought you couldn't. However, if you meant, "Siemens saved all images separately without averaging", then you are correct. 2) DtiStudio can read repeated scans and combine them for one DTI calculation. On Sun, Feb 28, 2010 at 7:54 PM, Darren Gitelman < d-gitelman at northwestern.edu> wrote: > Hello: > > Is there a way to combine data across several repeats of a DTI sequence? > > The reason I ask is that we have a Siemens Trio scanner but are > working with another group that has a GE scanner. On the GE scanner > the DTI sequence allows NEX > 1 (they are getting 4), which appears to > improve their SNR considerably. The Siemens sequences do not allow > this, so we are repeating the DTI sequence several times, and want to > combine the data across runs. Can this be done within DTIstudio or > some other program? Would it be best to do this at the level of the > DTI images or the FA maps? > > Thanks, > Darren > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100228/251a3ecc/attachment.html From d-gitelman at northwestern.edu Sun Feb 28 22:17:16 2010 From: d-gitelman at northwestern.edu (Darren Gitelman) Date: Sun, 28 Feb 2010 21:17:16 -0600 Subject: [Mristudio-users] How to combine DTI data from different runs Message-ID: Dear Susumu Thanks for the speedy reply. Regarding the 2 issues you mentioned > 1) You can specify the number of signal averaging in Siemens. I'm not sure > why you thought you couldn't. However, if you meant, "Siemens saved all > images separately without averaging", then you are correct. Our physicist said for this particular sequence repeats were not possible. He is not sure why and also seemed surprised that the choice was grayed out. > 2) DtiStudio can read repeated scans and combine them for one DTI > calculation. Excellent. So the next question is how to do this? I read through the manual, but I did not see where this type of calculation was specified. - I loaded all 3 repeated scans by adding the folders to the Dicom Image File Folders, and all the scans loaded properly. - My guess is the next step is to realign all the images using AIR. I have a couple of questions about this. - What is the optional upper bound? - Which cost function is best to use? - Should I adjust the gradients for the diffusion weighted images? - Once Air finishes I have a bunch of images labeled Air-series-blah\ -1, Air-series-blah\ -2, etc. - How do I save these images so I can just reload them later and not have to redo-air. - How do I get DTI studio to use these images rather than the original images for the FA calculation? - How do I tell DTIstudio to combine the images across the repeats? Thanks again, Darren > Hi Darren, > > In a previous communication in the mailing list, I explained why we can not > use regular k-space averaging for DTI and, therefore, we average data after > magnitude calculation (we average images, not k-space data). If anybody > remembers which thread it was, I would appreciate it. > > Anyway, because we first have to calculate image before averaging, there is > no point to ask scanners to do the averaging. One downside of the > averaging-by-the-scanner is, if the images are mis-registered or there are > corrupted images, we can not undo the averaging. > > I believe that is why Siemens always save all images separately (without > creating an "averaged image" even if multiple averaging is specified. > > Please note the difference between "repeated scans (you submitted the same > protocol twice)" and "averaged scans (you specified 2 signal averaging)" > when you use Siemens. Either way, all images are saved individually and they > are basically the same studies. However, in the former case, the "repeated > images" are stored in different directories and Siemens console can not > combine them for DTI calculation. With the latter case, the repeated images > are stored in the same directory and Siemens console can combine them to > calculate one DTI data. > > Either way, when you use DtiStudio, you need to load all files at once and > DtiStudio can combine them to calculate one DTI. > > Now going back to your question; > > 1) You can specify the number of signal averaging in Siemens. I'm not sure > why you thought you couldn't. However, if you meant, "Siemens saved all > images separately without averaging", then you are correct. > 2) DtiStudio can read repeated scans and combine them for one DTI > calculation. > > On Sun, Feb 28, 2010 at 7:54 PM, Darren Gitelman < > d-gitelman at northwestern.edu> wrote: > > > Hello: > > > > Is there a way to combine data across several repeats of a DTI sequence? > > > > The reason I ask is that we have a Siemens Trio scanner but are > > working with another group that has a GE scanner. On the GE scanner > > the DTI sequence allows NEX > 1 (they are getting 4), which appears to > > improve their SNR considerably. The Siemens sequences do not allow > > this, so we are repeating the DTI sequence several times, and want to > > combine the data across runs. Can this be done within DTIstudio or > > some other program? Would it be best to do this at the level of the > > DTI images or the FA maps? > > > > Thanks, > > Darren From 7by3 at queensu.ca Sun Feb 28 23:19:29 2010 From: 7by3 at queensu.ca (7by3 at queensu.ca) Date: Sun, 28 Feb 2010 23:19:29 -0500 Subject: [Mristudio-users] FA values and define ROI Message-ID: Dear users: We are doing a DTI project and planning to use DTIstudio. I have some questions hope you could help me answer. 1. How could I define ROI? (we are interested in the DMN brain structures, such as medial prefrontal cortex, medial temporal lobe, PCC etc). I just do not know how can I find these areas in the brain? Is there anyway that brain regions could be marked in the brain? Do I need to use atlas or I can just find it from DTI studio? (Hope it makes sense) 2. I want to get FA values. After clicking tensor, color map etc. tab from DTImap. I could not find FA values. Could you let me know how and where to find these FA values? 3. We are also looking at the fiber tract. For example, we want to look at the fiber tract from PCC to medial temporal lobe. Therefore, we need to find the seed region PCC. But how can I find the location of PCC in the brain? (this question is similar to question 1). Could you help me with these questions? Thank you! Bing -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100228/4a88690c/attachment.html From susumu at mri.jhu.edu Mon Mar 1 08:59:36 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 01 Mar 2010 08:59:36 -0500 Subject: [Mristudio-users] FA values and define ROI In-Reply-To: References: Message-ID: Hi Bing, 1) Manual ROI approach Many papers use manual ROI approach and it's still one of the best ways. The downside is, you have to be an expert neuroanatomist and even so, the ROI placement reproducibility is often a concern. For the manual ROI approach, you can use the DtiStudio "ROI" tab, but I recommend you to use RoiEditor, which has a much stronger interface. Using DtiStudio, you need to load an FA map to get FA values. You can directly draw ROIs on an FA map in the "ROI" tab and determine the average FA within the ROI. You can also load both color and FA map, draw ROIs on the color map, and measure FA. In this case, first choose the color map as an active image in the display in the "Image" tab, go to the "ROI" tab, draw an ROI, go back to the "Image" tab, choose the FA map as an active image, and go back to the "ROI" tab to find the FA value. Using RoiEditor, you need to grasp the concept of "Object", which allows drawing of multiple 3D ROIs. Our manual is still weak, but you can find some in www.mristudio.org. There is also a video of our tutorial. 2) Automated ROI You can use our atlas with more than 170 pre-defined ROIs, warped to your data. For this approach, you need to get DiffeoMap and RoiEditor from www.mristudio.org. Also, please read our recent papers by Mori et al, and Oishi et al, all in NeuroImage. Again, there is online manual in www.mristudio.org. 3) fiber tracking Once you successfully segment your brain, you can use the segmented regions as ROIs for fiber tracking. #2 and #3 are a bit advanced usage of our tools. #2 could be figured out through our website, I believe. We are planning to have a tutorial in ISMRM this year. Hope you can join. Susumu On Sun, Feb 28, 2010 at 11:19 PM, <7by3 at queensu.ca> wrote: > Dear users: > > We are doing a DTI project and planning to use DTIstudio. I have some > questions hope you could help me answer. > > 1. How could I define ROI? (we are interested in the DMN brain structures, > such as medial prefrontal cortex, medial temporal lobe, PCC etc). I just do > not know how can I find these areas in the brain? Is there anyway that brain > regions could be marked in the brain? Do I need to use atlas or I can just > find it from DTI studio? (Hope it makes sense) > > 2. I want to get FA values. After clicking tensor, color map etc. tab from > DTImap. I could not find FA values. Could you let me know how and where to > find these FA values? > > 3. We are also looking at the fiber tract. For example, we want to look at > the fiber tract from PCC to medial temporal lobe. Therefore, we need to find > the seed region PCC. But how can I find the location of PCC in the brain? > (this question is similar to question 1). > > Could you help me with these questions? > > Thank you! > > Bing > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100301/e93d59e9/attachment-0001.html From susumu at mri.jhu.edu Mon Mar 1 09:23:59 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 01 Mar 2010 09:23:59 -0500 Subject: [Mristudio-users] How to combine DTI data from different runs In-Reply-To: References: Message-ID: > - I loaded all 3 repeated scans by adding the folders to the Dicom > Image File Folders, and all the scans loaded properly. > - My guess is the next step is to realign all the images using AIR. I > have a couple of questions about this. > - What is the optional upper bound? > AIR requires us to define a threshold to remove the background signals. Otherwise, it tries to register the noise floor too. Also, AIR is sensitive to the threshold. We usually do not use upper bound, but this is to remove the CSF signals in b0 image to make the contrast closer to DWIs. Because you have 3 repeated images, I recommend you to calculate STD of the repeated scan using one of the buttons in the "DtiMapping" tab ("Mean, STD, etc"). Then click "Original-ADC-Mean-STD" button. You can find two extra rows of images; one is the average of the 3 repeated scans and the other is the STD. Usually the STD images should look like nothing but noise. If the subject moved, you can see clear anatomy due to image shift and thus a king of edge-enhanced STD images. You have to monitor what AIR does using this window. If the STD images look like noise, you don't have to do AIR but because AIR smooths the images (and thus enhance SNR), you'd better do AIR for all data. Make sure that AIR don't make such a data worse. If you find mis-registration in the STD images, AIR should correct them. AIR results are sensitive to threshold and also cost function. It is purely try & error. Usually once it works, you don't have to change often. My experience says, threshold tends to be high side for robust performance. > - Which cost function is best to use? > - Should I adjust the gradients for the diffusion weighted images? > I don't use this function. If the subject moves so much that this gradient correction based on image registration makes a significant impact on your data (namely, if AIR rotates the brain by 5 degree, the gradient vector also has to be rotated by 5 degree), you'd better worry so many other things about the validity of the data itself. However, it is true that some reviewers believe in this and ask you "did you do it?" > > - Once Air finishes I have a bunch of images labeled Air-series-blah\ > -1, Air-series-blah\ -2, etc. > - How do I save these images so I can just reload them later and not > have to redo-air. > - How do I get DTI studio to use these images rather than the > original images for the FA calculation? > - How do I tell DTIstudio to combine the images across the repeats? > If you unclick "create new image after registration", you registered images overwirte you original data and subsequent calculation will be based on the registered images. if you leave it checked, you get an extra dataset called "AIR_xxx". In this case, you need to save the registered "AIR_xxx" images and reload them for tensor calculation. For this, you use the "save" icon in the "Image" tab. Choose the entire data (b0 + DWIs) and save them into 1 file (if you have three repetitions, into 3 files) as "raw" format. This is so-called REC format in DtiStudio. When you have 3 repeated scans and load all of them, there is no particular steps to combine them. DtiStudio uses all 3 scans to fit one tensor. > Thanks again, > Darren > > > > > Hi Darren, > > > > In a previous communication in the mailing list, I explained why we can > not > > use regular k-space averaging for DTI and, therefore, we average data > after > > magnitude calculation (we average images, not k-space data). If anybody > > remembers which thread it was, I would appreciate it. > > > > Anyway, because we first have to calculate image before averaging, there > is > > no point to ask scanners to do the averaging. One downside of the > > averaging-by-the-scanner is, if the images are mis-registered or there > are > > corrupted images, we can not undo the averaging. > > > > I believe that is why Siemens always save all images separately (without > > creating an "averaged image" even if multiple averaging is specified. > > > > Please note the difference between "repeated scans (you submitted the > same > > protocol twice)" and "averaged scans (you specified 2 signal averaging)" > > when you use Siemens. Either way, all images are saved individually and > they > > are basically the same studies. However, in the former case, the > "repeated > > images" are stored in different directories and Siemens console can not > > combine them for DTI calculation. With the latter case, the repeated > images > > are stored in the same directory and Siemens console can combine them to > > calculate one DTI data. > > > > Either way, when you use DtiStudio, you need to load all files at once > and > > DtiStudio can combine them to calculate one DTI. > > > > Now going back to your question; > > > > 1) You can specify the number of signal averaging in Siemens. I'm not > sure > > why you thought you couldn't. However, if you meant, "Siemens saved all > > images separately without averaging", then you are correct. > > 2) DtiStudio can read repeated scans and combine them for one DTI > > calculation. > > > > On Sun, Feb 28, 2010 at 7:54 PM, Darren Gitelman < > > d-gitelman at northwestern.edu> wrote: > > > > > Hello: > > > > > > Is there a way to combine data across several repeats of a DTI > sequence? > > > > > > The reason I ask is that we have a Siemens Trio scanner but are > > > working with another group that has a GE scanner. On the GE scanner > > > the DTI sequence allows NEX > 1 (they are getting 4), which appears to > > > improve their SNR considerably. The Siemens sequences do not allow > > > this, so we are repeating the DTI sequence several times, and want to > > > combine the data across runs. Can this be done within DTIstudio or > > > some other program? Would it be best to do this at the level of the > > > DTI images or the FA maps? > > > > > > Thanks, > > > Darren > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100301/963d3321/attachment.html From saksena.sona at gmail.com Tue Mar 2 10:16:20 2010 From: saksena.sona at gmail.com (Sona Saksena) Date: Tue, 02 Mar 2010 10:16:20 -0500 Subject: [Mristudio-users] hello Message-ID: <9018fecc1003020716g3180072dx13044c749b395cf3@mail.gmail.com> Hello, Is there a video tutorial of Diffeomap and ROI editor. I wanted to know that whether there is an option in the ROI drawing section of the DTI studio in which I can change the shape of the ROI and drag the ROI from one place to another. Any help is highly appreciated. -- Sona -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100302/90a33442/attachment.html From Michael.Nelles at ukb.uni-bonn.de Fri Mar 5 10:15:14 2010 From: Michael.Nelles at ukb.uni-bonn.de (Michael.Nelles at ukb.uni-bonn.de) Date: Fri, 05 Mar 2010 16:15:14 +0100 Subject: [Mristudio-users] Michael Nelles is out of the office. Message-ID: Ich werde ab 02.03.2010 nicht im B?ro sein. Ich kehre zur?ck am 07.03.2010. I will be out of the office starting 03/02/2010 and will not return until 03/07/2010. I will respond to your message when I return. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100305/dd3c66d0/attachment.html From caoaize at hotmail.com Tue Mar 9 12:43:15 2010 From: caoaize at hotmail.com (caoaize) Date: Wed, 10 Mar 2010 01:43:15 +0800 Subject: [Mristudio-users] Outlier image slice rejection and data format Message-ID: Hi, There, It is my first time to run through DTIStudio, but I met some problems: 1. The new version has automatic outlier image slice rejection, based on the relative error >3%, I wonder whether there is document or paper illustrates this method, what relative error here refers? 2. The DWI data saved as NRRD, it is after outlier removal, correct? With any other processing? 3. I am thinking to use the updated FA and DWI data from DTI studio to FSL FDT module, but do not know how to convert the .nrrd file or the .dat file into Analyze format. My colleage save in analyzed format in DTI studio, but it is not recognized both other programs. I wish some body give me a help. Thanks. Aize _________________________________________________________________ MSN????????????????25???????????2010????????? http://kaba.msn.com.cn/?k=1 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100310/419618e7/attachment.html From susumu at mri.jhu.edu Wed Mar 10 09:59:13 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 10 Mar 2010 09:59:13 -0500 Subject: [Mristudio-users] Outlier image slice rejection and data format In-Reply-To: References: Message-ID: Hi Aize, > 1. The new version has automatic outlier image slice rejection, based on > the relative error >3%, I wonder whether there is document or paper > illustrates this method, what relative error here refers? > We are still testing several different types of outliever rejection methods. At this point, I recommend you to use the simple linear fitting option without the outlier rejection option (sorry, the default should not be the slice rejection option). It is, however, advisable to make sure that your data are free from corruption by carefully inspecting your data using the data inspection window. If you do find corruption, you can manually remove it ( https://www.mristudio.org/wiki/user_manual/DTI_Studio_User_Manual/original_image_view) or try one of the options for automated rejection. There are two types of automated rejection; slice rejection and pixel rejection. I hope that we can post the latest version with some documents this month. Meanwhile, if you are interested in, please try 2-4% of error threshold. If you didn't find any motion-related image corruption, there is no need to do the outlier rejection. > 2. The DWI data saved as NRRD, it is after outlier removal, correct? With > any other processing? > Do you mean your original DWI data are saved as NRRD (before imported to DtiStudio) or did you save your data in NRRD using DtiStudio? Why did you use NRRD? The outlier removal is a procedure for tensor calculation (it simply doesn't use some DWIs) and it does not touch the original DWI data. > 3. I am thinking to use the updated FA and DWI data from DTI studio to FSL > FDT module, but do not know how to convert the .nrrd file or the .dat file > into Analyze format. My colleage save in analyzed format in DTI studio, but > it is not recognized both other programs. > > Hangyi, do you know anything about the compatibility issue of Analyze? > I wish some body give me a help. Thanks. > > Aize > > ------------------------------ > ????? Windows Live Messenger ???????? ????? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100310/cfe43de8/attachment-0001.html From aamirabadi at hotmail.com Wed Mar 10 11:07:57 2010 From: aamirabadi at hotmail.com (Afsaneh Amirabadi) Date: Wed, 10 Mar 2010 16:07:57 +0000 Subject: [Mristudio-users] How to change the number of b0-image Message-ID: Hi, I wonder how I can change the number of b0-image? Is there any other way beside using the diffusion option page while we prescribe the exam? Thank you so mych in advance for your help. Regards, Afsaneh _________________________________________________________________ IM on the go with Messenger on your phone http://go.microsoft.com/?linkid=9712960 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100310/9011727d/attachment.html From weiguoli1 at gmail.com Wed Mar 10 18:38:48 2010 From: weiguoli1 at gmail.com (Weiguo Li) Date: Wed, 10 Mar 2010 17:38:48 -0600 Subject: [Mristudio-users] What is the definition of Linear Index(CI), Planar Index(Cp) and Spherical Index (Cs)? Thank you so much. Message-ID: What is the definition of Linear Index(CI), Planar Index(Cp) and Spherical Index (Cs)? Thank you so much. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100310/0337fb9c/attachment.html From rajagov2 at ccf.org Wed Mar 10 21:08:04 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Wed, 10 Mar 2010 21:08:04 -0500 Subject: [Mristudio-users] What is the definition of Linear Index(CI), Planar Index(Cp) and Spherical Index (Cs)? Thank you so much. References: Message-ID: <77A88E90A851594AAEF830450587C39D01EDAC21@CCHSCLEXMB56.cc.ad.cchs.net> Please refer to the following articles Westin CF, Maier SE, Mamata H, Nabavi A, Jolesz FA, Kikinis R. Processing and visualization for diffusion tensor MRI. Med Image Anal. Jun 2002;6(2):93-108. Westin C- F PS, Gudbjartsson H, Kikinis R, Jolesz FA. Geometrical Diffusion Measures for MRI from Tensor Basis Analysis. Paper presented at: ISMRM, 1997. ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of Weiguo Li Sent: Wed 3/10/2010 6:38 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] What is the definition of Linear Index(CI), Planar Index(Cp) and Spherical Index (Cs)? Thank you so much. What is the definition of Linear Index(CI), Planar Index(Cp) and Spherical Index (Cs)? Thank you so much. =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 4468 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100310/c1e6fb77/attachment.bin From d-gitelman at northwestern.edu Thu Mar 11 01:16:17 2010 From: d-gitelman at northwestern.edu (Darren Gitelman) Date: Thu, 11 Mar 2010 00:16:17 -0600 Subject: [Mristudio-users] How to tell if AIR worked Message-ID: Hi How can one tell if AIR realigned a set of images correctly? Darren Gitelman, MD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100311/36d28584/attachment.html From dafnab at tasmc.health.gov.il Thu Mar 11 06:19:20 2010 From: dafnab at tasmc.health.gov.il (Dafna Ben Bashat) Date: Thu, 11 Mar 2010 13:19:20 +0200 Subject: [Mristudio-users] CC in elderly patients Message-ID: <5EDAC8080B8BEF4E8F13D293108E58980EACD325@EXCH-VS.tasmc.corp> Hi all, We are currently working on data from elderly stroke/TIA patients. In many of the TIA patients, who have good DTI data, for some reason the CC does not built well, we can't see the fan. This is not due to incorrect directions (the CST is built OK). ROI measurements give reasonable values. We even changed the flip-angel for the FACT, and got the same results. Any suggestions? Is it a known phenomenon in elderly / stroke / TIA patients? Thank you in advance. Dafna Dafna Ben Bashat Ph.D. Senior Physicist, In charge of MR systems The Wohl institute for Advanced Imaging Brain Imaging Center Tel Aviv Sourasky Medical Center Phone: 972-3-6973953 (o) Fax: 972-3-6973080 972-52-4262515 (m) Mail: dafnab at tasmc.health.gov.il -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100311/bb9ddc8d/attachment.html From junyiwang2002 at yahoo.com Thu Mar 11 11:52:25 2010 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Thu, 11 Mar 2010 08:52:25 -0800 (PST) Subject: [Mristudio-users] CC in elderly patients In-Reply-To: <5EDAC8080B8BEF4E8F13D293108E58980EACD325@EXCH-VS.tasmc.corp> References: <5EDAC8080B8BEF4E8F13D293108E58980EACD325@EXCH-VS.tasmc.corp> Message-ID: <274361.60960.qm@web50506.mail.re2.yahoo.com> Hi Dafna, I only have a few subjects in 80s, but I have subjects from 16-65 years old. I do see a substantial decrease of the amount of corpus callosum fibers projecting towards the cortex as we age. Some fibers still project to the cortex although a lot of them project downwards instead. I don't know whether this is caused by aging or DTI artifacts such as the termination of line propagation because of the lower FA or the crossing fiber issue. Jun Yi Wang Postdoctoral Research Scholar Fragile X Research and Treatment Center UC Davis M.I.N.D. Institute 530.747.3808 (Lab) ________________________________ From: Dafna Ben Bashat To: mristudio-users at mristudio.org Sent: Thu, March 11, 2010 3:19:20 AM Subject: [Mristudio-users] CC in elderly patients Hi all, We are currently working on data from elderly stroke/TIA patients. In many of the TIA patients, who have good DTI data, for some reason the CC does not built well, we can't see the fan. This is not due to incorrect directions (the CST is built OK). ROI measurements give reasonable values. We even changed the flip-angel for the FACT, and got the same results. Any suggestions? Is it a known phenomenon in elderly / stroke / TIA patients? Thank you in advance. Dafna Dafna Ben Bashat Ph.D. Senior Physicist, In charge of MR systems The Wohl institute for Advanced Imaging Brain Imaging Center Tel Aviv Sourasky Medical Center Phone: 972-3-6973953 (o) Fax: 972-3-6973080 972-52-4262515 (m) Mail: dafnab at tasmc.health.gov.il -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100311/acb7d3e1/attachment-0001.html From susumu at mri.jhu.edu Thu Mar 11 15:01:50 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 11 Mar 2010 15:01:50 -0500 Subject: [Mristudio-users] CC in elderly patients In-Reply-To: <274361.60960.qm@web50506.mail.re2.yahoo.com> References: <5EDAC8080B8BEF4E8F13D293108E58980EACD325@EXCH-VS.tasmc.corp> <274361.60960.qm@web50506.mail.re2.yahoo.com> Message-ID: Hi all, We have noticed the same phenomena and also got several inquiries from outside. Here is my understanding; 1) For young subjects, the shape of the CC has a clean U shape in coronal sections. If you do fiber tracking, you usually can reconstruct the U-shape trajectory, which makes some anatomical sense. 2) For the population with enlarged ventricles, such as elderly, AD, and stroke patients, the trajectory of the CC becomes more like a "W" shape with a sharp turn where the CC merges to the corona radiata. I believe that this is the primary reason that most streamlines end up in going downward toward the internal capsule, which doesn't make much anatomical sense. 3) Think about the 90 degree rotated "T" shape and the vertical line is the corona radiata and the horizontal line is the CC. If the horizontal line merges at the right angle, the probability of the tracking to go upward and downward is 50/50. If the horizontal line is slightly tiled upward, the CC tracking merges to the vertical line (corona radiata) and continues to travel upward. It's as simple as this. Once we get a vector (or tensor) field and ask a computer to reconstruct a path, the computer doesn't know the anatomy. All it knows is just a bunch of vectors. One may think that probabilistic tracking can deal with it but the connectivity strength could be influenced by the merging angle too. 4) This exemplifies what tractography is. It is just a region growing (or pixel-connection) tool based on pixel-by-pixel information, no matter which algorithm we use. It is just a feature extraction tool from MRI that observes water molecules. Some results look right and some results do not. 5) Then many people ask, "how do we know the validity". Here we (both who ask the question and who is asked the question) have to think very hard. To show the validity, we need to compare our observation (in this case tractography result) and gold standard (real anatomy). Then what do we really mean by "real anatomy" or "real connectivity"? What is connectivity anyway? First of all many of the macroscopic anatomical definition such as "superior longitudinal fasciculs" and "corona radiata" are defined by human eyes based on anatomical features, which doesn't have a clear definition and boundary. It's like a cloud. Everybody can see it at the core but at the boundary, we don't know how to define. Then how about the microscopic anatomical definition? Yes, we have a very clear definition, which is axonal connection. However, we know that one neuron communicate with multiple neurons through a *branching* axon. We have 100 billion neurons. Even if one neuron communicate with one neuron, this is a 100 billion x 100 billion question. For MRI, even if you do 1,000-orientation Q-ball imaging, we are talking about merely few GB of data. With a tensor fitting, what we have is 20 MB. On top of it, we are measuring water properties. So, we can understand that we are on a very shaky ground when we talk about "validation" because we can't even define what is the gold standard we are shooting for and our data is so small compared to what we are interested in. 6) Then next question is, "why do we do tractography". Here, we should go back and think why we do MRI first of all and what is the real power of it. The real power is that we can examine the entire brain within 30 min non-invasively and quantitatively. This is something no other modality, certainly histology, can't do. By performing a feature extraction such as tractography, we can quickly and quantitatively assess the anatomical status. 7) As long as we apply the same data acquisition method and the same analysis method, the results itself is always correct. There is nothing wrong with the results whatever they are. In this example, in some population, the CC goes downward while it goes upward in the normal subjects. The tractography sensitively detected some differences between the two population. 8) If we make mistake in this situation, that is when we interpret the data. For example, if we interpret the data like, "in young brains, the CC goes up and in aged brain the CC goes down because the connectivity changed", now such a statement becomes the subject of "right or wrong". 9) So, it is very important to evaluate why you got different results between two groups. The real reason could be something not the measurement was intended. For the case of the CC trajectory, the real reason could be "enlarged ventricles" and the DTI + tractography could be just an expensive and indirect way to show it. 10) This is a very typical issue in MRI, not just DTI. When we observe cortical thinning in T1, it may be just a change in contrast due to myelination status or other things. What we really observe is the thinning of T1-indicated-cortical-compartment and the direct translation into the real cortical thickness is sometimes dangerous or even erroneous. As long as we are dealing with 10 MB of water information, biological or cellular interpretation always requires caution. 11) Fiber reconstruction is a high-level image analysis tool, which is sensitive to so many anatomical factors including both micro and macroscopic factors. The microscopic factors are myelination, axonal loss, cellular loss, edema, etc that would affect the FA and anatomy. The microscopic factors are multiple compartments (e.g. crossing fibers) within the 2 mm pixel. So, in general, the interpretation would be difficult. It is a good tool to survey the overall white matter anatomy but you need to exercise the caution when you interpret it. I guess what I mentioned above contains a lot of my personal opinions and please take it as just one of the opinions, but hope it helps to understand the issue of the downard CC projection. Susumu On Thu, Mar 11, 2010 at 11:52 AM, Jun Yi Wang wrote: > Hi Dafna, > > I only have a few subjects in 80s, but I have subjects from 16-65 years > old. I do see a substantial decrease of the amount of corpus callosum > fibers projecting towards the cortex as we age. Some fibers still project > to the cortex although a lot of them project downwards instead. I don't > know whether this is caused by aging or DTI artifacts such as the > termination of line propagation because of the lower FA or the crossing > fiber issue. > > Jun Yi Wang > Postdoctoral Research Scholar > Fragile X Research and Treatment Center > UC Davis M.I.N.D. Institute > 530.747.3808 (Lab) > > ------------------------------ > *From:* Dafna Ben Bashat > *To:* mristudio-users at mristudio.org > *Sent:* Thu, March 11, 2010 3:19:20 AM > *Subject:* [Mristudio-users] CC in elderly patients > > Hi all, > > We are currently working on data from elderly stroke/TIA patients. > > In many of the TIA patients, who have good DTI data, for some reason the CC > does not built well, we can't see the fan. > > This is not due to incorrect directions (the CST is built OK). > > ROI measurements give reasonable values. We even changed the flip-angel for > the FACT, and got the same results. > > Any suggestions? Is it a known phenomenon in elderly / stroke / TIA > patients? > > > > Thank you in advance. > > > > Dafna > > > > > > Dafna Ben Bashat Ph.D. > > > > Senior Physicist, In charge of MR systems > > The Wohl institute for Advanced Imaging > > Brain Imaging Center > > Tel Aviv Sourasky Medical Center > > > > Phone: 972-3-6973953 (o) Fax: 972-3-6973080 > > > > 972-52-4262515 (m) Mail: dafnab at tasmc.health.gov.il > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100311/1609332d/attachment.html From junyiwang2002 at yahoo.com Thu Mar 11 15:34:50 2010 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Thu, 11 Mar 2010 12:34:50 -0800 (PST) Subject: [Mristudio-users] CC in elderly patients In-Reply-To: References: <5EDAC8080B8BEF4E8F13D293108E58980EACD325@EXCH-VS.tasmc.corp> <274361.60960.qm@web50506.mail.re2.yahoo.com> Message-ID: <554941.43033.qm@web50505.mail.re2.yahoo.com> Hi Susumu, Thank you very much for the detailed explanation! It is very useful. I have the same impression of the difficulty of defining a gold standard for tractography after I read the paper by Dauguet et al. (2007): Comparison of fiber tracts derived from in-vivo DTI tractography with 3D histological neural tract tracer reconstruction in a macaque brain. Jun Yi ________________________________ From: susumu mori To: "DTI Studio, ROI Editor, Landmarker Questions/Support" ; Xin Li Sent: Thu, March 11, 2010 12:01:50 PM Subject: Re: [Mristudio-users] CC in elderly patients Hi all, We have noticed the same phenomena and also got several inquiries from outside. Here is my understanding; 1) For young subjects, the shape of the CC has a clean U shape in coronal sections. If you do fiber tracking, you usually can reconstruct the U-shape trajectory, which makes some anatomical sense. 2) For the population with enlarged ventricles, such as elderly, AD, and stroke patients, the trajectory of the CC becomes more like a "W" shape with a sharp turn where the CC merges to the corona radiata. I believe that this is the primary reason that most streamlines end up in going downward toward the internal capsule, which doesn't make much anatomical sense. 3) Think about the 90 degree rotated "T" shape and the vertical line is the corona radiata and the horizontal line is the CC. If the horizontal line merges at the right angle, the probability of the tracking to go upward and downward is 50/50. If the horizontal line is slightly tiled upward, the CC tracking merges to the vertical line (corona radiata) and continues to travel upward. It's as simple as this. Once we get a vector (or tensor) field and ask a computer to reconstruct a path, the computer doesn't know the anatomy. All it knows is just a bunch of vectors. One may think that probabilistic tracking can deal with it but the connectivity strength could be influenced by the merging angle too. 4) This exemplifies what tractography is. It is just a region growing (or pixel-connection) tool based on pixel-by-pixel information, no matter which algorithm we use. It is just a feature extraction tool from MRI that observes water molecules. Some results look right and some results do not. 5) Then many people ask, "how do we know the validity". Here we (both who ask the question and who is asked the question) have to think very hard. To show the validity, we need to compare our observation (in this case tractography result) and gold standard (real anatomy). Then what do we really mean by "real anatomy" or "real connectivity"? What is connectivity anyway? First of all many of the macroscopic anatomical definition such as "superior longitudinal fasciculs" and "corona radiata" are defined by human eyes based on anatomical features, which doesn't have a clear definition and boundary. It's like a cloud. Everybody can see it at the core but at the boundary, we don't know how to define. Then how about the microscopic anatomical definition? Yes, we have a very clear definition, which is axonal connection. However, we know that one neuron communicate with multiple neurons through a branching axon. We have 100 billion neurons. Even if one neuron communicate with one neuron, this is a 100 billion x 100 billion question. For MRI, even if you do 1,000-orientation Q-ball imaging, we are talking about merely few GB of data. With a tensor fitting, what we have is 20 MB. On top of it, we are measuring water properties. So, we can understand that we are on a very shaky ground when we talk about "validation" because we can't even define what is the gold standard we are shooting for and our data is so small compared to what we are interested in. 6) Then next question is, "why do we do tractography". Here, we should go back and think why we do MRI first of all and what is the real power of it. The real power is that we can examine the entire brain within 30 min non-invasively and quantitatively. This is something no other modality, certainly histology, can't do. By performing a feature extraction such as tractography, we can quickly and quantitatively assess the anatomical status. 7) As long as we apply the same data acquisition method and the same analysis method, the results itself is always correct. There is nothing wrong with the results whatever they are. In this example, in some population, the CC goes downward while it goes upward in the normal subjects. The tractography sensitively detected some differences between the two population. 8) If we make mistake in this situation, that is when we interpret the data. For example, if we interpret the data like, "in young brains, the CC goes up and in aged brain the CC goes down because the connectivity changed", now such a statement becomes the subject of "right or wrong". 9) So, it is very important to evaluate why you got different results between two groups. The real reason could be something not the measurement was intended. For the case of the CC trajectory, the real reason could be "enlarged ventricles" and the DTI + tractography could be just an expensive and indirect way to show it. 10) This is a very typical issue in MRI, not just DTI. When we observe cortical thinning in T1, it may be just a change in contrast due to myelination status or other things. What we really observe is the thinning of T1-indicated-cortical-compartment and the direct translation into the real cortical thickness is sometimes dangerous or even erroneous. As long as we are dealing with 10 MB of water information, biological or cellular interpretation always requires caution. 11) Fiber reconstruction is a high-level image analysis tool, which is sensitive to so many anatomical factors including both micro and macroscopic factors. The microscopic factors are myelination, axonal loss, cellular loss, edema, etc that would affect the FA and anatomy. The microscopic factors are multiple compartments (e.g. crossing fibers) within the 2 mm pixel. So, in general, the interpretation would be difficult. It is a good tool to survey the overall white matter anatomy but you need to exercise the caution when you interpret it. I guess what I mentioned above contains a lot of my personal opinions and please take it as just one of the opinions, but hope it helps to understand the issue of the downard CC projection. Susumu On Thu, Mar 11, 2010 at 11:52 AM, Jun Yi Wang wrote: Hi Dafna, > >I only have a few subjects in 80s, but I have subjects from 16-65 years old. I do see a substantial decrease of the amount of corpus callosum fibers projecting towards the cortex as we age. Some fibers still project to the cortex although a lot of them project downwards instead. I don't know whether this is caused by aging or DTI artifacts such as the termination of line propagation because of the lower FA or the crossing fiber issue. > >Jun Yi Wang > >Postdoctoral > Research Scholar >Fragile X Research and Treatment Center >UC Davis M.I.N.D. Institute >530.747.3808 (Lab) > > > ________________________________ From: Dafna Ben Bashat >To: mristudio-users at mristudio.org >Sent: Thu, March 11, 2010 3:19:20 AM >Subject: [Mristudio-users] CC in elderly patients > > > >> >Hi >all, >We >are currently working on data from elderly stroke/TIA patients. >In >many of the TIA patients, who have good DTI data, for some reason the CC does >not built well, we can't see the fan. >This >is not due to incorrect directions (the CST is built OK). >ROI >measurements give reasonable values. We even changed the flip-angel for the >FACT, and got the same results. >Any >suggestions? Is it a known phenomenon in elderly / stroke / TIA patients? > >Thank >you in advance. > >Dafna > > > >Dafna Ben Bashat Ph.D. > >Senior Physicist, In charge of MR systems >The Wohl institute for Advanced Imaging >Brain Imaging Center >Tel Aviv Sourasky Medical Center > >Phone: 972-3-6973953 >(o) Fax: 972-3-6973080 > > 972-52-4262515 >(m) Mail: dafnab at tasmc.health.gov.il > > >_______________________________________________ >>Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100311/d4519ecc/attachment-0001.html From junyiwang2002 at yahoo.com Thu Mar 11 15:45:45 2010 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Thu, 11 Mar 2010 12:45:45 -0800 (PST) Subject: [Mristudio-users] CC in elderly patients Message-ID: <142131.47283.qm@web50505.mail.re2.yahoo.com> Hi Susumu, Just realized that I have a question to ask: are you working on a way to handle the crossing fiber issue such as the two-tensor streamline tractography proposed by Qazi et al. (2009), NeuroImage 47:T98-106? Jun Yi ________________________________ From: Jun Yi Wang To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Thu, March 11, 2010 12:34:50 PM Subject: Re: [Mristudio-users] CC in elderly patients Hi Susumu, Thank you very much for the detailed explanation! It is very useful. I have the same impression of the difficulty of defining a gold standard for tractography after I read the paper by Dauguet et al. (2007): Comparison of fiber tracts derived from in-vivo DTI tractography with 3D histological neural tract tracer reconstruction in a macaque brain. Jun Yi ________________________________ From: susumu mori To: "DTI Studio, ROI Editor, Landmarker Questions/Support" ; Xin Li Sent: Thu, March 11, 2010 12:01:50 PM Subject: Re: [Mristudio-users] CC in elderly patients Hi all, We have noticed the same phenomena and also got several inquiries from outside. Here is my understanding; 1) For young subjects, the shape of the CC has a clean U shape in coronal sections. If you do fiber tracking, you usually can reconstruct the U-shape trajectory, which makes some anatomical sense. 2) For the population with enlarged ventricles, such as elderly, AD, and stroke patients, the trajectory of the CC becomes more like a "W" shape with a sharp turn where the CC merges to the corona radiata. I believe that this is the primary reason that most streamlines end up in going downward toward the internal capsule, which doesn't make much anatomical sense. 3) Think about the 90 degree rotated "T" shape and the vertical line is the corona radiata and the horizontal line is the CC. If the horizontal line merges at the right angle, the probability of the tracking to go upward and downward is 50/50. If the horizontal line is slightly tiled upward, the CC tracking merges to the vertical line (corona radiata) and continues to travel upward. It's as simple as this. Once we get a vector (or tensor) field and ask a computer to reconstruct a path, the computer doesn't know the anatomy. All it knows is just a bunch of vectors. One may think that probabilistic tracking can deal with it but the connectivity strength could be influenced by the merging angle too. 4) This exemplifies what tractography is. It is just a region growing (or pixel-connection) tool based on pixel-by-pixel information, no matter which algorithm we use. It is just a feature extraction tool from MRI that observes water molecules. Some results look right and some results do not. 5) Then many people ask, "how do we know the validity". Here we (both who ask the question and who is asked the question) have to think very hard. To show the validity, we need to compare our observation (in this case tractography result) and gold standard (real anatomy). Then what do we really mean by "real anatomy" or "real connectivity"? What is connectivity anyway? First of all many of the macroscopic anatomical definition such as "superior longitudinal fasciculs" and "corona radiata" are defined by human eyes based on anatomical features, which doesn't have a clear definition and boundary. It's like a cloud. Everybody can see it at the core but at the boundary, we don't know how to define. Then how about the microscopic anatomical definition? Yes, we have a very clear definition, which is axonal connection. However, we know that one neuron communicate with multiple neurons through a branching axon. We have 100 billion neurons. Even if one neuron communicate with one neuron, this is a 100 billion x 100 billion question. For MRI, even if you do 1,000-orientation Q-ball imaging, we are talking about merely few GB of data. With a tensor fitting, what we have is 20 MB. On top of it, we are measuring water properties. So, we can understand that we are on a very shaky ground when we talk about "validation" because we can't even define what is the gold standard we are shooting for and our data is so small compared to what we are interested in. 6) Then next question is, "why do we do tractography". Here, we should go back and think why we do MRI first of all and what is the real power of it. The real power is that we can examine the entire brain within 30 min non-invasively and quantitatively. This is something no other modality, certainly histology, can't do. By performing a feature extraction such as tractography, we can quickly and quantitatively assess the anatomical status. 7) As long as we apply the same data acquisition method and the same analysis method, the results itself is always correct. There is nothing wrong with the results whatever they are. In this example, in some population, the CC goes downward while it goes upward in the normal subjects. The tractography sensitively detected some differences between the two population. 8) If we make mistake in this situation, that is when we interpret the data. For example, if we interpret the data like, "in young brains, the CC goes up and in aged brain the CC goes down because the connectivity changed", now such a statement becomes the subject of "right or wrong". 9) So, it is very important to evaluate why you got different results between two groups. The real reason could be something not the measurement was intended. For the case of the CC trajectory, the real reason could be "enlarged ventricles" and the DTI + tractography could be just an expensive and indirect way to show it. 10) This is a very typical issue in MRI, not just DTI. When we observe cortical thinning in T1, it may be just a change in contrast due to myelination status or other things. What we really observe is the thinning of T1-indicated-cortical-compartment and the direct translation into the real cortical thickness is sometimes dangerous or even erroneous. As long as we are dealing with 10 MB of water information, biological or cellular interpretation always requires caution. 11) Fiber reconstruction is a high-level image analysis tool, which is sensitive to so many anatomical factors including both micro and macroscopic factors. The microscopic factors are myelination, axonal loss, cellular loss, edema, etc that would affect the FA and anatomy. The microscopic factors are multiple compartments (e.g. crossing fibers) within the 2 mm pixel. So, in general, the interpretation would be difficult. It is a good tool to survey the overall white matter anatomy but you need to exercise the caution when you interpret it. I guess what I mentioned above contains a lot of my personal opinions and please take it as just one of the opinions, but hope it helps to understand the issue of the downard CC projection. Susumu On Thu, Mar 11, 2010 at 11:52 AM, Jun Yi Wang wrote: Hi Dafna, > >I only have a few subjects in 80s, but I have subjects from 16-65 years old. I do see a substantial decrease of the amount of corpus callosum fibers projecting towards the cortex as we age. Some fibers still project to the cortex although a lot of them project downwards instead. I don't know whether this is caused by aging or DTI artifacts such as the termination of line propagation because of the lower FA or the crossing fiber issue. > >Jun Yi Wang > >Postdoctoral > Research Scholar >Fragile X Research and Treatment Center >UC Davis M.I.N.D. Institute >530.747.3808 (Lab) > > > ________________________________ From: Dafna Ben Bashat >To: mristudio-users at mristudio.org >Sent: Thu, March 11, 2010 3:19:20 AM >Subject: [Mristudio-users] CC in elderly patients > > > >> >Hi >all, >We >are currently working on data from elderly stroke/TIA patients. >In >many of the TIA patients, who have good DTI data, for some reason the CC does >not built well, we can't see the fan. >This >is not due to incorrect directions (the CST is built OK). >ROI >measurements give reasonable values. We even changed the flip-angel for the >FACT, and got the same results. >Any >suggestions? Is it a known phenomenon in elderly / stroke / TIA patients? > >Thank >you in advance. > >Dafna > > > >Dafna Ben Bashat Ph.D. > >Senior Physicist, In charge of MR systems >The Wohl institute for Advanced Imaging >Brain Imaging Center >Tel Aviv Sourasky Medical Center > >Phone: 972-3-6973953 >(o) Fax: 972-3-6973080 > > 972-52-4262515 >(m) Mail: dafnab at tasmc.health.gov.il > > >_______________________________________________ >>Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100311/8ad59bce/attachment.html From susumu at mri.jhu.edu Thu Mar 11 16:48:32 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 11 Mar 2010 16:48:32 -0500 Subject: [Mristudio-users] CC in elderly patients In-Reply-To: <142131.47283.qm@web50505.mail.re2.yahoo.com> References: <142131.47283.qm@web50505.mail.re2.yahoo.com> Message-ID: No I don't. My research is application-driven and I haven't requested by any application to resolve fibers within a pixel to answer an important clinical question. Most of application research is talking about inter-pixel or pixel-cluster anatomical information (e.g. what is the size of a structure) but not intra-pixel information (e.g. how much water population is going up-down and how much in right-left). On Thu, Mar 11, 2010 at 3:45 PM, Jun Yi Wang wrote: > Hi Susumu, > > Just realized that I have a question to ask: are you working on a way to > handle the crossing fiber issue such as the two-tensor streamline > tractography proposed by Qazi et al. (2009), NeuroImage 47:T98-106? > > Jun Yi > > ------------------------------ > *From:* Jun Yi Wang > > *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > *Sent:* Thu, March 11, 2010 12:34:50 PM > > *Subject:* Re: [Mristudio-users] CC in elderly patients > > Hi Susumu, > > Thank you very much for the detailed explanation! It is very useful. I > have the same impression of the difficulty of defining a gold standard for > tractography after I read the paper by Dauguet et al. (2007): Comparison of > fiber tracts derived from in-vivo DTI tractography with 3D histological > neural tract tracer reconstruction in a macaque brain. > > Jun Yi > > ------------------------------ > *From:* susumu mori > *To:* "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org>; Xin Li > *Sent:* Thu, March 11, 2010 12:01:50 PM > *Subject:* Re: [Mristudio-users] CC in elderly patients > > Hi all, > > We have noticed the same phenomena and also got several inquiries from > outside. Here is my understanding; > > 1) For young subjects, the shape of the CC has a clean U shape in coronal > sections. If you do fiber tracking, you usually can reconstruct the U-shape > trajectory, which makes some anatomical sense. > 2) For the population with enlarged ventricles, such as elderly, AD, and > stroke patients, the trajectory of the CC becomes more like a "W" shape with > a sharp turn where the CC merges to the corona radiata. I believe that this > is the primary reason that most streamlines end up in going downward toward > the internal capsule, which doesn't make much anatomical sense. > 3) Think about the 90 degree rotated "T" shape and the vertical line is the > corona radiata and the horizontal line is the CC. If the horizontal line > merges at the right angle, the probability of the tracking to go upward and > downward is 50/50. If the horizontal line is slightly tiled upward, the CC > tracking merges to the vertical line (corona radiata) and continues to > travel upward. It's as simple as this. Once we get a vector (or tensor) > field and ask a computer to reconstruct a path, the computer doesn't know > the anatomy. All it knows is just a bunch of vectors. One may think that > probabilistic tracking can deal with it but the connectivity strength could > be influenced by the merging angle too. > 4) This exemplifies what tractography is. It is just a region growing (or > pixel-connection) tool based on pixel-by-pixel information, no matter which > algorithm we use. It is just a feature extraction tool from MRI that > observes water molecules. Some results look right and some results do not. > 5) Then many people ask, "how do we know the validity". Here we (both who > ask the question and who is asked the question) have to think very hard. To > show the validity, we need to compare our observation (in this case > tractography result) and gold standard (real anatomy). Then what do we > really mean by "real anatomy" or "real connectivity"? What is connectivity > anyway? First of all many of the macroscopic anatomical definition such as > "superior longitudinal fasciculs" and "corona radiata" are defined by human > eyes based on anatomical features, which doesn't have a clear definition and > boundary. It's like a cloud. Everybody can see it at the core but at the > boundary, we don't know how to define. Then how about the microscopic > anatomical definition? Yes, we have a very clear definition, which is axonal > connection. However, we know that one neuron communicate with multiple > neurons through a *branching* axon. We have 100 billion neurons. Even if > one neuron communicate with one neuron, this is a 100 billion x 100 billion > question. For MRI, even if you do 1,000-orientation Q-ball imaging, we are > talking about merely few GB of data. With a tensor fitting, what we have is > 20 MB. On top of it, we are measuring water properties. So, we can > understand that we are on a very shaky ground when we talk about > "validation" because we can't even define what is the gold standard we are > shooting for and our data is so small compared to what we are interested in. > 6) Then next question is, "why do we do tractography". Here, we should go > back and think why we do MRI first of all and what is the real power of it. > The real power is that we can examine the entire brain within 30 min > non-invasively and quantitatively. This is something no other modality, > certainly histology, can't do. By performing a feature extraction such as > tractography, we can quickly and quantitatively assess the anatomical > status. > 7) As long as we apply the same data acquisition method and the same > analysis method, the results itself is always correct. There is nothing > wrong with the results whatever they are. In this example, in some > population, the CC goes downward while it goes upward in the normal > subjects. The tractography sensitively detected some differences between the > two population. > 8) If we make mistake in this situation, that is when we interpret the > data. For example, if we interpret the data like, "in young brains, the CC > goes up and in aged brain the CC goes down because the connectivity > changed", now such a statement becomes the subject of "right or wrong". > 9) So, it is very important to evaluate why you got different results > between two groups. The real reason could be something not the measurement > was intended. For the case of the CC trajectory, the real reason could be > "enlarged ventricles" and the DTI + tractography could be just an expensive > and indirect way to show it. > 10) This is a very typical issue in MRI, not just DTI. When we observe > cortical thinning in T1, it may be just a change in contrast due to > myelination status or other things. What we really observe is the thinning > of T1-indicated-cortical-compartment and the direct translation into the > real cortical thickness is sometimes dangerous or even erroneous. As long as > we are dealing with 10 MB of water information, biological or cellular > interpretation always requires caution. > 11) Fiber reconstruction is a high-level image analysis tool, which is > sensitive to so many anatomical factors including both micro and macroscopic > factors. The microscopic factors are myelination, axonal loss, cellular > loss, edema, etc that would affect the FA and anatomy. The microscopic > factors are multiple compartments (e.g. crossing fibers) within the 2 mm > pixel. So, in general, the interpretation would be difficult. It is a good > tool to survey the overall white matter anatomy but you need to exercise the > caution when you interpret it. > > > I guess what I mentioned above contains a lot of my personal opinions and > please take it as just one of the opinions, but hope it helps to understand > the issue of the downard CC projection. > > Susumu > > > On Thu, Mar 11, 2010 at 11:52 AM, Jun Yi Wang wrote: > >> Hi Dafna, >> >> I only have a few subjects in 80s, but I have subjects from 16-65 years >> old. I do see a substantial decrease of the amount of corpus callosum >> fibers projecting towards the cortex as we age. Some fibers still project >> to the cortex although a lot of them project downwards instead. I don't >> know whether this is caused by aging or DTI artifacts such as the >> termination of line propagation because of the lower FA or the crossing >> fiber issue. >> >> Jun Yi Wang >> Postdoctoral Research Scholar >> Fragile X Research and Treatment Center >> UC Davis M.I.N.D. Institute >> 530.747.3808 (Lab) >> >> ------------------------------ >> *From:* Dafna Ben Bashat >> *To:* mristudio-users at mristudio.org >> *Sent:* Thu, March 11, 2010 3:19:20 AM >> *Subject:* [Mristudio-users] CC in elderly patients >> >> Hi all, >> >> We are currently working on data from elderly stroke/TIA patients. >> >> In many of the TIA patients, who have good DTI data, for some reason the >> CC does not built well, we can't see the fan. >> >> This is not due to incorrect directions (the CST is built OK). >> >> ROI measurements give reasonable values. We even changed the flip-angel >> for the FACT, and got the same results. >> >> Any suggestions? Is it a known phenomenon in elderly / stroke / TIA >> patients? >> >> >> >> Thank you in advance. >> >> >> >> Dafna >> >> >> >> >> >> Dafna Ben Bashat Ph.D. >> >> >> >> Senior Physicist, In charge of MR systems >> >> The Wohl institute for Advanced Imaging >> >> Brain Imaging Center >> >> Tel Aviv Sourasky Medical Center >> >> >> >> Phone: 972-3-6973953 (o) Fax: 972-3-6973080 >> >> >> >> 972-52-4262515 (m) Mail: dafnab at tasmc.health.gov.il >> >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100311/28d6a1ac/attachment-0001.html From dafnab at tasmc.health.gov.il Sat Mar 13 16:42:19 2010 From: dafnab at tasmc.health.gov.il (Dafna Ben Bashat) Date: Sat, 13 Mar 2010 23:42:19 +0200 Subject: [Mristudio-users] CC in elderly patients In-Reply-To: References: <142131.47283.qm@web50505.mail.re2.yahoo.com> Message-ID: <5EDAC8080B8BEF4E8F13D293108E58980EC6502E@EXCH-VS.tasmc.corp> Dear Susumu, I would like to thank you and all other, for the detailed answers. The interpretation of the data is indeed problematic, since in some patients we get the CC in the u shape and in other we don't. It seems that the comparison of the mean values of FA, MD and eigen values of the CC, is wrong. In addition, the parameter of the size of the CC obtained from the number of fibers in the reconstructed fiber is also unreliable. We found it to be highly dependent on the one who make the tractography, while the mean of the other parameters are much more repeatable. Thanks again Dafna Thank you very much for the detailed explanation Dafna Ben Bashat Ph.D. Senior Physicist, In charge of MR systems The Wohl institute for Advanced Imaging Brain Imaging Center Tel Aviv Sourasky Medical Center Phone: 972-3-6973953 (o) Fax: 972-3-6973080 972-52-4262515 (m) Mail: dafnab at tasmc.health.gov.il ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Thursday, March 11, 2010 11:49 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] CC in elderly patients No I don't. My research is application-driven and I haven't requested by any application to resolve fibers within a pixel to answer an important clinical question. Most of application research is talking about inter-pixel or pixel-cluster anatomical information (e.g. what is the size of a structure) but not intra-pixel information (e.g. how much water population is going up-down and how much in right-left). On Thu, Mar 11, 2010 at 3:45 PM, Jun Yi Wang wrote: Hi Susumu, Just realized that I have a question to ask: are you working on a way to handle the crossing fiber issue such as the two-tensor streamline tractography proposed by Qazi et al. (2009), NeuroImage 47:T98-106? Jun Yi ________________________________ From: Jun Yi Wang To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Thu, March 11, 2010 12:34:50 PM Subject: Re: [Mristudio-users] CC in elderly patients Hi Susumu, Thank you very much for the detailed explanation! It is very useful. I have the same impression of the difficulty of defining a gold standard for tractography after I read the paper by Dauguet et al. (2007): Comparison of fiber tracts derived from in-vivo DTI tractography with 3D histological neural tract tracer reconstruction in a macaque brain. Jun Yi ________________________________ From: susumu mori To: "DTI Studio, ROI Editor, Landmarker Questions/Support" ; Xin Li Sent: Thu, March 11, 2010 12:01:50 PM Subject: Re: [Mristudio-users] CC in elderly patients Hi all, We have noticed the same phenomena and also got several inquiries from outside. Here is my understanding; 1) For young subjects, the shape of the CC has a clean U shape in coronal sections. If you do fiber tracking, you usually can reconstruct the U-shape trajectory, which makes some anatomical sense. 2) For the population with enlarged ventricles, such as elderly, AD, and stroke patients, the trajectory of the CC becomes more like a "W" shape with a sharp turn where the CC merges to the corona radiata. I believe that this is the primary reason that most streamlines end up in going downward toward the internal capsule, which doesn't make much anatomical sense. 3) Think about the 90 degree rotated "T" shape and the vertical line is the corona radiata and the horizontal line is the CC. If the horizontal line merges at the right angle, the probability of the tracking to go upward and downward is 50/50. If the horizontal line is slightly tiled upward, the CC tracking merges to the vertical line (corona radiata) and continues to travel upward. It's as simple as this. Once we get a vector (or tensor) field and ask a computer to reconstruct a path, the computer doesn't know the anatomy. All it knows is just a bunch of vectors. One may think that probabilistic tracking can deal with it but the connectivity strength could be influenced by the merging angle too. 4) This exemplifies what tractography is. It is just a region growing (or pixel-connection) tool based on pixel-by-pixel information, no matter which algorithm we use. It is just a feature extraction tool from MRI that observes water molecules. Some results look right and some results do not. 5) Then many people ask, "how do we know the validity". Here we (both who ask the question and who is asked the question) have to think very hard. To show the validity, we need to compare our observation (in this case tractography result) and gold standard (real anatomy). Then what do we really mean by "real anatomy" or "real connectivity"? What is connectivity anyway? First of all many of the macroscopic anatomical definition such as "superior longitudinal fasciculs" and "corona radiata" are defined by human eyes based on anatomical features, which doesn't have a clear definition and boundary. It's like a cloud. Everybody can see it at the core but at the boundary, we don't know how to define. Then how about the microscopic anatomical definition? Yes, we have a very clear definition, which is axonal connection. However, we know that one neuron communicate with multiple neurons through a branching axon. We have 100 billion neurons. Even if one neuron communicate with one neuron, this is a 100 billion x 100 billion question. For MRI, even if you do 1,000-orientation Q-ball imaging, we are talking about merely few GB of data. With a tensor fitting, what we have is 20 MB. On top of it, we are measuring water properties. So, we can understand that we are on a very shaky ground when we talk about "validation" because we can't even define what is the gold standard we are shooting for and our data is so small compared to what we are interested in. 6) Then next question is, "why do we do tractography". Here, we should go back and think why we do MRI first of all and what is the real power of it. The real power is that we can examine the entire brain within 30 min non-invasively and quantitatively. This is something no other modality, certainly histology, can't do. By performing a feature extraction such as tractography, we can quickly and quantitatively assess the anatomical status. 7) As long as we apply the same data acquisition method and the same analysis method, the results itself is always correct. There is nothing wrong with the results whatever they are. In this example, in some population, the CC goes downward while it goes upward in the normal subjects. The tractography sensitively detected some differences between the two population. 8) If we make mistake in this situation, that is when we interpret the data. For example, if we interpret the data like, "in young brains, the CC goes up and in aged brain the CC goes down because the connectivity changed", now such a statement becomes the subject of "right or wrong". 9) So, it is very important to evaluate why you got different results between two groups. The real reason could be something not the measurement was intended. For the case of the CC trajectory, the real reason could be "enlarged ventricles" and the DTI + tractography could be just an expensive and indirect way to show it. 10) This is a very typical issue in MRI, not just DTI. When we observe cortical thinning in T1, it may be just a change in contrast due to myelination status or other things. What we really observe is the thinning of T1-indicated-cortical-compartment and the direct translation into the real cortical thickness is sometimes dangerous or even erroneous. As long as we are dealing with 10 MB of water information, biological or cellular interpretation always requires caution. 11) Fiber reconstruction is a high-level image analysis tool, which is sensitive to so many anatomical factors including both micro and macroscopic factors. The microscopic factors are myelination, axonal loss, cellular loss, edema, etc that would affect the FA and anatomy. The microscopic factors are multiple compartments (e.g. crossing fibers) within the 2 mm pixel. So, in general, the interpretation would be difficult. It is a good tool to survey the overall white matter anatomy but you need to exercise the caution when you interpret it. I guess what I mentioned above contains a lot of my personal opinions and please take it as just one of the opinions, but hope it helps to understand the issue of the downard CC projection. Susumu On Thu, Mar 11, 2010 at 11:52 AM, Jun Yi Wang wrote: Hi Dafna, I only have a few subjects in 80s, but I have subjects from 16-65 years old. I do see a substantial decrease of the amount of corpus callosum fibers projecting towards the cortex as we age. Some fibers still project to the cortex although a lot of them project downwards instead. I don't know whether this is caused by aging or DTI artifacts such as the termination of line propagation because of the lower FA or the crossing fiber issue. Jun Yi Wang Postdoctoral Research Scholar Fragile X Research and Treatment Center UC Davis M.I.N.D. Institute 530.747.3808 (Lab) ________________________________ From: Dafna Ben Bashat To: mristudio-users at mristudio.org Sent: Thu, March 11, 2010 3:19:20 AM Subject: [Mristudio-users] CC in elderly patients Hi all, We are currently working on data from elderly stroke/TIA patients. In many of the TIA patients, who have good DTI data, for some reason the CC does not built well, we can't see the fan. This is not due to incorrect directions (the CST is built OK). ROI measurements give reasonable values. We even changed the flip-angel for the FACT, and got the same results. Any suggestions? Is it a known phenomenon in elderly / stroke / TIA patients? Thank you in advance. Dafna Dafna Ben Bashat Ph.D. Senior Physicist, In charge of MR systems The Wohl institute for Advanced Imaging Brain Imaging Center Tel Aviv Sourasky Medical Center Phone: 972-3-6973953 (o) Fax: 972-3-6973080 972-52-4262515 (m) Mail: dafnab at tasmc.health.gov.il _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100313/586a1838/attachment-0001.html From kevinspitler at ucla.edu Wed Mar 17 23:32:17 2010 From: kevinspitler at ucla.edu (Kevin Spitler) Date: Wed, 17 Mar 2010 20:32:17 -0700 Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio Message-ID: <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> Hello, We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue). The study was performed on a 3T Trio scanner in Siemens. b values are b=0, b=600, b=1200 Direction is 12 I can provide more information or attach files if that would help solve the problem. Thanks for your help Best, Kevin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100317/937441f7/attachment.html From susumu at mri.jhu.edu Thu Mar 18 09:54:02 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 18 Mar 2010 09:54:02 -0400 Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> References: <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> Message-ID: Have you recently upgraded the operating system? Can I see the gradient table you used? On Wed, Mar 17, 2010 at 11:32 PM, Kevin Spitler wrote: > Hello, > > We have recently starting acquiring high resolution scans and I am having > difficulty loading them into DTI Studio. I am using the same 12 direction > gradient that worked on the low resolution (large slice thickness). > Although the DTI Studio program does not crash, the color map 0 generated is > not correct (random color patterns over the tissue). > > The study was performed on a 3T Trio scanner in Siemens. > b values are b=0, b=600, b=1200 > Direction is 12 > > I can provide more information or attach files if that would help solve the > problem. Thanks for your help > > Best, > Kevin > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100318/3743a76e/attachment.html From Helen.Carlson at albertahealthservices.ca Thu Mar 18 14:07:32 2010 From: Helen.Carlson at albertahealthservices.ca (Helen Carlson) Date: Thu, 18 Mar 2010 12:07:32 -0600 Subject: [Mristudio-users] Tractography: More decimal places for ADC mean values? Message-ID: Hi all, I am taking FA and ADC measurements of the Cingulum and Fornix in epilepsy patients using tractography in DTI Studio. I have noticed that the ADC values of the selected fibres in the Cingulum are in the region of 0.0007 but that this measurement only goes to 4 decimal places. In order to detect any differences in ADC across patient groups I would need more decimal places. I have clicked the statistics profile button in the Fiber Statistics window and have gotten a list of ADC values for each slice with a greater number of decimal places (i.e., 7.11e-004 which I assume is 0.000711) for my tract. So my question is, can I take the mean of all these values in the Statistics Profile window (for a given slice orientation) and use that as my mean ADC value for the selected tract? OR is there an easier way for me to get the mean ADC for a selected fiber tract with a greater number of decimal places? Thanks in advance for your help. Helen. Helen Carlson, Ph.D. Neuropsychology Department of Neurosciences Alberta Children's Hospital 2888 Shaganappi Trail NW, Calgary ________________________________ This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100318/e97a6f06/attachment.html From cwber at 126.com Sat Mar 20 04:20:16 2010 From: cwber at 126.com (cwber at 126.com) Date: Sat, 20 Mar 2010 16:20:16 +0800 (CST) Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> References: <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> Message-ID: You should first make sure you select the right data format? and make sure there is not mistakes in your Gradient table. Then try again, Best wishes! weibo ?2010-03-18 11:32:17?"Kevin Spitler" ??? Hello, We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue). The study was performed on a 3T Trio scanner in Siemens. b values are b=0, b=600, b=1200 Direction is 12 I can provide more information or attach files if that would help solve the problem. Thanks for your help Best, Kevin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100320/1a39cec0/attachment.html From kevinspitler at ucla.edu Sat Mar 20 10:09:12 2010 From: kevinspitler at ucla.edu (Kevin Spitler) Date: Sat, 20 Mar 2010 07:09:12 -0700 Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: References: <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> Message-ID: <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> I haven't upgraded the operating system.? I am still using Windows XP. Here is the gradient table: 0: 0.000, 0.000, 0.000 1: 0.500, 0.000, 0.500 2: -0.500, 0.000, 0.500 3: 0.000, 0.500, 0.500 4: 0.000, 0.500, -0.500 5: 0.500, 0.500, 0.000 6: -0.500, 0.500, 0.000 7: 1.000, 0.000, 1.000 8: -1.000, 0.000, 1.000 9: 0.000, 1.000, 1.000 10: 0.000, 1.000, -1.000 11: 1.000, 1.000, 0.000 12: -1.000, 1.000, 0.000 Thanks for your help! Please let me know what else I can send Best, Kevin On Thu, Mar 18, 2010 at 6:54 AM, susumu mori wrote: > > Have you recently upgraded the operating system? Can I see the gradient table you used? > > On Wed, Mar 17, 2010 at 11:32 PM, Kevin Spitler wrote: >> >> Hello, >> >> We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio.? I am using the same 12 direction gradient that worked on the low resolution (large slice thickness).? Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue). >> >> The study was performed on a 3T Trio scanner in Siemens. >> b values are b=0, b=600, b=1200 >> Direction is 12 >> >> I can provide more information or attach files if that would help solve the problem.? Thanks for your help >> >> Best, >> Kevin >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From cwber at 126.com Sat Mar 20 10:38:59 2010 From: cwber at 126.com (cwber) Date: Sat, 20 Mar 2010 22:38:59 +0800 (CST) Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> References: <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> Message-ID: <196b712.d396.1277c033c9b.Coremail.cwber@126.com> How did you get the gradient table, there maybe something wrong in your gradient table, you can check it, and which factory's machine did you use philips, GE,or Semense? -- ??? ?2010-03-20 22:09:12?"Kevin Spitler" ??? >I haven't upgraded the operating system. I am still using Windows XP. > >Here is the gradient table: > >0: 0.000, 0.000, 0.000 > 1: 0.500, 0.000, 0.500 > 2: -0.500, 0.000, 0.500 > 3: 0.000, 0.500, 0.500 > 4: 0.000, 0.500, -0.500 > 5: 0.500, 0.500, 0.000 > 6: -0.500, 0.500, 0.000 > 7: 1.000, 0.000, 1.000 > 8: -1.000, 0.000, 1.000 > 9: 0.000, 1.000, 1.000 > 10: 0.000, 1.000, -1.000 > 11: 1.000, 1.000, 0.000 > 12: -1.000, 1.000, 0.000 > >Thanks for your help! Please let me know what else I can send > >Best, >Kevin > > >On Thu, Mar 18, 2010 at 6:54 AM, susumu mori wrote: >> >> Have you recently upgraded the operating system? Can I see the gradient table you used? >> >> On Wed, Mar 17, 2010 at 11:32 PM, Kevin Spitler wrote: >>> >>> Hello, >>> >>> We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue). >>> >>> The study was performed on a 3T Trio scanner in Siemens. >>> b values are b=0, b=600, b=1200 >>> Direction is 12 >>> >>> I can provide more information or attach files if that would help solve the problem. Thanks for your help >>> >>> Best, >>> Kevin >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100320/bfc572a4/attachment-0001.html From kevinspitler at ucla.edu Sat Mar 20 12:42:58 2010 From: kevinspitler at ucla.edu (Kevin Spitler) Date: Sat, 20 Mar 2010 09:42:58 -0700 Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: <196b712.d396.1277c033c9b.Coremail.cwber@126.com> References: <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> <196b712.d396.1277c033c9b.Coremail.cwber@126.com> Message-ID: <9770ef211003200942p3f5a467ctbfb185ca1c48374b@mail.gmail.com> I am using the same gradient table as before, which worked with the low resolution data (large slice thickness). We are using a 3T Trio scanner in Siemens. Would it help if I attached one of the files from a recent scan? Best, Kevin 2010/3/20 cwber : > How did you get the gradient table, there maybe something wrong in your > gradient table, you can check it, and which factory's machine did you use > philips, GE,or Semense? > -- > ??? > > ?2010-03-20 22:09:12?"Kevin Spitler" ??? >>I haven't upgraded the operating system. I am still using Windows XP. >> >>Here is the gradient table: >> >>0: 0.000, 0.000, 0.000 >> 1: 0.500, 0.000, 0.500 >> 2: -0.500, 0.000, 0.500 >> 3: 0.000, 0.500, 0.500 >> 4: 0.000, 0.500, -0.500 >> 5: 0.500, 0.500, 0.000 >> 6: -0.500, 0.500, 0.000 >> 7: 1.000, 0.000, 1.000 >> 8: -1.000, 0.000, 1.000 >> 9: 0.000, 1.000, 1.000 >> 10: 0.000, 1.000, -1.000 >> 11: 1.000, 1.000, 0.000 >> 12: -1.000, 1.000, 0.000 >> >>Thanks for your help! Please let me know what else I can send >> >>Best, >>Kevin >> >> >>On Thu, Mar 18, 2010 at 6:54 AM, susumu mori wrote: >>> >>> Have you recently upgraded the operating system? Can I see the gradient table you used? >>> >>> On Wed, Mar 17, 2010 at 11:32 PM, Kevin Spitler wrote: >>>> >>>> Hello, >>>> >>>> We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue). >>>> >>>> The study was performed on a 3T Trio scanner in Siemens. >>>> b values are b=0, b=600, b=1200 >>>> Direction is 12 >>>> >>>> I can provide more information or attach files if that would help solve the problem. Thanks for your help >>>> >>>> Best, >>>> Kevin >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>>> >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>> >> >>_______________________________________________ >>Mristudio-users mailing list >>Mristudio-users at mristudio.org >>http://lists.mristudio.org/mailman/listinfo/ >>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > From mithamahesh at gmail.com Sat Mar 20 13:45:35 2010 From: mithamahesh at gmail.com (smitha mahesh) Date: Sat, 20 Mar 2010 10:45:35 -0700 Subject: [Mristudio-users] smitha mahesh wants to chat Message-ID: <994d85681003201045w36369b2p@mail.gmail.com> ----------------------------------------------------------------------- smitha mahesh wants to stay in better touch using some of Google's coolest new products. If you already have Gmail or Google Talk, visit: http://mail.google.com/mail/b-d72015a172-35cf53bd1f-a3033b0b08607283 You'll need to click this link to be able to chat with smitha mahesh. To get Gmail - a free email account from Google with over 2,800 megabytes of storage - and chat with smitha mahesh, visit: http://mail.google.com/mail/a-d72015a172-35cf53bd1f-a3033b0b08607283 Gmail offers: - Instant messaging right inside Gmail - Powerful spam protection - Built-in search for finding your messages and a helpful way of organizing emails into "conversations" - No pop-up ads or untargeted banners - just text ads and related information that are relevant to the content of your messages All this, and its yours for free. But wait, there's more! 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From cwber at 126.com Sat Mar 20 21:15:20 2010 From: cwber at 126.com (cwber) Date: Sun, 21 Mar 2010 09:15:20 +0800 (CST) Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: <9770ef211003200942p3f5a467ctbfb185ca1c48374b@mail.gmail.com> References: <9770ef211003200942p3f5a467ctbfb185ca1c48374b@mail.gmail.com> <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> <196b712.d396.1277c033c9b.Coremail.cwber@126.com> Message-ID: <11ca3d1.489.1277e49d7de.Coremail.cwber@126.com> HI, >>0: 0.000, 0.000, 0.000 >> 1: 0.500, 0.000, 0.500 >> 2: -0.500, 0.000, 0.500 >> 3: 0.000, 0.500, 0.500 >> 4: 0.000, 0.500, -0.500 >> 5: 0.500, 0.500, 0.000 >> 6: -0.500, 0.500, 0.000 >> 7: 1.000, 0.000, 1.000 >> 8: -1.000, 0.000, 1.000 >> 9: 0.000, 1.000, 1.000 >> 10: 0.000, 1.000, -1.000 >> 11: 1.000, 1.000, 0.000 >> 12: -1.000, 1.000, 0.000 As i know, the gradient table must be normalization.such as: (x)^2+(y)^2+(z)^2 == 1 but your gradient table doesn't satisfy this condition.i am not sure if there is any problem in your table. and senmens trio's Dicom file saved as mosaic format, so when you choose the data format you should paid attention to choose the right format. and you should ask semens's engineer to check your gradient talbe. good luck! -- weibo ?2010-03-21 00:42:58?"Kevin Spitler" ??? >I am using the same gradient table as before, which worked with the >low resolution data (large slice thickness). > >We are using a 3T Trio scanner in Siemens. > >Would it help if I attached one of the files from a recent scan? > >Best, >Kevin > >2010/3/20 cwber : >> How did you get the gradient table, there maybe something wrong in your >> gradient table, you can check it, and which factory's machine did you use >> philips, GE,or Semense? >> -- >> ??? >> >> ?2010-03-20 22:09:12?"Kevin Spitler" ??? >>>I haven't upgraded the operating system. I am still using Windows XP. >>> >>>Here is the gradient table: >>> >>>0: 0.000, 0.000, 0.000 >>> 1: 0.500, 0.000, 0.500 >>> 2: -0.500, 0.000, 0.500 >>> 3: 0.000, 0.500, 0.500 >>> 4: 0.000, 0.500, -0.500 >>> 5: 0.500, 0.500, 0.000 >>> 6: -0.500, 0.500, 0.000 >>> 7: 1.000, 0.000, 1.000 >>> 8: -1.000, 0.000, 1.000 >>> 9: 0.000, 1.000, 1.000 >>> 10: 0.000, 1.000, -1.000 >>> 11: 1.000, 1.000, 0.000 >>> 12: -1.000, 1.000, 0.000 >>> >>>Thanks for your help! Please let me know what else I can send >>> >>>Best, >>>Kevin >>> >>> >>>On Thu, Mar 18, 2010 at 6:54 AM, susumu mori wrote: >>>> >>>> Have you recently upgraded the operating system? Can I see the gradient table you used? >>>> >>>> On Wed, Mar 17, 2010 at 11:32 PM, Kevin Spitler wrote: >>>>> >>>>> Hello, >>>>> >>>>> We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue). >>>>> >>>>> The study was performed on a 3T Trio scanner in Siemens. >>>>> b values are b=0, b=600, b=1200 >>>>> Direction is 12 >>>>> >>>>> I can provide more information or attach files if that would help solve the problem. Thanks for your help >>>>> >>>>> Best, >>>>> Kevin >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>>> >>> >>>_______________________________________________ >>>Mristudio-users mailing list >>>Mristudio-users at mristudio.org >>>http://lists.mristudio.org/mailman/listinfo/ >>>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100321/12198104/attachment.html From leggwork at yahoo.com Sun Mar 21 12:09:30 2010 From: leggwork at yahoo.com (Bruce Leggett) Date: Sun, 21 Mar 2010 09:09:30 -0700 (PDT) Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: <11ca3d1.489.1277e49d7de.Coremail.cwber@126.com> References: <9770ef211003200942p3f5a467ctbfb185ca1c48374b@mail.gmail.com> <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> <196b712.d396.1277c033c9b.Coremail.cwber@126.com> <11ca3d1.489.1277e49d7de.Coremail.cwber@126.com> Message-ID: <284019.52203.qm@web110809.mail.gq1.yahoo.com> this is the gradient table that I use for standard siemens 12 direction X="-0.5197" Y="0.8541" Z="-0.0216" X="0.5197" Y="-0.8541" Z="0.0216" X="-0.1182" Y="0.4291" Z="-0.8955" X="-0.7689" Y="0.0718" Z="0.6353" X="0.5215" Y="0.8367" Z="-0.1673" X="0.1193" Y="0.6159" Z="0.7788" X="0.9157" Y="0.0436" Z="0.3994" X="0.7689" Y="-0.0718" Z="-0.6353" X="0.1182" Y="-0.4291" Z="0.8955" X="-0.5215" Y="-0.8367" Z="0.1673" X="-0.9157" Y="-0.0436" Z="-0.3994" X="-0.1193" Y="-0.6159" Z="-0.7788" thanks, bruce ________________________________ From: cwber To: "DTI Studio, ROI Editor; Landmarker Questions/Support" Sent: Sat, March 20, 2010 7:15:20 PM Subject: Re: [Mristudio-users] Problem loading high resolution scans into DTI Studio HI, >>0: 0.000, 0.000, 0.000 >> 1: 0.500, 0.000, 0.500 >> 2: -0.500, 0.000, 0.500 >> 3: 0.000, 0.500, 0.500 >> 4: 0.000, 0.500, -0.500 >> 5: 0.500, 0.500, 0.000 >> 6: -0.500, 0.500, 0.000 >> 7: 1.000, 0.000, 1.000 >> 8: -1.000, 0.000, 1.000 >> 9: 0.000, 1.000, 1.000 >> 10: 0.000, 1.000, -1.000 >> 11: 1.000, 1.000, 0.000 >> 12: -1.000, 1.000, 0.000 As i know, the gradient table must be normalization.such as: (x)^2+(y)^2+(z)^2 == 1 but your gradient table doesn't satisfy this condition.i am not sure if there is any problem in your table. and senmens trio's Dicom file saved as mosaic format, so when you choose the data format you should paid attention to choose the right format. and you should ask semens's engineer to check your gradient talbe. good luck! -- weibo ?2010-03-21 00:42:58?"Kevin Spitler" ??? >I am using the same gradient table as before, which worked with the >low resolution data (large slice thickness). > >We are using a 3T Trio scanner in Siemens. > >Would it help if I attached one of the files from a recent scan? > >Best, >Kevin > >2010/3/20 cwber : >> How did you get the gradient table, there maybe something wrong in your >> gradient table, you can check it, and which factory's machine did you use >> philips, GE,or Semense? >> -- >> ??? >> >> ?2010-03-20 22:09:12?"Kevin Spitler" ??? >>>I haven't upgraded the operating system. I am still using Windows XP. >>> >>>Here is the gradient table: >>> >>>0: 0.000, 0.000, 0.000 >>> 1: 0.500, 0.000, 0.500 >>> 2: -0.500, 0.000, 0.500 >>> 3: 0.000, 0.500, 0.500 >>> 4: 0.000, 0.500, -0.500 >>> 5: 0.500, 0.500, 0.000 >>> 6: -0.500, 0.500, 0.000 >>> 7: 1.000, 0.000, 1.000 >>> 8: -1.000, 0.000, 1.000 >>> 9: 0.000, 1.000, 1.000 >>> 10: 0.000, 1.000, -1.000 >>> 11: 1.000, 1.000, 0.000 >>> 12: -1.000, 1.000, 0.000 >>> >>>Thanks for your help! Please let me know what else I can send >>> >>>Best, >>>Kevin >>> >>> >>>On Thu, Mar 18, 2010 at 6:54 AM, susumu mori wrote: >>>> >>>> Have you recently upgraded the operating system? Can I see the gradient table you used? >>>> >>>> On Wed, Mar 17, 2010 at 11:32 PM, Kevin Spitler wrote: >>>>> >>>>> Hello, >>>>> >>>>> We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue). >>>>> >>>>> The study was performed on a 3T Trio scanner in Siemens. >>>>> b values are b=0, b=600, b=1200 >>>>> Direction is 12 >>>>> >>>>> I can provide more information or attach files if that would help solve the problem. Thanks for your help >>>>> >>>>> Best, >>>>> Kevin >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>>> >>> >>>_______________________________________________ >>>Mristudio-users mailing list >>>Mristudio-users at mristudio.org >>>http://lists.mristudio.org/mailman/listinfo/ >>>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100321/8a7b74c8/attachment-0001.html From kevinspitler at gmail.com Thu Mar 11 15:07:32 2010 From: kevinspitler at gmail.com (Kevin Spitler) Date: Thu, 11 Mar 2010 12:07:32 -0800 Subject: [Mristudio-users] Loading high resolution scans in DTI Studio Message-ID: <9770ef211003111207y7a2cc8d4p9ff2eda6166cff61@mail.gmail.com> Hello, We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue). The study was performed on a 3T Trio scanner in Siemens. b values are b=0, b=600, b=1200 Direction is 12 I can provide more information or attach files if that would help solve the problem. Thanks for your help Best, Kevin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100311/3591f891/attachment.html From kevinspitler at gmail.com Sat Mar 20 11:15:38 2010 From: kevinspitler at gmail.com (Kevin Spitler) Date: Sat, 20 Mar 2010 08:15:38 -0700 Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: <196b712.d396.1277c033c9b.Coremail.cwber@126.com> References: <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> <196b712.d396.1277c033c9b.Coremail.cwber@126.com> Message-ID: <9770ef211003200815v24766d3dmc942180dd446bf69@mail.gmail.com> I am using the same gradient table as before, which worked with the low resolution data (large slice thickness). We are using a 3T Trio scanner in Siemens. Would it help if I attached one of the files from a recent scan? Best, Kevin 2010/3/20 cwber > How did you get the gradient table, there maybe something wrong in your > gradient table, you can check it, and which factory's machine did you use > philips, GE,or Semense? > -- > ??? > > ?2010-03-20 22:09:12?"Kevin Spitler" ??? > >I haven't upgraded the operating system. I am still using Windows XP. > > > >Here is the gradient table: > > > >0: 0.000, 0.000, 0.000 > > 1: 0.500, 0.000, 0.500 > > 2: -0.500, 0.000, 0.500 > > 3: 0.000, 0.500, 0.500 > > 4: 0.000, 0.500, -0.500 > > 5: 0.500, 0.500, 0.000 > > 6: -0.500, 0.500, 0.000 > > 7: 1.000, 0.000, 1.000 > > 8: -1.000, 0.000, 1.000 > > 9: 0.000, 1.000, 1.000 > > 10: 0.000, 1.000, -1.000 > > 11: 1.000, 1.000, 0.000 > > 12: -1.000, 1.000, 0.000 > > > >Thanks for your help! Please let me know what else I can send > > > >Best, > >Kevin > > > > > >On Thu, Mar 18, 2010 at 6:54 AM, susumu mori wrote: > >> > >> Have you recently upgraded the operating system? Can I see the gradient table you used? > >> > >> On Wed, Mar 17, 2010 at 11:32 PM, Kevin Spitler wrote: > >>> > >>> Hello, > >>> > >>> We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue). > >>> > >>> The study was performed on a 3T Trio scanner in Siemens. > >>> b values are b=0, b=600, b=1200 > >>> Direction is 12 > >>> > >>> I can provide more information or attach files if that would help solve the problem. Thanks for your help > >>> > >>> Best, > >>> Kevin > >>> _______________________________________________ > >>> Mristudio-users mailing list > >>> Mristudio-users at mristudio.org > > >>> http://lists.mristudio.org/mailman/listinfo/ > >>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > >>> > >> > >> > >> _______________________________________________ > >> Mristudio-users mailing list > >> Mristudio-users at mristudio.org > >> http://lists.mristudio.org/mailman/listinfo/ > >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > >> > > > >_______________________________________________ > >Mristudio-users mailing list > >Mristudio-users at mristudio.org > >http://lists.mristudio.org/mailman/listinfo/ > >Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100320/ee61864f/attachment.html From shiye.chen at gmail.com Tue Mar 23 01:46:34 2010 From: shiye.chen at gmail.com (Syeira) Date: Tue, 23 Mar 2010 13:46:34 +0800 Subject: [Mristudio-users] Help on the DTI Studio stop working problem Message-ID: <4ba855c1.1708c00a.1836.ffff8397@mx.google.com> Hi, I have confront a problem which I don't know how it happen and how to deal with it, showed as below: cid:image003.jpg at 01CACA8F.38E5F890 Is it something wrong with the data? Or is it something wrong with the configuration? Did someone have the same problem with me? Would someone help me? Thanks a lot. BR Syeira -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100323/02806200/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/jpeg Size: 14703 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100323/02806200/attachment-0001.jpe From susumu at mri.jhu.edu Tue Mar 23 18:39:46 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 23 Mar 2010 18:39:46 -0400 Subject: [Mristudio-users] Help on the DTI Studio stop working problem In-Reply-To: <4ba855c1.1708c00a.1836.ffff8397@mx.google.com> References: <4ba855c1.1708c00a.1836.ffff8397@mx.google.com> Message-ID: If you are reading DICOM files, it happens when your gradient table doesn't match with the data. On Tue, Mar 23, 2010 at 1:46 AM, Syeira wrote: > Hi, > > > > I have confront a problem which I don?t know how it happen and how to deal > with it, showed as below: > > > > [image: cid:image003.jpg at 01CACA8F.38E5F890] > > > > Is it something wrong with the data? > > Or is it something wrong with the configuration? > > Did someone have the same problem with me? > > > > Would someone help me? Thanks a lot. > > > > BR > > Syeira > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100323/a1163f24/attachment.html From sandyavenugopal at gmail.com Tue Mar 23 19:20:02 2010 From: sandyavenugopal at gmail.com (sandya venugopal) Date: Tue, 23 Mar 2010 16:20:02 -0700 Subject: [Mristudio-users] Help on the DTI Studio stop working problem In-Reply-To: <4ba855c1.1708c00a.1836.ffff8397@mx.google.com> References: <4ba855c1.1708c00a.1836.ffff8397@mx.google.com> Message-ID: <2fa93621003231620r962d7a7rafec722f05073a6d@mail.gmail.com> I have the same problem, and the system crashes. Not sure what the issue is. Only happens on my desktop, not on my laptop. Both desk and lap top are superfast computers with plenty of memory, so that is not the issue. I don't use DICOM files. Any ideas or sugegstions? Sandya On 22 March 2010 22:46, Syeira wrote: > Hi, > > > > I have confront a problem which I don?t know how it happen and how to deal > with it, showed as below: > > > > [image: cid:image003.jpg at 01CACA8F.38E5F890] > > > > Is it something wrong with the data? > > Or is it something wrong with the configuration? > > Did someone have the same problem with me? > > > > Would someone help me? Thanks a lot. > > > > BR > > Syeira > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100323/de27b32b/attachment.html From kevinspitler at gmail.com Wed Mar 24 00:10:06 2010 From: kevinspitler at gmail.com (Kevin Spitler) Date: Tue, 23 Mar 2010 21:10:06 -0700 Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: <284019.52203.qm@web110809.mail.gq1.yahoo.com> References: <9770ef211003200942p3f5a467ctbfb185ca1c48374b@mail.gmail.com> <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> <196b712.d396.1277c033c9b.Coremail.cwber@126.com> <11ca3d1.489.1277e49d7de.Coremail.cwber@126.com> <284019.52203.qm@web110809.mail.gq1.yahoo.com> Message-ID: <9770ef211003232110o6ea1fb96id36f8c5d0a0abedf@mail.gmail.com> Hi Bruce, Thanks for your gradient table. I can't get this to load the data. I get the error message "forgot gradient table" which may be because there are only 12 lines, instead of 13 (0 to 12), so when I number the lines provided, I get a different error message "forget gradient of B0-image?" How do you use this gradient table? Thanks, Kevin On Sun, Mar 21, 2010 at 9:09 AM, Bruce Leggett wrote: > this is the gradient table that I use for standard siemens 12 direction > > > ?X="-0.5197" Y="0.8541" Z="-0.0216" > ?X="0.5197" Y="-0.8541" Z="0.0216" > ?X="-0.1182" Y="0.4291" Z="-0.8955" > ?X="-0.7689" Y="0.0718" Z="0.6353" > ?X="0.5215" Y="0.8367" Z="-0.1673" > ?X="0.1193" Y="0.6159" Z="0.7788" > ?X="0.9157" Y="0.0436" Z="0.3994" > ?X="0.7689" Y="-0.0718" Z="-0.6353" > ?X="0.1182" Y="-0.4291" Z="0.8955" > ?X="-0.5215" Y="-0.8367" Z="0.1673" > ?X="-0.9157" Y="-0.0436" Z="-0.3994" > ?X="-0.1193" Y="-0.6159" Z="-0.7788" > > thanks, > bruce > > > ________________________________ > From: cwber > To: "DTI Studio, ROI Editor; Landmarker Questions/Support" > > Sent: Sat, March 20, 2010 7:15:20 PM > Subject: Re: [Mristudio-users] Problem loading high resolution scans into > DTI Studio > > HI, >>>0: 0.000, 0.000, 0.000 >>> 1: 0.500, 0.000, 0.500 >>> 2: -0.500, 0.000, 0.500 >>> 3: 0.000, 0.500, 0.500 >>> 4: 0.000, 0.500, -0.500 >>> 5: 0.500, 0.500, 0.000 >>> 6: -0.500, 0.500, 0.000 >>> 7: 1.000, 0.000, 1.000 >>> 8: -1.000, 0.000, 1.000 >>> 9: 0.000, 1.000, 1.000 >>> 10: 0.000, 1.000, -1.000 >>> 11: 1.000, 1.000, 0.000 >>> 12: -1.000, 1.000, 0.000 > As i know, the?gradient table must be normalization.such as: > (x)^2+(y)^2+(z)^2 == 1 but your gradient table doesn't satisfy this > condition.i am not sure if there is any problem in your table. and senmens > trio's Dicom file saved as mosaic format, so when you choose the data format > you should paid attention to choose the right format. and you should ask > semens's engineer to check your gradient talbe. > good luck! > -- > weibo > > ?2010-03-21?00:42:58?"Kevin?Spitler"????? >>I?am?using?the?same?gradient?table?as?before,?which?worked?with?the >>low?resolution?data?(large?slice?thickness). >> >>We?are?using?a?3T?Trio?scanner?in?Siemens. >> >>Would?it?help?if?I?attached?one?of?the?files?from?a?recent?scan? >> >>Best, >>Kevin >> >>2010/3/20?cwber?: >>>?How?did?you?get?the?gradient?table,?there?maybe?something?wrong?in?your >>>?gradient?table,?you?can?check?it,?and?which?factory's?machine > did?you?use >>>?philips,?GE,or?Semense? >>>?-- >>>???? >>> >>>??2010-03-20?22:09:12?"Kevin?Spitler"????? >>>>I?haven't?upgraded?the?operating?system.??I?am?still?using?Windows?XP. >>>> >>>>Here?is?the?gradient?table: >>>> >>>>0:?0.000,?0.000,?0.000 >>>>?1:?0.500,?0.000,?0.500 >>>>?2:?-0.500,?0.000,?0.500 >>>>?3:?0.000,?0.500,?0.500 >>>>?4:?0.000,?0.500,?-0.500 >>>>?5:?0.500,?0.500,?0.000 >>>>?6:?-0.500,?0.500,?0.000 >>>>?7:?1.000,?0.000,?1.000 >> >>>?8:?-1.000,?0.000,?1.000 >>>>?9:?0.000,?1.000,?1.000 >>>>?10:?0.000,?1.000,?-1.000 >>>>?11:?1.000,?1.000,?0.000 >>>>?12:?-1.000,?1.000,?0.000 >>>> >>>>Thanks?for?your?help!??Please?let?me?know?what?else?I?can?send >>>> >>>>Best, >>>>Kevin >>>> >>>> >>>>On?Thu,?Mar?18,?2010?at?6:54?AM,?susumu?mori??wrote: >>>>> >>>>>?Have?you?recently?upgraded?the?operating?system??Can?I?see?the?gradient?table?you?used? >>>>> >>>>>?On?Wed,?Mar > 17,?2010?at?11:32?PM,?Kevin?Spitler??wrote: >>>>>> >>>>>>?Hello, >>>>>> >>>>>>?We?have?recently?starting?acquiring?high?resolution?scans?and?I?am?having?difficulty?loading?them?into?DTI?Studio.??I?am?using?the?same?12?direction?gradient?that?worked?on?the?low?resolution?(large?slice?thickness).??Although?the?DTI?Studio?program?does?not?crash,?the?color?map?0?generated?is?not?correct?(random?color?patterns?over?the?tissue). >>>>>> >>>>>>?The?study?was?performed?on&nbs > p;a?3T?Trio?scanner?in?Siemens. >>>>>>?b?values?are?b=0,?b=600,?b=1200 >>>>>>?Direction?is?12 >>>>>> >>>>>>?I?can?provide?more?information?or?attach?files?if?that?would?help?solve?the?problem.??Thanks?for?your?help >>>>>> >>>>>>?Best, >>>>>>?Kevin >>>>>>?_______________________________________________ >>>>>>?Mristudio-users?mailing?list >>>>>>?Mristudio-users at mristudio.org >>>>>>?http://lists.mristudio.org/mailman/listinfo/ >>>>>>?Unsubscribe,?send?a?blank?email?to:?Mristudio-users-unsubscribe at mristudio.org >>>>>> >>>>> >>>>> >>>>>?_______________________________________________ >>>>>?Mristudio-users?mailing?list >>>>>?Mristudio-users at mristudio.org >>>>>?http://lists.mristudio.org/mailman/listinfo/ >>>>>?Unsubscribe,?send?a?blank?email?to:?Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>>>_______________________________________________ >>>>Mristudio-users?mailing?list >>>>Mristudio-users at mristudio.org >>>>http://lists.mristudio.org/mailman/listinfo/ >>>>Unsubscribe,?send?a?blank?email?to:?Mristudio-users-unsubscribe at mristudio.org >>> >>> >>> >>>?_______________________________________________ >>>?Mristudio-users?mailing?list >>>?Mristudio-users at mristudio.org >>>?http://lists.mristudio.org/mailman/listinfo/ >>>?Unsubscribe,?send?a?blank?email?to: >>>?Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >>_______________________________________________ >>Mristudio-users?mailing?list >>Mristudio-users at mristudio.org >>http://lists.mristudio.org/mailman/listinfo/ >>Unsubscribe,?send?a?blank?email?to:?Mristudio-users-unsubscribe at mristudio.org > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > From cwber at 126.com Wed Mar 24 04:23:48 2010 From: cwber at 126.com (cwber) Date: Wed, 24 Mar 2010 16:23:48 +0800 (CST) Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: <9770ef211003232110o6ea1fb96id36f8c5d0a0abedf@mail.gmail.com> References: <9770ef211003232110o6ea1fb96id36f8c5d0a0abedf@mail.gmail.com> <9770ef211003200942p3f5a467ctbfb185ca1c48374b@mail.gmail.com> <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> <196b712.d396.1277c033c9b.Coremail.cwber@126.com> <11ca3d1.489.1277e49d7de.Coremail.cwber@126.com> <284019.52203.qm@web110809.mail.gq1.yahoo.com> Message-ID: <1838111.10300.1278f4530fb.Coremail.cwber@126.com> Hi, you should add the B=0 gradient, as follow, 0: 0.000, 0.000, 0.000 and then use the table below. you should make sure your b=0 images is arranged firstly. best wishes! -- weber ?2010-03-24 12:10:06?"Kevin Spitler" ??? >Hi Bruce, >Thanks for your gradient table. I can't get this to load the data. I >get the error message "forgot gradient table" which may be because >there are only 12 lines, instead of 13 (0 to 12), so when I number the >lines provided, I get a different error message "forget gradient of >B0-image?" > >How do you use this gradient table? > >Thanks, >Kevin > >On Sun, Mar 21, 2010 at 9:09 AM, Bruce Leggett wrote: >> this is the gradient table that I use for standard siemens 12 direction >> >> >> X="-0.5197" Y="0.8541" Z="-0.0216" >> X="0.5197" Y="-0.8541" Z="0.0216" >> X="-0.1182" Y="0.4291" Z="-0.8955" >> X="-0.7689" Y="0.0718" Z="0.6353" >> X="0.5215" Y="0.8367" Z="-0.1673" >> X="0.1193" Y="0.6159" Z="0.7788" >> X="0.9157" Y="0.0436" Z="0.3994" >> X="0.7689" Y="-0.0718" Z="-0.6353" >> X="0.1182" Y="-0.4291" Z="0.8955" >> X="-0.5215" Y="-0.8367" Z="0.1673" >> X="-0.9157" Y="-0.0436" Z="-0.3994" >> X="-0.1193" Y="-0.6159" Z="-0.7788" >> >> thanks, >> bruce >> >> >> ________________________________ >> From: cwber >> To: "DTI Studio, ROI Editor; Landmarker Questions/Support" >> >> Sent: Sat, March 20, 2010 7:15:20 PM >> Subject: Re: [Mristudio-users] Problem loading high resolution scans into >> DTI Studio >> >> HI, >>>>0: 0.000, 0.000, 0.000 >>>> 1: 0.500, 0.000, 0.500 >>>> 2: -0.500, 0.000, 0.500 >>>> 3: 0.000, 0.500, 0.500 >>>> 4: 0.000, 0.500, -0.500 >>>> 5: 0.500, 0.500, 0.000 >>>> 6: -0.500, 0.500, 0.000 >>>> 7: 1.000, 0.000, 1.000 >>>> 8: -1.000, 0.000, 1.000 >>>> 9: 0.000, 1.000, 1.000 >>>> 10: 0.000, 1.000, -1.000 >>>> 11: 1.000, 1.000, 0.000 >>>> 12: -1.000, 1.000, 0.000 >> As i know, the gradient table must be normalization.such as: >> (x)^2+(y)^2+(z)^2 == 1 but your gradient table doesn't satisfy this >> condition.i am not sure if there is any problem in your table. and senmens >> trio's Dicom file saved as mosaic format, so when you choose the data format >> you should paid attention to choose the right format. and you should ask >> semens's engineer to check your gradient talbe. >> good luck! >> -- >> weibo >> >> ?2010-03-21 00:42:58?"Kevin Spitler" ??? >>>I am using the same gradient table as before, which worked with the >>>low resolution data (large slice thickness). >>> >>>We are using a 3T Trio scanner in Siemens. >>> >>>Would it help if I attached one of the files from a recent scan? >>> >>>Best, >>>Kevin >>> >>>2010/3/20 cwber : >>>> How did you get the gradient table, there maybe something wrong in your >>>> gradient table, you can check it, and which factory's machine >> did you use >>>> philips, GE,or Semense? >>>> -- >>>> ??? >>>> >>>> ?2010-03-20 22:09:12?"Kevin Spitler" ??? >>>>>I haven't upgraded the operating system. I am still using Windows XP. >>>>> >>>>>Here is the gradient table: >>>>> >>>>>0: 0.000, 0.000, 0.000 >>>>> 1: 0.500, 0.000, 0.500 >>>>> 2: -0.500, 0.000, 0.500 >>>>> 3: 0.000, 0.500, 0.500 >>>>> 4: 0.000, 0.500, -0.500 >>>>> 5: 0.500, 0.500, 0.000 >>>>> 6: -0.500, 0.500, 0.000 >>>>> 7: 1.000, 0.000, 1.000 >>> >>>> 8: -1.000, 0.000, 1.000 >>>>> 9: 0.000, 1.000, 1.000 >>>>> 10: 0.000, 1.000, -1.000 >>>>> 11: 1.000, 1.000, 0.000 >>>>> 12: -1.000, 1.000, 0.000 >>>>> >>>>>Thanks for your help! Please let me know what else I can send >>>>> >>>>>Best, >>>>>Kevin >>>>> >>>>> >>>>>On Thu, Mar 18, 2010 at 6:54 AM, susumu mori wrote: >>>>>> >>>>>> Have you recently upgraded the operating system? Can I see the gradient table you used? >>>>>> >>>>>> On Wed, Mar >> 17, 2010 at 11:32 PM, Kevin Spitler wrote: >>>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue). >>>>>>> >>>>>>> The study was performed on&nbs >> p;a 3T Trio scanner in Siemens. >>>>>>> b values are b=0, b=600, b=1200 >>>>>>> Direction is 12 >>>>>>> >>>>>>> I can provide more information or attach files if that would help solve the problem. Thanks for your help >>>>>>> >>>>>>> Best, >>>>>>> Kevin >>>>>>> _______________________________________________ >>>>>>> Mristudio-users mailing list >>>>>>> Mristudio-users at mristudio.org >>>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Mristudio-users mailing list >>>>>> Mristudio-users at mristudio.org >>>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>>>>> >>>>> >>>>>_______________________________________________ >>>>>Mristudio-users mailing list >>>>>Mristudio-users at mristudio.org >>>>>http://lists.mristudio.org/mailman/listinfo/ >>>>>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>> >>>_______________________________________________ >>>Mristudio-users mailing list >>>Mristudio-users at mristudio.org >>>http://lists.mristudio.org/mailman/listinfo/ >>>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100324/9831af52/attachment-0001.html From susumu at mri.jhu.edu Wed Mar 24 07:09:02 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 24 Mar 2010 07:09:02 -0400 Subject: [Mristudio-users] Help on the DTI Studio stop working problem In-Reply-To: <2fa93621003231620r962d7a7rafec722f05073a6d@mail.gmail.com> References: <4ba855c1.1708c00a.1836.ffff8397@mx.google.com> <2fa93621003231620r962d7a7rafec722f05073a6d@mail.gmail.com> Message-ID: Are you using a 32-bit operating system in one of the computers? The 32-bit system can allocate only 1-1.5GB RAM to a single program no matter how much RAM you have, which limits the size of the data you are processing. On Tue, Mar 23, 2010 at 7:20 PM, sandya venugopal wrote: > I have the same problem, and the system crashes. Not sure what the issue > is. Only happens on my desktop, not on my laptop. Both desk and lap top are > superfast computers with plenty of memory, so that is not the issue. I don't > use DICOM files. Any ideas or sugegstions? > > Sandya > > > On 22 March 2010 22:46, Syeira wrote: > >> Hi, >> >> >> >> I have confront a problem which I don?t know how it happen and how to deal >> with it, showed as below: >> >> >> >> [image: cid:image003.jpg at 01CACA8F.38E5F890] >> >> >> >> Is it something wrong with the data? >> >> Or is it something wrong with the configuration? >> >> Did someone have the same problem with me? >> >> >> >> Would someone help me? Thanks a lot. >> >> >> >> BR >> >> Syeira >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100324/2c229cdb/attachment.html From sandyavenugopal at gmail.com Wed Mar 24 11:50:08 2010 From: sandyavenugopal at gmail.com (sandya venugopal) Date: Wed, 24 Mar 2010 08:50:08 -0700 Subject: [Mristudio-users] Help on the DTI Studio stop working problem In-Reply-To: References: <4ba855c1.1708c00a.1836.ffff8397@mx.google.com> <2fa93621003231620r962d7a7rafec722f05073a6d@mail.gmail.com> Message-ID: <2fa93621003240850k2d76e19cg5996bcd13bd44d3@mail.gmail.com> I use 64 bit system. On 24 March 2010 04:09, susumu mori wrote: > Are you using a 32-bit operating system in one of the computers? > The 32-bit system can allocate only 1-1.5GB RAM to a single program no > matter how much RAM you have, which limits the size of the data you are > processing. > > > On Tue, Mar 23, 2010 at 7:20 PM, sandya venugopal < > sandyavenugopal at gmail.com> wrote: > >> I have the same problem, and the system crashes. Not sure what the issue >> is. Only happens on my desktop, not on my laptop. Both desk and lap top are >> superfast computers with plenty of memory, so that is not the issue. I don't >> use DICOM files. Any ideas or sugegstions? >> >> Sandya >> >> >> On 22 March 2010 22:46, Syeira wrote: >> >>> Hi, >>> >>> >>> >>> I have confront a problem which I don?t know how it happen and how to >>> deal with it, showed as below: >>> >>> >>> >>> [image: cid:image003.jpg at 01CACA8F.38E5F890] >>> >>> >>> >>> Is it something wrong with the data? >>> >>> Or is it something wrong with the configuration? >>> >>> Did someone have the same problem with me? >>> >>> >>> >>> Would someone help me? Thanks a lot. >>> >>> >>> >>> BR >>> >>> Syeira >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100324/7914637f/attachment.html From susumu at mri.jhu.edu Wed Mar 24 16:16:55 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 24 Mar 2010 16:16:55 -0400 Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: <9770ef211003232110o6ea1fb96id36f8c5d0a0abedf@mail.gmail.com> References: <9770ef211003200942p3f5a467ctbfb185ca1c48374b@mail.gmail.com> <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> <196b712.d396.1277c033c9b.Coremail.cwber@126.com> <11ca3d1.489.1277e49d7de.Coremail.cwber@126.com> <284019.52203.qm@web110809.mail.gq1.yahoo.com> <9770ef211003232110o6ea1fb96id36f8c5d0a0abedf@mail.gmail.com> Message-ID: Hi all, Please try the following. I think Siemens changed their 12-orientation scheme some time ago and this should work for VB13 and also VB15, I believe. 0: 0, 0, 0 1: 1.000000, 0.414250, -0.414250 2: 1.000000, -0.414250, -0.414250 3: 1.000000, -0.414250, 0.414250 4: 1.000000, 0.414250, 0.414250 5: 0.414250, 0.414250, 1.000000 6: 0.414250, 1.000000, 0.414250 7: 0.414250, 1.000000, -0.414250 8: 0.414250, 0.414250, -1.000000 9: 0.414250, -0.414250, -1.000000 10: 0.414250, -1.000000, -0.414250 11: 0.414250, -1.000000, 0.414250 12: 0.414250, -0.414250, 1.000000 On Wed, Mar 24, 2010 at 12:10 AM, Kevin Spitler wrote: > Hi Bruce,Thanks for your gradient table. I can't get this to load the > data. Iget the error message "forgot gradient table" which may be > becausethere are only 12 lines, instead of 13 (0 to 12), so when I number > thelines provided, I get a different error message "forget gradient > ofB0-image?" > How do you use this gradient table? > Thanks,Kevin > On Sun, Mar 21, 2010 at 9:09 AM, Bruce Leggett > wrote:> this is the gradient table that I use for standard siemens 12 > direction>>> X="-0.5197" Y="0.8541" Z="-0.0216"> X="0.5197" Y="-0.8541" > Z="0.0216"> X="-0.1182" Y="0.4291" Z="-0.8955"> X="-0.7689" Y="0.0718" > Z="0.6353"> X="0.5215" Y="0.8367" Z="-0.1673"> X="0.1193" Y="0.6159" > Z="0.7788"> X="0.9157" Y="0.0436" Z="0.3994"> X="0.7689" Y="-0.0718" > Z="-0.6353"> X="0.1182" Y="-0.4291" Z="0.8955"> X="-0.5215" Y="-0.8367" > Z="0.1673"> X="-0.9157" Y="-0.0436" Z="-0.3994"> X="-0.1193" Y="-0.6159" > Z="-0.7788">> thanks,> bruce>>> ________________________________> From: > cwber > To: "DTI Studio, ROI Editor; Landmarker > Questions/Support"> > Sent: Sat, March 20, > 2010 7:15:20 PM> Subject: Re: [Mristudio-users] Problem loading high > resolution scans into> DTI Studio>> HI,>>>0: 0.000, 0.000, 0.000>>> 1: > 0.500, 0.000, 0.500>>> 2: -0.500, 0.000, 0.500>>> 3: 0.000, 0.500, 0.500>>> > 4: 0.000, 0.500, -0.500>>> 5: 0.500, 0.500, 0.000>>> 6: -0.500, 0.500, > 0.000>>> 7: 1.000, 0.000, 1.000>>> 8: -1.000, 0.000, 1.000>>> 9: 0.000, > 1.000, 1.000>>> 10: 0.000, 1.000, -1.000>>> 11: 1.000, 1.000, 0.000>>> 12: > -1.000, 1.000, 0.000> As i know, the gradient table must be > normalization.such as:> (x)^2+(y)^2+(z)^2 == 1 but your gradient table > doesn't satisfy this> condition.i am not sure if there is any problem in > your table. and senmens> trio's Dicom file saved as mosaic format, so when > you choose the data format> you should paid attention to choose the right > format. and you should ask> semens's engineer to check your gradient talbe.> > good luck!> --> weibo>> ?2010-03-21 00:42:58?"Kevin Spitler" < > kevinspitler at ucla.edu > > ???>>I am using the same gradient table as before, which worked with the>>low resolution data (large slice thickness).>>>>We are using a 3T Trio scanner in Siemens.>>>>Would it help if I attached one of the files from a recent scan?>>>>Best,>>Kevin>>>>2010/3/20 cwber < > cwber at 126.com>:>>> How did you get the gradient table, there maybe something wrong in your>>> gradient table, you can check it, and which factory's machine> > did you use>>> philips, GE,or Semense?>>> -->>> ???>>>>>> ?2010-03-20 22:09:12?"Kevin Spitler" < > kevinspitler at ucla.edu > > ???>>>>I haven't upgraded the operating system. I am still using Windows XP.>>>>>>>>Here is the gradient table:>>>>>>>>0: 0.000, 0.000, 0.000>>>> 1: 0.500, 0.000, 0.500>>>> 2: -0.500, 0.000, 0.500>>>> 3: 0.000, 0.500, 0.500>>>> 4: 0.000, 0.500, -0.500>>>> 5: 0.500, 0.500, 0.000>>>> 6: -0.500, 0.500, 0.000>>>> 7: 1.000, 0.000, 1.000>>>>> 8: -1.000, 0.000, 1.000>>>> 9: 0.000, 1.000, 1.000>>>> 10: 0.000, 1.000, -1.000>>>> 11: 1.000, 1.000, 0.000>>>> 12: -1.000, 1.000, 0.000>>>>>>>>Thanks for your help! Please let me know what else I can send>>>>>>>>Best,>>>>Kevin>>>>>>>>>>>>On Thu, Mar 18, 2010 at 6:54 AM, susumu mori < > susumu at mri.jhu.edu> wrote:>>>>>>>>>> Have you recently upgraded the operating system? Can I see the gradient table you used?>>>>>>>>>> On Wed, Mar> > 17, 2010 at 11:32 PM, Kevin Spitler wrote:>>>>>>>>>>>> Hello,>>>>>>>>>>>> We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue).>>>>>>>>>>>> The study was performed on&nbs> > p;a 3T Trio scanner in Siemens.>>>>>> b values are b=0, b=600, b=1200>>>>>> Direction is 12>>>>>>>>>>>> I can provide more information or attach files if that would help solve the problem. Thanks for your help>>>>>>>>>>>> Best,>>>>>> Kevin>>>>>> _______________________________________________>>>>>> Mristudio-users mailing list>>>>>> > Mristudio-users at mristudio.org>>>>>> > http://lists.mristudio.org/mailman/listinfo/ > >>>>>> Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > >>>>>>>>>>>>>>>>>>>>> _______________________________________________>>>>> Mristudio-users mailing list>>>>> > Mristudio-users at mristudio.org>>>>> > http://lists.mristudio.org/mailman/listinfo/ > >>>>> Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > >>>>>>>>>>>>>_______________________________________________>>>>Mristudio-users mailing list>>>> > Mristudio-users at mristudio.org>>>> > http://lists.mristudio.org/mailman/listinfo/ > >>>>Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > >>>>>>>>>>>> _______________________________________________>>> Mristudio-users mailing list>>> > Mristudio-users at mristudio.org>>> > http://lists.mristudio.org/mailman/listinfo/ > >>> Unsubscribe, send a blank email to:>>> > Mristudio-users-unsubscribe at mristudio.org > >>>>>>>>>>_______________________________________________>>Mristudio-users mailing list>> > Mristudio-users at mristudio.org>> > http://lists.mristudio.org/mailman/listinfo/ > >>Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org>>>>> > _______________________________________________> Mristudio-users mailing > list> Mristudio-users at mristudio.org> > http://lists.mristudio.org/mailman/listinfo/> Unsubscribe, send a blank > email to:> Mristudio-users-unsubscribe at mristudio.org>> > _______________________________________________Mristudio-users mailing > listMristudio-users at mristudio.orghttp:// > lists.mristudio.org/mailman/listinfo/Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100324/6fd54768/attachment-0001.html From mithra at mail.utexas.edu Thu Mar 25 11:37:34 2010 From: mithra at mail.utexas.edu (Mithra) Date: Thu, 25 Mar 2010 10:37:34 -0500 Subject: [Mristudio-users] DTI Studio in Parallels Message-ID: <42fe38b81003250837s8e7763andcc0ccdfaa621e90@mail.gmail.com> Hello, I downloaded DTI Studio in parallels in my Mac. The 'Fit tensor' tab seems to have disappeared under 'MRI View 3D'. The other 2 tabs ('Image' and 'ROI') are present. I wanted to check this with another version of DTI studio. I transferred the version I had in my windows laptop to the parallels in my mac and I get the same problem (Even though the same version works fine in my windows laptop). Am I missing something here. I am not sure what went wrong. Any help would be appreciated. Thanks. - Mithra. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100325/9dfc30d4/attachment.html From susumu at mri.jhu.edu Fri Mar 26 15:04:38 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 26 Mar 2010 15:04:38 -0400 Subject: [Mristudio-users] How to tell if AIR worked In-Reply-To: References: Message-ID: Hi all, Recently, we've been receiving multiple inquiries about how we can assess image quality of diffusion images, which often suffer from co-registration errors, image corruption, and eddy current. There are many tools to correct them but it is still difficult to judge when we need them and how to tell the correction efficacy. I wrote a small description regarding these issues and posted at https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2. The file name is "DtiStudioUpdate.doc" and there are 5 associated PowerPoint files. I hope this will help answering some of the questions. Also, please check out the new release (DtiStudio V3.0.2), which has all the new functions described in this document. Sincerely, Susumu Mori On Thu, Mar 11, 2010 at 2:16 AM, Darren Gitelman < d-gitelman at northwestern.edu> wrote: > Hi > > How can one tell if AIR realigned a set of images correctly? > > Darren Gitelman, MD > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100326/e020ec02/attachment.html From kevinspitler at gmail.com Tue Mar 30 21:34:59 2010 From: kevinspitler at gmail.com (Kevin Spitler) Date: Tue, 30 Mar 2010 18:34:59 -0700 Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: References: <9770ef211003200942p3f5a467ctbfb185ca1c48374b@mail.gmail.com> <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> <196b712.d396.1277c033c9b.Coremail.cwber@126.com> <11ca3d1.489.1277e49d7de.Coremail.cwber@126.com> <284019.52203.qm@web110809.mail.gq1.yahoo.com> <9770ef211003232110o6ea1fb96id36f8c5d0a0abedf@mail.gmail.com> Message-ID: Thanks all for your help! I am having some progress with this last gradient although I still have a few things that I am checking. Thanks, Kevin 2010/3/24 susumu mori : > Hi all, > > Please try the following. I think Siemens changed their 12-orientation > scheme some time ago and this should work for VB13 and also VB15, I believe. > > 0: 0, 0, 0 > 1: 1.000000, 0.414250, -0.414250 > 2: 1.000000, -0.414250, -0.414250 > 3: 1.000000, -0.414250, 0.414250 > 4: 1.000000, 0.414250, 0.414250 > 5: 0.414250, 0.414250, 1.000000 > 6: 0.414250, 1.000000, 0.414250 > 7: 0.414250, 1.000000, -0.414250 > 8: 0.414250, 0.414250, -1.000000 > 9: 0.414250, -0.414250, -1.000000 > 10: 0.414250, -1.000000, -0.414250 > 11: 0.414250, -1.000000, 0.414250 > 12: 0.414250, -0.414250, 1.000000 > > > On Wed, Mar 24, 2010 at 12:10 AM, Kevin Spitler > wrote: >> >> Hi Bruce,Thanks for your gradient table. I can't get this to load the >> data. Iget the error message "forgot gradient table" which may be >> becausethere are only 12 lines, instead of 13 (0 to 12), so when I number >> thelines provided, I get a different error message "forget gradient >> ofB0-image?" >> How do you use this gradient table? >> Thanks,Kevin >> On Sun, Mar 21, 2010 at 9:09 AM, Bruce Leggett >> wrote:> this is the gradient table that I use for standard siemens 12 >> direction>>> X="-0.5197" Y="0.8541" Z="-0.0216"> X="0.5197" Y="-0.8541" >> Z="0.0216"> X="-0.1182" Y="0.4291" Z="-0.8955"> X="-0.7689" Y="0.0718" >> Z="0.6353"> X="0.5215" Y="0.8367" Z="-0.1673"> X="0.1193" Y="0.6159" >> Z="0.7788"> X="0.9157" Y="0.0436" Z="0.3994"> X="0.7689" Y="-0.0718" >> Z="-0.6353"> X="0.1182" Y="-0.4291" Z="0.8955"> X="-0.5215" Y="-0.8367" >> Z="0.1673"> X="-0.9157" Y="-0.0436" Z="-0.3994"> X="-0.1193" Y="-0.6159" >> Z="-0.7788">> thanks,> bruce>>> ________________________________> From: >> cwber > To: "DTI Studio, ROI Editor; Landmarker >> Questions/Support"> > Sent: Sat, March 20, >> 2010 7:15:20 PM> Subject: Re: [Mristudio-users] Problem loading high >> resolution scans into> DTI Studio>> HI,>>>0: 0.000, 0.000, 0.000>>> 1: >> 0.500, 0.000, 0.500>>> 2: -0.500, 0.000, 0.500>>> 3: 0.000, 0.500, 0.500>>> >> 4: 0.000, 0.500, -0.500>>> 5: 0.500, 0.500, 0.000>>> 6: -0.500, 0.500, >> 0.000>>> 7: 1.000, 0.000, 1.000>>> 8: -1.000, 0.000, 1.000>>> 9: 0.000, >> 1.000, 1.000>>> 10: 0.000, 1.000, -1.000>>> 11: 1.000, 1.000, 0.000>>> 12: >> -1.000, 1.000, 0.000> As i know, the gradient table must be >> normalization.such as:> (x)^2+(y)^2+(z)^2 == 1 but your gradient table >> doesn't satisfy this> condition.i am not sure if there is any problem in >> your table. and senmens> trio's Dicom file saved as mosaic format, so when >> you choose the data format> you should paid attention to choose the right >> format. and you should ask> semens's engineer to check your gradient talbe.> >> good luck!> --> weibo>> >> ?2010-03-21 00:42:58?"Kevin Spitler" ???>>I am using the same gradient table as before, which worked with the>>low resolution data (large slice thickness).>>>>We are using a 3T Trio scanner in Siemens.>>>>Would it help if I attached one of the files from a recent scan?>>>>Best,>>Kevin>>>>2010/3/20 cwber :>>> How did you get the gradient table, there maybe something wrong in your>>> gradient table, you can check it, and which factory's machine> >> did you use>>> philips, GE,or Semense?>>> -->>> ???>>>>>> ?2010-03-20 22:09:12?"Kevin Spitler" ???>>>>I haven't upgraded the operating system. I am still using Windows XP.>>>>>>>>Here is the gradient table:>>>>>>>>0: 0.000, 0.000, 0.000>>>> 1: 0.500, 0.000, 0.500>>>> 2: -0.500, 0.000, 0.500>>>> 3: 0.000, 0.500, 0.500>>>> 4: 0.000, 0.500, -0.500>>>> 5: 0.500, 0.500, 0.000>>>> 6: -0.500, 0.500, 0.000>>>> 7: 1.000, 0.000, 1.000>>>>> 8: -1.000, 0.000, 1.000>>>> 9: 0.000, 1.000, 1.000>>>> 10: 0.000, 1.000, -1.000>>>> 11: 1.000, 1.000, 0.000>>>> 12: -1.000, 1.000, 0.000>>>>>>>>Thanks for your help! Please let me know what else I can send>>>>>>>>Best,>>>>Kevin>>>>>>>>>>>>On Thu, Mar 18, 2010 at 6:54 AM, susumu mori wrote:>>>>>>>>>> Have you recently upgraded the operating system? Can I see the gradient table you used?>>>>>>>>>> On Wed, Mar> >> 17, 2010 at 11:32 PM, Kevin Spitler wrote:>>>>>>>>>>>> Hello,>>>>>>>>>>>> We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue).>>>>>>>>>>>> The study was performed on&nbs> >> p;a 3T Trio scanner in Siemens.>>>>>> b values are b=0, b=600, b=1200>>>>>> Direction is 12>>>>>>>>>>>> I can provide more information or attach files if that would help solve the problem. Thanks for your help>>>>>>>>>>>> Best,>>>>>> Kevin>>>>>> _______________________________________________>>>>>> Mristudio-users mailing list>>>>>> Mristudio-users at mristudio.org>>>>>> http://lists.mristudio.org/mailman/listinfo/>>>>>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org>>>>>>>>>>>>>>>>>>>>> _______________________________________________>>>>> Mristudio-users mailing list>>>>> Mristudio-users at mristudio.org>>>>> http://lists.mristudio.org/mailman/listinfo/>>>>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org>>>>>>>>>>>>>_______________________________________________>>>>Mristudio-users mailing list>>>>Mristudio-users at mristudio.org>>>>http://lists.mristudio.org/mailman/listinfo/>>>>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org>>>>>>>>>>>> _______________________________________________>>> Mristudio-users mailing list>>> Mristudio-users at mristudio.org>>> http://lists.mristudio.org/mailman/listinfo/>>> Unsubscribe, send a blank email to:>>> Mristudio-users-unsubscribe at mristudio.org>>>>>>>>>>_______________________________________________>>Mristudio-users mailing list>>Mristudio-users at mristudio.org>>http://lists.mristudio.org/mailman/listinfo/>>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org>>>>> >> _______________________________________________> Mristudio-users mailing >> list> Mristudio-users at mristudio.org> >> http://lists.mristudio.org/mailman/listinfo/> Unsubscribe, send a blank >> email to:> Mristudio-users-unsubscribe at mristudio.org>> >> _______________________________________________Mristudio-users mailing >> listMristudio-users at mristudio.orghttp://lists.mristudio.org/mailman/listinfo/Unsubscribe, >> send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > From kevinspitler at ucla.edu Tue Mar 30 23:32:37 2010 From: kevinspitler at ucla.edu (Kevin Spitler) Date: Tue, 30 Mar 2010 20:32:37 -0700 Subject: [Mristudio-users] Problem loading high resolution scans into DTI Studio In-Reply-To: References: <9770ef211003200942p3f5a467ctbfb185ca1c48374b@mail.gmail.com> <9770ef211003172032x5bda836dua58762f2f150927@mail.gmail.com> <9770ef211003200709tc75a8a3h8682361685ad650a@mail.gmail.com> <196b712.d396.1277c033c9b.Coremail.cwber@126.com> <11ca3d1.489.1277e49d7de.Coremail.cwber@126.com> <284019.52203.qm@web110809.mail.gq1.yahoo.com> <9770ef211003232110o6ea1fb96id36f8c5d0a0abedf@mail.gmail.com> Message-ID: Thanks all for your help! I am having some progress with this last gradient although I still have a few things that I am checking. Thanks, Kevin 2010/3/24 susumu mori : > Hi all, > > Please try the following. I think Siemens changed their 12-orientation > scheme some time ago and this should work for VB13 and also VB15, I believe. > > 0: 0, 0, 0 > 1: 1.000000, 0.414250, -0.414250 > 2: 1.000000, -0.414250, -0.414250 > 3: 1.000000, -0.414250, 0.414250 > 4: 1.000000, 0.414250, 0.414250 > 5: 0.414250, 0.414250, 1.000000 > 6: 0.414250, 1.000000, 0.414250 > 7: 0.414250, 1.000000, -0.414250 > 8: 0.414250, 0.414250, -1.000000 > 9: 0.414250, -0.414250, -1.000000 > 10: 0.414250, -1.000000, -0.414250 > 11: 0.414250, -1.000000, 0.414250 > 12: 0.414250, -0.414250, 1.000000 > > > On Wed, Mar 24, 2010 at 12:10 AM, Kevin Spitler > wrote: >> >> Hi Bruce,Thanks for your gradient table. I can't get this to load the >> data. Iget the error message "forgot gradient table" which may be >> becausethere are only 12 lines, instead of 13 (0 to 12), so when I number >> thelines provided, I get a different error message "forget gradient >> ofB0-image?" >> How do you use this gradient table? >> Thanks,Kevin >> On Sun, Mar 21, 2010 at 9:09 AM, Bruce Leggett >> wrote:> this is the gradient table that I use for standard siemens 12 >> direction>>> X="-0.5197" Y="0.8541" Z="-0.0216"> X="0.5197" Y="-0.8541" >> Z="0.0216"> X="-0.1182" Y="0.4291" Z="-0.8955"> X="-0.7689" Y="0.0718" >> Z="0.6353"> X="0.5215" Y="0.8367" Z="-0.1673"> X="0.1193" Y="0.6159" >> Z="0.7788"> X="0.9157" Y="0.0436" Z="0.3994"> X="0.7689" Y="-0.0718" >> Z="-0.6353"> X="0.1182" Y="-0.4291" Z="0.8955"> X="-0.5215" Y="-0.8367" >> Z="0.1673"> X="-0.9157" Y="-0.0436" Z="-0.3994"> X="-0.1193" Y="-0.6159" >> Z="-0.7788">> thanks,> bruce>>> ________________________________> From: >> cwber > To: "DTI Studio, ROI Editor; Landmarker >> Questions/Support"> > Sent: Sat, March 20, >> 2010 7:15:20 PM> Subject: Re: [Mristudio-users] Problem loading high >> resolution scans into> DTI Studio>> HI,>>>0: 0.000, 0.000, 0.000>>> 1: >> 0.500, 0.000, 0.500>>> 2: -0.500, 0.000, 0.500>>> 3: 0.000, 0.500, 0.500>>> >> 4: 0.000, 0.500, -0.500>>> 5: 0.500, 0.500, 0.000>>> 6: -0.500, 0.500, >> 0.000>>> 7: 1.000, 0.000, 1.000>>> 8: -1.000, 0.000, 1.000>>> 9: 0.000, >> 1.000, 1.000>>> 10: 0.000, 1.000, -1.000>>> 11: 1.000, 1.000, 0.000>>> 12: >> -1.000, 1.000, 0.000> As i know, the gradient table must be >> normalization.such as:> (x)^2+(y)^2+(z)^2 == 1 but your gradient table >> doesn't satisfy this> condition.i am not sure if there is any problem in >> your table. and senmens> trio's Dicom file saved as mosaic format, so when >> you choose the data format> you should paid attention to choose the right >> format. and you should ask> semens's engineer to check your gradient talbe.> >> good luck!> --> weibo>> >> ?2010-03-21 00:42:58?"Kevin Spitler" ???>>I am using the same gradient table as before, which worked with the>>low resolution data (large slice thickness).>>>>We are using a 3T Trio scanner in Siemens.>>>>Would it help if I attached one of the files from a recent scan?>>>>Best,>>Kevin>>>>2010/3/20 cwber :>>> How did you get the gradient table, there maybe something wrong in your>>> gradient table, you can check it, and which factory's machine> >> did you use>>> philips, GE,or Semense?>>> -->>> ???>>>>>> ?2010-03-20 22:09:12?"Kevin Spitler" ???>>>>I haven't upgraded the operating system. I am still using Windows XP.>>>>>>>>Here is the gradient table:>>>>>>>>0: 0.000, 0.000, 0.000>>>> 1: 0.500, 0.000, 0.500>>>> 2: -0.500, 0.000, 0.500>>>> 3: 0.000, 0.500, 0.500>>>> 4: 0.000, 0.500, -0.500>>>> 5: 0.500, 0.500, 0.000>>>> 6: -0.500, 0.500, 0.000>>>> 7: 1.000, 0.000, 1.000>>>>> 8: -1.000, 0.000, 1.000>>>> 9: 0.000, 1.000, 1.000>>>> 10: 0.000, 1.000, -1.000>>>> 11: 1.000, 1.000, 0.000>>>> 12: -1.000, 1.000, 0.000>>>>>>>>Thanks for your help! Please let me know what else I can send>>>>>>>>Best,>>>>Kevin>>>>>>>>>>>>On Thu, Mar 18, 2010 at 6:54 AM, susumu mori wrote:>>>>>>>>>> Have you recently upgraded the operating system? Can I see the gradient table you used?>>>>>>>>>> On Wed, Mar> >> 17, 2010 at 11:32 PM, Kevin Spitler wrote:>>>>>>>>>>>> Hello,>>>>>>>>>>>> We have recently starting acquiring high resolution scans and I am having difficulty loading them into DTI Studio. I am using the same 12 direction gradient that worked on the low resolution (large slice thickness). Although the DTI Studio program does not crash, the color map 0 generated is not correct (random color patterns over the tissue).>>>>>>>>>>>> The study was performed on&nbs> >> p;a 3T Trio scanner in Siemens.>>>>>> b values are b=0, b=600, b=1200>>>>>> Direction is 12>>>>>>>>>>>> I can provide more information or attach files if that would help solve the problem. Thanks for your help>>>>>>>>>>>> Best,>>>>>> Kevin>>>>>> _______________________________________________>>>>>> Mristudio-users mailing list>>>>>> Mristudio-users at mristudio.org>>>>>> http://lists.mristudio.org/mailman/listinfo/>>>>>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org>>>>>>>>>>>>>>>>>>>>> _______________________________________________>>>>> Mristudio-users mailing list>>>>> Mristudio-users at mristudio.org>>>>> http://lists.mristudio.org/mailman/listinfo/>>>>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org>>>>>>>>>>>>>_______________________________________________>>>>Mristudio-users mailing list>>>>Mristudio-users at mristudio.org>>>>http://lists.mristudio.org/mailman/listinfo/>>>>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org>>>>>>>>>>>> _______________________________________________>>> Mristudio-users mailing list>>> Mristudio-users at mristudio.org>>> http://lists.mristudio.org/mailman/listinfo/>>> Unsubscribe, send a blank email to:>>> Mristudio-users-unsubscribe at mristudio.org>>>>>>>>>>_______________________________________________>>Mristudio-users mailing list>>Mristudio-users at mristudio.org>>http://lists.mristudio.org/mailman/listinfo/>>Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org>>>>> >> _______________________________________________> Mristudio-users mailing >> list> Mristudio-users at mristudio.org> >> http://lists.mristudio.org/mailman/listinfo/> Unsubscribe, send a blank >> email to:> Mristudio-users-unsubscribe at mristudio.org>> >> _______________________________________________Mristudio-users mailing >> listMristudio-users at mristudio.orghttp://lists.mristudio.org/mailman/listinfo/Unsubscribe, >> send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > From sailasuta at hmri.org Thu Apr 1 19:42:08 2010 From: sailasuta at hmri.org (Pom Sailasuta) Date: Thu, 01 Apr 2010 16:42:08 -0700 Subject: [Mristudio-users] DTI protocol (resending using my registered email) Message-ID: Dear Dr. Susumu, I am looking for recommended DTI scanning protocol on a 3T Philips Achieva scanner with 8-ch SENSE head coil. Can you point me to the location where I can find it? thanks Napapon -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100401/f83aeeba/attachment.html From jsadino.queens at gmail.com Mon Apr 5 22:18:05 2010 From: jsadino.queens at gmail.com (Jeff Sadino) Date: Mon, 05 Apr 2010 16:18:05 -1000 Subject: [Mristudio-users] command file Message-ID: Hello Everyone, I am interested in using the command/script based files to run a lot of datasets. I read Xin's posting about doing this in DiffeoMap with the following commands. Is there anywhere I can look to see all of the available commands? And are the instructions the same for DTI Studio as they are for DiffeoMap? Thank you! Jeff Sadino Govind, You need to create a command txt file named as "xx.cf" first. The attached is an example. It decribes the syntax of the commands. The Load Command File option process all the loaded subject images based on these commands. Hope this will help you. Xin //.cf file Format // Lines that begin with "//" are comment lines. // Commands are enclosed by "Begin/End" clauses. // The commands use reserved keywords, such as "crop", "format", "orientation". // Crop Slices in Axial Projection Command Syntax // crop startslicenumber endslicenumber // Change Format Command Syntax // format byte(word, float) // Change Slice Orientation Command Syntax // orientation axial(sagittal, coronal) // Rotate Image Command Syntax // rotate x degree y degree z degree trilinear(neighbor) // Shift Image Command Syntax // shift point(mm) x shift y shift z shift // Resample Image Command Syntax // resample imagewidth imageheight numberofslices fovwidth fovheight slicethickness trilinear(neighbor) // example // Begin // crop 20 180 // format byte // orientation axial // rotate x 45 y 0 z 10 neighbor // shift point x 10 y 0 z 5 // resample 181 217 181 181 217 1 trilinear // End -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100405/a8033eac/attachment.html From JLaMarche at tams.com Tue Apr 6 07:01:08 2010 From: JLaMarche at tams.com (John LaMarche) Date: Tue, 06 Apr 2010 04:01:08 -0700 Subject: [Mristudio-users] John LaMarche is out of the office. Message-ID: I will be out of the office starting 04/03/2010 and will not return until 04/12/2010. I will respond to your message when I return. From Surya.Gnyawali at osumc.edu Tue Apr 6 09:45:24 2010 From: Surya.Gnyawali at osumc.edu (Gnyawali, Surya) Date: Tue, 06 Apr 2010 09:45:24 -0400 Subject: [Mristudio-users] Gradient table DTI References: Message-ID: <4190FD92443D18458C90D47347B761E40156B98F@msxc05.OSUMC.EDU> Hi everyone, I want to start using MRI DTI track software. I don't know how to make gradient table. Can any one explains the every minute details to make the table and use it to track neuron activities in DTI mouse brain images. Thanks in advance. Surya Phone: 614-247-4559 E-mail: Surya.Gnyawali at osumc.edu ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of Jeff Sadino Sent: Mon 4/5/2010 10:18 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] command file Hello Everyone, I am interested in using the command/script based files to run a lot of datasets. I read Xin's posting about doing this in DiffeoMap with the following commands. Is there anywhere I can look to see all of the available commands? And are the instructions the same for DTI Studio as they are for DiffeoMap? Thank you! Jeff Sadino Govind, You need to create a command txt file named as "xx.cf " first. The attached is an example. It decribes the syntax of the commands. The Load Command File option process all the loaded subject images based on these commands. Hope this will help you. Xin //.cf file Format // Lines that begin with "//" are comment lines. // Commands are enclosed by "Begin/End" clauses. // The commands use reserved keywords, such as "crop", "format", "orientation". // Crop Slices in Axial Projection Command Syntax // crop startslicenumber endslicenumber // Change Format Command Syntax // format byte(word, float) // Change Slice Orientation Command Syntax // orientation axial(sagittal, coronal) // Rotate Image Command Syntax // rotate x degree y degree z degree trilinear(neighbor) // Shift Image Command Syntax // shift point(mm) x shift y shift z shift // Resample Image Command Syntax // resample imagewidth imageheight numberofslices fovwidth fovheight slicethickness trilinear(neighbor) // example // Begin // crop 20 180 // format byte // orientation axial // rotate x 45 y 0 z 10 neighbor // shift point x 10 y 0 z 5 // resample 181 217 181 181 217 1 trilinear // End -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100406/3045ef22/attachment.html From susumu at mri.jhu.edu Wed Apr 7 11:16:52 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 07 Apr 2010 11:16:52 -0400 Subject: [Mristudio-users] command file In-Reply-To: References: Message-ID: Hi Jeff, we are working on the command-line programs, but if I'm not mistaken, the current commands are limited to the pre-processing of the images such as changes matrix and resolution conversion, translation, and rotation. DiffeoMap does image registration and our experience tells it is still difficult to automate the process because quality control at each step is essential. Susumu On Mon, Apr 5, 2010 at 10:18 PM, Jeff Sadino wrote: > Hello Everyone, > I am interested in using the command/script based files to run a lot of > datasets. I read Xin's posting about doing this in DiffeoMap with the > following commands. Is there anywhere I can look to see all of the > available commands? And are the instructions the same for DTI Studio as > they are for DiffeoMap? > > Thank you! > Jeff Sadino > > > Govind, > > You need to create a command txt file named as "xx.cf" first. The attached > is an example. It decribes the syntax of the commands. The Load Command File > option process all the loaded subject images based on these commands. > > Hope this will help you. > > Xin > > > //.cf file Format > > // Lines that begin with "//" are comment lines. > // Commands are enclosed by "Begin/End" clauses. > > // The commands use reserved keywords, such as "crop", "format", > "orientation". > > // Crop Slices in Axial Projection Command Syntax > // crop startslicenumber endslicenumber > > // Change Format Command Syntax > // format byte(word, float) > > // Change Slice Orientation Command Syntax > // orientation axial(sagittal, coronal) > > // Rotate Image Command Syntax > // rotate x degree y degree z degree trilinear(neighbor) > > // Shift Image Command Syntax > // shift point(mm) x shift y shift z shift > > // Resample Image Command Syntax > // resample imagewidth imageheight numberofslices fovwidth fovheight > slicethickness trilinear(neighbor) > > // example > > // Begin > // crop 20 180 > // format byte > // orientation axial > // rotate x 45 y 0 z 10 neighbor > // shift point x 10 y 0 z 5 > // resample 181 217 181 181 217 1 trilinear > // End > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100407/1611e6bf/attachment.html From yj3 at duke.edu Wed Apr 7 17:21:08 2010 From: yj3 at duke.edu (Yi Jiang) Date: Wed, 07 Apr 2010 17:21:08 -0400 Subject: [Mristudio-users] second and tertiary eigenvalue equal to 0 References: Message-ID: <949BA53CF83A4B62A2A969748F9424F4@panpan> Dear All, I computed diffusion tensors and FA, va0 (primary eigenvalue), va1 (secondary eigenvalue), and va2 (tertiary eigenvalue) by linear fitting in DTIStudio. Then I save them into raw matrix and read them in matlab. I found the number of non-zero (the background is all zero) voxels for va1 and va2 is less than that of va0 or FA. Such as: number of non-zeros voxels for va0 = 6311454 number of non-zeros voxels for va1 = 6310767 number of non-zeros voxels for va2 = 6248757 number of non-zeros voxels for va0 = 6311454 This happens in all my datasets, consistently. The voxels where va0~=0 & va1==0 are not a lot (a few hundred), and they mostly are at the edge of the brain, not inside white mattter. But the voxels where va0~=0 & va2==0 are quite a lot (tens of thousand), and they resides mostly inside white matter, such as corpus callosum. I would like to know why this happens. Moreover, when I try to, for example, calculate the mean va2 within corpus callosum, how can I deal with those voxels where va2==0 ? I think to treat them as equal to 0 sounds not correct physiologically. But because there are a lot, I want to count those points in, especially for small white matter structures (sometimes those va2==0 voxels can take up to 10% of a white matter structure). Also, when I calculate radial diffusivity (va1+va2)/2, the va2==0 points generate incorrect radial diffusivity. Thank you very much! Best, Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100407/9e43c343/attachment-0001.html From susumu at mri.jhu.edu Wed Apr 7 17:25:30 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 07 Apr 2010 17:25:30 -0400 Subject: [Mristudio-users] DTI protocol (resending using my registered email) In-Reply-To: References: Message-ID: Here is what I would do; 1) resolution: 2-2.2mm isotropic. The latest RF coils are good enough to deliver 2mm resolution with decent SNR. The smaller the image matrix, the less distortion and higher SNR. 2.2mm: 112x112 matrix (zerofilled (interpolated) to 224x224 or 256x256) for 246x246 mm FOV or 96x96 (->192x192 or 256x256) for 211x211 mm FOV. 2.2 mm slice 2mm: 112x112 matrix for 224x224 mm FOV. 96x96 for 192x192mm FOV could be too small for some subjects. 2mm slice 2) the total number of DWIs: We do about 60 DWIs which should take 8-9 min. 30 DWI could provide decent SNR with 2.2 mm but a bit push for 2mm. 60 DWIs mean; 30 orientation x 2, 20 x 3, 15 x 4, 12 x 5. In my opinion, they provide very similar results but some reviewers believe the more orientations the better. With simulation or extremely high SNR data (e.g. >30 min scan), you start to see slight differences among these schemes but with <10 min scan, they are usually indistinguishable. Add 5-6 b0 images. 3) TR: decided by the number of slices. Choose the shortest. Philips and Siemens should be in 6-10s range. Old GE may have >10s due to a gradient duty cycle issue. 4) TE: shortest. Siemens and GE should use double-echo type option (default for Siemens and option for GE). Philips users may want to add few ms, which would shorten the scan time drastically and reduce Eddy-current distortion. Systematically increase the TE until you reach the shortest scan time. The shortest TE often leads to longer scan time due to gradient duty cycle. 5) SENSE/GRAPPA/ASSET: On, factor = 2 - 2.5. Latest 32-channel head coil could push to 3 but check the image quality before you decide to use. 6) Partial fourier: I prefer 100% and I feel the image is more robust against motion, but this is just my subjective experience. Many use 70-80%, which may improve SNR by using shorter TE. Susumu On Thu, Apr 1, 2010 at 7:42 PM, Pom Sailasuta wrote: > Dear Dr. Susumu, > > I am looking for recommended DTI scanning protocol on a 3T Philips Achieva > scanner with 8-ch SENSE head coil. Can you point me to the location where I > can find it? > > thanks > > Napapon > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100407/df2d3acf/attachment.html From susumu at mri.jhu.edu Wed Apr 7 17:39:44 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 07 Apr 2010 17:39:44 -0400 Subject: [Mristudio-users] second and tertiary eigenvalue equal to 0 In-Reply-To: <949BA53CF83A4B62A2A969748F9424F4@panpan> References: <949BA53CF83A4B62A2A969748F9424F4@panpan> Message-ID: Hi Yi, I want to hear from Hangyi for detailed response, but there are known issues in tensor fitting. In the linear tensor fitting, we assume that the tensor has positive diagonal elements. This means, for example, when gradients are applied (diffusion-weighted), signal becomes lower than non-weighted images (b0). However, there are situation when this assumption is violated. At the edge of the brain, subject motion (non-reproducible) and eddy current (reproducible) causes pixel mis-registration, meaning, the pixel is sometimes inside and sometime outside the brain. Then the fitting blows up. Also, for the very highly anisotropic area such as CC, DWIs with the gradients applied perpendicular to the fiber (say, we expect only 5% signal loss) could have higher intensity than b0 due to SNR (say more than 5% signal fluctuation). In this case, the fitting blows up again. In these situations, it is not uncommon to get negative diagonal elements or FA higher than 1.0. To prevent this, there are several proposed methods. I believe DtiStudio simply replace the negative diagonal elements with 0. The issues of the CC should be reduced if you have higher SNR (or more DWIs). What is the resolution and the number of DWIs you are using? For the brain edge, please check the fitting error map based on the DtiStudio Updage file I recently distributed. Susumu On Wed, Apr 7, 2010 at 5:21 PM, Yi Jiang wrote: > Dear All, > > > > I computed diffusion tensors and FA, va0 (primary eigenvalue), va1 > (secondary eigenvalue), and va2 (tertiary eigenvalue) by linear fitting in > DTIStudio. Then I save them into raw matrix and read them in matlab. > > > > I found the number of non-zero (the background is all zero) voxels for va1 > and va2 is less than that of va0 or FA. Such as: > > > > number of non-zeros voxels for va0 = 6311454 > number of non-zeros voxels for va1 = 6310767 > number of non-zeros voxels for va2 = 6248757 > number of non-zeros voxels for va0 = 6311454 > > > > This happens in all my datasets, consistently. > > > > The voxels where va0~=0 & va1==0 are not a lot (a few hundred), and they > mostly are at the edge of the brain, not inside white mattter. > > > > But the voxels where va0~=0 & va2==0 are quite a lot (tens of thousand), > and they resides mostly inside white matter, such as corpus callosum. > > > > I would like to know why this happens. > > > > Moreover, when I try to, for example, calculate the mean va2 within corpus > callosum, how can I deal with those voxels where va2==0 ? I think to treat > them as equal to 0 sounds not correct physiologically. But because there are > a lot, I want to count those points in, especially for small white matter > structures (sometimes those va2==0 voxels can take up to 10% of a white > matter structure). > > > > Also, when I calculate radial diffusivity (va1+va2)/2, the va2==0 points > generate incorrect radial diffusivity. > > > > Thank you very much! > > > > Best, > > Yi > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100407/eac5d6e6/attachment.html From hjiang at jhmi.edu Thu Apr 8 09:18:42 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Thu, 08 Apr 2010 09:18:42 -0400 Subject: [Mristudio-users] second and tertiary eigenvalue equal to 0 In-Reply-To: References: <949BA53CF83A4B62A2A969748F9424F4@panpan> Message-ID: <145933A2BE9E4F48AE079A201379BF2F210B80504C@RAD-EXCH1.win.ad.jhu.edu> hi, theoretically, the tensor is positive definite matrix. practically, it is not. the eigen values could be zero or negative. in DtiStudio, the zeros are kept there, the negatives are forced as zeros. regards, hangyi ________________________________________ From: smoriw at gmail.com [smoriw at gmail.com] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: Wednesday, April 07, 2010 5:39 PM To: Yi Jiang; DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang Subject: Re: [Mristudio-users] second and tertiary eigenvalue equal to 0 Hi Yi, I want to hear from Hangyi for detailed response, but there are known issues in tensor fitting. In the linear tensor fitting, we assume that the tensor has positive diagonal elements. This means, for example, when gradients are applied (diffusion-weighted), signal becomes lower than non-weighted images (b0). However, there are situation when this assumption is violated. At the edge of the brain, subject motion (non-reproducible) and eddy current (reproducible) causes pixel mis-registration, meaning, the pixel is sometimes inside and sometime outside the brain. Then the fitting blows up. Also, for the very highly anisotropic area such as CC, DWIs with the gradients applied perpendicular to the fiber (say, we expect only 5% signal loss) could have higher intensity than b0 due to SNR (say more than 5% signal fluctuation). In this case, the fitting blows up again. In these situations, it is not uncommon to get negative diagonal elements or FA higher than 1.0. To prevent this, there are several proposed methods. I believe DtiStudio simply replace the negative diagonal elements with 0. The issues of the CC should be reduced if you have higher SNR (or more DWIs). What is the resolution and the number of DWIs you are using? For the brain edge, please check the fitting error map based on the DtiStudio Updage file I recently distributed. Susumu On Wed, Apr 7, 2010 at 5:21 PM, Yi Jiang > wrote: Dear All, I computed diffusion tensors and FA, va0 (primary eigenvalue), va1 (secondary eigenvalue), and va2 (tertiary eigenvalue) by linear fitting in DTIStudio. Then I save them into raw matrix and read them in matlab. I found the number of non-zero (the background is all zero) voxels for va1 and va2 is less than that of va0 or FA. Such as: number of non-zeros voxels for va0 = 6311454 number of non-zeros voxels for va1 = 6310767 number of non-zeros voxels for va2 = 6248757 number of non-zeros voxels for va0 = 6311454 This happens in all my datasets, consistently. The voxels where va0~=0 & va1==0 are not a lot (a few hundred), and they mostly are at the edge of the brain, not inside white mattter. But the voxels where va0~=0 & va2==0 are quite a lot (tens of thousand), and they resides mostly inside white matter, such as corpus callosum. I would like to know why this happens. Moreover, when I try to, for example, calculate the mean va2 within corpus callosum, how can I deal with those voxels where va2==0 ? I think to treat them as equal to 0 sounds not correct physiologically. But because there are a lot, I want to count those points in, especially for small white matter structures (sometimes those va2==0 voxels can take up to 10% of a white matter structure). Also, when I calculate radial diffusivity (va1+va2)/2, the va2==0 points generate incorrect radial diffusivity. Thank you very much! Best, Yi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From joanne.powell at hotmail.com Thu Apr 8 12:20:08 2010 From: joanne.powell at hotmail.com (joanne powell) Date: Thu, 08 Apr 2010 17:20:08 +0100 Subject: [Mristudio-users] reading .hdr .img files Message-ID: Hi Is there a way for DTI studio to read .hdr .img files. I would like to perform motion correction on the images before performing tractography and have used FSL to do this (as I do not know any other way). The file comes out as a .hdr .img file and I am unsure how to open these images in DTI studio to perform tractography. Would anybody kindly be able to offer me any help or advice here? Kindest regards Joanne _________________________________________________________________ http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100408/ca38c4fc/attachment-0001.html From ccapeland at anatomicaltravel.com Thu Apr 8 12:31:47 2010 From: ccapeland at anatomicaltravel.com (Chad Capeland) Date: Thu, 08 Apr 2010 12:31:47 -0400 Subject: [Mristudio-users] reading .hdr .img files In-Reply-To: References: Message-ID: <4BBE04F3.4000800@anatomicaltravel.com> joanne powell wrote: > Hi > > Is there a way for DTI studio to read .hdr .img files. > I would like to perform motion correction on the images before > performing tractography and have used FSL to do this (as I do not know > any other way). > The file comes out as a .hdr .img file and I am unsure how to open > these images in DTI studio to perform tractography. > > Would anybody kindly be able to offer me any help or advice here? > The .img is probably just raw voxel data. The .hdr will give you the specs on how to interpret the data, like size, type, etc. -- Chad Capeland Director R&D Anatomical Travelogue LLC ccapeland at anatomicaltravel.com 212-625-6665 www.thevisualmd.com www.anatomicaltravel.com/research -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From jmcentee at jhmi.edu Thu Apr 8 12:38:14 2010 From: jmcentee at jhmi.edu (Julie McEntee) Date: Thu, 08 Apr 2010 12:38:14 -0400 Subject: [Mristudio-users] reading .hdr .img files In-Reply-To: Message-ID: I would avoid ANALYZE format in DtiStudio as the .hdr does not store enough info to display R/L, and sometimes other directions, properly (DtiStudio uses radiological convention- R is L). DtiStudio has motion correction algorithms (e.g., AIR)- see new posted doc on website under User manual, DtiStudio, 3.0.2 new features, DtiStudioUpdate.doc. New version (3.0.2) has multiple options; beta version only one (AIR). -Julie Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676 On 4/8/10 12:20 PM, "joanne powell" wrote: > Hi > > Is there a way for DTI studio to read .hdr .img files. > I would like to perform motion correction on the images before performing > tractography and have used FSL to do this (as I do not know any other way). > The file comes out as a .hdr .img file and I am unsure how to open these > images in DTI studio to perform tractography. > > Would anybody kindly be able to offer me any help or advice here? > > Kindest regards > Joanne > > > Get a free e-mail account with Hotmail. Sign-up now. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100408/b4bfcf6f/attachment.html From afzaliesfahan at yahoo.com Thu Apr 8 12:42:52 2010 From: afzaliesfahan at yahoo.com (maryam afzali) Date: Thu, 08 Apr 2010 09:42:52 -0700 (PDT) Subject: [Mristudio-users] reading .hdr .img files In-Reply-To: References: Message-ID: <7115.32411.qm@web57901.mail.re3.yahoo.com> Hi You should follow these steps: File> MRI view 3D? (Select your image)> Image file format (analyze)> ok You should change your image file format to 'analyze format'. ________________________________ From: joanne powell To: mristudio-users at mristudio.org Sent: Thu, April 8, 2010 9:20:08 AM Subject: [Mristudio-users] reading .hdr .img files Hi ? Is there a way for DTI studio to read .hdr .img files. I would like to perform motion correction on the images before performing tractography and have used FSL to do this (as I do not know any other way). The file comes out as a .hdr .img file and I am unsure how to open these images in DTI studio to perform tractography. ? Would anybody kindly?be able to offer me any help or advice here? ? Kindest regards Joanne ________________________________ Get a free e-mail account with Hotmail. Sign-up now. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100408/caf90727/attachment.html From mithra at mail.utexas.edu Tue Apr 13 11:28:38 2010 From: mithra at mail.utexas.edu (Mithra) Date: Tue, 13 Apr 2010 10:28:38 -0500 Subject: [Mristudio-users] Regarding the data viewing Message-ID: Hello, I have a basic question about image viewing. Are the data displayed in radiological format or neurological format. I have some data collected some time ago and would like to make sure which side is left and which one is right. It looked like the screen left side shows the left side of the brain. Am I right. Thank you for your help. Regards, - Mithra. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100413/2adbf44e/attachment.html From susumu at mri.jhu.edu Tue Apr 13 11:45:14 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 13 Apr 2010 11:45:14 -0400 Subject: [Mristudio-users] Regarding the data viewing In-Reply-To: References: Message-ID: Hi Mithra, Please see Q15 of the FAQ section of https://www.mristudio.org/wiki/faq. Susumu On Tue, Apr 13, 2010 at 11:28 AM, Mithra wrote: > Hello, > I have a basic question about image viewing. Are the data displayed in > radiological format or neurological format. I have some data collected some > time ago and would like to make sure which side is left and which one is > right. > > It looked like the screen left side shows the left side of the brain. Am I > right. > > Thank you for your help. > > Regards, > - Mithra. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100413/b78e1e96/attachment.html From rajagov2 at ccf.org Tue Apr 13 12:16:59 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Tue, 13 Apr 2010 12:16:59 -0400 Subject: [Mristudio-users] Absence of CST in subcortical motor cortex Message-ID: <77A88E90A851594AAEF830450587C39D01EDAC80@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, In our study we tried to evaluate changes in CST between our patient and control groups using DTI metrics. We reconstructed CST using tracography and measured changes in DTI metrics. We used same protocol for DTI imaging and the DTI images were processed the same way in DTI studio like setting same the FA threshold for tracking in all the subjects, tracts reconstructed using Wakana et al's two ROI approach i.e we placed our first ROI in cerebral peduncle and then the second ROI in subcortical Motor cortex, used cut operation in all the subjects, then similar kind of outlier rejection of bad DW images.By this i mean same processing steps. The question i have is in some of these patients CST doesn't go all the way up to motor cortex i.e.after reconstruction CST is available only between cerebral peduncle to top of lateral ventricle and after that ( i.e. higher up) CST is absent, this is seen only in some of our patients not in all the cases. Can i attribute this to the disease process or is there somewhere i am making mistake in my image processing steps. Thanks in advance. venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100413/014364bd/attachment-0001.html From susumu at mri.jhu.edu Tue Apr 13 16:25:51 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 13 Apr 2010 16:25:51 -0400 Subject: [Mristudio-users] Absence of CST in subcortical motor cortex In-Reply-To: <77A88E90A851594AAEF830450587C39D01EDAC80@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D01EDAC80@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Hi Venkat, If you apply the same method to both groups and only one of the groups show the truncated CST, it tells there is some difference between the two groups detected by DTI. I think this is a fact. Our interpretation, on the other hand, may not be a fact and there are many ways to interpret the same data. I believe this is the source of your question. When we do MRI and find something (e.g. FA drops, ADC increases, fibers thinner, etc), we try to directly relate it to underlying neuroanatomy. For example, FA tells something about myelination and tractography about connectivity. However, MRI/DTI measures water properties at each pixel, which is a decidedly indirect indicator of any cellular entity. The level of biological question we are asking often require astronomical amount of data. For example, if we want to know myelination status, we are asking questions in micrometer scale of 100 billion axons. On the other hand, DTI data is merely 20 MB of information. This is a huge degeneration problem. You can predict what would happen in DTI/MRI if you know the anatomy, but it's much tougher to define what really happens from DTI/MRI results. By applying the same tractography protocol, you found consistent difference between two groups. If you use Wakana's protocol, there are more subjects in the patient group that return "null". If you quantify the results in some way (e.g. the number of "null" subjects, the average number of pixels, etc), you may be able to find a statistical difference. So far so good. However, you have to interpret this data, where the difficulty arises. If you literary take the results and claim, "there are more patients who lack the CST", that may not be true. This is because there could be multiple reasons that lead to the same tractography results; there is one area with low FA, enlargement of the ventricle made the CST trajectory more tortuous, thinning of one anatomical area made the tractography less reproducible (partial volume effect), reduction of the CST axon leads to the higher contribution of a small population of crossing fibers, and so on. By having only 20 MB of the data, MRI/DTI/tractography can only be a screening tool, I think. To obtain more information, you may need to do more analysis to come closer to the true reason of your results. You can modify the CST protocol so that you can get more fibers. If you lower the second ROI away from the motor cortex, you get more fiber with an expense of less specificity to the CST. You can monitor FA values along the fiber. You can do voxel-based analysis to find a group of pixels that accounts for the different tractography results. If you can identify the reason (e.g. locations of pixels with different FA/vector values), you have more specific information about the difference between the two groups. Sorry that I'm not providing a solution to your answer. If your control group shows good CSTs, then I think you are not making a mistake. It's possible that the corona radiata has lower FA in the patients. I would try to find out the reason of the truncated CST. Susumu On Tue, Apr 13, 2010 at 12:16 PM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > > Dear All, > > In our study we tried to evaluate changes in CST between our patient and > control groups using DTI metrics. We reconstructed CST using tracography and > measured changes in DTI metrics. > > We used same protocol for DTI imaging and the DTI images were processed the > same way in DTI studio like setting same the FA threshold for tracking in > all the subjects, tracts reconstructed using Wakana et al's two ROI approach > i.e we placed our first ROI in cerebral peduncle and then the second ROI in > subcortical Motor cortex, used cut operation in all the subjects, then > similar kind of outlier rejection of bad DW images.By this i mean same > processing steps. > > > The question i have is in some of these patients CST doesn't go all the way > up to motor cortex i.e.after reconstruction CST is available only between > cerebral peduncle to top of lateral ventricle and after that ( i.e. higher > up) CST is absent, this is seen only in some of our patients not in all the > cases. Can i attribute this to the disease process or is there somewhere i > am making mistake in my image processing steps. > > Thanks in advance. > > venkat > > =================================== > > P Please consider the environment before printing this e-mail > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100413/db5a0144/attachment.html From rajagov2 at ccf.org Wed Apr 14 10:22:04 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Wed, 14 Apr 2010 10:22:04 -0400 Subject: [Mristudio-users] Absence of CST in subcortical motor cortex References: <77A88E90A851594AAEF830450587C39D01EDAC80@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D01EDAC82@CCHSCLEXMB56.cc.ad.cchs.net> Dear Dr.Mori, Thanks very much for your informative and insightful answer. As you mentioned i don't see any CST abnormality i.e absence of CST in controls, so this relieves me from being worried as processing error. Thanks very much. Regards venkat ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Tue 4/13/2010 4:25 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Absence of CST in subcortical motor cortex Hi Venkat, If you apply the same method to both groups and only one of the groups show the truncated CST, it tells there is some difference between the two groups detected by DTI. I think this is a fact. Our interpretation, on the other hand, may not be a fact and there are many ways to interpret the same data. I believe this is the source of your question. When we do MRI and find something (e.g. FA drops, ADC increases, fibers thinner, etc), we try to directly relate it to underlying neuroanatomy. For example, FA tells something about myelination and tractography about connectivity. However, MRI/DTI measures water properties at each pixel, which is a decidedly indirect indicator of any cellular entity. The level of biological question we are asking often require astronomical amount of data. For example, if we want to know myelination status, we are asking questions in micrometer scale of 100 billion axons. On the other hand, DTI data is merely 20 MB of information. This is a huge degeneration problem. You can predict what would happen in DTI/MRI if you know the anatomy, but it's much tougher to define what really happens from DTI/MRI results. By applying the same tractography protocol, you found consistent difference between two groups. If you use Wakana's protocol, there are more subjects in the patient group that return "null". If you quantify the results in some way (e.g. the number of "null" subjects, the average number of pixels, etc), you may be able to find a statistical difference. So far so good. However, you have to interpret this data, where the difficulty arises. If you literary take the results and claim, "there are more patients who lack the CST", that may not be true. This is because there could be multiple reasons that lead to the same tractography results; there is one area with low FA, enlargement of the ventricle made the CST trajectory more tortuous, thinning of one anatomical area made the tractography less reproducible (partial volume effect), reduction of the CST axon leads to the higher contribution of a small population of crossing fibers, and so on. By having only 20 MB of the data, MRI/DTI/tractography can only be a screening tool, I think. To obtain more information, you may need to do more analysis to come closer to the true reason of your results. You can modify the CST protocol so that you can get more fibers. If you lower the second ROI away from the motor cortex, you get more fiber with an expense of less specificity to the CST. You can monitor FA values along the fiber. You can do voxel-based analysis to find a group of pixels that accounts for the different tractography results. If you can identify the reason (e.g. locations of pixels with different FA/vector values), you have more specific information about the difference between the two groups. Sorry that I'm not providing a solution to your answer. If your control group shows good CSTs, then I think you are not making a mistake. It's possible that the corona radiata has lower FA in the patients. I would try to find out the reason of the truncated CST. Susumu On Tue, Apr 13, 2010 at 12:16 PM, Rajagopalan, Venkateswaran wrote: Dear All, In our study we tried to evaluate changes in CST between our patient and control groups using DTI metrics. We reconstructed CST using tracography and measured changes in DTI metrics. We used same protocol for DTI imaging and the DTI images were processed the same way in DTI studio like setting same the FA threshold for tracking in all the subjects, tracts reconstructed using Wakana et al's two ROI approach i.e we placed our first ROI in cerebral peduncle and then the second ROI in subcortical Motor cortex, used cut operation in all the subjects, then similar kind of outlier rejection of bad DW images.By this i mean same processing steps. The question i have is in some of these patients CST doesn't go all the way up to motor cortex i.e.after reconstruction CST is available only between cerebral peduncle to top of lateral ventricle and after that ( i.e. higher up) CST is absent, this is seen only in some of our patients not in all the cases. Can i attribute this to the disease process or is there somewhere i am making mistake in my image processing steps. Thanks in advance. venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 8453 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100414/aee17cfa/attachment-0001.bin From haitao.ge at hotmail.com Thu Apr 15 09:41:45 2010 From: haitao.ge at hotmail.com (haitao.ge at hotmail.com) Date: Thu, 15 Apr 2010 21:41:45 +0800 Subject: [Mristudio-users] makeaheader.exe + alignlinear.exe + align_warp.exe Message-ID: Hi everyone, I am trying to use DiffeoMap to process diffusion tensor images. The instruction indicates that if one wants to use the function "Automatic Image Linear Registration", the user needs to build makeaheader.exe, alignlinear.exe and align_warp.exe independently. However, after I downloaded the AIR, it was said that this program should be modified by C compiler firstly before it could be used in Windows. I wonder if there are ready-compiled execute format files to simplify the above procedures. Thanks in advance, ------------------------------------------------------- Haitao Ge, Ph.D. Center for Sectional and Imaging Anatomy Shandong University School of Medicine 44#, West Wenhua Rd. Jinan 250012, Shandong P.R.China Tel: +86-15965644699 haitao.ge at hotmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100415/4fd5dcbe/attachment.html From pom4pom at gmail.com Wed Apr 7 23:38:31 2010 From: pom4pom at gmail.com (Pom Sailasuta) Date: Wed, 07 Apr 2010 20:38:31 -0700 Subject: [Mristudio-users] DTI protocol (resending using my registered email) In-Reply-To: References: Message-ID: thank you, Dr. Susumu. I will give it a try. Pom On Wed, Apr 7, 2010 at 2:25 PM, susumu mori wrote: > Here is what I would do; > > 1) resolution: 2-2.2mm isotropic. The latest RF coils are good enough to > deliver 2mm resolution with decent SNR. The smaller the image matrix, the > less distortion and higher SNR. > 2.2mm: 112x112 matrix (zerofilled (interpolated) to 224x224 or 256x256) for > 246x246 mm FOV or 96x96 (->192x192 or 256x256) for 211x211 mm FOV. 2.2 mm > slice > > 2mm: 112x112 matrix for 224x224 mm FOV. 96x96 for 192x192mm FOV could be > too small for some subjects. 2mm slice > > 2) the total number of DWIs: We do about 60 DWIs which should take 8-9 min. > 30 DWI could provide decent SNR with 2.2 mm but a bit push for 2mm. 60 DWIs > mean; 30 orientation x 2, 20 x 3, 15 x 4, 12 x 5. In my opinion, they > provide very similar results but some reviewers believe the more > orientations the better. With simulation or extremely high SNR data (e.g. > >30 min scan), you start to see slight differences among these schemes but > with <10 min scan, they are usually indistinguishable. Add 5-6 b0 images. > > 3) TR: decided by the number of slices. Choose the shortest. Philips and > Siemens should be in 6-10s range. Old GE may have >10s due to a gradient > duty cycle issue. > > 4) TE: shortest. Siemens and GE should use double-echo type option (default > for Siemens and option for GE). Philips users may want to add few ms, which > would shorten the scan time drastically and reduce Eddy-current distortion. > Systematically increase the TE until you reach the shortest scan time. The > shortest TE often leads to longer scan time due to gradient duty cycle. > > 5) SENSE/GRAPPA/ASSET: On, factor = 2 - 2.5. Latest 32-channel head coil > could push to 3 but check the image quality before you decide to use. > > 6) Partial fourier: I prefer 100% and I feel the image is more robust > against motion, but this is just my subjective experience. Many use 70-80%, > which may improve SNR by using shorter TE. > > Susumu > > On Thu, Apr 1, 2010 at 7:42 PM, Pom Sailasuta wrote: > >> Dear Dr. Susumu, >> >> I am looking for recommended DTI scanning protocol on a 3T Philips Achieva >> scanner with 8-ch SENSE head coil. Can you point me to the location where I >> can find it? >> >> thanks >> >> Napapon >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100407/1614e124/attachment-0001.html From bfling at umich.edu Fri Apr 9 15:03:15 2010 From: bfling at umich.edu (Brett W Fling) Date: Fri, 09 Apr 2010 15:03:15 -0400 Subject: [Mristudio-users] motion / eddy current correction Message-ID: <574AF378-C7BE-4B68-8146-AF482E277753@umich.edu> Hello, We are fairly new to using the DTIstudio (version 3.0.2.) and I was hoping you could help us out with some of our questions. We were able to load in our DICOM files and create different tensor images (i.e. FA map), however I wasn't sure if the program automatically does all the preprocessing (motion and eddy current correction). The images look fairly reasonable however there seems to be some background noise outside the brain. Thanks for you comments. ********************************************** Brett W Fling, M.S. Neuromotor Behavior Laboratory School of Kinesiology University of Michigan 401 Washtenaw Ave Ann Arbor, MI 48109-2214 Office Phone: 734-615-9330 Email: bfling at umich.edu http://sitemaker.umich.edu/neuromotorbehaviorlab/home -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100409/1fa72644/attachment-0001.html From mmzeineh at gmail.com Thu Apr 15 18:57:20 2010 From: mmzeineh at gmail.com (Michael Zeineh) Date: Thu, 15 Apr 2010 15:57:20 -0700 Subject: [Mristudio-users] Question re displaying of ROIs Message-ID: If I draw ROIs under the fiber tab, once I draw more than one ROI, I cannot see any of the drawn ROIs. Similarly, if I load an ROI, it will only display the fibers under the fibertrack tab. Is there any way to display the ROIs under the fiber tab? Thank you. From jmcentee at jhmi.edu Fri Apr 16 10:00:02 2010 From: jmcentee at jhmi.edu (Julie McEntee) Date: Fri, 16 Apr 2010 10:00:02 -0400 Subject: [Mristudio-users] motion / eddy current correction In-Reply-To: <574AF378-C7BE-4B68-8146-AF482E277753@umich.edu> Message-ID: Have a look/read at the DtiStudioUpdate.doc on the MRIStudio website under User Manual, DtiStudio, 3.0.2 version. Julie Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676 On 4/9/10 3:03 PM, "Brett W Fling" wrote: > Hello, > > We are fairly new to using the DTIstudio (version 3.0.2.) and I was hoping you > could help us out with some of our questions. > We were able to load in our DICOM files and create different tensor images > (i.e. FA map), however I wasn't sure if the program automatically does all the > preprocessing (motion and eddy current correction). The images look fairly > reasonable however there seems to be some background noise outside the brain. > > Thanks for you comments. > > > > ********************************************** > Brett W Fling, M.S. > Neuromotor Behavior Laboratory > School of Kinesiology > University of Michigan > 401 Washtenaw Ave > Ann Arbor, MI 48109-2214 > Office Phone: 734-615-9330 > Email: bfling at umich.edu > http://sitemaker.umich.edu/neuromotorbehaviorlab/home > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100416/e862c86a/attachment.html From Michael.Nelles at ukb.uni-bonn.de Wed Apr 21 05:32:27 2010 From: Michael.Nelles at ukb.uni-bonn.de (Michael.Nelles at ukb.uni-bonn.de) Date: Wed, 21 Apr 2010 11:32:27 +0200 Subject: [Mristudio-users] Fiber-Tracking Menu Options Message-ID: Hi all, I have questions concerning the two Fiber Tracking methods one can choose when starting Fiber-Tracking: what is the difference between tracking "using principal vector and FA map" and tracking "using tensor images" ? Are there any relevant differences of tracking results (of e.g. the CST) to be expected ? Is it true that you have to flip the z-component of the Eigen-Vector when processing Philips DTI data ? Thanks in advance ! M. Nelles -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100421/e6d7f715/attachment.html From susumu at mri.jhu.edu Wed Apr 21 08:26:46 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 21 Apr 2010 08:26:46 -0400 Subject: [Mristudio-users] Fiber-Tracking Menu Options In-Reply-To: References: Message-ID: Hi Nelles, I believe they are the same (Hangyi, correct me if I'm wrong). Usually after tensor calculation, we save tensor-derived images such as FA, eigenvalues, and eigenvectors. However, sometimes we save only a tensor file to save the disc space, because as long as we save the raw tensor file, we can re-generate all the derived images. To perform tracking, you need to load the tensor file, calculate FA and eigenvectors, save them, and load them again for tracking. The "using the tensor images" option save time by eliminating these steps when you have only the tensor file. You just load the tensor file and start tracking. Susumu On Wed, Apr 21, 2010 at 5:32 AM, wrote: > > Hi all, > > I have questions concerning the two Fiber Tracking methods one can choose > when starting Fiber-Tracking: > what is the difference between tracking "using principal vector and FA map" > and tracking "using tensor images" ? > Are there any relevant differences of tracking results (of e.g. the CST) to > be expected ? > > Is it true that you have to flip the z-component of the Eigen-Vector when > processing Philips DTI data ? > > Thanks in advance ! > > M. Nelles > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100421/15ef891a/attachment.html From Michael.Nelles at ukb.uni-bonn.de Wed Apr 21 10:11:47 2010 From: Michael.Nelles at ukb.uni-bonn.de (Michael.Nelles at ukb.uni-bonn.de) Date: Wed, 21 Apr 2010 16:11:47 +0200 Subject: [Mristudio-users] Fiber-Tracking Menu Options In-Reply-To: Message-ID: Hi Susumu, thanks very much for the quick reply. With kind regards, M. Nelles ------------------------------------------------------------------------------- Michael Nelles, MD Dept. of Radiology / Neuroradiology University of Bonn Medical Center Sigmund Freud Str. 25, D - 53105 Bonn, Germany Phone: (+49) 228 287 16389 Fax: (+49) 228 287 14321 Email: michael.nelles at ukb.uni-bonn.de susumu mori An Gesendet von: "DTI Studio, ROI Editor, DiffeoMap mristudio-users-b Questions/Support" ounces at mristudio. , org Hangyi Jiang Kopie 21.04.2010 14:26 Thema Re: [Mristudio-users] Fiber-Tracking Menu Options Bitte antworten an "DTI Studio, ROI Editor, DiffeoMap Questions/Support " Hi Nelles, I believe they are the same (Hangyi, correct me if I'm wrong). Usually after tensor calculation, we save tensor-derived images such as FA, eigenvalues, and eigenvectors. However, sometimes we save only a tensor file to save the disc space, because as long as we save the raw tensor file, we can re-generate all the derived images. To perform tracking, you need to load the tensor file, calculate FA and eigenvectors, save them, and load them again for tracking. The "using the tensor images" option save time by eliminating these steps when you have only the tensor file. You just load the tensor file and start tracking. Susumu On Wed, Apr 21, 2010 at 5:32 AM, wrote: Hi all, I have questions concerning the two Fiber Tracking methods one can choose when starting Fiber-Tracking: what is the difference between tracking "using principal vector and FA map" and tracking "using tensor images" ? Are there any relevant differences of tracking results (of e.g. the CST) to be expected ? Is it true that you have to flip the z-component of the Eigen-Vector when processing Philips DTI data ? Thanks in advance ! M. Nelles _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100421/f9e9da29/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: graycol.gif Type: image/gif Size: 105 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100421/f9e9da29/attachment-0003.gif -------------- next part -------------- A non-text attachment was scrubbed... Name: pic14237.gif Type: image/gif Size: 1255 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100421/f9e9da29/attachment-0004.gif -------------- next part -------------- A non-text attachment was scrubbed... Name: ecblank.gif Type: image/gif Size: 45 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100421/f9e9da29/attachment-0005.gif From Malek.Makki at kispi.uzh.ch Thu Apr 22 03:04:50 2010 From: Malek.Makki at kispi.uzh.ch (Makki Malek) Date: Thu, 22 Apr 2010 09:04:50 +0200 Subject: [Mristudio-users] Need help! Message-ID: Dear DTIstudio users I just received a set DT-MRI acquired on a Phillips Achiva 3T with 1b0 + 33 directions. We are not Philips site thus I do not have access to the table gradient directions Can someone email it to me please Regards ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Malek I. Makki, PhD Diagnostic Imaging Department MRI Center Kinderspital Zurich Phone. +41(0)44 266 3130 Fax: +41(0)44 266 7153 malek.makki at kispi.uzh.ch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100422/0076e98d/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: PGP.sig Type: application/pgp-signature Size: 489 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100422/0076e98d/attachment.bin From M.L.Schouw at amc.uva.nl Thu Apr 22 03:36:08 2010 From: M.L.Schouw at amc.uva.nl (M.L.J. Schouw) Date: Thu, 22 Apr 2010 09:36:08 +0200 Subject: [Mristudio-users] Need help! In-Reply-To: References: Message-ID: Hi Malek, DTI-studio has a Philips 32 (the 33rd is the b0) gradient table under 'select predefined gradient table', otherwise, when you open de REC file in notepad or something like that, it gives the gradients in the last couple of information columns. Probably then you will need to flip x with z. Regards, Marieke M.L.J. Schouw, arts-onderzoeker Dept. Radiology, G2-241 Academic Medical Center Meibergdreef 9 1105 AZ Amsterdam the Netherlands Tel: + 31 20 5668323 Fax: + 31 20 5669119 ----- Original Message ----- From: Makki Malek Date: Thursday, April 22, 2010 9:07 am Subject: [Mristudio-users] Need help! To: mristudio-users at mristudio.org > Dear DTIstudio users > > > > I just received a set DT-MRI acquired on a Phillips Achiva 3T with 1b0 > + 33 directions. We are not Philips site thus I do not have access to > the table gradient directions > > > > Can someone email it to me please > > > > Regards > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Malek I. Makki, PhD > > Diagnostic Imaging Department > > MRI Center > > Kinderspital Zurich > > > > Phone. +41(0)44 266 3130 > > Fax: +41(0)44 266 7153 > > malek.makki at kispi.uzh.ch < > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From zamyadim at sri.utoronto.ca Thu Apr 22 11:40:46 2010 From: zamyadim at sri.utoronto.ca (Mojdeh) Date: Thu, 22 Apr 2010 11:40:46 -0400 Subject: [Mristudio-users] pixel rejection Message-ID: <4BD06DFE.2080200@sri.utoronto.ca> Could you please refer me to a paper explaining how the automatic outlier pixel rejection is performed in the new version of DTIstudio? Thanks, Mojdeh Zamyadi From hjiang at jhmi.edu Thu Apr 22 13:58:41 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Thu, 22 Apr 2010 13:58:41 -0400 Subject: [Mristudio-users] pixel rejection In-Reply-To: <4BD06DFE.2080200@sri.utoronto.ca> References: <4BD06DFE.2080200@sri.utoronto.ca> Message-ID: <145933A2BE9E4F48AE079A201379BF2F210B80507A@RAD-EXCH1.win.ad.jhu.edu> Please see the attached abstracts represented in ISMRM, to get some ideas about the outlier rejection method. hangyi ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Mojdeh [zamyadim at sri.utoronto.ca] Sent: Thursday, April 22, 2010 11:40 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] pixel rejection Could you please refer me to a paper explaining how the automatic outlier pixel rejection is performed in the new version of DTIstudio? Thanks, Mojdeh Zamyadi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- A non-text attachment was scrubbed... Name: ISMRM_Proc_01404.pdf Type: application/pdf Size: 123991 bytes Desc: ISMRM_Proc_01404.pdf Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100422/d728d0d0/attachment-0002.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: ISMRM_p1582_2007.pdf Type: application/pdf Size: 113310 bytes Desc: ISMRM_p1582_2007.pdf Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100422/d728d0d0/attachment-0003.pdf From hjiang at jhmi.edu Thu Apr 22 14:24:34 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Thu, 22 Apr 2010 14:24:34 -0400 Subject: [Mristudio-users] pixel rejection In-Reply-To: <4BD06DFE.2080200@sri.utoronto.ca> References: <4BD06DFE.2080200@sri.utoronto.ca> Message-ID: <145933A2BE9E4F48AE079A201379BF2F210B80507C@RAD-EXCH1.win.ad.jhu.edu> please see the attached for the abstract presented in ISMRM for the basic idea about outlier rejection. hangyi ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Mojdeh [zamyadim at sri.utoronto.ca] Sent: Thursday, April 22, 2010 11:40 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] pixel rejection Could you please refer me to a paper explaining how the automatic outlier pixel rejection is performed in the new version of DTIstudio? Thanks, Mojdeh Zamyadi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- A non-text attachment was scrubbed... Name: ISMRM_p1582_2007.pdf Type: application/pdf Size: 113310 bytes Desc: ISMRM_p1582_2007.pdf Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100422/e4042efe/attachment-0001.pdf From hjiang at jhmi.edu Thu Apr 22 14:25:37 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Thu, 22 Apr 2010 14:25:37 -0400 Subject: [Mristudio-users] pixel rejection In-Reply-To: <4BD06DFE.2080200@sri.utoronto.ca> References: <4BD06DFE.2080200@sri.utoronto.ca> Message-ID: <145933A2BE9E4F48AE079A201379BF2F210B80507D@RAD-EXCH1.win.ad.jhu.edu> here is another one. thanks, hangyi ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Mojdeh [zamyadim at sri.utoronto.ca] Sent: Thursday, April 22, 2010 11:40 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] pixel rejection Could you please refer me to a paper explaining how the automatic outlier pixel rejection is performed in the new version of DTIstudio? Thanks, Mojdeh Zamyadi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- A non-text attachment was scrubbed... Name: ISMRM_p1404_2009.pdf Type: application/pdf Size: 123991 bytes Desc: ISMRM_p1404_2009.pdf Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100422/9031b929/attachment-0001.pdf From Michael.Nelles at ukb.uni-bonn.de Fri Apr 23 02:26:14 2010 From: Michael.Nelles at ukb.uni-bonn.de (Michael.Nelles at ukb.uni-bonn.de) Date: Fri, 23 Apr 2010 08:26:14 +0200 Subject: [Mristudio-users] Display fibers in FA color coding Message-ID: Hi, is it somehow possible to display fibers in FA color coding (i.e., whole selected fiber is displayed in the cFA color convention) ? [sometimes useful to detect erroneous fibers] thanks in advance, Michael ------------------------------------------------------------------------------- Michael Nelles, MD Dept. of Radiology / Neuroradiology University of Bonn Medical Center Sigmund Freud Str. 25, D - 53105 Bonn, Germany Phone: (+49) 228 287 16389 Fax: (+49) 228 287 14321 Email: michael.nelles at ukb.uni-bonn.de -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100423/04093d66/attachment.html From susumu at mri.jhu.edu Fri Apr 23 06:47:27 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 23 Apr 2010 06:47:27 -0400 Subject: [Mristudio-users] Display fibers in FA color coding In-Reply-To: References: Message-ID: Hi Mike, Sorry, but DtiStudio can't do it. Susumu On Fri, Apr 23, 2010 at 2:26 AM, wrote: > Hi, > > is it somehow possible to display fibers in FA color coding (i.e., whole > selected fiber is displayed in the cFA color convention) ? > [sometimes useful to detect erroneous fibers] > > thanks in advance, > > Michael > > > ------------------------------------------------------------------------------- > Michael Nelles, MD > Dept. of Radiology / Neuroradiology > University of Bonn Medical Center > Sigmund Freud Str. 25, > D - 53105 Bonn, Germany > Phone: (+49) 228 287 16389 > Fax: (+49) 228 287 14321 > Email: michael.nelles at ukb.uni-bonn.de > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100423/45ed143e/attachment.html From blue.year at msa.hinet.net Mon Apr 26 14:37:30 2010 From: blue.year at msa.hinet.net (Syu-JyunPeng) Date: Tue, 27 Apr 2010 02:37:30 +0800 (CST) Subject: [Mristudio-users] DTI question Message-ID: <1074955848.1272307050763.JavaMail.nobody@sg2000-ap-1> An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100427/9f4522ee/attachment.html From choisj70 at gmail.com Mon Apr 26 22:37:15 2010 From: choisj70 at gmail.com (Seongjin) Date: Mon, 26 Apr 2010 22:37:15 -0400 Subject: [Mristudio-users] Reference for AIR in DTI Studio Message-ID: Using a fixed noise level, I tried two reference images for AIR. This was done only for intra-individual registration not for spatial normalization. Because I did not want to wash out individual difference. 1. b=0 image 2. aDWI (generated using DTI studio, average of all raw DWIs) Test results for some data sets, AIR results from 2 visually appeared to be better, i.e. less motion. Is there any better suggestion for reference image for AIR in DTI studio? -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100426/4044a884/attachment.html From drajaygarg at gmail.com Tue Apr 27 00:40:23 2010 From: drajaygarg at gmail.com (Ajay Garg) Date: Tue, 27 Apr 2010 10:10:23 +0530 Subject: [Mristudio-users] Gradient Table Message-ID: Dear All, I am looking for gradient table for Philips Achieve MR System. I had acquired high resolution DT images (32-directions, 2mm iso). Thanks , Ajay -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100427/3139f9cb/attachment.html From cwber at 126.com Tue Apr 27 01:19:02 2010 From: cwber at 126.com (cwber) Date: Tue, 27 Apr 2010 13:19:02 +0800 (CST) Subject: [Mristudio-users] Gradient Table In-Reply-To: References: Message-ID: Dear Ajay, You can get the gradient table from the web http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html best wishes! -- weber ?2010-04-27 12:40:23?"Ajay Garg" ??? Dear All, I am looking for gradient table for Philips Achieve MR System. I had acquired high resolution DT images (32-directions, 2mm iso). Thanks , Ajay -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100427/5284de6d/attachment.html From drajaygarg at gmail.com Tue Apr 27 01:38:25 2010 From: drajaygarg at gmail.com (Ajay Garg) Date: Tue, 27 Apr 2010 11:08:25 +0530 Subject: [Mristudio-users] Gradient Table In-Reply-To: References: Message-ID: Dear Weber, Thanks. Ajay 2010/4/27 cwber > Dear Ajay, > You can get the gradient table from the web > http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html > best wishes! > -- > weber > > ?2010-04-27 12:40:23?"Ajay Garg" ??? > > Dear All, > > I am looking for gradient table for Philips Achieve MR System. I had > acquired high resolution DT images (32-directions, 2mm iso). > Thanks , > > Ajay > > > > ------------------------------ > ?????????????200??????? > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100427/a82238cf/attachment-0001.html From susumu at mri.jhu.edu Tue Apr 27 09:35:30 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 27 Apr 2010 09:35:30 -0400 Subject: [Mristudio-users] Reference for AIR in DTI Studio In-Reply-To: References: Message-ID: Cross-contrast image registration is always difficult. This applies for regular intra-data DTI image registration in which DWIs are registered to b0. If you have aDWI, the contrasts between two images will be much closer and co-registration may work better, but in theory, you can not correct the eddy current for which b0 is used as the non-distorted reference, although modern scanners should not have much eddy current distortion anymore. Another issue you need to worry is that aDWI may contain motion-caused mis-registration in it. Then aDWI may not be a good reference. If you haven't read DtiStudioUpdate.doc in https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2, please study it, although it doesn't completely answer your question. On Mon, Apr 26, 2010 at 10:37 PM, [Seongjin] wrote: > Using a fixed noise level, I tried two reference images for AIR. > This was done only for intra-individual registration not for spatial > normalization. > Because I did not want to wash out individual difference. > > 1. b=0 image > > 2. aDWI (generated using DTI studio, average of all raw DWIs) > > Test results for some data sets, AIR results from 2 visually appeared to be > better, i.e. less motion. > > Is there any better suggestion for reference image for AIR in DTI studio? > > -SC > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100427/b9221383/attachment.html From choisj70 at gmail.com Tue Apr 27 12:51:17 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 27 Apr 2010 12:51:17 -0400 Subject: [Mristudio-users] Reference for AIR in DTI Studio In-Reply-To: References: Message-ID: Thanks for your reply to my question. -SC On Tue, Apr 27, 2010 at 9:35 AM, susumu mori wrote: > Cross-contrast image registration is always difficult. This applies for > regular intra-data DTI image registration in which DWIs are registered to > b0. If you have aDWI, the contrasts between two images will be much closer > and co-registration may work better, but in theory, you can not correct the > eddy current for which b0 is used as the non-distorted reference, although > modern scanners should not have much eddy current distortion anymore. > > Another issue you need to worry is that aDWI may contain motion-caused > mis-registration in it. Then aDWI may not be a good reference. > > If you haven't read DtiStudioUpdate.doc in > https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2, please study it, > although it doesn't completely answer your question. > > On Mon, Apr 26, 2010 at 10:37 PM, [Seongjin] wrote: > >> Using a fixed noise level, I tried two reference images for AIR. >> This was done only for intra-individual registration not for spatial >> normalization. >> Because I did not want to wash out individual difference. >> >> 1. b=0 image >> >> 2. aDWI (generated using DTI studio, average of all raw DWIs) >> >> Test results for some data sets, AIR results from 2 visually appeared to >> be better, i.e. less motion. >> >> Is there any better suggestion for reference image for AIR in DTI studio? >> >> -SC >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100427/1ef8570d/attachment.html From wgh0805 at 126.com Thu Apr 29 01:45:35 2010 From: wgh0805 at 126.com (wgh0805) Date: Thu, 29 Apr 2010 13:45:35 +0800 (CST) Subject: [Mristudio-users] Gradient Table Message-ID: <139777b.4b37.12848194708.Coremail.wgh0805@126.com> Dear all: I have the data of Siemens DICOM ,but I can not find the gradient table for it. How can I find it? Thanks , Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100429/0f4b681b/attachment.html From khua1 at jhu.edu Thu Apr 29 06:27:27 2010 From: khua1 at jhu.edu (HUA KEGANG) Date: Thu, 29 Apr 2010 10:27:27 +0000 Subject: [Mristudio-users] Gradient Table In-Reply-To: <139777b.4b37.12848194708.Coremail.wgh0805@126.com> References: <139777b.4b37.12848194708.Coremail.wgh0805@126.com> Message-ID: I found the tag (0019,100e) has the gradient direction info for Siemens Mosiac DICOM file. You can try if it works for your data. Thanks? Date: Thu, 29 Apr 2010 13:45:35 +0800 From: wgh0805 at 126.com Subject: [Mristudio-users] Gradient Table To: mristudio-users at mristudio.org Dear all: I have the data of Siemens DICOM ,but I can not find the gradient table for it. How can I find it? Thanks , Mark ????????????????????? _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100429/e43a5f76/attachment.html From susumu at mri.jhu.edu Thu Apr 22 15:36:44 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 22 Apr 2010 15:36:44 -0400 Subject: [Mristudio-users] pixel rejection In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F210B80507D@RAD-EXCH1.win.ad.jhu.edu> References: <4BD06DFE.2080200@sri.utoronto.ca> <145933A2BE9E4F48AE079A201379BF2F210B80507D@RAD-EXCH1.win.ad.jhu.edu> Message-ID: Hi all, If you used "image-based" rejection, in which rejection takes place in a image-by-image base, the abstracts Hangyi sent is the one you want to refer. If you use "pixel-based", please refer to the attached one which will be an abstract of up coming ISMRM. Thanks, Susumu On Thu, Apr 22, 2010 at 2:25 PM, Hangyi Jiang wrote: > here is another one. > > thanks, > > hangyi > > > > ________________________________________ > From: mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of Mojdeh [ > zamyadim at sri.utoronto.ca] > Sent: Thursday, April 22, 2010 11:40 AM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] pixel rejection > > Could you please refer me to a paper explaining how the automatic > outlier pixel rejection is performed in the new version of DTIstudio? > > Thanks, > Mojdeh Zamyadi > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100422/d11e6eb8/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: YueISMRM2010abstract.pdf Type: application/pdf Size: 144911 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100422/d11e6eb8/attachment-0001.pdf From susumu at mri.jhu.edu Thu Apr 29 08:17:28 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 29 Apr 2010 08:17:28 -0400 Subject: [Mristudio-users] Gradient Table In-Reply-To: <139777b.4b37.12848194708.Coremail.wgh0805@126.com> References: <139777b.4b37.12848194708.Coremail.wgh0805@126.com> Message-ID: Hi Mark, If you are using the standard Siemens 12-orientation scheme or other pre-defined tables available in the scanner, we have a file that contains all tables. It seems that Siemens Mosaic/Dicom contains some gradient orientation information, but we still haven't completely figured out how to use them. There are several important points you need to know. 1) Here is the usual 12 orientations in DtiStudio format (you can cut&paste); 0: 0, 0, 0 1: 1.000000, 0.414250, -0.414250 2: 1.000000, -0.414250, -0.414250 3: 1.000000, -0.414250, 0.414250 4: 1.000000, 0.414250, 0.414250 5: 0.414250, 0.414250, 1.000000 6: 0.414250, 1.000000, 0.414250 7: 0.414250, 1.000000, -0.414250 8: 0.414250, 0.414250, -1.000000 9: 0.414250, -0.414250, -1.000000 10: 0.414250, -1.000000, -0.414250 11: 0.414250, -1.000000, 0.414250 12: 0.414250, -0.414250, 1.000000 2) Some old operating system uses different types of the tables. So the current table may not work. If you find a problem with the above table, please let us know. 3) If you are using another pre-defined table, please refer to the attached file. This lists all the tables in VB13 (and after, I believe). You need to convert the format to DtiStudio format. If you look at the 20-orientation scheme in the file, you can find that I converted the Siemens format to the DtiStudio format. 4) Unless you are using VB15, the gradient table needs to be recalculated when you use oblique-plane imaging. VB15 does it automatically and you don't have to worry. With older operating systems, you need to click "Rotate Gradient if Applicable" checkbox in the initial parameter input window of DtiStudio. Susumu 2010/4/29 wgh0805 > Dear all: > > I have the data of *Siemens DICOM* ,but I can not find the gradient > table for it. How can I find it? > Thanks , > > Mark > > > > ------------------------------ > ????????????????????? > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100429/a8d48cdd/attachment-0001.html -------------- next part -------------- case 1: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = PRS ; switch (cFlag) { case 'P': setVector (0, 1.0, 0, 0) ; break ; case 'R': setVector (0, 0, 1.0, 0) ; break ; case 'S': setVector (0, 0, 0, 1.0) ; break ; default: if ( ! isContextPrepForBinarySearch || (m_lDebugLevel & DEBUG_RETURN) ) TRACE_PUT2 (TC_INFO, TF_SEQ, "%s ERROR: Invalid control flag '%c' in sequence code.", ptModule, cFlag) ; return false ; } break ; case 3: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; switch (cFlag) { case 'O': m_eCoordinateSystem = PRS ; setVector (0, 1.0, 0, 0) ; setVector (1, 0, 1.0, 0) ; setVector (2, 0, 0, 1.0) ; break ; case 'T': m_eCoordinateSystem = XYZ ; setVector (0, 1.0, 1.0, -0.5) ; setVector (1, 1.0, -0.5, 1.0) ; setVector (2, -0.5, 1.0, 1.0) ; break ; default: if ( ! isContextPrepForBinarySearch || (m_lDebugLevel & DEBUG_RETURN) ) TRACE_PUT2 (TC_INFO, TF_SEQ, "%s ERROR: Invalid control flag '%c' in sequence code.", ptModule, cFlag) ; return false ; } break ; case 6: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // (Note: do not modify the following comments - doxygen greps for them) // vector set for 6 directions (normalised to maximum) setVector (0, 1.0, 0.0, 1.0) ; setVector (1, -1.0, 0.0, 1.0) ; setVector (2, 0.0, 1.0, 1.0) ; setVector (3, 0.0, 1.0, -1.0) ; setVector (4, 1.0, 1.0, 0.0) ; setVector (5, -1.0, 1.0, 0.0) ; break ; case 10: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 10 directions (normalised to maximum) setVector (0, 0.000000, 0.809017, 0.618034 ) ; setVector (1, 0.000000, 0.190983, 1.000000 ) ; setVector (2, -0.587785, 0.809017, 0.190983 ) ; setVector (3, -0.951057, 0.190983, 0.309017 ) ; setVector (4, -0.363271, 0.809017, -0.500000 ) ; setVector (5, -0.587785, 0.190983, -0.809017 ) ; setVector (6, 0.363271, 0.809017, -0.500000 ) ; setVector (7, 0.587785, 0.190983, -0.809017 ) ; setVector (8, 0.587785, 0.809017, 0.190983 ) ; setVector (9, 0.951057, 0.190983, 0.309017 ) ; break ; case 12: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 12 directions (normalised to maximum) setVector (0, 1.000000, 0.414250, -0.414250 ); setVector (1, 1.000000, -0.414250, -0.414250 ); setVector (2, 1.000000, -0.414250, 0.414250 ); setVector (3, 1.000000, 0.414250, 0.414250 ); setVector (4, 0.414250, 0.414250, 1.000000 ); setVector (5, 0.414250, 1.000000, 0.414250 ); setVector (6, 0.414250, 1.000000, -0.414250 ); setVector (7, 0.414250, 0.414250, -1.000000 ); setVector (8, 0.414250, -0.414250, -1.000000 ); setVector (9, 0.414250, -1.000000, -0.414250 ); setVector (10, 0.414250, -1.000000, 0.414250 ); setVector (11, 0.414250, -0.414250, 1.000000 ); break ; case 20: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 20 directions (normalised to maximum) setVector (0, 1.000000, 0.000000, 0.000000) ; setVector (1, 0.000000, 1.000000, 0.000000) ; setVector (2, -0.031984, 0.799591, 0.599693) ; setVector (3, 0.856706, 0.493831, -0.148949) ; setVector (4, 0.834429, 0.309159, 0.456234) ; setVector (5, 0.834429, -0.309159, 0.456234) ; setVector (6, 0.856706, -0.493831, -0.148949) ; setVector (7, 0.822228, 0.000000, -0.569158) ; setVector (8, 0.550834, 0.425872, -0.717784) ; setVector (9, 0.468173, 0.834308, -0.291108) ; setVector (10, 0.515933, 0.808894, 0.281963) ; setVector (11, 0.391890, 0.515855, 0.761785) ; setVector (12, 0.478151, 0.000000, 0.878278) ; setVector (13, 0.391890, -0.515855, 0.761785) ; setVector (14, 0.515933, -0.808894, 0.281963) ; setVector (15, 0.468173, -0.834308, -0.291108) ; setVector (16, 0.550834, -0.425872, -0.717784) ; setVector (17, 0.111012, -0.264029, -0.958105) ; setVector (18, 0.111012, 0.264029, -0.958105) ; setVector (19, 0.031984, 0.799591, -0.599693) ; break ; 0: 0, 0, 0 1: 1.000000, 0.000000, 0.000000; 2: 0.000000, 1.000000, 0.000000; 3: -0.031984, 0.799591, 0.599693; 4: 0.856706, 0.493831, -0.148949; 5: 0.834429, 0.309159, 0.456234; 6: 0.834429, -0.309159, 0.456234; 7: 0.856706, -0.493831, -0.148949; 8: 0.822228, 0.000000, -0.569158; 9: 0.550834, 0.425872, -0.717784 ; 10: 0.468173, 0.834308, -0.291108 ; 11: 0.515933, 0.808894, 0.281963 ; 12: 0.391890, 0.515855, 0.761785 ; 13: 0.478151, 0.000000, 0.878278 ; 14: 0.391890, -0.515855, 0.761785 ; 15: 0.515933, -0.808894, 0.281963 ; 16: 0.468173, -0.834308, -0.291108 ; 17: 0.550834, -0.425872, -0.717784 ; 18: 0.111012, -0.264029, -0.958105 ; 19: 0.111012, 0.264029, -0.958105 ; 20: 0.031984, 0.799591, -0.599693 ; case 30: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 30 directions (normalised to maximum) setVector (0, -0.208098, 0.525514, 0.850005 ) ; setVector (1, 0.202387, 0.526131, 0.851002 ) ; setVector (2, 0.409956, 0.175267, 0.918257 ) ; setVector (3, -0.412630, 0.742620, 0.565889 ) ; setVector (4, -0.207127, 0.959492, 0.280092 ) ; setVector (5, -0.872713, 0.525505, 0.064764 ) ; setVector (6, -0.746815, 0.526129, 0.455449 ) ; setVector (7, -0.415238, 0.175473, 0.915841 ) ; setVector (8, -0.746636, 0.175268, 0.673642 ) ; setVector (9, -0.665701, 0.742619, -0.217574 ) ; setVector (10, -0.330391, 0.959489, -0.110458 ) ; setVector (11, -0.331275, 0.525513, -0.809983 ) ; setVector (12, -0.663936, 0.526130, -0.569521 ) ; setVector (13, -0.999332, 0.175474, -0.111904 ) ; setVector (14, -0.871398, 0.175267, -0.501922 ) ; setVector (15, 0.001214, 0.742616, -0.700356 ) ; setVector (16, 0.002949, 0.959483, -0.348370 ) ; setVector (17, 0.667975, 0.525509, -0.565356 ) ; setVector (18, 0.336490, 0.526126, -0.807431 ) ; setVector (19, 0.202383, -0.175470, 0.985002 ) ; setVector (20, 0.208094, 0.175265, -0.983848 ) ; setVector (21, 0.666452, 0.742619, -0.215262 ) ; setVector (22, 0.332212, 0.959489, -0.104850 ) ; setVector (23, 0.205064, 0.958364, 0.285421 ) ; setVector (24, 0.412630, 0.742620, 0.565889 ) ; setVector (25, 0.746093, 0.175315, 0.674232 ) ; setVector (26, 0.744110, 0.525505, 0.460568 ) ; setVector (27, 0.871894, 0.526125, 0.070507 ) ; setVector (28, 0.874264, 0.175471, -0.496841 ) ; setVector (29, 1.000000, 0.175267, -0.106112 ) ; break ; case 64: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 64 directions (normalised to maximum) setVector (0, 1.000000, 0.000000, 0.000000); setVector (1, 0.000000, 1.000000, 0.000000); setVector (2, -0.026007, 0.649170, 0.760199); setVector (3, 0.591136, -0.766176, 0.252058); setVector (4, -0.236071, -0.524158, 0.818247); setVector (5, -0.893021, -0.259006, 0.368008); setVector (6, 0.796184, 0.129030, 0.591137); setVector (7, 0.233964, 0.929855, 0.283956); setVector (8, 0.935686, 0.139953, 0.323891); setVector (9, 0.505827, -0.844710, -0.174940); setVector (10, 0.346220, -0.847539, -0.402256); setVector (11, 0.456968, -0.630956, -0.626956); setVector (12, -0.486997, -0.388997, 0.781995); setVector (13, -0.617845, 0.672831, 0.406898); setVector (14, -0.576984, -0.104997, -0.809978); setVector (15, -0.826695, -0.520808, 0.212921); setVector (16, 0.893712, -0.039987, -0.446856); setVector (17, 0.290101, -0.541189, -0.789276); setVector (18, 0.115951, -0.962591, -0.244896); setVector (19, -0.800182, 0.403092, -0.444101); setVector (20, 0.513981, 0.839970, 0.173994); setVector (21, -0.788548, 0.152912, -0.595659); setVector (22, 0.949280, -0.233069, 0.211062); setVector (23, 0.232964, 0.782880, 0.576911); setVector (24, -0.020999, -0.187990, -0.981946); setVector (25, 0.216932, -0.955701, 0.198938); setVector (26, 0.774003, -0.604002, 0.190001); setVector (27, -0.160928, 0.355840, 0.920587); setVector (28, -0.147035, 0.731173, -0.666158); setVector (29, 0.888141, 0.417066, 0.193031); setVector (30, -0.561971, 0.231988, -0.793959); setVector (31, -0.380809, 0.142928, 0.913541); setVector (32, -0.306000, -0.199000, -0.931001); setVector (33, -0.332086, -0.130034, 0.934243); setVector (34, -0.963226, -0.265062, 0.044010); setVector (35, -0.959501, 0.205107, 0.193101); setVector (36, 0.452965, -0.888932, 0.067995); setVector (37, -0.773133, 0.628108, 0.088015); setVector (38, 0.709082, 0.408047, 0.575066); setVector (39, -0.692769, 0.023992, 0.720760); setVector (40, 0.681659, 0.528735, -0.505747); setVector (41, -0.141995, -0.724976, 0.673978); setVector (42, -0.740168, 0.388088, 0.549125); setVector (43, -0.103006, 0.822044, 0.560030); setVector (44, 0.584037, -0.596038, 0.551035); setVector (45, -0.088008, -0.335031, 0.938088); setVector (46, -0.552263, -0.792377, 0.259123); setVector (47, 0.838158, -0.458086, -0.296056); setVector (48, 0.362995, -0.560993, 0.743990); setVector (49, -0.184062, 0.392133, -0.901306); setVector (50, -0.720938, -0.692941, 0.008999); setVector (51, 0.433101, 0.682159, -0.589137); setVector (52, 0.502114, 0.690157, 0.521119); setVector (53, -0.170944, -0.508833, -0.843722); setVector (54, 0.462968, 0.422971, 0.778946); setVector (55, 0.385030, -0.809064, 0.444035); setVector (56, -0.713102, -0.247035, 0.656094); setVector (57, 0.259923, 0.884737, -0.386885); setVector (58, 0.001000, 0.077002, -0.997030); setVector (59, 0.037002, -0.902057, 0.430027); setVector (60, 0.570320, -0.303170, -0.763428); setVector (61, -0.282105, 0.145054, -0.948354); setVector (62, 0.721098, 0.608082, 0.332045); setVector (63, 0.266985, 0.959945, -0.084995); break ; case 256: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 256 directions (normalised to maximum) setVector (0, 0.059010, -0.013002, 0.998173); setVector (1, 0.070008, 0.157018, 0.985111); setVector (2, -0.078038, 0.083041, 0.993486); setVector (3, -0.092987, -0.086988, 0.991860); setVector (4, 0.046987, -0.178952, 0.982735); setVector (5, 0.199944, -0.108970, 0.973729); setVector (6, 0.211021, 0.052005, 0.976097); setVector (7, 0.210999, 0.212999, 0.953997); setVector (8, -0.050982, 0.250913, 0.966666); setVector (9, -0.208056, 0.186050, 0.960259); setVector (10, -0.355044, 0.120015, 0.927114); setVector (11, -0.225050, 0.016004, 0.974216); setVector (12, -0.239998, -0.156999, 0.957994); setVector (13, -0.107055, -0.253129, 0.961491); setVector (14, 0.031988, -0.337873, 0.940648); setVector (15, 0.191053, -0.268075, 0.944264); setVector (16, 0.333011, -0.202007, 0.921030); setVector (17, 0.350043, -0.034004, 0.936116); setVector (18, 0.353962, 0.131986, 0.925900); setVector (19, 0.321087, 0.303082, 0.897243); setVector (20, 0.124035, 0.337095, 0.933264); setVector (21, -0.028007, 0.395092, 0.918214); setVector (22, -0.189921, 0.343856, 0.919616); setVector (23, -0.340929, 0.281942, 0.896814); setVector (24, -0.483028, 0.214012, 0.849048); setVector (25, -0.492017, 0.052002, 0.869031); setVector (26, -0.364886, -0.049984, 0.929710); setVector (27, -0.376988, -0.226993, 0.897972); setVector (28, -0.251019, -0.327024, 0.911068); setVector (29, -0.116041, -0.415148, 0.902323); setVector (30, 0.027007, -0.490130, 0.871231); setVector (31, 0.176089, -0.413208, 0.893450); setVector (32, 0.323985, -0.380982, 0.865960); setVector (33, 0.451026, -0.272016, 0.850049); setVector (34, 0.477203, -0.106045, 0.872371); setVector (35, 0.487906, 0.059988, 0.870832); setVector (36, 0.468001, 0.231001, 0.853003); setVector (37, 0.426147, 0.394136, 0.814282); setVector (38, 0.266963, 0.442939, 0.855883); setVector (39, 0.120952, 0.485807, 0.865657); setVector (40, -0.024989, 0.534766, 0.844631); setVector (41, -0.176029, 0.491082, 0.853142); setVector (42, -0.323126, 0.437171, 0.839328); setVector (43, -0.463978, 0.371982, 0.803961); setVector (44, -0.613900, 0.139977, 0.776874); setVector (45, -0.617975, -0.018999, 0.785968); setVector (46, -0.493054, -0.117013, 0.862094); setVector (47, -0.503790, -0.292878, 0.812661); setVector (48, -0.383865, -0.394861, 0.834705); setVector (49, -0.253926, -0.486859, 0.835757); setVector (50, -0.113952, -0.565762, 0.816657); setVector (51, 0.037997, -0.625950, 0.778937); setVector (52, 0.182983, -0.543949, 0.818924); setVector (53, 0.328974, -0.543956, 0.771938); setVector (54, 0.446988, -0.437988, 0.779979); setVector (55, 0.565718, -0.320840, 0.759621); setVector (56, 0.595011, -0.163003, 0.787015); setVector (57, 0.611304, -0.002001, 0.791393); setVector (58, 0.600103, 0.163028, 0.783134); setVector (59, 0.568061, 0.325035, 0.756081); setVector (60, 0.512003, 0.482003, 0.711004); setVector (61, 0.362192, 0.543287, 0.757401); setVector (62, 0.211049, 0.594139, 0.776181); setVector (63, 0.058967, 0.640642, 0.765572); setVector (64, -0.119057, 0.637302, 0.761361); setVector (65, -0.274102, 0.590219, 0.759282); setVector (66, -0.421992, 0.527990, 0.736986); setVector (67, -0.560010, 0.454008, 0.693012); setVector (68, -0.598017, 0.298008, 0.744021); setVector (69, -0.730015, 0.044001, 0.682014); setVector (70, -0.718931, -0.123988, 0.683934); setVector (71, -0.607904, -0.181971, 0.772878); setVector (72, -0.643781, -0.311894, 0.698762); setVector (73, -0.524667, -0.433725, 0.732535); setVector (74, -0.395115, -0.537156, 0.745217); setVector (75, -0.255897, -0.624749, 0.737703); setVector (76, -0.106010, -0.694064, 0.712066); setVector (77, 0.051982, -0.740746, 0.669771); setVector (78, 0.198017, -0.665057, 0.720062); setVector (79, 0.338997, -0.682994, 0.646994); setVector (80, 0.455869, -0.583832, 0.671807); setVector (81, 0.567210, -0.477177, 0.671249); setVector (82, 0.670100, -0.360054, 0.649097); setVector (83, 0.704211, -0.210063, 0.678203); setVector (84, 0.723245, -0.057019, 0.688233); setVector (85, 0.720289, 0.101041, 0.686276); setVector (86, 0.696042, 0.258015, 0.670040); setVector (87, 0.650084, 0.411053, 0.639082); setVector (88, 0.582844, 0.557851, 0.590842); setVector (89, 0.441061, 0.629087, 0.640089); setVector (90, 0.292091, 0.685213, 0.667208); setVector (91, 0.136935, 0.732653, 0.666684); setVector (92, -0.035006, 0.744130, 0.667117); setVector (93, -0.207001, 0.724004, 0.658004); setVector (94, -0.361776, 0.671585, 0.646600); setVector (95, -0.506971, 0.602966, 0.615965); setVector (96, -0.641109, 0.517088, 0.567097); setVector (97, -0.690897, 0.366945, 0.622907); setVector (98, -0.718746, 0.206927, 0.663766); setVector (99, -0.821800, 0.110973, 0.558864); setVector (100, -0.820917, -0.048995, 0.568942); setVector (101, -0.787722, -0.210926, 0.578796); setVector (102, -0.733198, -0.353096, 0.581157); setVector (103, -0.632761, -0.470822, 0.614768); setVector (104, -0.516033, -0.577036, 0.633040); setVector (105, -0.386042, -0.669073, 0.635069); setVector (106, -0.244127, -0.745387, 0.620322); setVector (107, -0.092982, -0.802848, 0.588888); setVector (108, 0.061971, -0.837608, 0.542746); setVector (109, 0.207049, -0.774182, 0.598141); setVector (110, 0.355042, -0.784093, 0.509061); setVector (111, 0.480125, -0.691179, 0.540140); setVector (112, 0.596018, -0.585017, 0.550016); setVector (113, 0.703421, -0.465279, 0.537322); setVector (114, 0.781234, -0.304091, 0.545163); setVector (115, 0.812165, -0.145029, 0.565115); setVector (116, 0.821641, 0.016993, 0.569751); setVector (117, 0.808928, 0.175984, 0.560950); setVector (118, 0.774726, 0.330883, 0.538810); setVector (119, 0.718831, 0.477888, 0.504881); setVector (120, 0.642730, 0.615741, 0.455808); setVector (121, 0.509022, 0.697030, 0.505021); setVector (122, 0.366176, 0.758364, 0.539259); setVector (123, 0.213039, 0.808148, 0.549100); setVector (124, 0.045984, 0.830708, 0.554805); setVector (125, -0.123006, 0.826039, 0.550026); setVector (126, -0.288131, 0.793361, 0.536244); setVector (127, -0.439982, 0.734970, 0.515979); setVector (128, -0.579687, 0.658644, 0.479741); setVector (129, -0.705004, 0.567003, 0.426002); setVector (130, -0.764589, 0.424772, 0.484740); setVector (131, -0.800709, 0.269902, 0.534806); setVector (132, -0.892958, 0.161992, 0.419980); setVector (133, -0.900927, 0.002000, 0.433965); setVector (134, -0.879831, -0.158969, 0.447914); setVector (135, -0.833019, -0.319007, 0.452010); setVector (136, -0.747071, -0.470045, 0.470045); setVector (137, -0.637748, -0.587767, 0.497803); setVector (138, -0.513898, -0.689863, 0.509899); setVector (139, -0.377037, -0.775076, 0.507050); setVector (140, -0.230976, -0.842913, 0.485950); setVector (141, -0.081983, -0.889811, 0.448905); setVector (142, 0.074014, -0.912169, 0.403075); setVector (143, 0.219092, -0.860361, 0.460193); setVector (144, 0.362034, -0.861080, 0.357033); setVector (145, 0.490041, -0.778065, 0.393033); setVector (146, 0.608025, -0.678028, 0.413017); setVector (147, 0.718996, -0.558997, 0.412998); setVector (148, 0.810079, -0.408040, 0.421041); setVector (149, 0.870877, -0.239966, 0.428940); setVector (150, 0.894955, -0.073996, 0.439978); setVector (151, 0.896096, 0.088009, 0.435047); setVector (152, 0.874684, 0.243912, 0.418849); setVector (153, 0.831860, 0.391934, 0.392934); 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setVector (238, -0.026001, 0.988038, 0.152006); setVector (239, -0.200088, 0.969424, 0.142062); setVector (240, -0.365992, 0.922979, 0.118997); setVector (241, -0.510695, 0.856488, 0.074955); setVector (242, -0.640958, 0.766950, 0.030998); setVector (243, -0.764977, 0.643980, 0.010000); setVector (244, 0.857996, -0.512998, 0.026000); setVector (245, -0.901024, 0.423011, 0.096003); setVector (246, 0.938499, -0.343182, 0.038020); setVector (247, 0.983769, -0.177958, 0.022995); setVector (248, 0.999898, -0.012999, 0.005999); setVector (249, -0.988633, -0.149944, 0.010996); setVector (250, -0.949788, -0.310931, 0.034992); setVector (251, -0.883406, -0.464213, 0.064029); setVector (252, -0.783923, -0.615940, 0.077992); setVector (253, -0.660104, -0.746118, 0.087014); setVector (254, -0.521822, -0.848711, 0.085971); setVector (255, -0.380935, -0.922844, 0.056990); break ; From naamab at stanford.edu Thu Apr 29 10:07:54 2010 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Thu, 29 Apr 2010 07:07:54 -0700 Subject: [Mristudio-users] Gradient Table In-Reply-To: References: <139777b.4b37.12848194708.Coremail.wgh0805@126.com> Message-ID: We are using VB15. Like Susumu said, the Siemens scanner recalculates the gradient table slightly per each subject, and the revised table is in the header (but it is not obvious). You can get that information from the header using MRIconvert (you still have to edit it to dtistudio format). Naama On Apr 29, 2010, at 5:17 AM, susumu mori wrote: > Hi Mark, > > If you are using the standard Siemens 12-orientation scheme or other > pre-defined tables available in the scanner, we have a file that > contains all tables. It seems that Siemens Mosaic/Dicom contains > some gradient orientation information, but we still haven't > completely figured out how to use them. There are several important > points you need to know. > > 1) Here is the usual 12 orientations in DtiStudio format (you can > cut&paste); > 0: 0, 0, 0 > 1: 1.000000, 0.414250, -0.414250 > 2: 1.000000, -0.414250, -0.414250 > 3: 1.000000, -0.414250, 0.414250 > 4: 1.000000, 0.414250, 0.414250 > 5: 0.414250, 0.414250, 1.000000 > 6: 0.414250, 1.000000, 0.414250 > 7: 0.414250, 1.000000, -0.414250 > 8: 0.414250, 0.414250, -1.000000 > 9: 0.414250, -0.414250, -1.000000 > 10: 0.414250, -1.000000, -0.414250 > 11: 0.414250, -1.000000, 0.414250 > 12: 0.414250, -0.414250, 1.000000 > > 2) Some old operating system uses different types of the tables. So > the current table may not work. If you find a problem with the above > table, please let us know. > > 3) If you are using another pre-defined table, please refer to the > attached file. This lists all the tables in VB13 (and after, I > believe). You need to convert the format to DtiStudio format. If you > look at the 20-orientation scheme in the file, you can find that I > converted the Siemens format to the DtiStudio format. > > 4) Unless you are using VB15, the gradient table needs to be > recalculated when you use oblique-plane imaging. VB15 does it > automatically and you don't have to worry. With older operating > systems, you need to click "Rotate Gradient if Applicable" checkbox > in the initial parameter input window of DtiStudio. > > Susumu > > 2010/4/29 wgh0805 > Dear all: > > I have the data of Siemens DICOM ,but I can not find the gradient > table for it. How can I find it? > Thanks , > > Mark > > > > ????????????????????? > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100429/efad554d/attachment.html From wgh0805 at 126.com Thu Apr 29 11:37:45 2010 From: wgh0805 at 126.com (wgh0805) Date: Thu, 29 Apr 2010 23:37:45 +0800 (CST) Subject: [Mristudio-users] Gradient Table In-Reply-To: References: <139777b.4b37.12848194708.Coremail.wgh0805@126.com> Message-ID: <6daf14.cabd.1284a376b73.Coremail.wgh0805@126.com> Thanks,I will tell the result if I have some progress. ?2010-04-29 22:07:54?"Naama Barnea-Goraly" ??? We are using VB15. Like Susumu said, the Siemens scanner recalculates the gradient table slightly per each subject, and the revised table is in the header (but it is not obvious). You can get that information from the header using MRIconvert (you still have to edit it to dtistudio format). Naama On Apr 29, 2010, at 5:17 AM, susumu mori wrote: Hi Mark, If you are using the standard Siemens 12-orientation scheme or other pre-defined tables available in the scanner, we have a file that contains all tables. It seems that Siemens Mosaic/Dicom contains some gradient orientation information, but we still haven't completely figured out how to use them. There are several important points you need to know. 1) Here is the usual 12 orientations in DtiStudio format (you can cut&paste); 0: 0, 0, 0 1: 1.000000, 0.414250, -0.414250 2: 1.000000, -0.414250, -0.414250 3: 1.000000, -0.414250, 0.414250 4: 1.000000, 0.414250, 0.414250 5: 0.414250, 0.414250, 1.000000 6: 0.414250, 1.000000, 0.414250 7: 0.414250, 1.000000, -0.414250 8: 0.414250, 0.414250, -1.000000 9: 0.414250, -0.414250, -1.000000 10: 0.414250, -1.000000, -0.414250 11: 0.414250, -1.000000, 0.414250 12: 0.414250, -0.414250, 1.000000 2) Some old operating system uses different types of the tables. So the current table may not work. If you find a problem with the above table, please let us know. 3) If you are using another pre-defined table, please refer to the attached file. This lists all the tables in VB13 (and after, I believe). You need to convert the format to DtiStudio format. If you look at the 20-orientation scheme in the file, you can find that I converted the Siemens format to the DtiStudio format. 4) Unless you are using VB15, the gradient table needs to be recalculated when you use oblique-plane imaging. VB15 does it automatically and you don't have to worry. With older operating systems, you need to click "Rotate Gradient if Applicable" checkbox in the initial parameter input window of DtiStudio. Susumu 2010/4/29 wgh0805 Dear all: I have the data of Siemens DICOM ,but I can not find the gradient table for it. How can I find it? Thanks , Mark ????????????????????? _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100429/927f9790/attachment.html From naamab at stanford.edu Fri Apr 30 09:41:32 2010 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Fri, 30 Apr 2010 06:41:32 -0700 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio Message-ID: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> The output from the Siemens scanner are slice dicom images. How do I separate them into individual images like the ones we get from GE? Thanks, Naama From ASHTARI at email.chop.edu Fri Apr 30 09:53:24 2010 From: ASHTARI at email.chop.edu (Ashtari, Manzar) Date: Fri, 30 Apr 2010 09:53:24 -0400 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> Message-ID: This is done as an option on the scanner. You can also perform this after the images are reconstructed. Best, MA ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] Sent: Friday, April 30, 2010 9:41 AM To: DiffeoMap Questions/Support DTI Studio ROI Editor Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio The output from the Siemens scanner are slice dicom images. How do I separate them into individual images like the ones we get from GE? Thanks, Naama _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From naamab at stanford.edu Fri Apr 30 10:16:52 2010 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Fri, 30 Apr 2010 07:16:52 -0700 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> Message-ID: <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> Thank you - is there a way to separate them off the scanner? Thanks, Naama On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: > This is done as an option on the scanner. You can also perform this > after the images are reconstructed. > Best, > > MA > ________________________________________ > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] > Sent: Friday, April 30, 2010 9:41 AM > To: DiffeoMap Questions/Support DTI Studio ROI Editor > Subject: [Mristudio-users] Importing Siemens slice dicom images to > dtistudio > > The output from the Siemens scanner are slice dicom images. How do I > separate them into individual images like the ones we get from GE? > > Thanks, > > Naama > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. From ASHTARI at email.chop.edu Fri Apr 30 10:46:57 2010 From: ASHTARI at email.chop.edu (Ashtari, Manzar) Date: Fri, 30 Apr 2010 10:46:57 -0400 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> Message-ID: Yes you will have a separate series listed along with others. Best, MA ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] Sent: Friday, April 30, 2010 10:16 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to dtistudio Thank you - is there a way to separate them off the scanner? Thanks, Naama On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: > This is done as an option on the scanner. You can also perform this > after the images are reconstructed. > Best, > > MA > ________________________________________ > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] > Sent: Friday, April 30, 2010 9:41 AM > To: DiffeoMap Questions/Support DTI Studio ROI Editor > Subject: [Mristudio-users] Importing Siemens slice dicom images to > dtistudio > > The output from the Siemens scanner are slice dicom images. How do I > separate them into individual images like the ones we get from GE? > > Thanks, > > Naama > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Fri Apr 30 12:25:02 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 30 Apr 2010 12:25:02 -0400 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> Message-ID: Naama, I'm not exactly sure about what you are asking but maybe related to what I experienced in the past? For Siemens, GE, and Philips, I got an impression that you need a research agreement to store DICOM files into separate directories based on imaging type such as T1, T2, DTI. If you run scans and burn a CD for clinical purpose, you find DICOM files all mixed up in 1 or multiple directories with a generic names, from which it is very difficult to sort. These CD usually includes a DICOM viewer and you need to use it for the viewing purpose. So, I would first check if your scanner has an option to save DICOM in separate directories based on the modalities. If not, we wrote a small program to sort out the clinical DICOM files. We don't use this very often and may not work for some type of operating systems, but you can at least give it a try. Please contact Hangyi if you want it. Susumu On Fri, Apr 30, 2010 at 10:46 AM, Ashtari, Manzar wrote: > Yes you will have a separate series listed along with others. > Best, > > MA > ________________________________________ > From: mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly [ > naamab at stanford.edu] > Sent: Friday, April 30, 2010 10:16 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to > dtistudio > > Thank you - is there a way to separate them off the scanner? > > Thanks, > > Naama > > > > On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: > > > This is done as an option on the scanner. You can also perform this > > after the images are reconstructed. > > Best, > > > > MA > > ________________________________________ > > From: mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org > > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] > > Sent: Friday, April 30, 2010 9:41 AM > > To: DiffeoMap Questions/Support DTI Studio ROI Editor > > Subject: [Mristudio-users] Importing Siemens slice dicom images to > > dtistudio > > > > The output from the Siemens scanner are slice dicom images. How do I > > separate them into individual images like the ones we get from GE? > > > > Thanks, > > > > Naama > > > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > Naama Barnea-Goraly M.D. > Instructor > Center for Interdisciplinary Brain Sciences Research > Stanford University Division of Child and Adolescent Psychiatry > 401 Quarry Rd. MC 5795 > Stanford University School of Medicine > Stanford, CA 94305-5795 > Phone: (650) 736-1874, fax: (650) 724-4794 > > > CONFIDENTIALITY NOTICE: This e-mail communication and any attachments > may contain confidential information for the use of the designated > recipients named above. If you are not the intended recipient, you > are hereby notified that you have received this communication in error > and that any review, disclosure, dissemination, distribution or > copying of it or its contents is prohibited. If you have received > this communication in error, please notify Stanford Medical Center > immediately by telephone at (650) 725-5722 and destroy all copies of > this communication and any attachments. Thank you. > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100430/7fa0aa4d/attachment.html From ASHTARI at email.chop.edu Fri Apr 30 14:34:21 2010 From: ASHTARI at email.chop.edu (Ashtari, Manzar) Date: Fri, 30 Apr 2010 14:34:21 -0400 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> Message-ID: I know what Naama is asking for. Siemens images come in mosaic form and she wants to have them none mosaic. I know you can convert them on the scanner but don't know of any program that does it in a lab setting. Best, MA ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: Friday, April 30, 2010 12:25 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to dtistudio Naama, I'm not exactly sure about what you are asking but maybe related to what I experienced in the past? For Siemens, GE, and Philips, I got an impression that you need a research agreement to store DICOM files into separate directories based on imaging type such as T1, T2, DTI. If you run scans and burn a CD for clinical purpose, you find DICOM files all mixed up in 1 or multiple directories with a generic names, from which it is very difficult to sort. These CD usually includes a DICOM viewer and you need to use it for the viewing purpose. So, I would first check if your scanner has an option to save DICOM in separate directories based on the modalities. If not, we wrote a small program to sort out the clinical DICOM files. We don't use this very often and may not work for some type of operating systems, but you can at least give it a try. Please contact Hangyi if you want it. Susumu On Fri, Apr 30, 2010 at 10:46 AM, Ashtari, Manzar > wrote: Yes you will have a separate series listed along with others. Best, MA ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] Sent: Friday, April 30, 2010 10:16 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to dtistudio Thank you - is there a way to separate them off the scanner? Thanks, Naama On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: > This is done as an option on the scanner. You can also perform this > after the images are reconstructed. > Best, > > MA > ________________________________________ > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] > Sent: Friday, April 30, 2010 9:41 AM > To: DiffeoMap Questions/Support DTI Studio ROI Editor > Subject: [Mristudio-users] Importing Siemens slice dicom images to > dtistudio > > The output from the Siemens scanner are slice dicom images. How do I > separate them into individual images like the ones we get from GE? > > Thanks, > > Naama > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100430/d62d33be/attachment-0001.html From susumu at mri.jhu.edu Fri Apr 30 14:37:51 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 30 Apr 2010 14:37:51 -0400 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> Message-ID: Oh I see. I'm not sure why Naama wants it.... On Fri, Apr 30, 2010 at 2:34 PM, Ashtari, Manzar wrote: > I know what Naama is asking for. Siemens images come in mosaic form and > she wants to have them none mosaic. I know you can convert them on the > scanner but don't know of any program that does it in a lab setting. > > > Best, > > MA > * > > * > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ > susumu at mri.jhu.edu] > *Sent:* Friday, April 30, 2010 12:25 PM > *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang > *Subject:* Re: [Mristudio-users] Importing Siemens slice dicom images to > dtistudio > > Naama, > > I'm not exactly sure about what you are asking but maybe related to what I > experienced in the past? > > For Siemens, GE, and Philips, I got an impression that you need a research > agreement to store DICOM files into separate directories based on imaging > type such as T1, T2, DTI. If you run scans and burn a CD for clinical > purpose, you find DICOM files all mixed up in 1 or multiple directories with > a generic names, from which it is very difficult to sort. These CD usually > includes a DICOM viewer and you need to use it for the viewing purpose. > > So, I would first check if your scanner has an option to save DICOM in > separate directories based on the modalities. If not, we wrote a small > program to sort out the clinical DICOM files. We don't use this very often > and may not work for some type of operating systems, but you can at least > give it a try. Please contact Hangyi if you want it. > > Susumu > > > On Fri, Apr 30, 2010 at 10:46 AM, Ashtari, Manzar wrote: > >> Yes you will have a separate series listed along with others. >> Best, >> >> MA >> ________________________________________ >> From: mristudio-users-bounces at mristudio.org [ >> mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly [ >> naamab at stanford.edu] >> Sent: Friday, April 30, 2010 10:16 AM >> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >> Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to >> dtistudio >> >> Thank you - is there a way to separate them off the scanner? >> >> Thanks, >> >> Naama >> >> >> >> On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: >> >> > This is done as an option on the scanner. You can also perform this >> > after the images are reconstructed. >> > Best, >> > >> > MA >> > ________________________________________ >> > From: mristudio-users-bounces at mristudio.org [ >> mristudio-users-bounces at mristudio.org >> > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] >> > Sent: Friday, April 30, 2010 9:41 AM >> > To: DiffeoMap Questions/Support DTI Studio ROI Editor >> > Subject: [Mristudio-users] Importing Siemens slice dicom images to >> > dtistudio >> > >> > The output from the Siemens scanner are slice dicom images. How do I >> > separate them into individual images like the ones we get from GE? >> > >> > Thanks, >> > >> > Naama >> > >> > >> > >> > >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> Naama Barnea-Goraly M.D. >> Instructor >> Center for Interdisciplinary Brain Sciences Research >> Stanford University Division of Child and Adolescent Psychiatry >> 401 Quarry Rd. MC 5795 >> Stanford University School of Medicine >> Stanford, CA 94305-5795 >> Phone: (650) 736-1874, fax: (650) 724-4794 >> >> >> CONFIDENTIALITY NOTICE: This e-mail communication and any attachments >> may contain confidential information for the use of the designated >> recipients named above. If you are not the intended recipient, you >> are hereby notified that you have received this communication in error >> and that any review, disclosure, dissemination, distribution or >> copying of it or its contents is prohibited. If you have received >> this communication in error, please notify Stanford Medical Center >> immediately by telephone at (650) 725-5722 and destroy all copies of >> this communication and any attachments. Thank you. >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100430/d09b0399/attachment.html From naamab at stanford.edu Fri Apr 30 15:23:26 2010 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Fri, 30 Apr 2010 12:23:26 -0700 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> Message-ID: <69FA5B5C-A93D-4C9F-BEEC-3E9104F48A32@stanford.edu> Manzar is right, I would like to see the images individually - like the GE output. Susumu's reply makes me think I am missing something. Right now I can only look at a whole slice so I can't compare the different repetitions, also in the image window I can only see the whole slice in axial view (2D). Anyway I can view this scan differently? Thanks, Naama On Apr 30, 2010, at 11:37 AM, susumu mori wrote: > Oh I see. I'm not sure why Naama wants it.... > > On Fri, Apr 30, 2010 at 2:34 PM, Ashtari, Manzar > wrote: > I know what Naama is asking for. Siemens images come in mosaic form > and she wants to have them none mosaic. I know you can convert them > on the scanner but don't know of any program that does it in a lab > setting. > > > Best, > > MA > > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org > ] On Behalf Of susumu mori [susumu at mri.jhu.edu] > Sent: Friday, April 30, 2010 12:25 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang > Subject: Re: [Mristudio-users] Importing Siemens slice dicom images > to dtistudio > > Naama, > > I'm not exactly sure about what you are asking but maybe related to > what I experienced in the past? > > For Siemens, GE, and Philips, I got an impression that you need a > research agreement to store DICOM files into separate directories > based on imaging type such as T1, T2, DTI. If you run scans and burn > a CD for clinical purpose, you find DICOM files all mixed up in 1 or > multiple directories with a generic names, from which it is very > difficult to sort. These CD usually includes a DICOM viewer and you > need to use it for the viewing purpose. > > So, I would first check if your scanner has an option to save DICOM > in separate directories based on the modalities. If not, we wrote a > small program to sort out the clinical DICOM files. We don't use > this very often and may not work for some type of operating systems, > but you can at least give it a try. Please contact Hangyi if you > want it. > > Susumu > > > On Fri, Apr 30, 2010 at 10:46 AM, Ashtari, Manzar > wrote: > Yes you will have a separate series listed along with others. > Best, > > MA > ________________________________________ > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] > Sent: Friday, April 30, 2010 10:16 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] Importing Siemens slice dicom images > to dtistudio > > Thank you - is there a way to separate them off the scanner? > > Thanks, > > Naama > > > > On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: > > > This is done as an option on the scanner. You can also perform this > > after the images are reconstructed. > > Best, > > > > MA > > ________________________________________ > > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org > > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] > > Sent: Friday, April 30, 2010 9:41 AM > > To: DiffeoMap Questions/Support DTI Studio ROI Editor > > Subject: [Mristudio-users] Importing Siemens slice dicom images to > > dtistudio > > > > The output from the Siemens scanner are slice dicom images. How do I > > separate them into individual images like the ones we get from GE? > > > > Thanks, > > > > Naama > > > > > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > Naama Barnea-Goraly M.D. > Instructor > Center for Interdisciplinary Brain Sciences Research > Stanford University Division of Child and Adolescent Psychiatry > 401 Quarry Rd. MC 5795 > Stanford University School of Medicine > Stanford, CA 94305-5795 > Phone: (650) 736-1874, fax: (650) 724-4794 > > > CONFIDENTIALITY NOTICE: This e-mail communication and any attachments > may contain confidential information for the use of the designated > recipients named above. If you are not the intended recipient, you > are hereby notified that you have received this communication in error > and that any review, disclosure, dissemination, distribution or > copying of it or its contents is prohibited. If you have received > this communication in error, please notify Stanford Medical Center > immediately by telephone at (650) 725-5722 and destroy all copies of > this communication and any attachments. Thank you. > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100430/5bd5bcf7/attachment-0001.html From susumu at mri.jhu.edu Fri Apr 30 15:29:12 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 30 Apr 2010 15:29:12 -0400 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: <69FA5B5C-A93D-4C9F-BEEC-3E9104F48A32@stanford.edu> References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> <69FA5B5C-A93D-4C9F-BEEC-3E9104F48A32@stanford.edu> Message-ID: Hmmmm, reading the Mosaic into DtiStudio let you see individual images. You can save them as separate raw or Analyze files. If you want DICOM, I thought there was a way. Hangyi, I thought there was a DICOM save option? On Fri, Apr 30, 2010 at 3:23 PM, Naama Barnea-Goraly wrote: > > Manzar is right, I would like to see the images individually - like the GE > output. Susumu's reply makes me think I am missing something. Right now I > can only look at a whole slice so I can't compare the different repetitions, > also in the image window I can only see the whole slice in axial view (2D). > Anyway I can view this scan differently? > > Thanks, > > Naama > > > > > > > > On Apr 30, 2010, at 11:37 AM, susumu mori wrote: > > Oh I see. I'm not sure why Naama wants it.... > > On Fri, Apr 30, 2010 at 2:34 PM, Ashtari, Manzar wrote: > >> I know what Naama is asking for. Siemens images come in mosaic form >> and she wants to have them none mosaic. I know you can convert them on the >> scanner but don't know of any program that does it in a lab setting. >> >> >> Best, >> >> MA >> * >> >> * >> ------------------------------ >> *From:* mristudio-users-bounces at mristudio.org [ >> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ >> susumu at mri.jhu.edu] >> *Sent:* Friday, April 30, 2010 12:25 PM >> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang >> *Subject:* Re: [Mristudio-users] Importing Siemens slice dicom images to >> dtistudio >> >> Naama, >> >> I'm not exactly sure about what you are asking but maybe related to what I >> experienced in the past? >> >> For Siemens, GE, and Philips, I got an impression that you need a research >> agreement to store DICOM files into separate directories based on imaging >> type such as T1, T2, DTI. If you run scans and burn a CD for clinical >> purpose, you find DICOM files all mixed up in 1 or multiple directories with >> a generic names, from which it is very difficult to sort. These CD usually >> includes a DICOM viewer and you need to use it for the viewing purpose. >> >> So, I would first check if your scanner has an option to save DICOM in >> separate directories based on the modalities. If not, we wrote a small >> program to sort out the clinical DICOM files. We don't use this very often >> and may not work for some type of operating systems, but you can at least >> give it a try. Please contact Hangyi if you want it. >> >> Susumu >> >> >> On Fri, Apr 30, 2010 at 10:46 AM, Ashtari, Manzar > > wrote: >> >>> Yes you will have a separate series listed along with others. >>> Best, >>> >>> MA >>> ________________________________________ >>> From: mristudio-users-bounces at mristudio.org [ >>> mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly >>> [naamab at stanford.edu] >>> Sent: Friday, April 30, 2010 10:16 AM >>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >>> Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to >>> dtistudio >>> >>> Thank you - is there a way to separate them off the scanner? >>> >>> Thanks, >>> >>> Naama >>> >>> >>> >>> On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: >>> >>> > This is done as an option on the scanner. You can also perform this >>> > after the images are reconstructed. >>> > Best, >>> > >>> > MA >>> > ________________________________________ >>> > From: mristudio-users-bounces at mristudio.org [ >>> mristudio-users-bounces at mristudio.org >>> > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] >>> > Sent: Friday, April 30, 2010 9:41 AM >>> > To: DiffeoMap Questions/Support DTI Studio ROI Editor >>> > Subject: [Mristudio-users] Importing Siemens slice dicom images to >>> > dtistudio >>> > >>> > The output from the Siemens scanner are slice dicom images. How do I >>> > separate them into individual images like the ones we get from GE? >>> > >>> > Thanks, >>> > >>> > Naama >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > Mristudio-users mailing list >>> > Mristudio-users at mristudio.org >>> > http://lists.mristudio.org/mailman/listinfo/ >>> > Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> > _______________________________________________ >>> > Mristudio-users mailing list >>> > Mristudio-users at mristudio.org >>> > http://lists.mristudio.org/mailman/listinfo/ >>> > Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> Naama Barnea-Goraly M.D. >>> Instructor >>> Center for Interdisciplinary Brain Sciences Research >>> Stanford University Division of Child and Adolescent Psychiatry >>> 401 Quarry Rd. MC 5795 >>> Stanford University School of Medicine >>> Stanford, CA 94305-5795 >>> Phone: (650) 736-1874, fax: (650) 724-4794 >>> >>> >>> CONFIDENTIALITY NOTICE: This e-mail communication and any attachments >>> may contain confidential information for the use of the designated >>> recipients named above. If you are not the intended recipient, you >>> are hereby notified that you have received this communication in error >>> and that any review, disclosure, dissemination, distribution or >>> copying of it or its contents is prohibited. If you have received >>> this communication in error, please notify Stanford Medical Center >>> immediately by telephone at (650) 725-5722 and destroy all copies of >>> this communication and any attachments. Thank you. >>> >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > Naama Barnea-Goraly M.D. > Instructor > Center for Interdisciplinary Brain Sciences Research > Stanford University Division of Child and Adolescent Psychiatry > 401 Quarry Rd. MC 5795 > Stanford University School of Medicine > Stanford, CA 94305-5795 > Phone: (650) 736-1874, fax: (650) 724-4794 > > > CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may > contain confidential information for the use of the designated recipients > named above. If you are not the intended recipient, you are hereby notified > that you have received this communication in error and that any review, > disclosure, dissemination, distribution or copying of it or its contents is > prohibited. If you have received this communication in error, please notify > Stanford Medical Center immediately by telephone at (650) 725-5722 and > destroy all copies of this communication and any attachments. Thank you. > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100430/f2f9a168/attachment.html From ASHTARI at email.chop.edu Fri Apr 30 15:31:02 2010 From: ASHTARI at email.chop.edu (Ashtari, Manzar) Date: Fri, 30 Apr 2010 15:31:02 -0400 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> <69FA5B5C-A93D-4C9F-BEEC-3E9104F48A32@stanford.edu> Message-ID: There is no problem reading the siemens mosaic dicom images into the DTIStudio. Naama may want the individual images for something else. Or she may have gotten the images on a CD and exactly what you said had happened and she does not know what happened to the rest of the images. Best, MA ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: Friday, April 30, 2010 3:29 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to dtistudio Hmmmm, reading the Mosaic into DtiStudio let you see individual images. You can save them as separate raw or Analyze files. If you want DICOM, I thought there was a way. Hangyi, I thought there was a DICOM save option? On Fri, Apr 30, 2010 at 3:23 PM, Naama Barnea-Goraly > wrote: Manzar is right, I would like to see the images individually - like the GE output. Susumu's reply makes me think I am missing something. Right now I can only look at a whole slice so I can't compare the different repetitions, also in the image window I can only see the whole slice in axial view (2D). Anyway I can view this scan differently? Thanks, Naama On Apr 30, 2010, at 11:37 AM, susumu mori wrote: Oh I see. I'm not sure why Naama wants it.... On Fri, Apr 30, 2010 at 2:34 PM, Ashtari, Manzar > wrote: I know what Naama is asking for. Siemens images come in mosaic form and she wants to have them none mosaic. I know you can convert them on the scanner but don't know of any program that does it in a lab setting. Best, MA ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: Friday, April 30, 2010 12:25 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to dtistudio Naama, I'm not exactly sure about what you are asking but maybe related to what I experienced in the past? For Siemens, GE, and Philips, I got an impression that you need a research agreement to store DICOM files into separate directories based on imaging type such as T1, T2, DTI. If you run scans and burn a CD for clinical purpose, you find DICOM files all mixed up in 1 or multiple directories with a generic names, from which it is very difficult to sort. These CD usually includes a DICOM viewer and you need to use it for the viewing purpose. So, I would first check if your scanner has an option to save DICOM in separate directories based on the modalities. If not, we wrote a small program to sort out the clinical DICOM files. We don't use this very often and may not work for some type of operating systems, but you can at least give it a try. Please contact Hangyi if you want it. Susumu On Fri, Apr 30, 2010 at 10:46 AM, Ashtari, Manzar > wrote: Yes you will have a separate series listed along with others. Best, MA ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] Sent: Friday, April 30, 2010 10:16 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to dtistudio Thank you - is there a way to separate them off the scanner? Thanks, Naama On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: > This is done as an option on the scanner. You can also perform this > after the images are reconstructed. > Best, > > MA > ________________________________________ > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] > Sent: Friday, April 30, 2010 9:41 AM > To: DiffeoMap Questions/Support DTI Studio ROI Editor > Subject: [Mristudio-users] Importing Siemens slice dicom images to > dtistudio > > The output from the Siemens scanner are slice dicom images. How do I > separate them into individual images like the ones we get from GE? > > Thanks, > > Naama > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100430/2de720cd/attachment-0001.html From pieter.vandemaele at ugent.be Fri Apr 30 17:03:54 2010 From: pieter.vandemaele at ugent.be (Pieter Vandemaele) Date: Fri, 30 Apr 2010 23:03:54 +0200 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> <69FA5B5C-A93D-4C9F-BEEC-3E9104F48A32@stanford.edu> Message-ID: <9C1BAAC8-406D-48BC-BF35-22A1AA534CB2@ugent.be> You can use the free software MRIConvert (http://lcni.uoregon.edu/~jolinda/MRIConvert/) or XMedCon (http://xmedcon.sourceforge.net/) to do file conversion/splitting. Best Pieter Op 30-apr-2010, om 21:31 heeft Ashtari, Manzar het volgende geschreven: > There is no problem reading the siemens mosaic dicom images into the DTIStudio. Naama may want the individual images for something else. Or she may have gotten the images on a CD and exactly what you said had happened and she does not know what happened to the rest of the images. > Best, > > MA > > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] > Sent: Friday, April 30, 2010 3:29 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang > Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to dtistudio > > Hmmmm, reading the Mosaic into DtiStudio let you see individual images. You can save them as separate raw or Analyze files. If you want DICOM, I thought there was a way. Hangyi, I thought there was a DICOM save option? > > On Fri, Apr 30, 2010 at 3:23 PM, Naama Barnea-Goraly wrote: > > Manzar is right, I would like to see the images individually - like the GE output. Susumu's reply makes me think I am missing something. Right now I can only look at a whole slice so I can't compare the different repetitions, also in the image window I can only see the whole slice in axial view (2D). Anyway I can view this scan differently? > > Thanks, > > Naama > > > > > > > > On Apr 30, 2010, at 11:37 AM, susumu mori wrote: > >> Oh I see. I'm not sure why Naama wants it.... >> >> On Fri, Apr 30, 2010 at 2:34 PM, Ashtari, Manzar wrote: >> I know what Naama is asking for. Siemens images come in mosaic form and she wants to have them none mosaic. I know you can convert them on the scanner but don't know of any program that does it in a lab setting. >> >> >> Best, >> >> MA >> >> From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] >> Sent: Friday, April 30, 2010 12:25 PM >> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang >> Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to dtistudio >> >> Naama, >> >> I'm not exactly sure about what you are asking but maybe related to what I experienced in the past? >> >> For Siemens, GE, and Philips, I got an impression that you need a research agreement to store DICOM files into separate directories based on imaging type such as T1, T2, DTI. If you run scans and burn a CD for clinical purpose, you find DICOM files all mixed up in 1 or multiple directories with a generic names, from which it is very difficult to sort. These CD usually includes a DICOM viewer and you need to use it for the viewing purpose. >> >> So, I would first check if your scanner has an option to save DICOM in separate directories based on the modalities. If not, we wrote a small program to sort out the clinical DICOM files. We don't use this very often and may not work for some type of operating systems, but you can at least give it a try. Please contact Hangyi if you want it. >> >> Susumu >> >> >> On Fri, Apr 30, 2010 at 10:46 AM, Ashtari, Manzar wrote: >> Yes you will have a separate series listed along with others. >> Best, >> >> MA >> ________________________________________ >> From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] >> Sent: Friday, April 30, 2010 10:16 AM >> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >> Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to dtistudio >> >> Thank you - is there a way to separate them off the scanner? >> >> Thanks, >> >> Naama >> >> >> >> On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: >> >> > This is done as an option on the scanner. You can also perform this >> > after the images are reconstructed. >> > Best, >> > >> > MA >> > ________________________________________ >> > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org >> > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] >> > Sent: Friday, April 30, 2010 9:41 AM >> > To: DiffeoMap Questions/Support DTI Studio ROI Editor >> > Subject: [Mristudio-users] Importing Siemens slice dicom images to >> > dtistudio >> > >> > The output from the Siemens scanner are slice dicom images. How do I >> > separate them into individual images like the ones we get from GE? >> > >> > Thanks, >> > >> > Naama >> > >> > >> > >> > >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> >> Naama Barnea-Goraly M.D. >> Instructor >> Center for Interdisciplinary Brain Sciences Research >> Stanford University Division of Child and Adolescent Psychiatry >> 401 Quarry Rd. MC 5795 >> Stanford University School of Medicine >> Stanford, CA 94305-5795 >> Phone: (650) 736-1874, fax: (650) 724-4794 >> >> >> CONFIDENTIALITY NOTICE: This e-mail communication and any attachments >> may contain confidential information for the use of the designated >> recipients named above. If you are not the intended recipient, you >> are hereby notified that you have received this communication in error >> and that any review, disclosure, dissemination, distribution or >> copying of it or its contents is prohibited. If you have received >> this communication in error, please notify Stanford Medical Center >> immediately by telephone at (650) 725-5722 and destroy all copies of >> this communication and any attachments. Thank you. >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > Naama Barnea-Goraly M.D. > Instructor > Center for Interdisciplinary Brain Sciences Research > Stanford University Division of Child and Adolescent Psychiatry > 401 Quarry Rd. MC 5795 > Stanford University School of Medicine > Stanford, CA 94305-5795 > Phone: (650) 736-1874, fax: (650) 724-4794 > > > CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100430/00ad9202/attachment.html From mithra at mail.utexas.edu Fri Apr 30 17:15:24 2010 From: mithra at mail.utexas.edu (Mithra) Date: Fri, 30 Apr 2010 16:15:24 -0500 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: <9C1BAAC8-406D-48BC-BF35-22A1AA534CB2@ugent.be> References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> <69FA5B5C-A93D-4C9F-BEEC-3E9104F48A32@stanford.edu> <9C1BAAC8-406D-48BC-BF35-22A1AA534CB2@ugent.be> Message-ID: Hello, I have a similar issue. I have DTI data collected long ago from a Siemens Trio scanner. The raw data is in '.dat' format. Is there a way to convert the files into dicoms or Nifti files? Thank you for your help. Regards, Mithra. On Fri, Apr 30, 2010 at 4:03 PM, Pieter Vandemaele < pieter.vandemaele at ugent.be> wrote: > You can use the free software MRIConvert ( > http://lcni.uoregon.edu/~jolinda/MRIConvert/) > or XMedCon (http://xmedcon.sourceforge.net/) to do file > conversion/splitting. > > Best > > Pieter > > Op 30-apr-2010, om 21:31 heeft Ashtari, Manzar het volgende geschreven: > > There is no problem reading the siemens mosaic dicom images into the > DTIStudio. Naama may want the individual images for something else. Or > she may have gotten the images on a CD and exactly what you said had > happened and she does not know what happened to the rest of the images. > Best, > > MA > * > > * > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ > susumu at mri.jhu.edu] > *Sent:* Friday, April 30, 2010 3:29 PM > *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang > *Subject:* Re: [Mristudio-users] Importing Siemens slice dicom images to > dtistudio > > Hmmmm, reading the Mosaic into DtiStudio let you see individual images. You > can save them as separate raw or Analyze files. If you want DICOM, I thought > there was a way. Hangyi, I thought there was a DICOM save option? > > On Fri, Apr 30, 2010 at 3:23 PM, Naama Barnea-Goraly > wrote: > >> >> Manzar is right, I would like to see the images individually - like the GE >> output. Susumu's reply makes me think I am missing something. Right now I >> can only look at a whole slice so I can't compare the different repetitions, >> also in the image window I can only see the whole slice in axial view (2D). >> Anyway I can view this scan differently? >> >> Thanks, >> >> Naama >> >> >> >> >> >> >> >> On Apr 30, 2010, at 11:37 AM, susumu mori wrote: >> >> Oh I see. I'm not sure why Naama wants it.... >> >> On Fri, Apr 30, 2010 at 2:34 PM, Ashtari, Manzar >> wrote: >> >>> I know what Naama is asking for. Siemens images come in mosaic form and >>> she wants to have them none mosaic. I know you can convert them on the >>> scanner but don't know of any program that does it in a lab setting. >>> >>> >>> Best, >>> >>> MA >>> * >>> >>> * >>> ------------------------------ >>> *From:* mristudio-users-bounces at mristudio.org [ >>> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ >>> susumu at mri.jhu.edu] >>> *Sent:* Friday, April 30, 2010 12:25 PM >>> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang >>> *Subject:* Re: [Mristudio-users] Importing Siemens slice dicom images to >>> dtistudio >>> >>> Naama, >>> >>> I'm not exactly sure about what you are asking but maybe related to what >>> I experienced in the past? >>> >>> For Siemens, GE, and Philips, I got an impression that you need a >>> research agreement to store DICOM files into separate directories based on >>> imaging type such as T1, T2, DTI. If you run scans and burn a CD for >>> clinical purpose, you find DICOM files all mixed up in 1 or multiple >>> directories with a generic names, from which it is very difficult to sort. >>> These CD usually includes a DICOM viewer and you need to use it for the >>> viewing purpose. >>> >>> So, I would first check if your scanner has an option to save DICOM in >>> separate directories based on the modalities. If not, we wrote a small >>> program to sort out the clinical DICOM files. We don't use this very often >>> and may not work for some type of operating systems, but you can at least >>> give it a try. Please contact Hangyi if you want it. >>> >>> Susumu >>> >>> >>> On Fri, Apr 30, 2010 at 10:46 AM, Ashtari, Manzar < >>> ASHTARI at email.chop.edu> wrote: >>> >>>> Yes you will have a separate series listed along with others. >>>> Best, >>>> >>>> MA >>>> ________________________________________ >>>> From: mristudio-users-bounces at mristudio.org [ >>>> mristudio-users-bounces at mristudio.org] On Behalf Of Naama Barnea-Goraly >>>> [naamab at stanford.edu] >>>> Sent: Friday, April 30, 2010 10:16 AM >>>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >>>> Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to >>>> dtistudio >>>> >>>> Thank you - is there a way to separate them off the scanner? >>>> >>>> Thanks, >>>> >>>> Naama >>>> >>>> >>>> >>>> On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: >>>> >>>> > This is done as an option on the scanner. You can also perform this >>>> > after the images are reconstructed. >>>> > Best, >>>> > >>>> > MA >>>> > ________________________________________ >>>> > From: mristudio-users-bounces at mristudio.org [ >>>> mristudio-users-bounces at mristudio.org >>>> > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] >>>> > Sent: Friday, April 30, 2010 9:41 AM >>>> > To: DiffeoMap Questions/Support DTI Studio ROI Editor >>>> > Subject: [Mristudio-users] Importing Siemens slice dicom images to >>>> > dtistudio >>>> > >>>> > The output from the Siemens scanner are slice dicom images. How do I >>>> > separate them into individual images like the ones we get from GE? >>>> > >>>> > Thanks, >>>> > >>>> > Naama >>>> > >>>> > >>>> > >>>> > >>>> > _______________________________________________ >>>> > Mristudio-users mailing list >>>> > Mristudio-users at mristudio.org >>>> > http://lists.mristudio.org/mailman/listinfo/ >>>> > Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> > _______________________________________________ >>>> > Mristudio-users mailing list >>>> > Mristudio-users at mristudio.org >>>> > http://lists.mristudio.org/mailman/listinfo/ >>>> > Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> Naama Barnea-Goraly M.D. >>>> Instructor >>>> Center for Interdisciplinary Brain Sciences Research >>>> Stanford University Division of Child and Adolescent Psychiatry >>>> 401 Quarry Rd. MC 5795 >>>> Stanford University School of Medicine >>>> Stanford, CA 94305-5795 >>>> Phone: (650) 736-1874, fax: (650) 724-4794 >>>> >>>> >>>> CONFIDENTIALITY NOTICE: This e-mail communication and any attachments >>>> may contain confidential information for the use of the designated >>>> recipients named above. If you are not the intended recipient, you >>>> are hereby notified that you have received this communication in error >>>> and that any review, disclosure, dissemination, distribution or >>>> copying of it or its contents is prohibited. If you have received >>>> this communication in error, please notify Stanford Medical Center >>>> immediately by telephone at (650) 725-5722 and destroy all copies of >>>> this communication and any attachments. Thank you. >>>> >>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> >> Naama Barnea-Goraly M.D. >> Instructor >> Center for Interdisciplinary Brain Sciences Research >> Stanford University Division of Child and Adolescent Psychiatry >> 401 Quarry Rd. MC 5795 >> Stanford University School of Medicine >> Stanford, CA 94305-5795 >> Phone: (650) 736-1874, fax: (650) 724-4794 >> >> >> CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may >> contain confidential information for the use of the designated recipients >> named above. If you are not the intended recipient, you are hereby notified >> that you have received this communication in error and that any review, >> disclosure, dissemination, distribution or copying of it or its contents is >> prohibited. If you have received this communication in error, please notify >> Stanford Medical Center immediately by telephone at (650) 725-5722 and >> destroy all copies of this communication and any attachments. Thank you. >> >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100430/0efa21e3/attachment-0001.html From sophie.lafaille at gmail.com Fri Apr 30 17:44:42 2010 From: sophie.lafaille at gmail.com (Sophie Lafaille) Date: Fri, 30 Apr 2010 17:44:42 -0400 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> <69FA5B5C-A93D-4C9F-BEEC-3E9104F48A32@stanford.edu> <9C1BAAC8-406D-48BC-BF35-22A1AA534CB2@ugent.be> Message-ID: try SPM, it's the only program that allows me to convert my *.MR images from a 3T GE scanner. it's called dicom import. sophie also, maybe try Mango? http://ric.uthscsa.edu/mango/ On 30 April 2010 17:15, Mithra wrote: > Hello, > I have a similar issue. I have DTI data collected long ago from a Siemens > Trio scanner. The raw data is in '.dat' format. Is there a way to convert > the files into dicoms or Nifti files? > > > Thank you for your help. > > Regards, > Mithra. > > On Fri, Apr 30, 2010 at 4:03 PM, Pieter Vandemaele < > pieter.vandemaele at ugent.be> wrote: > >> You can use the free software MRIConvert ( >> http://lcni.uoregon.edu/~jolinda/MRIConvert/) >> or XMedCon (http://xmedcon.sourceforge.net/) to do file >> conversion/splitting. >> >> Best >> >> Pieter >> >> Op 30-apr-2010, om 21:31 heeft Ashtari, Manzar het volgende geschreven: >> >> There is no problem reading the siemens mosaic dicom images into the >> DTIStudio. Naama may want the individual images for something else. Or >> she may have gotten the images on a CD and exactly what you said had >> happened and she does not know what happened to the rest of the images. >> Best, >> >> MA >> * >> >> * >> ------------------------------ >> *From:* mristudio-users-bounces at mristudio.org [ >> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ >> susumu at mri.jhu.edu] >> *Sent:* Friday, April 30, 2010 3:29 PM >> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang >> *Subject:* Re: [Mristudio-users] Importing Siemens slice dicom images to >> dtistudio >> >> Hmmmm, reading the Mosaic into DtiStudio let you see individual images. >> You can save them as separate raw or Analyze files. If you want DICOM, I >> thought there was a way. Hangyi, I thought there was a DICOM save option? >> >> On Fri, Apr 30, 2010 at 3:23 PM, Naama Barnea-Goraly > > wrote: >> >>> >>> Manzar is right, I would like to see the images individually - like the >>> GE output. Susumu's reply makes me think I am missing something. Right now I >>> can only look at a whole slice so I can't compare the different repetitions, >>> also in the image window I can only see the whole slice in axial view (2D). >>> Anyway I can view this scan differently? >>> >>> Thanks, >>> >>> Naama >>> >>> >>> >>> >>> >>> >>> >>> On Apr 30, 2010, at 11:37 AM, susumu mori wrote: >>> >>> Oh I see. I'm not sure why Naama wants it.... >>> >>> On Fri, Apr 30, 2010 at 2:34 PM, Ashtari, Manzar >> > wrote: >>> >>>> I know what Naama is asking for. Siemens images come in mosaic form >>>> and she wants to have them none mosaic. I know you can convert them on the >>>> scanner but don't know of any program that does it in a lab setting. >>>> >>>> >>>> Best, >>>> >>>> MA >>>> * >>>> >>>> * >>>> ------------------------------ >>>> *From:* mristudio-users-bounces at mristudio.org [ >>>> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ >>>> susumu at mri.jhu.edu] >>>> *Sent:* Friday, April 30, 2010 12:25 PM >>>> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang >>>> *Subject:* Re: [Mristudio-users] Importing Siemens slice dicom images >>>> to dtistudio >>>> >>>> Naama, >>>> >>>> I'm not exactly sure about what you are asking but maybe related to what >>>> I experienced in the past? >>>> >>>> For Siemens, GE, and Philips, I got an impression that you need a >>>> research agreement to store DICOM files into separate directories based on >>>> imaging type such as T1, T2, DTI. If you run scans and burn a CD for >>>> clinical purpose, you find DICOM files all mixed up in 1 or multiple >>>> directories with a generic names, from which it is very difficult to sort. >>>> These CD usually includes a DICOM viewer and you need to use it for the >>>> viewing purpose. >>>> >>>> So, I would first check if your scanner has an option to save DICOM in >>>> separate directories based on the modalities. If not, we wrote a small >>>> program to sort out the clinical DICOM files. We don't use this very often >>>> and may not work for some type of operating systems, but you can at least >>>> give it a try. Please contact Hangyi if you want it. >>>> >>>> Susumu >>>> >>>> >>>> On Fri, Apr 30, 2010 at 10:46 AM, Ashtari, Manzar < >>>> ASHTARI at email.chop.edu> wrote: >>>> >>>>> Yes you will have a separate series listed along with others. >>>>> Best, >>>>> >>>>> MA >>>>> ________________________________________ >>>>> From: mristudio-users-bounces at mristudio.org [ >>>>> mristudio-users-bounces at mristudio.org] On Behalf Of Naama >>>>> Barnea-Goraly [naamab at stanford.edu] >>>>> Sent: Friday, April 30, 2010 10:16 AM >>>>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >>>>> Subject: Re: [Mristudio-users] Importing Siemens slice dicom images to >>>>> dtistudio >>>>> >>>>> Thank you - is there a way to separate them off the scanner? >>>>> >>>>> Thanks, >>>>> >>>>> Naama >>>>> >>>>> >>>>> >>>>> On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: >>>>> >>>>> > This is done as an option on the scanner. You can also perform this >>>>> > after the images are reconstructed. >>>>> > Best, >>>>> > >>>>> > MA >>>>> > ________________________________________ >>>>> > From: mristudio-users-bounces at mristudio.org [ >>>>> mristudio-users-bounces at mristudio.org >>>>> > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] >>>>> > Sent: Friday, April 30, 2010 9:41 AM >>>>> > To: DiffeoMap Questions/Support DTI Studio ROI Editor >>>>> > Subject: [Mristudio-users] Importing Siemens slice dicom images to >>>>> > dtistudio >>>>> > >>>>> > The output from the Siemens scanner are slice dicom images. How do I >>>>> > separate them into individual images like the ones we get from GE? >>>>> > >>>>> > Thanks, >>>>> > >>>>> > Naama >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > Mristudio-users mailing list >>>>> > Mristudio-users at mristudio.org >>>>> > http://lists.mristudio.org/mailman/listinfo/ >>>>> > Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> > _______________________________________________ >>>>> > Mristudio-users mailing list >>>>> > Mristudio-users at mristudio.org >>>>> > http://lists.mristudio.org/mailman/listinfo/ >>>>> > Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>>> Naama Barnea-Goraly M.D. >>>>> Instructor >>>>> Center for Interdisciplinary Brain Sciences Research >>>>> Stanford University Division of Child and Adolescent Psychiatry >>>>> 401 Quarry Rd. MC 5795 >>>>> Stanford University School of Medicine >>>>> Stanford, CA 94305-5795 >>>>> Phone: (650) 736-1874, fax: (650) 724-4794 >>>>> >>>>> >>>>> CONFIDENTIALITY NOTICE: This e-mail communication and any attachments >>>>> may contain confidential information for the use of the designated >>>>> recipients named above. If you are not the intended recipient, you >>>>> are hereby notified that you have received this communication in error >>>>> and that any review, disclosure, dissemination, distribution or >>>>> copying of it or its contents is prohibited. If you have received >>>>> this communication in error, please notify Stanford Medical Center >>>>> immediately by telephone at (650) 725-5722 and destroy all copies of >>>>> this communication and any attachments. Thank you. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> _______________________________________________ >>>>> Mristudio-users mailing list >>>>> Mristudio-users at mristudio.org >>>>> http://lists.mristudio.org/mailman/listinfo/ >>>>> Unsubscribe, send a blank email to: >>>>> Mristudio-users-unsubscribe at mristudio.org >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >>> Naama Barnea-Goraly M.D. >>> Instructor >>> Center for Interdisciplinary Brain Sciences Research >>> Stanford University Division of Child and Adolescent Psychiatry >>> 401 Quarry Rd. MC 5795 >>> Stanford University School of Medicine >>> Stanford, CA 94305-5795 >>> Phone: (650) 736-1874, fax: (650) 724-4794 >>> >>> >>> CONFIDENTIALITY NOTICE: This e-mail communication and any attachments >>> may contain confidential information for the use of the designated >>> recipients named above. If you are not the intended recipient, you are >>> hereby notified that you have received this communication in error and that >>> any review, disclosure, dissemination, distribution or copying of it or its >>> contents is prohibited. If you have received this communication in error, >>> please notify Stanford Medical Center immediately by telephone at (650) >>> 725-5722 and destroy all copies of this communication and any attachments. >>> Thank you. >>> >>> >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100430/b4a69c11/attachment.html From naamab at stanford.edu Fri Apr 30 18:28:02 2010 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Fri, 30 Apr 2010 15:28:02 -0700 Subject: [Mristudio-users] Importing Siemens slice dicom images to dtistudio In-Reply-To: References: <657B6A6C-855C-4E73-B40D-4AD375A083D4@stanford.edu> <7253149A-2639-411D-898B-2F78B0FCB2CF@stanford.edu> <69FA5B5C-A93D-4C9F-BEEC-3E9104F48A32@stanford.edu> <9C1BAAC8-406D-48BC-BF35-22A1AA534CB2@ugent.be> Message-ID: <6123FC7C-3F06-4BEA-B01C-D47870D123E5@stanford.edu> We had a similar issue with GE data and used Osirix to extract the files we needed (it is not the issue I currently have with Siemens data). On Apr 30, 2010, at 2:15 PM, Mithra wrote: > Hello, > I have a similar issue. I have DTI data collected long ago from a > Siemens Trio scanner. The raw data is in '.dat' format. Is there a > way to convert the files into dicoms or Nifti files? > > > Thank you for your help. > > Regards, > Mithra. > > On Fri, Apr 30, 2010 at 4:03 PM, Pieter Vandemaele > wrote: > You can use the free software MRIConvert (http://lcni.uoregon.edu/~jolinda/MRIConvert/ > ) or XMedCon (http://xmedcon.sourceforge.net/) to do file conversion/ > splitting. > > Best > > Pieter > > Op 30-apr-2010, om 21:31 heeft Ashtari, Manzar het volgende > geschreven: > >> There is no problem reading the siemens mosaic dicom images into >> the DTIStudio. Naama may want the individual images for something >> else. Or she may have gotten the images on a CD and exactly what >> you said had happened and she does not know what happened to the >> rest of the images. >> Best, >> >> MA >> >> From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org >> ] On Behalf Of susumu mori [susumu at mri.jhu.edu] >> Sent: Friday, April 30, 2010 3:29 PM >> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang >> Subject: Re: [Mristudio-users] Importing Siemens slice dicom images >> to dtistudio >> >> Hmmmm, reading the Mosaic into DtiStudio let you see individual >> images. You can save them as separate raw or Analyze files. If you >> want DICOM, I thought there was a way. Hangyi, I thought there was >> a DICOM save option? >> >> On Fri, Apr 30, 2010 at 3:23 PM, Naama Barnea-Goraly > > wrote: >> >> Manzar is right, I would like to see the images individually - like >> the GE output. Susumu's reply makes me think I am missing >> something. Right now I can only look at a whole slice so I can't >> compare the different repetitions, also in the image window I can >> only see the whole slice in axial view (2D). Anyway I can view this >> scan differently? >> >> Thanks, >> >> Naama >> >> >> >> >> >> >> >> On Apr 30, 2010, at 11:37 AM, susumu mori wrote: >> >>> Oh I see. I'm not sure why Naama wants it.... >>> >>> On Fri, Apr 30, 2010 at 2:34 PM, Ashtari, Manzar >> > wrote: >>> I know what Naama is asking for. Siemens images come in mosaic >>> form and she wants to have them none mosaic. I know you can >>> convert them on the scanner but don't know of any program that >>> does it in a lab setting. >>> >>> >>> Best, >>> >>> MA >>> >>> From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org >>> ] On Behalf Of susumu mori [susumu at mri.jhu.edu] >>> Sent: Friday, April 30, 2010 12:25 PM >>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi >>> Jiang >>> Subject: Re: [Mristudio-users] Importing Siemens slice dicom >>> images to dtistudio >>> >>> Naama, >>> >>> I'm not exactly sure about what you are asking but maybe related >>> to what I experienced in the past? >>> >>> For Siemens, GE, and Philips, I got an impression that you need a >>> research agreement to store DICOM files into separate directories >>> based on imaging type such as T1, T2, DTI. If you run scans and >>> burn a CD for clinical purpose, you find DICOM files all mixed up >>> in 1 or multiple directories with a generic names, from which it >>> is very difficult to sort. These CD usually includes a DICOM >>> viewer and you need to use it for the viewing purpose. >>> >>> So, I would first check if your scanner has an option to save >>> DICOM in separate directories based on the modalities. If not, we >>> wrote a small program to sort out the clinical DICOM files. We >>> don't use this very often and may not work for some type of >>> operating systems, but you can at least give it a try. Please >>> contact Hangyi if you want it. >>> >>> Susumu >>> >>> >>> On Fri, Apr 30, 2010 at 10:46 AM, Ashtari, Manzar >> > wrote: >>> Yes you will have a separate series listed along with others. >>> Best, >>> >>> MA >>> ________________________________________ >>> From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org >>> ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] >>> Sent: Friday, April 30, 2010 10:16 AM >>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >>> Subject: Re: [Mristudio-users] Importing Siemens slice dicom >>> images to dtistudio >>> >>> Thank you - is there a way to separate them off the scanner? >>> >>> Thanks, >>> >>> Naama >>> >>> >>> >>> On Apr 30, 2010, at 6:53 AM, Ashtari, Manzar wrote: >>> >>> > This is done as an option on the scanner. You can also perform >>> this >>> > after the images are reconstructed. >>> > Best, >>> > >>> > MA >>> > ________________________________________ >>> > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org >>> > ] On Behalf Of Naama Barnea-Goraly [naamab at stanford.edu] >>> > Sent: Friday, April 30, 2010 9:41 AM >>> > To: DiffeoMap Questions/Support DTI Studio ROI Editor >>> > Subject: [Mristudio-users] Importing Siemens slice dicom images to >>> > dtistudio >>> > >>> > The output from the Siemens scanner are slice dicom images. How >>> do I >>> > separate them into individual images like the ones we get from GE? >>> > >>> > Thanks, >>> > >>> > Naama >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > Mristudio-users mailing list >>> > Mristudio-users at mristudio.org >>> > http://lists.mristudio.org/mailman/listinfo/ >>> > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>> > _______________________________________________ >>> > Mristudio-users mailing list >>> > Mristudio-users at mristudio.org >>> > http://lists.mristudio.org/mailman/listinfo/ >>> > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>> >>> Naama Barnea-Goraly M.D. >>> Instructor >>> Center for Interdisciplinary Brain Sciences Research >>> Stanford University Division of Child and Adolescent Psychiatry >>> 401 Quarry Rd. MC 5795 >>> Stanford University School of Medicine >>> Stanford, CA 94305-5795 >>> Phone: (650) 736-1874, fax: (650) 724-4794 >>> >>> >>> CONFIDENTIALITY NOTICE: This e-mail communication and any >>> attachments >>> may contain confidential information for the use of the designated >>> recipients named above. If you are not the intended recipient, you >>> are hereby notified that you have received this communication in >>> error >>> and that any review, disclosure, dissemination, distribution or >>> copying of it or its contents is prohibited. If you have received >>> this communication in error, please notify Stanford Medical Center >>> immediately by telephone at (650) 725-5722 and destroy all copies of >>> this communication and any attachments. Thank you. >>> >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> >> Naama Barnea-Goraly M.D. >> Instructor >> Center for Interdisciplinary Brain Sciences Research >> Stanford University Division of Child and Adolescent Psychiatry >> 401 Quarry Rd. MC 5795 >> Stanford University School of Medicine >> Stanford, CA 94305-5795 >> Phone: (650) 736-1874, fax: (650) 724-4794 >> >> >> CONFIDENTIALITY NOTICE: This e-mail communication and any >> attachments may contain confidential information for the use of the >> designated recipients named above. If you are not the intended >> recipient, you are hereby notified that you have received this >> communication in error and that any review, disclosure, >> dissemination, distribution or copying of it or its contents is >> prohibited. If you have received this communication in error, >> please notify Stanford Medical Center immediately by telephone at >> (650) 725-5722 and destroy all copies of this communication and any >> attachments. Thank you. >> >> >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100430/d2635f28/attachment-0001.html From castilla at terra.com.br Thu May 6 09:46:18 2010 From: castilla at terra.com.br (Andre Coutinho Castilla) Date: Thu, 06 May 2010 10:46:18 -0300 Subject: [Mristudio-users] General Electric 25 directions gradient table Message-ID: Hello I am a newcommer to DTI. I am having problems on obtaining the gradient table of my examinations. Could someone provide me this table? I am using a GE 1,5T echospeed, 4 channel head coil and 25 directions. Thanks in advance Andre Castilla MD, PhD Sao Paulo Brazil -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100506/820add8b/attachment.html From wayne009007 at 126.com Thu May 6 10:04:58 2010 From: wayne009007 at 126.com (wayne_netease) Date: Thu, 06 May 2010 22:04:58 +0800 Subject: [Mristudio-users] General Electric 25 directions gradient table References: Message-ID: <30B55BD507F64986836295B1C364F035@bleach> Hi dear Andre: I'm sorry because I have never used GE MR scaner to perform DTI acquisition. On way, I think, may be applicable using the dcm2niigui.exe tool(one plugin of MRIcroN), which can convert the DTI raw data into nifti format and simultaneously generate one text containing the gradient vectors.This function have been tested applicable for Siemens data.You can try it! Bests! Qin Wen ----- Original Message ----- From: Andre Coutinho Castilla To: mristudio-users at mristudio.org Sent: Thursday, May 06, 2010 9:46 PM Subject: [Mristudio-users] General Electric 25 directions gradient table Hello I am a newcommer to DTI. I am having problems on obtaining the gradient table of my examinations. Could someone provide me this table? I am using a GE 1,5T echospeed, 4 channel head coil and 25 directions. Thanks in advance Andre Castilla MD, PhD Sao Paulo Brazil ------------------------------------------------------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100506/02dbe16c/attachment.html From Malek.Makki at kispi.uzh.ch Thu May 6 10:14:40 2010 From: Malek.Makki at kispi.uzh.ch (Makki Malek) Date: Thu, 06 May 2010 16:14:40 +0200 Subject: [Mristudio-users] General Electric 25 directions gradient table In-Reply-To: Message-ID: GE sequence uses a file called "tensor.dat" which you can find it in the scanner console under /usr/g/bin and here are the 25 directions in our system 1.000000 0.000000 0.000000 0.849000 0.528000 0.000000 -0.108000 0.565000 0.818000 0.884000 -0.345000 -0.315000 -0.003000 -0.736000 0.677000 -0.868000 -0.238000 0.436000 0.799000 0.370000 0.475000 -0.162000 0.987000 0.000000 0.866000 -0.129000 0.483000 -0.212000 -0.936000 0.281000 0.068000 -0.892000 -0.446000 0.550000 -0.544000 -0.634000 -0.435000 -0.422000 0.795000 -0.599000 0.780000 0.182000 -0.525000 0.030000 -0.851000 -0.600000 -0.688000 0.409000 0.653000 -0.060000 -0.755000 0.207000 -0.076000 -0.975000 -0.413000 -0.699000 -0.584000 -0.436000 0.822000 -0.366000 0.462000 0.874000 0.148000 -0.503000 0.488000 -0.713000 0.824000 -0.530000 0.202000 0.297000 0.349000 0.889000 -0.040000 0.318000 -0.947000 Malek ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andre Coutinho Castilla Sent: Thursday, May 06, 2010 3:46 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] General Electric 25 directions gradient table Hello I am a newcommer to DTI. I am having problems on obtaining the gradient table of my examinations. Could someone provide me this table? I am using a GE 1,5T echospeed, 4 channel head coil and 25 directions. Thanks in advance Andre Castilla MD, PhD Sao Paulo Brazil -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100506/5a5e4519/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: PGP.sig Type: application/pgp-signature Size: 489 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100506/5a5e4519/attachment.bin From LisaMarie.Langevin at albertahealthservices.ca Thu May 6 12:43:01 2010 From: LisaMarie.Langevin at albertahealthservices.ca (Lisa Marie Langevin) Date: Thu, 06 May 2010 10:43:01 -0600 Subject: [Mristudio-users] General Electric 25 directions gradient table In-Reply-To: References: Message-ID: <16D6DA47889FE44BA52573AAAE4493AE2CC92035@EXMBX10C.crha.bewell.ca> Dear All, I am having the same trouble with the gradient tables for a GE 3T scanner, 11 directions with an 8 direction head coil. Thank you if anyone else is using this too. LM :) Lisa Marie Langevin, Ph.D. Postdoctoral Research Fellow Alberta Children's Hospital Research Institute for Child and Maternal Health Behavioural Research Unit, Alberta Children's Hospital Tel: (403) 955-2785, Fax: (403) 955-2772 Email: lisamarie.langevin at albertahealthservices.ca ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Andre Coutinho Castilla [castilla at terra.com.br] Sent: May 6, 2010 7:46 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] General Electric 25 directions gradient table Hello I am a newcommer to DTI. I am having problems on obtaining the gradient table of my examinations. Could someone provide me this table? I am using a GE 1,5T echospeed, 4 channel head coil and 25 directions. Thanks in advance Andre Castilla MD, PhD Sao Paulo Brazil ________________________________ This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100506/901305f7/attachment-0001.html From susumu at mri.jhu.edu Thu May 6 16:02:45 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 06 May 2010 16:02:45 -0400 Subject: [Mristudio-users] General Electric 25 directions gradient table In-Reply-To: <16D6DA47889FE44BA52573AAAE4493AE2CC92035@EXMBX10C.crha.bewell.ca> References: <16D6DA47889FE44BA52573AAAE4493AE2CC92035@EXMBX10C.crha.bewell.ca> Message-ID: Hi all, I'm in Stockholm for ISMRM. Next week, I'll post GE, Siemens, and Philips gradient tables in FAQ section. I'll notify once they are up. Susumu On Thu, May 6, 2010 at 12:43 PM, Lisa Marie Langevin < LisaMarie.Langevin at albertahealthservices.ca> wrote: > Dear All, > > I am having the same trouble with the gradient tables for a GE 3T scanner, > 11 directions with an 8 direction head coil. > > Thank you if anyone else is using this too. > > LM :) > > > Lisa Marie Langevin, Ph.D. > Postdoctoral Research Fellow > Alberta Children's Hospital Research Institute for Child and Maternal > Health > Behavioural Research Unit, Alberta Children's Hospital > Tel: (403) 955-2785, Fax: (403) 955-2772 > Email: lisamarie > .langevin at albertahealthservices.ca > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of Andre Coutinho > Castilla [castilla at terra.com.br] > *Sent:* May 6, 2010 7:46 AM > > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] General Electric 25 directions gradient table > > Hello > > I am a newcommer to DTI. > I am having problems on obtaining the gradient table of my examinations. > Could someone provide me this table? > I am using a GE 1,5T echospeed, 4 channel head coil and 25 directions. > > Thanks in advance > > Andre Castilla MD, PhD > Sao Paulo > Brazil > > ------------------------------ > This message and any attached documents are only for the use of the > intended recipient(s), are confidential and may contain privileged > information. Any unauthorized review, use, retransmission, or other > disclosure is strictly prohibited. If you have received this message in > error, please notify the sender immediately, and then delete the original > message. Thank you. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100506/4eca6a72/attachment.html From castillabr at gmail.com Thu May 6 20:42:42 2010 From: castillabr at gmail.com (Andre Castilla) Date: Thu, 06 May 2010 21:42:42 -0300 Subject: [Mristudio-users] General Electric 25 directions gradient table In-Reply-To: References: <16D6DA47889FE44BA52573AAAE4493AE2CC92035@EXMBX10C.crha.bewell.ca> Message-ID: Thank you very much. Andre 2010/5/6 susumu mori > Hi all, > > I'm in Stockholm for ISMRM. Next week, I'll post GE, Siemens, and Philips > gradient tables in FAQ section. I'll notify once they are up. > > Susumu > > On Thu, May 6, 2010 at 12:43 PM, Lisa Marie Langevin < > LisaMarie.Langevin at albertahealthservices.ca> wrote: > >> Dear All, >> >> I am having the same trouble with the gradient tables for a GE 3T scanner, >> 11 directions with an 8 direction head coil. >> >> Thank you if anyone else is using this too. >> >> LM :) >> >> >> Lisa Marie Langevin, Ph.D. >> Postdoctoral Research Fellow >> Alberta Children's Hospital Research Institute for Child and Maternal >> Health >> Behavioural Research Unit, Alberta Children's Hospital >> Tel: (403) 955-2785, Fax: (403) 955-2772 >> Email: lisamarie >> .langevin at albertahealthservices.ca >> ------------------------------ >> *From:* mristudio-users-bounces at mristudio.org [ >> mristudio-users-bounces at mristudio.org] On Behalf Of Andre Coutinho >> Castilla [castilla at terra.com.br] >> *Sent:* May 6, 2010 7:46 AM >> >> *To:* mristudio-users at mristudio.org >> *Subject:* [Mristudio-users] General Electric 25 directions gradient >> table >> >> Hello >> >> I am a newcommer to DTI. >> I am having problems on obtaining the gradient table of my examinations. >> Could someone provide me this table? >> I am using a GE 1,5T echospeed, 4 channel head coil and 25 directions. >> >> Thanks in advance >> >> Andre Castilla MD, PhD >> Sao Paulo >> Brazil >> >> ------------------------------ >> This message and any attached documents are only for the use of the >> intended recipient(s), are confidential and may contain privileged >> information. Any unauthorized review, use, retransmission, or other >> disclosure is strictly prohibited. If you have received this message in >> error, please notify the sender immediately, and then delete the original >> message. Thank you. >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100506/3ccf68ac/attachment.html From evangelouI at ninds.nih.gov Mon May 10 14:54:07 2010 From: evangelouI at ninds.nih.gov (Evangelou, Iordanis (NIH/NINDS) [E]) Date: Mon, 10 May 2010 14:54:07 -0400 Subject: [Mristudio-users] General Electric 25 directions gradient table In-Reply-To: References: <16D6DA47889FE44BA52573AAAE4493AE2CC92035@EXMBX10C.crha.bewell.ca> Message-ID: <794DFDD3C128EF44AC49ADC58FD0090C77A8FF8C@NIHMLBX10.nih.gov> GE has changed their gradient table in 2005, Not sure what would be the ones for your case. ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Staff Scientist Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 ________________________________________ From: susumu mori [susumu at mri.jhu.edu] Sent: Thursday, May 06, 2010 4:02 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Xin Li Subject: Re: [Mristudio-users] General Electric 25 directions gradient table Hi all, I'm in Stockholm for ISMRM. Next week, I'll post GE, Siemens, and Philips gradient tables in FAQ section. I'll notify once they are up. Susumu On Thu, May 6, 2010 at 12:43 PM, Lisa Marie Langevin > wrote: Dear All, I am having the same trouble with the gradient tables for a GE 3T scanner, 11 directions with an 8 direction head coil. Thank you if anyone else is using this too. LM :) Lisa Marie Langevin, Ph.D. Postdoctoral Research Fellow Alberta Children's Hospital Research Institute for Child and Maternal Health Behavioural Research Unit, Alberta Children's Hospital Tel: (403) 955-2785, Fax: (403) 955-2772 Email: lisamarie.langevin at albertahealthservices.ca ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Andre Coutinho Castilla [castilla at terra.com.br] Sent: May 6, 2010 7:46 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] General Electric 25 directions gradient table Hello I am a newcommer to DTI. I am having problems on obtaining the gradient table of my examinations. Could someone provide me this table? I am using a GE 1,5T echospeed, 4 channel head coil and 25 directions. Thanks in advance Andre Castilla MD, PhD Sao Paulo Brazil ________________________________ This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From LisaMarie.Langevin at albertahealthservices.ca Mon May 10 18:19:58 2010 From: LisaMarie.Langevin at albertahealthservices.ca (Lisa Marie Langevin) Date: Mon, 10 May 2010 16:19:58 -0600 Subject: [Mristudio-users] DTI files concatamerized Message-ID: <16D6DA47889FE44BA52573AAAE4493AE2CC9205C@EXMBX10C.crha.bewell.ca> Hi gang! The data I am getting from my GE scanner is not showing all the .dcm files for each direction separately. It is averaging the replicates for each of my directions (11 + B0) and then concatamerizing the images into a single .dcm file. In FSL, I can see all the directions individually. Is there a way to separate all the directions so they can load in DTIStudio? The program crashes when I try to open the single .dcm file. Thank you so much in advance! LM :) Lisa Marie Langevin, Ph.D. Postdoctoral Research Fellow Alberta Children's Hospital Research Institute for Child and Maternal Health Behavioural Research Unit, Alberta Children's Hospital Tel: (403) 955-2785, Fax: (403) 955-2772 Email: lisamarie.langevin at albertahealthservices.ca ________________________________ This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100510/13b1921a/attachment-0001.html From susumu at mri.jhu.edu Mon May 10 21:18:06 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 10 May 2010 21:18:06 -0400 Subject: [Mristudio-users] DTI files concatamerized In-Reply-To: <16D6DA47889FE44BA52573AAAE4493AE2CC9205C@EXMBX10C.crha.bewell.ca> References: <16D6DA47889FE44BA52573AAAE4493AE2CC9205C@EXMBX10C.crha.bewell.ca> Message-ID: Hi Lisa, Is it a new DICOM format of GE? Or is it something very specific to your study? If former is the case, we need to add a capability in DtiStudio so that you can read the data directly. If you could ftp the data, we can take a look. Susumu On Mon, May 10, 2010 at 6:19 PM, Lisa Marie Langevin < LisaMarie.Langevin at albertahealthservices.ca> wrote: > Hi gang! > > The data I am getting from my GE scanner is not showing all the .dcm files > for each direction separately. It is averaging the replicates for each of > my directions (11 + B0) and then concatamerizing the images into a single > .dcm file. > > In FSL, I can see all the directions individually. > > Is there a way to separate all the directions so they can load in > DTIStudio? The program crashes when I try to open the single .dcm file. > > Thank you so much in advance! > > LM :) > > > Lisa Marie Langevin, Ph.D. > Postdoctoral Research Fellow > Alberta Children's Hospital Research Institute for Child and Maternal > Health > Behavioural Research Unit, Alberta Children's Hospital > Tel: (403) 955-2785, Fax: (403) 955-2772 > Email: lisamarie.langevin at albertahealthservices.ca > > ------------------------------ > This message and any attached documents are only for the use of the > intended recipient(s), are confidential and may contain privileged > information. Any unauthorized review, use, retransmission, or other > disclosure is strictly prohibited. If you have received this message in > error, please notify the sender immediately, and then delete the original > message. Thank you. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100510/e55c66a0/attachment.html From basketballmouse at 163.com Mon May 10 20:39:36 2010 From: basketballmouse at 163.com (=?gb2312?B?u8a6o8fl?=) Date: Tue, 11 May 2010 08:39:36 +0800 Subject: [Mristudio-users] General Electric 25 directions gradient table References: <16D6DA47889FE44BA52573AAAE4493AE2CC92035@EXMBX10C.crha.bewell.ca> <794DFDD3C128EF44AC49ADC58FD0090C77A8FF8C@NIHMLBX10.nih.gov> Message-ID: <201005110839352183774@163.com> I have the two version of GE gradient tables. 2010-05-11 ??? ???? Evangelou, Iordanis (NIH/NINDS) [E] ????? 2010-05-11 02:55:23 ???? DTI Studio, ROI Editor, DiffeoMap Questions/Support; Xin Li ??? ??? Re: [Mristudio-users] General Electric 25 directions gradient table GE has changed their gradient table in 2005, Not sure what would be the ones for your case. ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Staff Scientist Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 ________________________________________ From: susumu mori [susumu at mri.jhu.edu] Sent: Thursday, May 06, 2010 4:02 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Xin Li Subject: Re: [Mristudio-users] General Electric 25 directions gradient table Hi all, I'm in Stockholm for ISMRM. Next week, I'll post GE, Siemens, and Philips gradient tables in FAQ section. I'll notify once they are up. Susumu On Thu, May 6, 2010 at 12:43 PM, Lisa Marie Langevin > wrote: Dear All, I am having the same trouble with the gradient tables for a GE 3T scanner, 11 directions with an 8 direction head coil. Thank you if anyone else is using this too. LM :) Lisa Marie Langevin, Ph.D. Postdoctoral Research Fellow Alberta Children's Hospital Research Institute for Child and Maternal Health Behavioural Research Unit, Alberta Children's Hospital Tel: (403) 955-2785, Fax: (403) 955-2772 Email: lisamarie.langevin at albertahealthservices.ca ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Andre Coutinho Castilla [castilla at terra.com.br] Sent: May 6, 2010 7:46 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] General Electric 25 directions gradient table Hello I am a newcommer to DTI. I am having problems on obtaining the gradient table of my examinations. Could someone provide me this table? I am using a GE 1,5T echospeed, 4 channel head coil and 25 directions. Thanks in advance Andre Castilla MD, PhD Sao Paulo Brazil ________________________________ This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100511/9f6bf878/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: ge_tensor_new.dat Type: application/octet-stream Size: 325504 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100511/9f6bf878/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: ge_tensor_old.dat Type: application/octet-stream Size: 390060 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100511/9f6bf878/attachment-0003.obj From wayne009007 at 126.com Tue May 11 05:29:26 2010 From: wayne009007 at 126.com (wayne_netease) Date: Tue, 11 May 2010 17:29:26 +0800 Subject: [Mristudio-users] General Electric 25 directions gradient table References: <16D6DA47889FE44BA52573AAAE4493AE2CC92035@EXMBX10C.crha.bewell.ca> <794DFDD3C128EF44AC49ADC58FD0090C77A8FF8C@NIHMLBX10.nih.gov> <201005110839352183774@163.com> Message-ID: <4C9D346BAA3F4764AB372EE2EE261509@bleach> thank you! ? ? (Qin Wen) ----- Original Message ----- From: ??? To: DTI Studio, ROI Editor,DiffeoMap Questions/Support Sent: Tuesday, May 11, 2010 8:39 AM Subject: Re: [Mristudio-users] General Electric 25 directions gradient table I have the two version of GE gradient tables. 2010-05-11 ------------------------------------------------------------------------------ ??? ------------------------------------------------------------------------------ ???? Evangelou, Iordanis (NIH/NINDS) [E] ????? 2010-05-11 02:55:23 ???? DTI Studio, ROI Editor, DiffeoMap Questions/Support; Xin Li ??? ??? Re: [Mristudio-users] General Electric 25 directions gradient table GE has changed their gradient table in 2005, Not sure what would be the ones for your case. ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Staff Scientist Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 ________________________________________ From: susumu mori [susumu at mri.jhu.edu] Sent: Thursday, May 06, 2010 4:02 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Xin Li Subject: Re: [Mristudio-users] General Electric 25 directions gradient table Hi all, I'm in Stockholm for ISMRM. Next week, I'll post GE, Siemens, and Philips gradient tables in FAQ section. I'll notify once they are up. Susumu On Thu, May 6, 2010 at 12:43 PM, Lisa Marie Langevin > wrote: Dear All, I am having the same trouble with the gradient tables for a GE 3T scanner, 11 directions with an 8 direction head coil. Thank you if anyone else is using this too. LM :) Lisa Marie Langevin, Ph.D. Postdoctoral Research Fellow Alberta Children's Hospital Research Institute for Child and Maternal Health Behavioural Research Unit, Alberta Children's Hospital Tel: (403) 955-2785, Fax: (403) 955-2772 Email: lisamarie.langevin at albertahealthservices.ca ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Andre Coutinho Castilla [castilla at terra.com.br] Sent: May 6, 2010 7:46 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] General Electric 25 directions gradient table Hello I am a newcommer to DTI. I am having problems on obtaining the gradient table of my examinations. Could someone provide me this table? I am using a GE 1,5T echospeed, 4 channel head coil and 25 directions. Thanks in advance Andre Castilla MD, PhD Sao Paulo Brazil ________________________________ This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ------------------------------------------------------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100511/179b8a44/attachment.html From susumu at mri.jhu.edu Tue May 11 15:22:21 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 11 May 2010 15:22:21 -0400 Subject: [Mristudio-users] General Electric 25 directions gradient table In-Reply-To: <201005110839352183774@163.com> References: <16D6DA47889FE44BA52573AAAE4493AE2CC92035@EXMBX10C.crha.bewell.ca> <794DFDD3C128EF44AC49ADC58FD0090C77A8FF8C@NIHMLBX10.nih.gov> <201005110839352183774@163.com> Message-ID: Thanks! This is really a nice info. 2010/5/10 ??? > I have the two version of GE gradient tables. > > > 2010-05-11 > ------------------------------ > ??? > ------------------------------ > *????* Evangelou, Iordanis (NIH/NINDS) [E] > *?????* 2010-05-11 02:55:23 > *????* DTI Studio, ROI Editor, DiffeoMap Questions/Support; Xin Li > *???* > *???* Re: [Mristudio-users] General Electric 25 directions gradient table > > GE has changed their gradient table in 2005, Not sure what would be the ones for your case. > ------------------------------------------------------------------- > Iordanis E. Evangelou, DPhil > Staff Scientist > Neuroimmunology Branch > National Institute of Neurological Disorders and Stroke > National Institutes of Health > Building 10, Room 5C203B > Bethesda, MD 20892 > ________________________________________ > From: susumu mori [susumu at mri.jhu.edu] > Sent: Thursday, May 06, 2010 4:02 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Xin Li > > Subject: Re: [Mristudio-users] General Electric 25 directions gradient table > Hi all, > > I'm in Stockholm for ISMRM. Next week, I'll post GE, Siemens, and Philips gradient tables in FAQ section. I'll notify once they are up. > Susumu > On Thu, May 6, 2010 at 12:43 PM, Lisa Marie Langevin < > LisaMarie.Langevin at albertahealthservices.ca LisaMarie.Langevin at albertahealthservices.ca>> wrote: > Dear All, > > I am having the same trouble with the gradient tables for a GE 3T scanner, 11 directions with an 8 direction head coil. > Thank you if anyone else is using this too. > LM :) > Lisa Marie Langevin, Ph.D. > Postdoctoral Research Fellow > > Alberta Children's Hospital Research Institute for Child and Maternal Health > Behavioural Research Unit, Alberta Children's Hospital > Tel: (403) 955-2785, Fax: (403) 955-2772 > Email: lisamarie. > langevin at albertahealthservices.ca lisamarie.langevin at albertahealthservices.ca> > ________________________________ > From: mristudio-users-bounces at mristudio.org mristudio-users-bounces at mristudio.org> [ > mristudio-users-bounces at mristudio.org mristudio-users-bounces at mristudio.org > >] On Behalf Of Andre Coutinho Castilla [castilla at terra.com.br castilla at terra.com.br>] > Sent: May 6, 2010 7:46 AM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] General Electric 25 directions gradient table > Hello > I am a newcommer to DTI. > I am having problems on obtaining the gradient table of my examinations. > Could someone provide me this table? > I am using a GE 1,5T echospeed, 4 channel head coil and 25 directions. > Thanks in advance > Andre Castilla MD, PhD > Sao Paulo > Brazil > ________________________________ > > This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org Mristudio-users-unsubscribe at mristudio.org> > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100511/085a6e4e/attachment-0001.html From vrajakar at uwo.ca Wed May 12 13:14:27 2010 From: vrajakar at uwo.ca (Velarny Rajakariar) Date: Wed, 12 May 2010 13:14:27 -0400 Subject: [Mristudio-users] DTI Map In-Reply-To: References: <16D6DA47889FE44BA52573AAAE4493AE2CC92035@EXMBX10C.crha.bewell.ca> <794DFDD3C128EF44AC49ADC58FD0090C77A8FF8C@NIHMLBX10.nih.gov> <201005110839352183774@163.com> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100512/ed758394/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: DiffeoMap.docx Type: application/octet-stream Size: 21574 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100512/ed758394/attachment-0001.obj From vrajakar at uwo.ca Wed May 12 13:36:49 2010 From: vrajakar at uwo.ca (Velarny Rajakariar) Date: Wed, 12 May 2010 13:36:49 -0400 Subject: [Mristudio-users] DTI Map In-Reply-To: References: <16D6DA47889FE44BA52573AAAE4493AE2CC92035@EXMBX10C.crha.bewell.ca> <794DFDD3C128EF44AC49ADC58FD0090C77A8FF8C@NIHMLBX10.nih.gov> <201005110839352183774@163.com> Message-ID: Hello, I've got the number from mristudio website. Thanks, Velarny ----- Original Message ----- From: Velarny Rajakariar Date: Wednesday, May 12, 2010 1:19 pm Subject: [Mristudio-users] DTI Map To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Hello, > My name is Velarny Rajakariar from Robarts Research Institute, London, Ontario. And, I'm new to Diffusion MRI. > I am trying to install DiffeoMap, but its ask for registration key number (please refer to the attached file). Do you have one or please advise me where I can obtain this number. > Your help in this matter is appreciated > Best Regards, > Velarny Rajakariar > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users- > unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100512/3d5d33cf/attachment.html From xli16 at jhmi.edu Wed May 12 14:07:47 2010 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 12 May 2010 14:07:47 -0400 Subject: [Mristudio-users] DTI Map In-Reply-To: References: <16D6DA47889FE44BA52573AAAE4493AE2CC92035@EXMBX10C.crha.bewell.ca> <794DFDD3C128EF44AC49ADC58FD0090C77A8FF8C@NIHMLBX10.nih.gov> <201005110839352183774@163.com> Message-ID: <72a0f33a3c3c5.4beab633@johnshopkins.edu> Rajakariar, Please go to www.mristudio.org and click "Register Software" in the "Registration" section. You will be asked to enter your user name, password and the machine ID. After you enter them, you would be able to get the registration key number. Regards, Xin ----- Original Message ----- From: Velarny Rajakariar Date: Wednesday, May 12, 2010 1:14 pm Subject: [Mristudio-users] DTI Map To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Hello, My name is Velarny Rajakariar from Robarts Research Institute, > London, Ontario. And, I'm new to Diffusion MRI.I am trying to install > DiffeoMap, but its ask for registration key number (please refer to > the attached file). Do you have one or please advise me where I can > obtain this number.Your help in this matter is appreciatedBest > Regards,Velarny Rajakariar > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From d-gitelman at northwestern.edu Wed May 12 16:08:52 2010 From: d-gitelman at northwestern.edu (Darren Gitelman) Date: Wed, 12 May 2010 15:08:52 -0500 Subject: [Mristudio-users] error opening NRRD files Message-ID: Hi I imported my 3 sets of diffusion images (Siemens Dicom) into DTIstudio. Then I saved the images by clicking the save icon in the menu area on the right. I selected all my images to save and used the single header nrrd format and all images in 1 file. If I try to open the image by clicking the open icon, it is loaded fine, but the DTImap tab is missing from the interface. If instead I choose file-> DTImapping and select NRRD and then choose the file, there is an error "NRRD-DWMRI header error: not a valid NRRD-DWMRI file". Please advise since the file was created by DTIstudio. thanks, Darren -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100512/e2936fcb/attachment.html From gaolion at gmail.com Thu May 13 08:07:52 2010 From: gaolion at gmail.com (lion gao) Date: Thu, 13 May 2010 20:07:52 +0800 Subject: [Mristudio-users] DTI method: VBA, MRIstudio vs. TBSS Message-ID: Dear Experts, I have one part of my thesis on DTI data analysis. The method I used is the voxel-based analysis (VBA) and I tried MRIstudio as well. One of the examiners pointed out that track-based spatial statistics (TBSS), as a state of art way, should have been considered. I am familiar with TBSS, only know that it may reduce systemic mis-registration inVBA and increasing papers published with the method. I am not sure whether: 1. VBA has become ?out of date?, 2. and TBSS has become a ?golden standard? for DTI data analysis. Can someone help to justify the situation or defense a little bit? Thank you very much in advance! Best wishes, Gao -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100513/328f89d3/attachment.html From miaomiaolong at 126.com Thu May 13 10:44:32 2010 From: miaomiaolong at 126.com (Longmm) Date: Thu, 13 May 2010 22:44:32 +0800 (CST) Subject: [Mristudio-users] DTI method: VBA, MRIstudio vs. TBSS In-Reply-To: References: Message-ID: <10f3d2c.b073.128921fbc14.Coremail.miaomiaolong@126.com> actually, the most amazing part of a good research is new techniqe, or fact, or idea from an well established traditional stable experiment or design , or facts. ?2010-05-13 20:07:52?"lion gao" ??? Dear Experts, I have one part of my thesis on DTI data analysis. The method I used is the voxel-based analysis (VBA) and I tried MRIstudio as well. One of the examiners pointed out that track-based spatial statistics (TBSS), as a state of art way, should have been considered. I am familiar with TBSS, only know that it may reduce systemic mis-registration inVBA and increasing papers published with the method. I am not sure whether: 1. VBA has become ?out of date?, 2. and TBSS has become a ?golden standard? for DTI data analysis. Can someone help to justify the situation or defense a little bit? Thank you very much in advance! Best wishes, Gao -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100513/2c3d0fcd/attachment.html From susumu at mri.jhu.edu Thu May 13 11:44:31 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 13 May 2010 11:44:31 -0400 Subject: [Mristudio-users] DTI method: VBA, MRIstudio vs. TBSS In-Reply-To: References: Message-ID: Good question Gao. Here is my thought (my personal opinion, of course); 1) you are comparing VBA and TBSS. These are methods to "define corresponding pixels (or areas) across subjects", so that you can compare pixel numbers such as FA and MD among different brains. This is called "registration". 2) These methods can be classified from different point of views; 2-1) granularity: One extreme is to define the entire brain as one ROI. You can get the whole brain volume, whole brain FA, or whole brain histogram. While there is not much use of this approach, it is precise (do 10 times and you get the same results) and accurate (nobody makes mistakes about where is the whole brain except for some ambiguity about where you cut the ROI in the brainstem). The other extreme is the pixel, which is the smallest unit. This mean, you identify the corresponding pixels across subjects. Once you map the entire 1 million pixels in one brain to the other, it is the same as transforming one brain to the other (two brains now have the same shape). This approach is called "normalization" and, of course, not accurate because it is not possible to completely solve the system and accurately map all 1 million pixels. VBA and TBSS are based on this normalization procedure. There are methods to ameliorate this accuracy issue. Usually VBA uses filters to blur the information. In my understanding, TBSS "re-register" nearby pixel information to the core of the white matter, which could be considered as a sort of filtering, reducing the granularity and hopefully increasing the accuracy. 2-2) Anatomy: When we do normalization, computer algorithm do not care about anatomy. It just does whatever it thinks best to register pixels. This is the pixel-based analysis. On the other hand, manual ROI is usually based on anatomical information we can perceive. This is anatomy-based analysis. Tractography-based analysis can also be considered as a kind of registration method. We do, for example, tractography of the cortico-spinal tract in 10 subjects. Then we can define a group of pixels that belong to the CST and compare the pixel values. In this way, we define a specific area across subjects based on anatomy. 3) In MriStudio, DiffeoMap does pixel-based registration just as VBA. You can do VBA analysis. In addition, you can superimpose our parcellation map and divide the brain into about 150 areas. In terms of granularity, it is much less than VBA (more than 1 million pixels vs 150 areas). This is also a conversion to pixel-based to anatomy-based analysis. 4) Now going back to your question, VBA and TBSS are looking at the same data with different point of view. First of all, the granularity is different; TBSS reduces the information to the white matter core. Also, VBA is completely pixel-based but TBSS, which is not completely anatomy-based but has some anatomy-based factors by reducing the information to the core of the white matter. 5) In my opinion, all methods described above have advantages and disadvantages. I don't think any one of them is better than the other. Quantification based on location information is definitely one of the most difficult problems we are all facing. 6) On the other hand, your reviewer is correct, in a sense that it is always important to compare different results to enrich your data and interpretation. This is especially true if there is a tool widely used like TBSS. However, it is not like, one method should be treated as the gold standard and other approaches should give a similar result. If you compare VBA and TBSS, you likely to get different results because as explained above they are operating at the different granularity, precision, and accuracy. MRI image anlaysis is very often a screening and hypothesis generating tool rather than a tool to draw a conclusion. We are simply looking at 6MB information based on water signal. So, in conclusion, > No, VBA is not out of date > Yes, it is a good idea to compare results from widely used tools, but any normalization-based method should not be considered as a gold standard in my opinion. We just have to understand how they operate and what are their advantages and disadvantages. On Thu, May 13, 2010 at 8:07 AM, lion gao wrote: > Dear Experts, > > > > I have one part of my thesis on DTI data analysis. The method I used is the > voxel-based analysis (VBA) and I tried MRIstudio as well. One of the > examiners pointed out that track-based spatial statistics (TBSS), as a state > of art way, should have been considered. > > > I am familiar with TBSS, only know that it may reduce systemic > mis-registration inVBA and increasing papers published with the method. I am > not sure whether: > 1. VBA has become ?out of date?, > 2. and TBSS has become a ?golden standard? for DTI data analysis. > > Can someone help to justify the situation or defense a little bit? Thank > you very much in advance! > > > Best wishes, > > Gao > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100513/5f5a046b/attachment-0001.html From stevie.ray28 at gmail.com Thu May 13 12:04:55 2010 From: stevie.ray28 at gmail.com (Stephen Ray) Date: Thu, 13 May 2010 10:04:55 -0600 Subject: [Mristudio-users] Beginner with question about getting started Message-ID: Hello, This is Stephen Ray. I am a physicist doing some volunteer work for analyzing DTI images for a research group. I am excited to do this because I am interested in the application, but I basically have no knowledge in terms of processing images, how the data is collected, and how the software. I tried going through the manual, but am still having trouble sorting out what to put where. Here is my current situation, any help you could offer would be fantastic. I was sent a folder of dicom files, so I open up DTI studio and select DTI mapping. From there I choose Siemens Dicom which takes me to the parameters. This is the point where I get lost. The folder sent to me as 520 images to process. The images are named as such: IM-0001-0001 through IM-0001-0520. So would I put 520 in the "images slices" box in the Image Dimension section. For the "Slices to be processed" section, would I put 1 and 520? Also, I have no idea what process/gradient table they used. Where would I get that information? Would that be information I need to get from the protocol of the image collection or from the person who ran the experiment? Also, in the Philips REC Image File section, is this where I load the dicom images? Do I have to load them individually or can I direct the software to the correct directory where the images are? Thanks for your help and assistance! Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100513/1cf19011/attachment.html From rajagov2 at ccf.org Thu May 13 12:50:40 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Thu, 13 May 2010 12:50:40 -0400 Subject: [Mristudio-users] Beginner with question about getting started References: Message-ID: <77A88E90A851594AAEF830450587C39D04183190@CCHSCLEXMB56.cc.ad.cchs.net> Hi Stephen, I can help you with few things but i am not an expert with DTI studio. 1) Before choosing DTI mapping option choose MRI3dview there you will find different options to open your files for instance my dicom files (from seimens) are .dcm and not IMA so try opening your files one of these options and see which one works. Once you have succeded in opening your files to your right top corner you will see "Orthogonal Views" there you will find slice marker slot by scrolling up and down the arrows you can find the number of slices. This is because for instance my DTI data is collected over 12 directions and 1 without diffusion weighting so 13 in total and we have acquires 30 slices so 13*30= 390, similarly in your case you have mentioned that you have 520 slices actually that is the total number of images acquired. So similar to my DTI data example you can try to figure out the number of gradient directions. 2) For the "Slices to be processed" section, would I put 1 and 520? So for this question you will get your answer from point 1) above. 3) Also, I have no idea what process/gradient table they used. Would that be information I need to get from the protocol of the image collection or from the person who ran the experiment? I got the gradient table information from our techs who ran the scans but if you search DTI studio archives you might find them for the magent field strength you used then version of the software used in siemens and the number of gradient directions. DTI studio manual will provide you more information . Venkat ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of Stephen Ray Sent: Thu 5/13/2010 12:04 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Beginner with question about getting started Hello, This is Stephen Ray. I am a physicist doing some volunteer work for analyzing DTI images for a research group. I am excited to do this because I am interested in the application, but I basically have no knowledge in terms of processing images, how the data is collected, and how the software. I tried going through the manual, but am still having trouble sorting out what to put where. Here is my current situation, any help you could offer would be fantastic. I was sent a folder of dicom files, so I open up DTI studio and select DTI mapping. From there I choose Siemens Dicom which takes me to the parameters. This is the point where I get lost. The folder sent to me as 520 images to process. The images are named as such: IM-0001-0001 through IM-0001-0520. So would I put 520 in the "images slices" box in the Image Dimension section. For the "Slices to be processed" section, would I put 1 and 520? Also, I have no idea what process/gradient table they used. Where would I get that information? Would that be information I need to get from the protocol of the image collection or from the person who ran the experiment? Also, in the Philips REC Image File section, is this where I load the dicom images? Do I have to load them individually or can I direct the software to the correct directory where the images are? Thanks for your help and assistance! Stephen =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6207 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100513/8e219b47/attachment.bin From d.gitelman at gmail.com Fri May 14 13:03:39 2010 From: d.gitelman at gmail.com (Gmail) Date: Fri, 14 May 2010 12:03:39 -0500 Subject: [Mristudio-users] error opening NRRD files In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F210CC23A49@RAD-EXCH1.win.ad.jhu.edu> References: <145933A2BE9E4F48AE079A201379BF2F210CC23A49@RAD-EXCH1.win.ad.jhu.edu> Message-ID: <19C9AC86-4969-425C-BFE5-F13FC975D042@gmail.com> Thanks. After rereading susumu's reply about saving data I saved it as raw and open it using a .dpf file. That works very well. ----- Darren sent from my iPhone On May 14, 2010, at 8:25 AM, Hangyi Jiang wrote: > the message "NRRD-DWMRI header error: not a valid NRRD-DWMRI file" > tells that the program cannot find gradient info. in the nrrd file. > the "image save" button can save the image into nrrd file, but not > the gradients. > > if the dataset can be processed as DICOM format, it is better to do > it in that way. > > hangyi > > > > > > > > ________________________________________ > From: mristudio-users-bounces at mristudio.org [mristudio-users- > bounces at mristudio.org] On Behalf Of Darren Gitelman [d- > gitelman at northwestern.edu] > Sent: Wednesday, May 12, 2010 4:08 PM > To: mristudio-users > Subject: [Mristudio-users] error opening NRRD files > > Hi > > I imported my 3 sets of diffusion images (Siemens Dicom) into > DTIstudio. Then I saved the images by clicking the save icon in the > menu area on the right. I selected all my images to save and used > the single header nrrd format and all images in 1 file. If I try to > open the image by clicking the open icon, it is loaded fine, but the > DTImap tab is missing from the interface. If instead I choose file-> > DTImapping and select NRRD and then choose the file, there is an > error "NRRD-DWMRI header error: not a valid NRRD-DWMRI file". > > Please advise since the file was created by DTIstudio. > > thanks, > Darren From gaolion at gmail.com Fri May 14 13:41:19 2010 From: gaolion at gmail.com (lion gao) Date: Sat, 15 May 2010 01:41:19 +0800 Subject: [Mristudio-users] DTI method: VBA, MRIstudio vs. TBSS In-Reply-To: References: Message-ID: Dear Susumu Mori, Thanks very much for your answer, it's very informative! One question is that when you mention granularity and anatomy, it finally all leads to the advantages of TBSS, the skeleton. so my answer looks a bit repeated for a same point. Another one is I do need to find some flaw in TBSS for defence use :P, so I find some limitation from the original paper. BTW, I am NOT familiar with TBSS. http://sirl.stanford.edu/~bob/pdf/DTI/Methods/Smith_TBSS_NeuroImage06.pdf Finally, I arranged some defences based on your comments below. Have a look if interested , or simply skip it :) Thanks again & Best Wishes, Gao It has been quite a time since VBA was popularly used in DTI data, while track-based spatial statistical gains popularity rapid in recent years. To compare the two methods, there two points of views need to the clarified: 1. Granularity. It represents the extent to which a system is divided into smaller parts. In VBA, the brain is broken into nearly one million of voxels, then it is normalized before comparing with one another. In MRIstudio, it can superimpose the parcellation map and divided the brain into 150 areas, thus it has less granularity than VBA (1 million vs. 150). Whereas TBSS re-registers nearby voxels to the skeleton of white matter, reduces the granularity and increases the accuracy of registration. 2. Anatomy. In VBA analysis, computer algorithm registers the voxels automatically, without considering any anatomical information. Another new method of Tissue-specific, smoothing-compensated (T-SPOON) can improve the tissue specificity in VBA method and compensation for images smoothing. TBSS can also apply some anatomical information, i.e., the skeleton of white matter, thus the registration would be better than totally automatic VBA method. TBSS definitely has its advantages in DTI analysis, nonetheless, it is not without flaw or limitation: 1.Partial volume effect still exists in TBSS method, and the problem may be greatly exacerbated in spatial smoothing; 2. Increased head motion can increase image blurring and bias FA value; 3. In regions of crossing tracts or junctions, TBSS may misinterpret the change of tracks in junction as apparently reduced FA; 4. Finally, in patients with apparent pathological changes, TBSS may exclude the areas from analysis. There are always advantages and disadvantages of each method in DTI studies. TBSS as new method, may be generally more accurate than VBA method, although it needs more sophisticated data projection approach in the future. We also need to keep in mind that DTI is based on information of water diffusion, it may help to screen and generate hypothesis rather than to draw a final conclusion. ------------------------------------------------------------------------------- On 13 May 2010 23:44, susumu mori wrote: > Good question Gao. > > Here is my thought (my personal opinion, of course); > > 1) you are comparing VBA and TBSS. These are methods to "define > corresponding pixels (or areas) across subjects", so that you can compare > pixel numbers such as FA and MD among different brains. This is called > "registration". > 2) These methods can be classified from different point of views; > 2-1) granularity: One extreme is to define the entire brain as one ROI. You > can get the whole brain volume, whole brain FA, or whole brain histogram. > While there is not much use of this approach, it is precise (do 10 times and > you get the same results) and accurate (nobody makes mistakes about where is > the whole brain except for some ambiguity about where you cut the ROI in the > brainstem). The other extreme is the pixel, which is the smallest unit. This > mean, you identify the corresponding pixels across subjects. Once you map > the entire 1 million pixels in one brain to the other, it is the same as > transforming one brain to the other (two brains now have the same shape). > This approach is called "normalization" and, of course, not accurate because > it is not possible to completely solve the system and accurately map all 1 > million pixels. VBA and TBSS are based on this normalization procedure. > There are methods to ameliorate this accuracy issue. Usually VBA uses > filters to blur the information. In my understanding, TBSS "re-register" > nearby pixel information to the core of the white matter, which could be > considered as a sort of filtering, reducing the granularity and hopefully > increasing the accuracy. > 2-2) Anatomy: When we do normalization, computer algorithm do not care > about anatomy. It just does whatever it thinks best to register pixels. This > is the pixel-based analysis. On the other hand, manual ROI is usually based > on anatomical information we can perceive. This is anatomy-based analysis. > Tractography-based analysis can also be considered as a kind of registration > method. We do, for example, tractography of the cortico-spinal tract in 10 > subjects. Then we can define a group of pixels that belong to the CST and > compare the pixel values. In this way, we define a specific area across > subjects based on anatomy. > 3) In MriStudio, DiffeoMap does pixel-based registration just as VBA. You > can do VBA analysis. In addition, you can superimpose our parcellation map > and divide the brain into about 150 areas. In terms of granularity, it is > much less than VBA (more than 1 million pixels vs 150 areas). This is also a > conversion to pixel-based to anatomy-based analysis. > 4) Now going back to your question, VBA and TBSS are looking at the same > data with different point of view. First of all, the granularity is > different; TBSS reduces the information to the white matter core. Also, VBA > is completely pixel-based but TBSS, which is not completely anatomy-based > but has some anatomy-based factors by reducing the information to the core > of the white matter. > 5) In my opinion, all methods described above have advantages and > disadvantages. I don't think any one of them is better than the other. > Quantification based on location information is definitely one of the most > difficult problems we are all facing. > 6) On the other hand, your reviewer is correct, in a sense that it is > always important to compare different results to enrich your data and > interpretation. This is especially true if there is a tool widely used like > TBSS. However, it is not like, one method should be treated as the gold > standard and other approaches should give a similar result. If you compare > VBA and TBSS, you likely to get different results because as explained above > they are operating at the different granularity, precision, and accuracy. > MRI image anlaysis is very often a screening and hypothesis generating tool > rather than a tool to draw a conclusion. We are simply looking at 6MB > information based on water signal. > > So, in conclusion, > > > No, VBA is not out of date > > Yes, it is a good idea to compare results from widely used tools, but any > normalization-based method should not be considered as a gold standard in my > opinion. We just have to understand how they operate and what are their > advantages and disadvantages. > > On Thu, May 13, 2010 at 8:07 AM, lion gao wrote: > >> Dear Experts, >> >> >> >> I have one part of my thesis on DTI data analysis. The method I used is >> the voxel-based analysis (VBA) and I tried MRIstudio as well. One of the >> examiners pointed out that track-based spatial statistics (TBSS), as a state >> of art way, should have been considered. >> >> >> I am familiar with TBSS, only know that it may reduce systemic >> mis-registration inVBA and increasing papers published with the method. I am >> not sure whether: >> 1. VBA has become ?out of date?, >> 2. and TBSS has become a ?golden standard? for DTI data analysis. >> >> Can someone help to justify the situation or defense a little bit? Thank >> you very much in advance! >> >> >> Best wishes, >> >> Gao >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100515/668d5561/attachment-0001.html From gaolion at gmail.com Fri May 14 13:48:29 2010 From: gaolion at gmail.com (lion gao) Date: Sat, 15 May 2010 01:48:29 +0800 Subject: [Mristudio-users] DTI method: VBA, MRIstudio vs. TBSS In-Reply-To: <10f3d2c.b073.128921fbc14.Coremail.miaomiaolong@126.com> References: <10f3d2c.b073.128921fbc14.Coremail.miaomiaolong@126.com> Message-ID: Yeah, New technique, fact, idea,etc. whatever, new things are eye-catching and can even generate new papers ~Joke- thank for your idea :) On 13 May 2010 22:44, Longmm wrote: > actually, the most amazing part of a good research is new techniqe, or > fact, or idea from an well established traditional stable experiment or > design , or facts. > > ?2010-05-13 20:07:52?"lion gao" ??? > > Dear Experts, > > > > I have one part of my thesis on DTI data analysis. The method I used is the > voxel-based analysis (VBA) and I tried MRIstudio as well. One of the > examiners pointed out that track-based spatial statistics (TBSS), as a state > of art way, should have been considered. > > > I am familiar with TBSS, only know that it may reduce systemic > mis-registration inVBA and increasing papers published with the method. I am > not sure whether: > 1. VBA has become ?out of date?, > 2. and TBSS has become a ?golden standard? for DTI data analysis. > > Can someone help to justify the situation or defense a little bit? Thank > you very much in advance! > > > Best wishes, > > Gao > > > > ------------------------------ > ????????????????????? > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100515/26feb93a/attachment.html From susumu at mri.jhu.edu Fri May 14 18:24:21 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 14 May 2010 18:24:21 -0400 Subject: [Mristudio-users] DTI method: VBA, MRIstudio vs. TBSS In-Reply-To: References: Message-ID: Well, I didn't mean TBSS was better than the other. Different granularity means different sensitivity/specificity to different types of diseases. For example, when we are studying brain growth and tissue atrophy in certain neurodegenerative disease, it happens in a global manner. There is an overall tendency like frontal lobe develop earlier than the occipital lobe. When you are going after this type of changes, it doesn't make sense to use the smallest granularity (pixel). If the change is only 5%, you can't find it by pixel-based methods because each pixel is too noisy. TBSS may also have too much granularity because each skeleton point may average only few adjacent pixels. In this case, an ROI drawn in the frontal lobe and occiptal lobe averaging thousands of pixels may be a better method. On the other hand if a lesion is sharply localized, then you want higher granularity. Pixels averaging always have a danger that abnormal pixels are averaged with normal pixels and thus dilute the effect. Raw pixel-based data is therefore always nice to have. It has low sensitivity and you can hardly get any statistical level once you do multiple-pixel comparison. But if you lower the statistical thresholding, you start to see some tendency. The filtering (pixel averaging) by TBSS may help to bring up such information above the surface of statistical power. However, you can also argue that if the abnormality is localized to one side of the tract, the projection to the center of the white matter core would decrease the sensitivity. Also, you can also argue that the skeletanization is somewhat a blackbox operation. When you are looking at the white matter away from the core where there are cross-subject variability, I'm not sure how the white matter is skeletanized and how they are aligned among subjects. Again, VBA data is one step closer to raw data before the high order image analysis such as TBSS do something on the pixel-by-pixel data. So you can argue that VBA and TBSS is not A or B, it is more like A or AxB Hope it helps. On Fri, May 14, 2010 at 1:41 PM, lion gao wrote: > Dear Susumu Mori, > > Thanks very much for your answer, it's very informative! > One question is that when you mention granularity and anatomy, it finally > all leads to the advantages of TBSS, the skeleton. so my answer looks a bit > repeated for a same point. Another one is I do need to find some flaw in > TBSS for defence use :P, so I find some limitation from the original paper. > BTW, I am NOT familiar with TBSS. > http://sirl.stanford.edu/~bob/pdf/DTI/Methods/Smith_TBSS_NeuroImage06.pdf > > Finally, I arranged some defences based on your comments below. Have a look > if interested , or simply skip it :) > > Thanks again & Best Wishes, > Gao > > > It has been quite a time since VBA was popularly used in DTI data, while > track-based spatial statistical gains popularity rapid in recent years. To > compare the two methods, there two points of views need to the clarified: > > 1. Granularity. It represents the extent to which a system is > divided into smaller parts. In VBA, the brain is broken into nearly one > million of voxels, then it is normalized before comparing with one another. > In MRIstudio, it can superimpose the parcellation map and divided the brain > into 150 areas, thus it has less granularity than VBA (1 million vs. 150). > Whereas TBSS re-registers nearby voxels to the skeleton of white matter, > reduces the granularity and increases the accuracy of registration. > > 2. Anatomy. In VBA analysis, computer algorithm registers the voxels > automatically, without considering any anatomical information. Another new > method of Tissue-specific, smoothing-compensated (T-SPOON) can improve the > tissue specificity in VBA method and compensation for images smoothing. TBSS > can also apply some anatomical information, i.e., the skeleton of white > matter, thus the registration would be better than totally automatic VBA > method. > > > > TBSS definitely has its advantages in DTI analysis, nonetheless, it is not > without flaw or limitation: 1.Partial volume effect still exists in TBSS > method, and the problem may be greatly exacerbated in spatial smoothing; 2. > Increased head motion can increase image blurring and bias FA value; 3. In > regions of crossing tracts or junctions, TBSS may misinterpret the change of > tracks in junction as apparently reduced FA; 4. Finally, in patients with > apparent pathological changes, TBSS may exclude the areas from analysis. > > > > There are always advantages and disadvantages of each method in DTI > studies. TBSS as new method, may be generally more accurate than VBA method, > although it needs more sophisticated data projection approach in the future. > We also need to keep in mind that DTI is based on information of water > diffusion, it may help to screen and generate hypothesis rather than to draw > a final conclusion. > > > > > > > > > ------------------------------------------------------------------------------- > > > > On 13 May 2010 23:44, susumu mori wrote: > >> Good question Gao. >> >> Here is my thought (my personal opinion, of course); >> >> 1) you are comparing VBA and TBSS. These are methods to "define >> corresponding pixels (or areas) across subjects", so that you can compare >> pixel numbers such as FA and MD among different brains. This is called >> "registration". >> 2) These methods can be classified from different point of views; >> 2-1) granularity: One extreme is to define the entire brain as one ROI. >> You can get the whole brain volume, whole brain FA, or whole brain >> histogram. While there is not much use of this approach, it is precise (do >> 10 times and you get the same results) and accurate (nobody makes mistakes >> about where is the whole brain except for some ambiguity about where you cut >> the ROI in the brainstem). The other extreme is the pixel, which is the >> smallest unit. This mean, you identify the corresponding pixels across >> subjects. Once you map the entire 1 million pixels in one brain to the >> other, it is the same as transforming one brain to the other (two brains now >> have the same shape). This approach is called "normalization" and, of >> course, not accurate because it is not possible to completely solve the >> system and accurately map all 1 million pixels. VBA and TBSS are based on >> this normalization procedure. There are methods to ameliorate this accuracy >> issue. Usually VBA uses filters to blur the information. In my >> understanding, TBSS "re-register" nearby pixel information to the core of >> the white matter, which could be considered as a sort of filtering, reducing >> the granularity and hopefully increasing the accuracy. >> 2-2) Anatomy: When we do normalization, computer algorithm do not care >> about anatomy. It just does whatever it thinks best to register pixels. This >> is the pixel-based analysis. On the other hand, manual ROI is usually based >> on anatomical information we can perceive. This is anatomy-based analysis. >> Tractography-based analysis can also be considered as a kind of registration >> method. We do, for example, tractography of the cortico-spinal tract in 10 >> subjects. Then we can define a group of pixels that belong to the CST and >> compare the pixel values. In this way, we define a specific area across >> subjects based on anatomy. >> 3) In MriStudio, DiffeoMap does pixel-based registration just as VBA. You >> can do VBA analysis. In addition, you can superimpose our parcellation map >> and divide the brain into about 150 areas. In terms of granularity, it is >> much less than VBA (more than 1 million pixels vs 150 areas). This is also a >> conversion to pixel-based to anatomy-based analysis. >> 4) Now going back to your question, VBA and TBSS are looking at the same >> data with different point of view. First of all, the granularity is >> different; TBSS reduces the information to the white matter core. Also, VBA >> is completely pixel-based but TBSS, which is not completely anatomy-based >> but has some anatomy-based factors by reducing the information to the core >> of the white matter. >> 5) In my opinion, all methods described above have advantages and >> disadvantages. I don't think any one of them is better than the other. >> Quantification based on location information is definitely one of the most >> difficult problems we are all facing. >> 6) On the other hand, your reviewer is correct, in a sense that it is >> always important to compare different results to enrich your data and >> interpretation. This is especially true if there is a tool widely used like >> TBSS. However, it is not like, one method should be treated as the gold >> standard and other approaches should give a similar result. If you compare >> VBA and TBSS, you likely to get different results because as explained above >> they are operating at the different granularity, precision, and accuracy. >> MRI image anlaysis is very often a screening and hypothesis generating tool >> rather than a tool to draw a conclusion. We are simply looking at 6MB >> information based on water signal. >> >> So, in conclusion, >> >> > No, VBA is not out of date >> > Yes, it is a good idea to compare results from widely used tools, but >> any normalization-based method should not be considered as a gold standard >> in my opinion. We just have to understand how they operate and what are >> their advantages and disadvantages. >> >> On Thu, May 13, 2010 at 8:07 AM, lion gao wrote: >> >>> Dear Experts, >>> >>> >>> >>> I have one part of my thesis on DTI data analysis. The method I used is >>> the voxel-based analysis (VBA) and I tried MRIstudio as well. One of the >>> examiners pointed out that track-based spatial statistics (TBSS), as a state >>> of art way, should have been considered. >>> >>> >>> I am familiar with TBSS, only know that it may reduce systemic >>> mis-registration inVBA and increasing papers published with the method. I am >>> not sure whether: >>> 1. VBA has become ?out of date?, >>> 2. and TBSS has become a ?golden standard? for DTI data analysis. >>> >>> Can someone help to justify the situation or defense a little bit? Thank >>> you very much in advance! >>> >>> >>> Best wishes, >>> >>> Gao >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100514/5ecd58ab/attachment-0001.html From gaolion at gmail.com Sat May 15 12:46:54 2010 From: gaolion at gmail.com (lion gao) Date: Sun, 16 May 2010 00:46:54 +0800 Subject: [Mristudio-users] DTI method: VBA, MRIstudio vs. TBSS In-Reply-To: References: Message-ID: Dear Susumu Mori, Sorry that I misunderstood some of your previous ellaboration. Now I get closer to your points, as well as the helpful arguements :) I guess I may add some points to my defense for VBA. Thanks again very much for your further explanation! Best wishes, Gao On 15 May 2010 06:24, susumu mori wrote: > Well, I didn't mean TBSS was better than the other. Different granularity > means different sensitivity/specificity to different types of diseases. > > For example, when we are studying brain growth and tissue atrophy in > certain neurodegenerative disease, it happens in a global manner. There is > an overall tendency like frontal lobe develop earlier than the occipital > lobe. When you are going after this type of changes, it doesn't make sense > to use the smallest granularity (pixel). If the change is only 5%, you can't > find it by pixel-based methods because each pixel is too noisy. TBSS may > also have too much granularity because each skeleton point may average only > few adjacent pixels. In this case, an ROI drawn in the frontal lobe and > occiptal lobe averaging thousands of pixels may be a better method. > > On the other hand if a lesion is sharply localized, then you want higher > granularity. Pixels averaging always have a danger that abnormal pixels are > averaged with normal pixels and thus dilute the effect. > > Raw pixel-based data is therefore always nice to have. It has low > sensitivity and you can hardly get any statistical level once you do > multiple-pixel comparison. But if you lower the statistical thresholding, > you start to see some tendency. The filtering (pixel averaging) by TBSS may > help to bring up such information above the surface of statistical power. > However, you can also argue that if the abnormality is localized to one side > of the tract, the projection to the center of the white matter core would > decrease the sensitivity. > > Also, you can also argue that the skeletanization is somewhat a blackbox > operation. When you are looking at the white matter away from the core where > there are cross-subject variability, I'm not sure how the white matter is > skeletanized and how they are aligned among subjects. > > Again, VBA data is one step closer to raw data before the high order image > analysis such as TBSS do something on the pixel-by-pixel data. So you can > argue that VBA and TBSS is not A or B, it is more like A or AxB > > Hope it helps. > > > On Fri, May 14, 2010 at 1:41 PM, lion gao wrote: > >> Dear Susumu Mori, >> >> Thanks very much for your answer, it's very informative! >> One question is that when you mention granularity and anatomy, it finally >> all leads to the advantages of TBSS, the skeleton. so my answer looks a bit >> repeated for a same point. Another one is I do need to find some flaw in >> TBSS for defence use :P, so I find some limitation from the original paper. >> BTW, I am NOT familiar with TBSS. >> http://sirl.stanford.edu/~bob/pdf/DTI/Methods/Smith_TBSS_NeuroImage06.pdf >> >> Finally, I arranged some defences based on your comments below. Have a >> look if interested , or simply skip it :) >> >> Thanks again & Best Wishes, >> Gao >> >> >> It has been quite a time since VBA was popularly used in DTI data, while >> track-based spatial statistical gains popularity rapid in recent years. To >> compare the two methods, there two points of views need to the clarified: >> >> 1. Granularity. It represents the extent to which a system is >> divided into smaller parts. In VBA, the brain is broken into nearly one >> million of voxels, then it is normalized before comparing with one another. >> In MRIstudio, it can superimpose the parcellation map and divided the brain >> into 150 areas, thus it has less granularity than VBA (1 million vs. 150). >> Whereas TBSS re-registers nearby voxels to the skeleton of white matter, >> reduces the granularity and increases the accuracy of registration. >> >> 2. Anatomy. In VBA analysis, computer algorithm registers the >> voxels automatically, without considering any anatomical information. >> Another new method of Tissue-specific, smoothing-compensated (T-SPOON) can >> improve the tissue specificity in VBA method and compensation for images >> smoothing. TBSS can also apply some anatomical information, i.e., the >> skeleton of white matter, thus the registration would be better than totally >> automatic VBA method. >> >> >> >> TBSS definitely has its advantages in DTI analysis, nonetheless, it is not >> without flaw or limitation: 1.Partial volume effect still exists in TBSS >> method, and the problem may be greatly exacerbated in spatial smoothing; 2. >> Increased head motion can increase image blurring and bias FA value; 3. In >> regions of crossing tracts or junctions, TBSS may misinterpret the change of >> tracks in junction as apparently reduced FA; 4. Finally, in patients with >> apparent pathological changes, TBSS may exclude the areas from analysis. >> >> >> >> There are always advantages and disadvantages of each method in DTI >> studies. TBSS as new method, may be generally more accurate than VBA method, >> although it needs more sophisticated data projection approach in the future. >> We also need to keep in mind that DTI is based on information of water >> diffusion, it may help to screen and generate hypothesis rather than to draw >> a final conclusion. >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------- >> >> >> >> On 13 May 2010 23:44, susumu mori wrote: >> >>> Good question Gao. >>> >>> Here is my thought (my personal opinion, of course); >>> >>> 1) you are comparing VBA and TBSS. These are methods to "define >>> corresponding pixels (or areas) across subjects", so that you can compare >>> pixel numbers such as FA and MD among different brains. This is called >>> "registration". >>> 2) These methods can be classified from different point of views; >>> 2-1) granularity: One extreme is to define the entire brain as one ROI. >>> You can get the whole brain volume, whole brain FA, or whole brain >>> histogram. While there is not much use of this approach, it is precise (do >>> 10 times and you get the same results) and accurate (nobody makes mistakes >>> about where is the whole brain except for some ambiguity about where you cut >>> the ROI in the brainstem). The other extreme is the pixel, which is the >>> smallest unit. This mean, you identify the corresponding pixels across >>> subjects. Once you map the entire 1 million pixels in one brain to the >>> other, it is the same as transforming one brain to the other (two brains now >>> have the same shape). This approach is called "normalization" and, of >>> course, not accurate because it is not possible to completely solve the >>> system and accurately map all 1 million pixels. VBA and TBSS are based on >>> this normalization procedure. There are methods to ameliorate this accuracy >>> issue. Usually VBA uses filters to blur the information. In my >>> understanding, TBSS "re-register" nearby pixel information to the core of >>> the white matter, which could be considered as a sort of filtering, reducing >>> the granularity and hopefully increasing the accuracy. >>> 2-2) Anatomy: When we do normalization, computer algorithm do not care >>> about anatomy. It just does whatever it thinks best to register pixels. This >>> is the pixel-based analysis. On the other hand, manual ROI is usually based >>> on anatomical information we can perceive. This is anatomy-based analysis. >>> Tractography-based analysis can also be considered as a kind of registration >>> method. We do, for example, tractography of the cortico-spinal tract in 10 >>> subjects. Then we can define a group of pixels that belong to the CST and >>> compare the pixel values. In this way, we define a specific area across >>> subjects based on anatomy. >>> 3) In MriStudio, DiffeoMap does pixel-based registration just as VBA. You >>> can do VBA analysis. In addition, you can superimpose our parcellation map >>> and divide the brain into about 150 areas. In terms of granularity, it is >>> much less than VBA (more than 1 million pixels vs 150 areas). This is also a >>> conversion to pixel-based to anatomy-based analysis. >>> 4) Now going back to your question, VBA and TBSS are looking at the same >>> data with different point of view. First of all, the granularity is >>> different; TBSS reduces the information to the white matter core. Also, VBA >>> is completely pixel-based but TBSS, which is not completely anatomy-based >>> but has some anatomy-based factors by reducing the information to the core >>> of the white matter. >>> 5) In my opinion, all methods described above have advantages and >>> disadvantages. I don't think any one of them is better than the other. >>> Quantification based on location information is definitely one of the most >>> difficult problems we are all facing. >>> 6) On the other hand, your reviewer is correct, in a sense that it is >>> always important to compare different results to enrich your data and >>> interpretation. This is especially true if there is a tool widely used like >>> TBSS. However, it is not like, one method should be treated as the gold >>> standard and other approaches should give a similar result. If you compare >>> VBA and TBSS, you likely to get different results because as explained above >>> they are operating at the different granularity, precision, and accuracy. >>> MRI image anlaysis is very often a screening and hypothesis generating tool >>> rather than a tool to draw a conclusion. We are simply looking at 6MB >>> information based on water signal. >>> >>> So, in conclusion, >>> >>> > No, VBA is not out of date >>> > Yes, it is a good idea to compare results from widely used tools, but >>> any normalization-based method should not be considered as a gold standard >>> in my opinion. We just have to understand how they operate and what are >>> their advantages and disadvantages. >>> >>> On Thu, May 13, 2010 at 8:07 AM, lion gao wrote: >>> >>>> Dear Experts, >>>> >>>> >>>> >>>> I have one part of my thesis on DTI data analysis. The method I used is >>>> the voxel-based analysis (VBA) and I tried MRIstudio as well. One of the >>>> examiners pointed out that track-based spatial statistics (TBSS), as a state >>>> of art way, should have been considered. >>>> >>>> >>>> I am familiar with TBSS, only know that it may reduce systemic >>>> mis-registration inVBA and increasing papers published with the method. I am >>>> not sure whether: >>>> 1. VBA has become ?out of date?, >>>> 2. and TBSS has become a ?golden standard? for DTI data analysis. >>>> >>>> Can someone help to justify the situation or defense a little bit? Thank >>>> you very much in advance! >>>> >>>> >>>> Best wishes, >>>> >>>> Gao >>>> >>>> _______________________________________________ >>>> Mristudio-users mailing list >>>> Mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> Mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100516/a8f3f3c8/attachment-0001.html From d-gitelman at northwestern.edu Mon May 17 00:04:23 2010 From: d-gitelman at northwestern.edu (Darren Gitelman) Date: Sun, 16 May 2010 23:04:23 -0500 Subject: [Mristudio-users] Theory registration Message-ID: Hi When using the theory registration method, which images are changed? The original images? It doesn't seem to produce new images such as with mutual information or AIR. Darren -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100516/21794e65/attachment.html From igor.yakushev at uni-mainz.de Mon May 17 06:53:08 2010 From: igor.yakushev at uni-mainz.de (Yakushev, Igor) Date: Mon, 17 May 2010 10:53:08 +0000 Subject: [Mristudio-users] Impact of white matter lesionson on accuracy of fiber tracking (FACT) Message-ID: Dear Colleagues, I wonder if there is any empirical evidence about impact of white matter lesions (WML) on accuracy of fiber tracking? The following questions are of specific interest: 1) what is the (at least expected) range of FA-values in a WML? Can FA-values within a WML (at least a proportion of voxels) be still within the range typical for "normal" WM? 2) To what extent can one exclude/minimize impact of WML on performance of FACT (in a specific brain region) by simply adjusting the FA-threshold? 3) In other words, if one tracts a specific fiber bundle within the brain with a pronounced vascular encephalopathy (VE) at a common FA-threshold of 0.2, and the resulting track looks fine, i.e. not worse as in a subject without any VE, can one conclude that there was just no WML over the course of this particular track and tracking is likely to be not biased by VE in this subject? 4) Let's lower the FA-threshold down to 0.05, repeat the above analysis and consider two possible outcomes: a) fiber tracking in the VE+ subject produced considerably less fibers than in the VE- subject; b) fiber tracking produced the same results in both subject. Can one now conclude that tracking of this particular bundle is a) biased b) not biased by VE, respectively? Thanks. Igor ****************************** Igor Yakushev, MD Department of Psychiatry University Medical Center Mainz Mainz, Germany From d-gitelman at northwestern.edu Mon May 17 09:42:14 2010 From: d-gitelman at northwestern.edu (Darren Gitelman) Date: Mon, 17 May 2010 08:42:14 -0500 Subject: [Mristudio-users] theory - registration Message-ID: Hi I am trying to use automatic outlier pixel rejection. Even though I click the button for a binary mask image no mask is produced that I can see. The second issue is that after running pixel rejection 3 of the images have a red X through them. Why should this occur? thanks, Darren -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100517/3e35c02c/attachment.html From susumu at mri.jhu.edu Mon May 17 14:30:33 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 17 May 2010 14:30:33 -0400 Subject: [Mristudio-users] theory - registration In-Reply-To: References: Message-ID: Hi Darren, When you choose, "pixel-rejection", I assume that you choose "Optional parameters" too. Then you should not get the red X. Please confirm that you are using the latest DtiStudio posted in the web currently. Susumu On Mon, May 17, 2010 at 9:42 AM, Darren Gitelman < d-gitelman at northwestern.edu> wrote: > Hi > > I am trying to use automatic outlier pixel rejection. Even though I click > the button for a binary mask image no mask is produced that I can see. > > The second issue is that after running pixel rejection 3 of the images have > a red X through them. Why should this occur? > > thanks, > Darren > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100517/4ffaa459/attachment.html From d-gitelman at northwestern.edu Tue May 18 03:15:56 2010 From: d-gitelman at northwestern.edu (Darren Gitelman) Date: Tue, 18 May 2010 02:15:56 -0500 Subject: [Mristudio-users] theory - registration In-Reply-To: References: Message-ID: Dear Susumu I am using the latest 64 bit version that I can download- 3.0.2 (Mar 2010). When I click pixel rejection, there is no dialog that says Yue's method, yes | no. There is just a button that says optional parameters. I filled in 30 for the min bad area, 3 for the min z value and 50 for the min B0- value. Then I clicked binary mask. Then OK to the options dialog. Then OK to the DTI-Map Options dialog. The calculation starts, but again the X appear on the slices and there is no binary pixel mask. While I'm at it I have some other questions about theory - registration 1) Should I run other registration methods such as AIR or MI before theory-registratin? Will theory-registration take care of eddy current correction? 2) What images are changed by theory registration? The original images? It doesn't seem to produce new images such as with mutual information or AIR. Thanks, Darren From hjiang at jhmi.edu Tue May 18 09:43:47 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Tue, 18 May 2010 09:43:47 -0400 Subject: [Mristudio-users] theory - registration In-Reply-To: References: Message-ID: <145933A2BE9E4F48AE079A201379BF2F210CC23A55@RAD-EXCH1.win.ad.jhu.edu> hi, for Yue's method, clicking "Optional parameters" in pixel rejection option, then a parameter dialog will pup up... clicking OK.... otherwise, the outlier pixel rejection uses default parameters. it is a good question about difference between "theory - registration" and "normal AIR" (in the "image" tab) basically, "normal AIR" will register ALL target images to a single user-selected reference image (usually a B0, or mean B0s). BEFORE tensor calculation. on the other hand, "theory - registration" do registration for each DWI INDIVIDUALLY with its theory-one iteratively DURING tensor calculation. in this procedure, the original images are not being changed. usually, AIR can do a better job if both the reference and target are in similar modality and intensity. from this point of view, "individual" registration during tensor calculation should be better than "normal AIR" before tensor calculation. however, this method may result in mis-alignment between different DWIs, since the registration is carried out for every single-pair (original and theory one) images, not for all DWIs. so it is hard to say which method is better. as my opinion, if the the mis-alignment between the DWIs is a dominant artifact, then "normal AIR" before tensor calculation is recommended. otherwise, "theory - registration" during tensor calculation is a good choice. regards, hangyi ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Darren Gitelman [d-gitelman at northwestern.edu] Sent: Tuesday, May 18, 2010 3:15 AM To: mristudio-users Subject: Re: [Mristudio-users] theory - registration Dear Susumu I am using the latest 64 bit version that I can download- 3.0.2 (Mar 2010). When I click pixel rejection, there is no dialog that says Yue's method, yes | no. There is just a button that says optional parameters. I filled in 30 for the min bad area, 3 for the min z value and 50 for the min B0- value. Then I clicked binary mask. Then OK to the options dialog. Then OK to the DTI-Map Options dialog. The calculation starts, but again the X appear on the slices and there is no binary pixel mask. While I'm at it I have some other questions about theory - registration 1) Should I run other registration methods such as AIR or MI before theory-registratin? Will theory-registration take care of eddy current correction? 2) What images are changed by theory registration? The original images? It doesn't seem to produce new images such as with mutual information or AIR. Thanks, Darren _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Tue May 18 10:48:41 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 18 May 2010 10:48:41 -0400 Subject: [Mristudio-users] theory - registration In-Reply-To: References: Message-ID: Darren, You are using the "Pixel rejection" correctly and we have to investigate why you are getting "Image rejection" results. 1) Should I run other registration methods such as AIR or MI before > theory-registratin? Will theory-registration take care of eddy current > correction? > >Theory registration should be used instead of AIR or MI. I have to confirm Hangyi if TheoryAIR does rigid or affine. I'll get back to you with this respect too. > > 2) What images are changed by theory registration? The original > images? It doesn't seem to produce new images such as with mutual > information or AIR. > >Yes, when you use TheoryAIR, you don't get a copy. The original images are overwritten. > > Thanks, > Darren > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100518/105757bf/attachment.html From susumu at mri.jhu.edu Tue May 18 10:48:41 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 18 May 2010 10:48:41 -0400 Subject: [Mristudio-users] theory - registration In-Reply-To: References: Message-ID: Darren, You are using the "Pixel rejection" correctly and we have to investigate why you are getting "Image rejection" results. 1) Should I run other registration methods such as AIR or MI before > theory-registratin? Will theory-registration take care of eddy current > correction? > >Theory registration should be used instead of AIR or MI. I have to confirm Hangyi if TheoryAIR does rigid or affine. I'll get back to you with this respect too. > > 2) What images are changed by theory registration? The original > images? It doesn't seem to produce new images such as with mutual > information or AIR. > >Yes, when you use TheoryAIR, you don't get a copy. The original images are overwritten. > > Thanks, > Darren > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100518/105757bf/attachment-0003.html From luca.binotto at unipd.it Tue May 18 11:24:36 2010 From: luca.binotto at unipd.it (luca.binotto at unipd.it) Date: Tue, 18 May 2010 17:24:36 +0200 Subject: [Mristudio-users] DTI Synthetic Dataset Message-ID: <201e7fe9c55fdb757725461a22eee369.squirrel@webmail.unipd.it> Hello there, does someone know where can I download a DTI synthetic dataset to compare different processing strategies in DtiStudio ? Many thanks in advance, best regards, Luca From susumu at mri.jhu.edu Tue May 18 11:39:40 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 18 May 2010 11:39:40 -0400 Subject: [Mristudio-users] DTI Synthetic Dataset In-Reply-To: <201e7fe9c55fdb757725461a22eee369.squirrel@webmail.unipd.it> References: <201e7fe9c55fdb757725461a22eee369.squirrel@webmail.unipd.it> Message-ID: If you were talking about synthetic data for fiber tracking, ISMRM diffusion/perfusion study group once set up a website to download such data. If you are talking bout synthetic DTI data, I'm not sure. Susumu On Tue, May 18, 2010 at 11:24 AM, wrote: > Hello there, > does someone know where can I download a DTI synthetic dataset > to compare different processing strategies in DtiStudio ? > > Many thanks in advance, > best regards, Luca > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100518/cfd8b025/attachment.html From mithra at mail.utexas.edu Tue May 18 14:58:05 2010 From: mithra at mail.utexas.edu (Mithra) Date: Tue, 18 May 2010 13:58:05 -0500 Subject: [Mristudio-users] Eddy Current correction Message-ID: Hello, Is there a way to do eddy current correction using DTI studio? Thanks. - Mithra. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100518/aaf7fe8e/attachment.html From susumu at mri.jhu.edu Tue May 18 15:28:00 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 18 May 2010 15:28:00 -0400 Subject: [Mristudio-users] Eddy Current correction In-Reply-To: References: Message-ID: When you do image corregistration using AIR, choose "Affine". Then it should reduce eddy current distortion as well as motion. If you choose "Rigid", then it corrects only motion. On Tue, May 18, 2010 at 2:58 PM, Mithra wrote: > Hello, > Is there a way to do eddy current correction using DTI studio? > > Thanks. > - Mithra. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100518/0228f6bb/attachment.html From choisj70 at gmail.com Tue May 18 15:28:48 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 18 May 2010 15:28:48 -0400 Subject: [Mristudio-users] Eddy Current correction In-Reply-To: References: Message-ID: Mithra, Load data into DTI Studio with your gradient table. Do AIR (Automatic Image Registration) or MI (Mutual-info img. registration) with Affine option. Registration with Affine option will do eddy-current correction. -SC On Tue, May 18, 2010 at 2:58 PM, Mithra wrote: > Hello, > Is there a way to do eddy current correction using DTI studio? > > Thanks. > - Mithra. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100518/83d66178/attachment.html From luca.binotto at unipd.it Wed May 19 10:00:16 2010 From: luca.binotto at unipd.it (luca.binotto at unipd.it) Date: Wed, 19 May 2010 16:00:16 +0200 Subject: [Mristudio-users] DTI Synthetic Dataset In-Reply-To: References: <201e7fe9c55fdb757725461a22eee369.squirrel@webmail.unipd.it> Message-ID: Yes, I was talking about synthetic data for fiber tracking. I gave a look at ISMRM study group website, it seems that to access their resources one must pay for membership. In any case, thanks for the reply. > If you were talking about synthetic data for fiber tracking, ISMRM > diffusion/perfusion study group once set up a website to download such > data. > If you are talking bout synthetic DTI data, I'm not sure. > > Susumu > > On Tue, May 18, 2010 at 11:24 AM, wrote: > >> Hello there, >> does someone know where can I download a DTI synthetic dataset >> to compare different processing strategies in DtiStudio ? >> >> Many thanks in advance, >> best regards, Luca >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > From susumu at mri.jhu.edu Wed May 19 12:01:33 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 19 May 2010 12:01:33 -0400 Subject: [Mristudio-users] Impact of white matter lesionson on accuracy of fiber tracking (FACT) In-Reply-To: References: Message-ID: On Mon, May 17, 2010 at 6:53 AM, Yakushev, Igor wrote: > Dear Colleagues, > > > > I wonder if there is any empirical evidence about impact of white matter > lesions (WML) on accuracy of fiber tracking? The following questions are of > specific interest: > > 1) what is the (at least expected) range of FA-values in a WML? Can > FA-values within a WML (at least a proportion of voxels) be still within the > range typical for "normal" WM? > > I think it depends. If the lesion is severe like stroke or some MS lesions, it is filled with fluid. So, FA could be as low as CSF. I think we can't make a generalized comment. > > 2) To what extent can one exclude/minimize impact of WML on performance of > FACT (in a specific brain region) by simply adjusting the FA-threshold? > > Lesion means FA decrease. Then it definitely affect FACT results. FACT is dependent on FA. If FA gets lower than FACT-FA threshold, you don't get a tract. Even if you get a tract, FA decrease could lead to higher uncertainty in eigenvectors. Then tracking through lesion could be more affected by noise. > In one sense, the high sensitivity of FACT to lesion is good because it can detect lesion (although you may not need to do FACT to identify lesions). > but in most case, the high sensitivity is not desirable. That is why we tested an atlas-based approach (Neuroimage. 2008 Jan 1;39(1):336-47), if you are interested in MRI-parameter (e.g. FA, MD, diffusivity, T2) along a tract of your interest > If you are interested in tract anatomy itself under the existence of lesions, then the atlas-based approach won't work. > One possible way to minimize the effect is to use multiple ROIs to increase the anatomical constraint and lower FA threshold. In this way, FACT results become less sensitive to FA decrease. > > 3) In other words, if one tracts a specific fiber bundle within the brain > with a pronounced vascular encephalopathy (VE) at a common FA-threshold of > 0.2, and the resulting track looks fine, i.e. not worse as in a subject > without any VE, can one conclude that there was just no WML over the course > of this particular track and tracking is likely to be not biased by VE in > this subject? > > > It is in general difficult to use tractography for quantitative purpose, but there are two types of information you can get; morphological parameters and pixel intensity parameters. For morphology, we are talking about the shape and size of the tracts. You can count the number of pixels occupied by the streamlines and call it tract volume. The shapes and trajectories are more difficult to quantify, but maybe you can do group analysis by normalizing the tract coordinates from the control and patient groups and compare. For the pixel intensity, you can measure, for example, FA of the tracts using DtiStudio. > It is therefore very important to understand if you want to know the morphology or intensity. In your case, you mentioned "tract looks fine", meaning you didn't see much morphological differences such as thinner or more curved. Then when you asked, "can one conclude that there was just no WML". Then here it seems you are asking more of pixel intensity because WML may cause FA drops and T2 increase, for example. Then you need to quantify FA values of the pixels occupied by the tract. You may find that FA of a portion of the trajectory is actually lower. 4) Let's lower the FA-threshold down to 0.05, repeat the above analysis and > consider two possible outcomes: a) fiber tracking in the VE+ subject > produced considerably less fibers than in the VE- subject; b) fiber tracking > produced the same results in both subject. Can one now conclude that > tracking of this particular bundle is a) biased b) not biased by VE, > respectively? > > Another inherent complication of tractography-based analysis is the coupling of the morphology and pixel intensity (FA). Suppose you have a cluster of pixels with low FA due to WML. Also assume that there is no change in tract size. If you do fiber tracking with FA>0.2, you may get smaller tracts in patients with WML simply because of the FA threshold. Then the result suggests there is a morphological change (the tract is smaller) in the patient, but the truth is FA drop.This is a common problem of many MRI-based study. We are observing signals from water and the entire brain information is contracted to mere tens of megabytes. We can do nice quantitative analysis of the images but interpretation is not always straightforward. > As you mentioned, you can approach the data from multiple angles, like changing the FA threshold. If the tract is thinner with FA>0.2 but not thinner with FA>0.05, then it may suggest that the tract is actually there with the normal size and the FA>0.05 results would yield lower FA values in the pixels within WML, which is the answer closer to the truth. This would certainly deepen your understanding of the pathology. > Tractography is just one way to probe the data and I would suggest you always combine it with other tools such as manual ROI and pixel-based SPM-type analysis. Recently we are using atlas-based analysis (see papers by K. Oishi et al). All these approaches looks at the same data with different angles. It is very difficult to come to a right conclusion with just one method. > > > > Thanks. > > Igor > > > > > > ****************************** > > Igor Yakushev, MD > > Department of Psychiatry > > University Medical Center Mainz > > Mainz, Germany > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100519/a74a5fe0/attachment-0001.html From youngbin at umich.edu Wed May 19 15:15:18 2010 From: youngbin at umich.edu (Youngbin Kwak) Date: Wed, 19 May 2010 15:15:18 -0400 Subject: [Mristudio-users] fiber tracking Message-ID: Hello, We would like to perform fiber tracking using FA maps created from other programs. FA maps are currently in all in MNI normalized space in analyze format. I've chosen the fiber-tracking option from the file menu of DTIstudio and then a window that says Fiber-tracking options pops up. I chose the continuous tracking using principal ventor and FA map and it brings me to the window where you have to set image parameters. For FA-map, I chose the analyze .img file. for the principal vector, I wasn't sure what I should choose.. Also for image dimension and voxel size, I wasn't sure what what values to put.. Can someone guide me here? Thanks! Youngbin -- Youngbin Kwak M.S. Ph.D. candidate, Neuroscience Graduate Program Cognitive Science & Cognitive Neuroscience Program University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100519/544f5377/attachment.html From susumu at mri.jhu.edu Wed May 19 21:52:49 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 19 May 2010 21:52:49 -0400 Subject: [Mristudio-users] fiber tracking In-Reply-To: References: Message-ID: Hi youngbin, The image dimension depends on your data and it's difficult to say what it is. Our MNI space is 181x217x181, but I know that there are several versions of MNI templates with different dimensions. For the vector map, it unfortunately has to be raw format without header, which is floating point with 3 vector components x D1 x D2 x D3. The software you are using needs to have a way to save the vector file in this raw format. susumu On Wed, May 19, 2010 at 3:15 PM, Youngbin Kwak wrote: > Hello, > > We would like to perform fiber tracking using FA maps created from other > programs. FA maps are currently in all in MNI normalized space in analyze > format. I've chosen the fiber-tracking option from the file menu of > DTIstudio and then a window that says Fiber-tracking options pops up. I > chose the continuous tracking using principal ventor and FA map and it > brings me to the window where you have to set image parameters. For FA-map, > I chose the analyze .img file. for the principal vector, I wasn't sure what > I should choose.. Also for image dimension and voxel size, I wasn't sure > what what values to put.. > Can someone guide me here? > > Thanks! > Youngbin > -- > Youngbin Kwak M.S. > Ph.D. candidate, Neuroscience Graduate Program > Cognitive Science & Cognitive Neuroscience Program > University of Michigan > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100519/0ff693eb/attachment.html From zamyadim at sri.utoronto.ca Thu May 20 09:59:26 2010 From: zamyadim at sri.utoronto.ca (Mojdeh) Date: Thu, 20 May 2010 09:59:26 -0400 Subject: [Mristudio-users] Image Quality Flag file Message-ID: <4BF5403E.1010701@sri.utoronto.ca> Hi all, I was wondering about the format of the "Image Quality Flag" file. I already have the number and location of the corrupted slices from past studies and I wanted to know how I can make my own flag file and later load it in the DTIstudio for further calculations. Thanks, Mojdeh From youngbin at umich.edu Thu May 20 10:12:19 2010 From: youngbin at umich.edu (Youngbin Kwak) Date: Thu, 20 May 2010 10:12:19 -0400 Subject: [Mristudio-users] fiber tracking In-Reply-To: References: Message-ID: Thanks Susumu, We have 6 tensor files (Dxx, Dxy, ...) each of them in .img/.hdr I saw that in DTIstudio it allows saving analyze files into raw .dat format? I'm wondering if we know how the principal vector file should look like, I should be able to convert and change the files we have into the format of data DTIstudio can take. Could you send me a sample file of pricipal vector that I could determine how the information is laid out so that I can figure out a way to change my files? Thanks! Youngbin On Wed, May 19, 2010 at 9:52 PM, susumu mori wrote: > Hi youngbin, > > The image dimension depends on your data and it's difficult to say what it > is. Our MNI space is 181x217x181, but I know that there are several versions > of MNI templates with different dimensions. > > For the vector map, it unfortunately has to be raw format without header, > which is floating point with 3 vector components x D1 x D2 x D3. The > software you are using needs to have a way to save the vector file in this > raw format. > > susumu > > On Wed, May 19, 2010 at 3:15 PM, Youngbin Kwak wrote: > >> Hello, >> >> We would like to perform fiber tracking using FA maps created from other >> programs. FA maps are currently in all in MNI normalized space in analyze >> format. I've chosen the fiber-tracking option from the file menu of >> DTIstudio and then a window that says Fiber-tracking options pops up. I >> chose the continuous tracking using principal ventor and FA map and it >> brings me to the window where you have to set image parameters. For FA-map, >> I chose the analyze .img file. for the principal vector, I wasn't sure what >> I should choose.. Also for image dimension and voxel size, I wasn't sure >> what what values to put.. >> Can someone guide me here? >> >> Thanks! >> Youngbin >> -- >> Youngbin Kwak M.S. >> Ph.D. candidate, Neuroscience Graduate Program >> Cognitive Science & Cognitive Neuroscience Program >> University of Michigan >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -- Youngbin Kwak M.S. Ph.D. candidate, Neuroscience Graduate Program Cognitive Science & Cognitive Neuroscience Program University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100520/8c3afef3/attachment.html From choisj70 at gmail.com Thu May 20 11:21:22 2010 From: choisj70 at gmail.com (Seongjin) Date: Thu, 20 May 2010 11:21:22 -0400 Subject: [Mristudio-users] Acquisition with slightly overlapping slice (i.e. negative gap between slices) Message-ID: This might be a stupid question. However, I would like ask your opinions in the community. Is there anyone tried DTI acquisition with a bit of overlapping adjacent slices (i.e. negative gap between slices: e.g. 2 mm slice thickness with -0.03 gap). What would be consequence of this acquisition and adverse influence on the DTI metrics? -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100520/49d9acf7/attachment.html From zamyadim at sri.utoronto.ca Thu May 20 12:05:43 2010 From: zamyadim at sri.utoronto.ca (Mojdeh) Date: Thu, 20 May 2010 12:05:43 -0400 Subject: [Mristudio-users] slice rejection Message-ID: <4BF55DD7.7030108@sri.utoronto.ca> Hi again :) Is there a way to find out which slices have been rejected when using the "Automatic outlier IMAGE_SLICE rejection" mode for DTI fitting? thanks, Mojdeh From naamab at stanford.edu Thu May 20 15:39:08 2010 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Thu, 20 May 2010 12:39:08 -0700 Subject: [Mristudio-users] How to skull strip in ROIeditor? Message-ID: <64133FBA-C47F-44C8-9A55-FB67BEFC1690@stanford.edu> Could anyone send out a step by step process for skull stripping in ROIeditor? (perhaps using a B0 image?). Thanks, Naama Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. From jmcentee at jhmi.edu Thu May 20 16:17:46 2010 From: jmcentee at jhmi.edu (Julie McEntee) Date: Thu, 20 May 2010 16:17:46 -0400 Subject: [Mristudio-users] How to skull strip in ROIeditor? In-Reply-To: <64133FBA-C47F-44C8-9A55-FB67BEFC1690@stanford.edu> Message-ID: Open ROIEditor Click folder icon (under File on top toolbar); choose b0 (change parameters according to your image dimensions/type) 1. Scroll down; under TOOL, click button with oval icon (Skull Stripping; last button on right) 1. Choose ?Skull strip the current archive image only.?; click OK 2. Change Segment Downsample (1,2,or 3) to 1; click OK Under IMAGE, click folder icon (Load Image File); choose FA.dat (same image parameters as b0) Under ROI, click icon with +/-/x/? signs (Operation; 1st button) 1. In left box choose SkullStrippedMaskByte_.b0 2. In center pull-down menu choose Multiplication 3. In right box choose FA.dat; click OK Under IMAGE, click disc icon (Save Image File) 1. In left box choose SkullStripped_.b0, click arrow, click OK 2. Save as .b0ss 3. Repeat save, choose Multiply_ SkullStrippedMaskByte_.b0_FA.dat, click arrow, click OK 4. Save as wrote: > > Could anyone send out a step by step process for skull stripping in > ROIeditor? (perhaps using a B0 image?). > > Thanks, > > Naama > > > > Naama Barnea-Goraly M.D. > Instructor > Center for Interdisciplinary Brain Sciences Research > Stanford University Division of Child and Adolescent Psychiatry > 401 Quarry Rd. MC 5795 > Stanford University School of Medicine > Stanford, CA 94305-5795 > Phone: (650) 736-1874, fax: (650) 724-4794 > > > CONFIDENTIALITY NOTICE: This e-mail communication and any attachments > may contain confidential information for the use of the designated > recipients named above. If you are not the intended recipient, you > are hereby notified that you have received this communication in error > and that any review, disclosure, dissemination, distribution or > copying of it or its contents is prohibited. If you have received > this communication in error, please notify Stanford Medical Center > immediately by telephone at (650) 725-5722 and destroy all copies of > this communication and any attachments. Thank you. > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From ftam-lists at rotman-baycrest.on.ca Fri May 21 07:21:32 2010 From: ftam-lists at rotman-baycrest.on.ca (Fred) Date: Fri, 21 May 2010 07:21:32 -0400 Subject: [Mristudio-users] gradient table options Message-ID: <1274440892.5506.35.camel@fissure.rotman-baycrest.on.ca> I'm trying to understand better why the "standard" vectors supplied by the vendor do not match the DICOM header, and what to do about it. I have read all I can find in the email list archive and the forum. It makes sense that the DICOM header should contain gradients that are already adjusted for the oblique acquisition. I believe you on that. However.... I am using Siemens with VB15, mosaic format, and oblique prescription. I understand from the email list that I should simply click "Get gradient from DICOM file header" and leave "Rotate gradients if applicable" *unchecked* because in VB15 the gradient table in the DICOM header is already rotated. Is that correct? What's strange: If my acquisition is straight axial (not oblique), the gradient table retrieved by DTIStudio from the DICOM header still does not match the gradient table supplied by Siemens. They are close, but not close enough to call them equal. Any idea why? More discrepancies turn up when comparing dcm2nii and MRIConvert with DTIStudio (with/without "Rotate gradients if applicable" option), running them against both straight axial and oblique scans: Straight Axial Scan -------------------- dcm2nii = mriconvert = dtistudio(read dicom) = dtistudio(read dicom + rotate) <> dtistudio(siemens + rotate) = siemens Oblique Scan (T>C30>S20,inplane10) ----------------------------------- dcm2nii = dtistudio(read dicom + rotate) <> dtistudio(read dicom) = mriconvert <> dtistudio(siemens + rotate) <> siemens Also, none of the gradient tables for the straight axial scan match the corresponding ones for the oblique scan, so obviously the gradient table is being adjusted somehow by Siemens before it is stored in the DICOM header. If that is the case, and we trust the Siemens DICOM field (which is not clear), we should *not* select the "Rotate gradients if applicable" option in DTIStudio (and similarly we should not use dcm2nii) for Siemens VB15, because that would over-rotate the gradient table. Does this sound reasonable? However, if that is true, then dcm2nii should cause problems for other Siemens users. I have not heard of that happening, although I noticed one thread on the FSL email list noting the discrepancy. What's going on and what should we do about it? Thanks in advance for any input, Fred From ftam-lists at rotman-baycrest.on.ca Fri May 21 07:23:01 2010 From: ftam-lists at rotman-baycrest.on.ca (Fred) Date: Fri, 21 May 2010 07:23:01 -0400 Subject: [Mristudio-users] gradient table options Message-ID: <1274440981.5506.39.camel@fissure.rotman-baycrest.on.ca> I'm trying to understand better why the "standard" vectors supplied by the vendor do not match the DICOM header, and what to do about it. I have read all I can find in the email list archive and the forum. It makes sense that the DICOM header should contain gradients that are already adjusted for the oblique acquisition. I believe you on that. However.... I am using Siemens with VB15, mosaic format, and oblique prescription. I understand from the email list that I should simply click "Get gradient from DICOM file header" and leave "Rotate gradients if applicable" *unchecked* because in VB15 the gradient table in the DICOM header is already rotated. Is that correct? What's strange: If my acquisition is straight axial (not oblique), the gradient table retrieved by DTIStudio from the DICOM header still does not match the gradient table supplied by Siemens. They are close, but not close enough to call them equal. Any idea why? More discrepancies turn up when comparing dcm2nii and MRIConvert with DTIStudio (with/without "Rotate gradients if applicable" option), running them against both straight axial and oblique scans: Straight Axial Scan -------------------- dcm2nii = mriconvert = dtistudio(read dicom) = dtistudio(read dicom + rotate) <> dtistudio(siemens + rotate) = siemens Oblique Scan (T>C30>S20,inplane10) ----------------------------------- dcm2nii = dtistudio(read dicom + rotate) <> dtistudio(read dicom) = mriconvert <> dtistudio(siemens + rotate) <> siemens Also, none of the gradient tables for the straight axial scan match the corresponding ones for the oblique scan, so obviously the gradient table is being adjusted somehow by Siemens before it is stored in the DICOM header. If that is the case, and we trust the Siemens DICOM field (which is not clear), we should *not* select the "Rotate gradients if applicable" option in DTIStudio (and similarly we should not use dcm2nii) for Siemens VB15, because that would over-rotate the gradient table. Does this sound reasonable? However, if that is true, then dcm2nii should cause problems for other Siemens users. I have not heard of that happening, although I noticed one thread on the FSL email list noting the discrepancy. What's going on and what should we do about it? Thanks in advance for any input, Fred From susumu at mri.jhu.edu Sat May 22 16:07:02 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sat, 22 May 2010 16:07:02 -0400 Subject: [Mristudio-users] Acquisition with slightly overlapping slice (i.e. negative gap between slices) In-Reply-To: References: Message-ID: Typically, the overlapping slice excitation (or even no-gap) leads to leakage of excitation to the adjacent slices and causes signal loss. So you pay a penalty of SNR. Usually, within one TR, which is typically around 6-8 seconds, even number slices are excited consecutively and then odd number slices. So, it take about 3-4 seconds before an adjacent slice is excited. Suppose you hit slice #1. If you have an overlap, you excite a part of slice #2. About 3-4 seconds later, you excite slice #2 but the spins of slice #2 has not been fully recovered and thus you loose signal. In your case, because it is just 1.5% overlap, you may not see much impact. Note that the slice excitation profile is not a step function, but has much broader shoulder. So, this SNR penalty by excitation leakage is always there even with gap = 0. When you reconstruct 3D volume, you have to make the slice thickness 0.03mm thinner (1.97mm). If you make sure that the scans are under steady-state (enough prescans), I think you don't have to worry about the effect on DTI calculation, except for SNR. On Thu, May 20, 2010 at 11:21 AM, [Seongjin] wrote: > This might be a stupid question. > However, I would like ask your opinions in the community. > Is there anyone tried DTI acquisition with a bit of overlapping adjacent > slices (i.e. negative gap between slices: e.g. 2 mm slice thickness with > -0.03 gap). > What would be consequence of this acquisition and adverse influence on the > DTI metrics? > > -SC > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100522/e7f7e70e/attachment.html From choisj70 at gmail.com Sat May 22 16:37:48 2010 From: choisj70 at gmail.com (Seongjin) Date: Sat, 22 May 2010 16:37:48 -0400 Subject: [Mristudio-users] Acquisition with slightly overlapping slice (i.e. negative gap between slices) In-Reply-To: References: Message-ID: Dr. Mori Thanks for the reply. -SC On Sat, May 22, 2010 at 4:07 PM, susumu mori wrote: > Typically, the overlapping slice excitation (or even no-gap) leads to > leakage of excitation to the adjacent slices and causes signal loss. So you > pay a penalty of SNR. > > Usually, within one TR, which is typically around 6-8 seconds, even number > slices are excited consecutively and then odd number slices. So, it take > about 3-4 seconds before an adjacent slice is excited. > > Suppose you hit slice #1. If you have an overlap, you excite a part of > slice #2. About 3-4 seconds later, you excite slice #2 but the spins of > slice #2 has not been fully recovered and thus you loose signal. > > In your case, because it is just 1.5% overlap, you may not see much impact. > Note that the slice excitation profile is not a step function, but has much > broader shoulder. So, this SNR penalty by excitation leakage is always there > even with gap = 0. > > When you reconstruct 3D volume, you have to make the slice thickness 0.03mm > thinner (1.97mm). > > If you make sure that the scans are under steady-state (enough prescans), I > think you don't have to worry about the effect on DTI calculation, except > for SNR. > > On Thu, May 20, 2010 at 11:21 AM, [Seongjin] wrote: > >> This might be a stupid question. >> However, I would like ask your opinions in the community. >> Is there anyone tried DTI acquisition with a bit of overlapping adjacent >> slices (i.e. negative gap between slices: e.g. 2 mm slice thickness with >> -0.03 gap). >> What would be consequence of this acquisition and adverse influence on the >> DTI metrics? >> >> -SC >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100522/efa99b4a/attachment-0001.html From youngbin at umich.edu Mon May 24 18:18:06 2010 From: youngbin at umich.edu (Youngbin Kwak) Date: Mon, 24 May 2010 18:18:06 -0400 Subject: [Mristudio-users] dwi images in analyze Message-ID: Hi all, If we have dwi images in analyze or NIFTI format, how can we load them up to DTI studio for tensor calculation and etc.? Thanks! Youngbin -- Youngbin Kwak M.S. Ph.D. candidate, Neuroscience Graduate Program Cognitive Science & Cognitive Neuroscience Program University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100524/26c87b48/attachment.html From junyiwang2002 at yahoo.com Mon May 24 18:32:18 2010 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Mon, 24 May 2010 15:32:18 -0700 (PDT) Subject: [Mristudio-users] dwi images in analyze In-Reply-To: References: Message-ID: <901657.27316.qm@web50505.mail.re2.yahoo.com> Hi Youngbin, You can first load it using the first choice under File. Save the image as a .dat file and then load it using DTI mapping under File. Jun Yi Wang Postdoctoral Scholar Center for Mind and Brain 202 Cousteau Place, Suite 225 Davis, CA 95618 ________________________________ From: Youngbin Kwak To: mristudio-users at mristudio.org Sent: Mon, May 24, 2010 3:18:06 PM Subject: [Mristudio-users] dwi images in analyze Hi all, If we have dwi images in analyze or NIFTI format, how can we load them up to DTI studio for tensor calculation and etc.? Thanks! Youngbin -- Youngbin Kwak M.S. Ph.D. candidate, Neuroscience Graduate Program Cognitive Science & Cognitive Neuroscience Program University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100524/28e9a381/attachment.html From MSedrak at mednet.ucla.edu Mon May 24 21:22:39 2010 From: MSedrak at mednet.ucla.edu (Sedrak, Mark M.D.) Date: Mon, 24 May 2010 18:22:39 -0700 Subject: [Mristudio-users] dwi images in analyze In-Reply-To: <901657.27316.qm@web50505.mail.re2.yahoo.com> References: <901657.27316.qm@web50505.mail.re2.yahoo.com> Message-ID: Can I be removed from this email chain... Thanks, Mark ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang [junyiwang2002 at yahoo.com] Sent: Monday, May 24, 2010 3:32 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] dwi images in analyze Hi Youngbin, You can first load it using the first choice under File. Save the image as a .dat file and then load it using DTI mapping under File. Jun Yi Wang Postdoctoral Scholar Center for Mind and Brain 202 Cousteau Place, Suite 225 Davis, CA 95618 ________________________________ From: Youngbin Kwak To: mristudio-users at mristudio.org Sent: Mon, May 24, 2010 3:18:06 PM Subject: [Mristudio-users] dwi images in analyze Hi all, If we have dwi images in analyze or NIFTI format, how can we load them up to DTI studio for tensor calculation and etc.? Thanks! Youngbin -- Youngbin Kwak M.S. Ph.D. candidate, Neuroscience Graduate Program Cognitive Science & Cognitive Neuroscience Program University of Michigan IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. From youngbin at umich.edu Tue May 25 14:42:56 2010 From: youngbin at umich.edu (Youngbin Kwak) Date: Tue, 25 May 2010 14:42:56 -0400 Subject: [Mristudio-users] image coregistration Message-ID: Hello all, I'm trying to create an ROI for performing tractography. What I'm planning on is to create an ROI that is defined in a normalized template and then convert it to native space. In order to do this, I'd first like to coregister a high-resolution anatomical image to the b0 image, so that however I create ROI on the anatomy file would parallel the location of DTI images. In order to do this, I've loaded the anatomical image and selected mutual-Info image registration option. I chose b0 image as reference and the anatomical image as image to be registered and used rigid body transformation. However there was an error message saying "RegImgFile.tmp was not found". Can someone help me out resolve this issue? Another question I have is, when I perform AIR registration for all the dwi images, there are new files created labled AIR_filename. Does the program know that it should use the newly created files (i.e. AIR_filename) to perform tensor calculation and the rest of the step? Or should I get rid of the original guys from the image tab and only have the new files available before performing tensor calculation? thanks a bunch! Youngbin -- Youngbin Kwak M.S. Ph.D. candidate, Neuroscience Graduate Program Cognitive Science & Cognitive Neuroscience Program University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100525/42ac78d0/attachment.html From ASHETTY at beaumont.edu Tue May 25 15:16:52 2010 From: ASHETTY at beaumont.edu (Anil Shetty) Date: Tue, 25 May 2010 15:16:52 -0400 Subject: [Mristudio-users] image coregistration In-Reply-To: References: Message-ID: <4BFBE9E4.5A9D.002E.1@beaumont.edu> HI Youngbin I am the newest one to use the program DTI-Studio. I am having lots of problems understanding structure of program steps. Do you have any manual or step by step recipe for doing tractography using Studio. I would greatly appreciate your help. anil shetty Anil N. Shetty, Ph.D. Chief, MR Physics Diagnostic Radiology William Beaumont Hospital Clinical Professor, Diagnostic Radiology, Oakland University William Beaumont School of Medicine. 3601 West 13 Mile Road Royal Oak, MI 48073 Voice: 248-551-1006 Fax: 248-551-3521 Page: 248-995-3357 e-mail: ashetty at beaumont.edu >>> Youngbin Kwak 5/25/2010 2:42 PM >>> Hello all, I'm trying to create an ROI for performing tractography. What I'm planning on is to create an ROI that is defined in a normalized template and then convert it to native space. In order to do this, I'd first like to coregister a high-resolution anatomical image to the b0 image, so that however I create ROI on the anatomy file would parallel the location of DTI images. In order to do this, I've loaded the anatomical image and selected mutual-Info image registration option. I chose b0 image as reference and the anatomical image as image to be registered and used rigid body transformation. However there was an error message saying "RegImgFile.tmp was not found". Can someone help me out resolve this issue? Another question I have is, when I perform AIR registration for all the dwi images, there are new files created labled AIR_filename. Does the program know that it should use the newly created files (i.e. AIR_filename) to perform tensor calculation and the rest of the step? Or should I get rid of the original guys from the image tab and only have the new files available before performing tensor calculation? thanks a bunch! Youngbin -- Youngbin Kwak M.S. Ph.D. candidate, Neuroscience Graduate Program Cognitive Science & Cognitive Neuroscience Program University of Michigan From youngbin at umich.edu Tue May 25 15:20:11 2010 From: youngbin at umich.edu (Youngbin Kwak) Date: Tue, 25 May 2010 15:20:11 -0400 Subject: [Mristudio-users] image coregistration In-Reply-To: <4BFBE9E4.5A9D.002E.1@beaumont.edu> References: <4BFBE9E4.5A9D.002E.1@beaumont.edu> Message-ID: Hi Anil, I'm a newby just like you and am feeling quite lost... I'll let you know if we figure out somewhat standard regime for us.. Youngbin On Tue, May 25, 2010 at 3:16 PM, Anil Shetty wrote: > HI Youngbin > > I am the newest one to use the program DTI-Studio. I am having lots of > problems understanding structure of program steps. Do you have any manual or > step by step recipe for doing tractography using Studio. I would greatly > appreciate your help. > > anil shetty > > > > > > Anil N. Shetty, Ph.D. > Chief, MR Physics > Diagnostic Radiology > William Beaumont Hospital > Clinical Professor, Diagnostic Radiology, Oakland University > William Beaumont School of Medicine. > 3601 West 13 Mile Road > Royal Oak, MI 48073 > > Voice: 248-551-1006 > Fax: 248-551-3521 > Page: 248-995-3357 > e-mail: ashetty at beaumont.edu > > > >>> Youngbin Kwak 5/25/2010 2:42 PM >>> > Hello all, > > I'm trying to create an ROI for performing tractography. What I'm planning > on is to create an ROI that is defined in a normalized template and then > convert it to native space. In order to do this, I'd first like to > coregister a high-resolution anatomical image to the b0 image, so that > however I create ROI on the anatomy file would parallel the location of DTI > images. > > In order to do this, I've loaded the anatomical image and selected > mutual-Info image registration option. I chose b0 image as reference and > the > anatomical image as image to be registered and used rigid body > transformation. However there was an error message saying "RegImgFile.tmp > was not found". Can someone help me out resolve this issue? > > Another question I have is, when I perform AIR registration for all the dwi > images, there are new files created labled AIR_filename. > Does the program know that it should use the newly created files (i.e. > AIR_filename) to perform tensor calculation and the rest of the step? > Or should I get rid of the original guys from the image tab and only have > the new files available before performing tensor calculation? > > thanks a bunch! > > Youngbin > > -- > Youngbin Kwak M.S. > Ph.D. candidate, Neuroscience Graduate Program > Cognitive Science & Cognitive Neuroscience Program > University of Michigan > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -- Youngbin Kwak M.S. Ph.D. candidate, Neuroscience Graduate Program Cognitive Science & Cognitive Neuroscience Program University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100525/8fcbd171/attachment-0001.html From ASHETTY at beaumont.edu Tue May 25 15:21:59 2010 From: ASHETTY at beaumont.edu (Anil Shetty) Date: Tue, 25 May 2010 15:21:59 -0400 Subject: [Mristudio-users] image coregistration In-Reply-To: References: <4BFBE9E4.5A9D.002E.1@beaumont.edu> Message-ID: <4BFBEB17.5A9D.002E.1@beaumont.edu> Thanks, Youngbin anil >>> Youngbin Kwak 5/25/2010 3:20 PM >>> Hi Anil, I'm a newby just like you and am feeling quite lost... I'll let you know if we figure out somewhat standard regime for us.. Youngbin On Tue, May 25, 2010 at 3:16 PM, Anil Shetty wrote: > HI Youngbin > > I am the newest one to use the program DTI-Studio. I am having lots of > problems understanding structure of program steps. Do you have any manual or > step by step recipe for doing tractography using Studio. I would greatly > appreciate your help. > > anil shetty > > > > > > Anil N. Shetty, Ph.D. > Chief, MR Physics > Diagnostic Radiology > William Beaumont Hospital > Clinical Professor, Diagnostic Radiology, Oakland University > William Beaumont School of Medicine. > 3601 West 13 Mile Road > Royal Oak, MI 48073 > > Voice: 248-551-1006 > Fax: 248-551-3521 > Page: 248-995-3357 > e-mail: ashetty at beaumont.edu > > > >>> Youngbin Kwak 5/25/2010 2:42 PM >>> > Hello all, > > I'm trying to create an ROI for performing tractography. What I'm planning > on is to create an ROI that is defined in a normalized template and then > convert it to native space. In order to do this, I'd first like to > coregister a high-resolution anatomical image to the b0 image, so that > however I create ROI on the anatomy file would parallel the location of DTI > images. > > In order to do this, I've loaded the anatomical image and selected > mutual-Info image registration option. I chose b0 image as reference and > the > anatomical image as image to be registered and used rigid body > transformation. However there was an error message saying "RegImgFile.tmp > was not found". Can someone help me out resolve this issue? > > Another question I have is, when I perform AIR registration for all the dwi > images, there are new files created labled AIR_filename. > Does the program know that it should use the newly created files (i.e. > AIR_filename) to perform tensor calculation and the rest of the step? > Or should I get rid of the original guys from the image tab and only have > the new files available before performing tensor calculation? > > thanks a bunch! > > Youngbin > > -- > Youngbin Kwak M.S. > Ph.D. candidate, Neuroscience Graduate Program > Cognitive Science & Cognitive Neuroscience Program > University of Michigan > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -- Youngbin Kwak M.S. Ph.D. candidate, Neuroscience Graduate Program Cognitive Science & Cognitive Neuroscience Program University of Michigan From charpentier.juliette at gmail.com Wed May 26 06:37:02 2010 From: charpentier.juliette at gmail.com (Juliette Charpentier) Date: Wed, 26 May 2010 12:37:02 +0200 Subject: [Mristudio-users] DtiStudio In-Reply-To: References: Message-ID: Hello all, In order to use DtiStudio properly, it seems that one needs a gradient table to go along with their data. Our lab is currently using a Philips MR Imaging. Within the dicom header of scanner, under the tag ?DiffusionGradientOrientation?, able to find the x,y,z information but it not seems to be correct. Is there a program that can generate gradient tables to go along with our dicom data, or can it be found on Philips website? Thank you very much for all of your help, it is much appreciated. Sincerely, Juliette Charpentier -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/579f18a5/attachment.html From support at mristudio.org Wed May 26 09:34:12 2010 From: support at mristudio.org (support at mristudio.org) Date: Wed, 26 May 2010 09:34:12 -0400 (EDT) Subject: [Mristudio-users] dwi images in analyze In-Reply-To: References: Message-ID: <49908.10.16.57.47.1274880852.squirrel@webmail.mristudio.org> load the images using "File->MriView 3D", re-save them as "RAW" format, and then use "File->DTI Mapping" for the re-saved file as "Philips REC" format. > Hi all, > > If we have dwi images in analyze or NIFTI format, how can we load them up to > DTI studio for tensor calculation and etc.? > > Thanks! > Youngbin > > -- > Youngbin Kwak M.S. > Ph.D. candidate, Neuroscience Graduate Program > Cognitive Science & Cognitive Neuroscience Program > University of Michigan > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From M.L.Schouw at amc.uva.nl Wed May 26 09:51:13 2010 From: M.L.Schouw at amc.uva.nl (M.L.J. Schouw) Date: Wed, 26 May 2010 15:51:13 +0200 Subject: [Mristudio-users] DtiStudio In-Reply-To: References: Message-ID: It's possible you need to swap the x with the z. That's what we do and this seems to work fine. Marieke. M.L.J. Schouw, arts-onderzoeker Dept. Radiology, G1-241 Academic Medical Center Meibergdreef 9 1105 AZ Amsterdam the Netherlands Tel: + 31 20 5668323 Fax: + 31 20 5669119 ----- Original Message ----- From: Juliette Charpentier Date: Wednesday, May 26, 2010 1:32 pm Subject: [Mristudio-users] DtiStudio To: mristudio-users at mristudio.org > Hello all, > > In order to use DtiStudio properly, it seems that one needs a gradient > table to go along with their data. Our lab is currently using a > Philips MR Imaging. > > > Within the dicom header of scanner, under the tag > ?DiffusionGradientOrientation?, able to find the x,y,z information but > it not seems to be correct. > > Is there a program that can generate gradient tables to go along with > our dicom data, or can it be found on Philips website? > > > Thank you very much for all of your help, it is much appreciated. > > Sincerely, > > Juliette Charpentier > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From susumu at mri.jhu.edu Wed May 26 09:55:52 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 26 May 2010 09:55:52 -0400 Subject: [Mristudio-users] DtiStudio In-Reply-To: References: Message-ID: Hi Juliette, We have been working on the gradient information inside DICOM. We start to understand Siemens but haven't finished Philips yet. This is a rather tricky issue and we have to be careful. Meanwhile, if you are using the standard "Low, Medium, High" gradient set, you can use the table provided from Philips. The latest DtiStudio has some pre-defined gradient table installed from which you can choose. However, this list contains only the tables that are used most frequently. Strictly speaking, there are 48 tables for Philips (although many of them are redundant), because there are combination of; 3 tables (6, 15, 32 orientations) Gradient overplus (on / off) 4 different releases (many releases share the same tables but not all) location of b0 image (beginning or end) On top of it, if you use gradient overplus = on (We DO NOT recommend this option = on), the table becomes sensitive to oblique angles. To solve all these issues at once, I recommend you to look into http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html. This nice software written by Jonathan Farrell can create a table for all possible combination. Susumu On Wed, May 26, 2010 at 6:37 AM, Juliette Charpentier < charpentier.juliette at gmail.com> wrote: > Hello all, > > In order to use DtiStudio properly, it seems that one needs a gradient table to go along with their data. Our lab is currently using a Philips MR Imaging. > > > > > Within the dicom header of scanner, under the tag ?DiffusionGradientOrientation?, able to find the x,y,z information but it not seems to be correct. > > Is there a program that can generate gradient tables to go along with our dicom data, or can it be found on Philips website? > > > > > Thank you very much for all of your help, it is much appreciated. > > Sincerely, > > Juliette Charpentier > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/59b480f9/attachment.html From susumu at mri.jhu.edu Wed May 26 10:43:19 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 26 May 2010 10:43:19 -0400 Subject: [Mristudio-users] DtiStudio In-Reply-To: References: Message-ID: That should be same as Y-swap. That's not very common, but can't deny the possibility. Is it old GE? On Wed, May 26, 2010 at 9:51 AM, M.L.J. Schouw wrote: > It's possible you need to swap the x with the z. That's what we do and this > seems to work fine. > > Marieke. > > M.L.J. Schouw, arts-onderzoeker > Dept. Radiology, G1-241 > Academic Medical Center > Meibergdreef 9 > 1105 AZ Amsterdam > the Netherlands > Tel: + 31 20 5668323 > Fax: + 31 20 5669119 > > > ----- Original Message ----- > From: Juliette Charpentier > Date: Wednesday, May 26, 2010 1:32 pm > Subject: [Mristudio-users] DtiStudio > To: mristudio-users at mristudio.org > > > > Hello all, > > > > In order to use DtiStudio properly, it seems that one needs a gradient > > table to go along with their data. Our lab is currently using a > > Philips MR Imaging. > > > > > > Within the dicom header of scanner, under the tag > > ?DiffusionGradientOrientation?, able to find the x,y,z information but > > it not seems to be correct. > > > > Is there a program that can generate gradient tables to go along with > > our dicom data, or can it be found on Philips website? > > > > > > Thank you very much for all of your help, it is much appreciated. > > > > Sincerely, > > > > Juliette Charpentier > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/2ec2aa2e/attachment-0001.html From LisaMarie.Langevin at albertahealthservices.ca Wed May 26 14:45:27 2010 From: LisaMarie.Langevin at albertahealthservices.ca (Lisa Marie Langevin) Date: Wed, 26 May 2010 12:45:27 -0600 Subject: [Mristudio-users] dwi images in analyze In-Reply-To: <49908.10.16.57.47.1274880852.squirrel@webmail.mristudio.org> References: <49908.10.16.57.47.1274880852.squirrel@webmail.mristudio.org> Message-ID: <16D6DA47889FE44BA52573AAAE4493AE2CC920C2@EXMBX10C.crha.bewell.ca> Hi guys, When I do this, I get an error message saying the file size is smaller than the DW-image size. What am I doing wrong? LM :) Lisa Marie Langevin, Ph.D. Postdoctoral Research Fellow Alberta Children's Hospital Research Institute for Child and Maternal Health Behavioural Research Unit, Alberta Children's Hospital Tel: (403) 955-2785, Fax: (403) 955-2772 Email: lisamarie.langevin at albertahealthservices.ca ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of support at mristudio.org [support at mristudio.org] Sent: May 26, 2010 7:34 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] dwi images in analyze load the images using "File->MriView 3D", re-save them as "RAW" format, and then use "File->DTI Mapping" for the re-saved file as "Philips REC" format. > Hi all, > > If we have dwi images in analyze or NIFTI format, how can we load them up to > DTI studio for tensor calculation and etc.? > > Thanks! > Youngbin > > -- > Youngbin Kwak M.S. > Ph.D. candidate, Neuroscience Graduate Program > Cognitive Science & Cognitive Neuroscience Program > University of Michigan > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. From susumu at mri.jhu.edu Wed May 26 15:31:01 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 26 May 2010 15:31:01 -0400 Subject: [Mristudio-users] dwi images in analyze In-Reply-To: <16D6DA47889FE44BA52573AAAE4493AE2CC920C2@EXMBX10C.crha.bewell.ca> References: <49908.10.16.57.47.1274880852.squirrel@webmail.mristudio.org> <16D6DA47889FE44BA52573AAAE4493AE2CC920C2@EXMBX10C.crha.bewell.ca> Message-ID: When you first time load the Analyze data, or when you reload it as the raw (REC) file, please go over the pull-down menu in the "image tab" to inspect all loaded images. Check these; >How many images are there? >Where is the b0 image? >Do they look correct images? >The brain positions are all the same? >what are the image dimensions and how many slices in each data? Then when you load the REC file for tensor calculation and specified the gradient table, check the image dimension, the number of slices, the total number of gradient orientations, and position of b0 (0, 0, 0). They should all match. When you got that message, one of these parameters are wrong. On Wed, May 26, 2010 at 2:45 PM, Lisa Marie Langevin < LisaMarie.Langevin at albertahealthservices.ca> wrote: > Hi guys, > > When I do this, I get an error message saying the file size is smaller than > the DW-image size. > > What am I doing wrong? > > LM :) > > > Lisa Marie Langevin, Ph.D. > Postdoctoral Research Fellow > Alberta Children's Hospital Research Institute for Child and Maternal > Health > Behavioural Research Unit, Alberta Children's Hospital > Tel: (403) 955-2785, Fax: (403) 955-2772 > Email: lisamarie.langevin at albertahealthservices.ca > ________________________________________ > From: mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of support at mristudio.org[ > support at mristudio.org] > Sent: May 26, 2010 7:34 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] dwi images in analyze > > load the images using "File->MriView 3D", re-save them as "RAW" format, and > then > use "File->DTI Mapping" for the re-saved file as "Philips REC" format. > > > > > > > Hi all, > > > > If we have dwi images in analyze or NIFTI format, how can we load them up > to > > DTI studio for tensor calculation and etc.? > > > > Thanks! > > Youngbin > > > > -- > > Youngbin Kwak M.S. > > Ph.D. candidate, Neuroscience Graduate Program > > Cognitive Science & Cognitive Neuroscience Program > > University of Michigan > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > This message and any attached documents are only for the use of the > intended recipient(s), are confidential and may contain privileged > information. Any unauthorized review, use, retransmission, or other > disclosure is strictly prohibited. If you have received this message in > error, please notify the sender immediately, and then delete the original > message. Thank you. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/99ec2121/attachment.html From LisaMarie.Langevin at albertahealthservices.ca Wed May 26 17:35:31 2010 From: LisaMarie.Langevin at albertahealthservices.ca (Lisa Marie Langevin) Date: Wed, 26 May 2010 15:35:31 -0600 Subject: [Mristudio-users] dwi images in analyze In-Reply-To: References: <49908.10.16.57.47.1274880852.squirrel@webmail.mristudio.org> <16D6DA47889FE44BA52573AAAE4493AE2CC920C2@EXMBX10C.crha.bewell.ca> Message-ID: <16D6DA47889FE44BA52573AAAE4493AE2CC920C3@EXMBX10C.crha.bewell.ca> If our images load in a different direction than we expect, how do we fix it? In our case, the top right image has anterior toward the bottom of the screen, instead of anterior oriented toward the top of the screen. LM :) Lisa Marie Langevin, Ph.D. Postdoctoral Research Fellow Alberta Children's Hospital Research Institute for Child and Maternal Health Behavioural Research Unit, Alberta Children's Hospital Tel: (403) 955-2785, Fax: (403) 955-2772 Email: lisamarie.langevin at albertahealthservices.ca ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: May 26, 2010 1:31 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] dwi images in analyze When you first time load the Analyze data, or when you reload it as the raw (REC) file, please go over the pull-down menu in the "image tab" to inspect all loaded images. Check these; >How many images are there? >Where is the b0 image? >Do they look correct images? >The brain positions are all the same? >what are the image dimensions and how many slices in each data? Then when you load the REC file for tensor calculation and specified the gradient table, check the image dimension, the number of slices, the total number of gradient orientations, and position of b0 (0, 0, 0). They should all match. When you got that message, one of these parameters are wrong. On Wed, May 26, 2010 at 2:45 PM, Lisa Marie Langevin > wrote: Hi guys, When I do this, I get an error message saying the file size is smaller than the DW-image size. What am I doing wrong? LM :) Lisa Marie Langevin, Ph.D. Postdoctoral Research Fellow Alberta Children's Hospital Research Institute for Child and Maternal Health Behavioural Research Unit, Alberta Children's Hospital Tel: (403) 955-2785, Fax: (403) 955-2772 Email: lisamarie.langevin at albertahealthservices.ca ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of support at mristudio.org [support at mristudio.org] Sent: May 26, 2010 7:34 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] dwi images in analyze load the images using "File->MriView 3D", re-save them as "RAW" format, and then use "File->DTI Mapping" for the re-saved file as "Philips REC" format. > Hi all, > > If we have dwi images in analyze or NIFTI format, how can we load them up to > DTI studio for tensor calculation and etc.? > > Thanks! > Youngbin > > -- > Youngbin Kwak M.S. > Ph.D. candidate, Neuroscience Graduate Program > Cognitive Science & Cognitive Neuroscience Program > University of Michigan > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ________________________________ This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/ba2347e3/attachment-0001.html From LisaMarie.Langevin at albertahealthservices.ca Wed May 26 17:39:24 2010 From: LisaMarie.Langevin at albertahealthservices.ca (Lisa Marie Langevin) Date: Wed, 26 May 2010 15:39:24 -0600 Subject: [Mristudio-users] dwi images in analyze In-Reply-To: References: <49908.10.16.57.47.1274880852.squirrel@webmail.mristudio.org> <16D6DA47889FE44BA52573AAAE4493AE2CC920C2@EXMBX10C.crha.bewell.ca> Message-ID: <16D6DA47889FE44BA52573AAAE4493AE2CC920C4@EXMBX10C.crha.bewell.ca> Dear Susumu, Thanks for your help. I got the images to load but: 1) the brain is oriented differently from how it looks on our scanner ie) the top right image has anterior pointing down, and the anterior of the brain in the bottom left image is facing right. 2) When I generate the colour map, all the colours are wrong ie) my callosum is coming out green. We have tried several ways to correct this over the last few weeks. If it's easier, I can load our .img raw files in a folder on the ftp site for you to try. LM :) Lisa Marie Langevin, Ph.D. Postdoctoral Research Fellow Alberta Children's Hospital Research Institute for Child and Maternal Health Behavioural Research Unit, Alberta Children's Hospital Tel: (403) 955-2785, Fax: (403) 955-2772 Email: lisamarie.langevin at albertahealthservices.ca ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: May 26, 2010 1:31 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] dwi images in analyze When you first time load the Analyze data, or when you reload it as the raw (REC) file, please go over the pull-down menu in the "image tab" to inspect all loaded images. Check these; >How many images are there? >Where is the b0 image? >Do they look correct images? >The brain positions are all the same? >what are the image dimensions and how many slices in each data? Then when you load the REC file for tensor calculation and specified the gradient table, check the image dimension, the number of slices, the total number of gradient orientations, and position of b0 (0, 0, 0). They should all match. When you got that message, one of these parameters are wrong. On Wed, May 26, 2010 at 2:45 PM, Lisa Marie Langevin > wrote: Hi guys, When I do this, I get an error message saying the file size is smaller than the DW-image size. What am I doing wrong? LM :) Lisa Marie Langevin, Ph.D. Postdoctoral Research Fellow Alberta Children's Hospital Research Institute for Child and Maternal Health Behavioural Research Unit, Alberta Children's Hospital Tel: (403) 955-2785, Fax: (403) 955-2772 Email: lisamarie.langevin at albertahealthservices.ca ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of support at mristudio.org [support at mristudio.org] Sent: May 26, 2010 7:34 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] dwi images in analyze load the images using "File->MriView 3D", re-save them as "RAW" format, and then use "File->DTI Mapping" for the re-saved file as "Philips REC" format. > Hi all, > > If we have dwi images in analyze or NIFTI format, how can we load them up to > DTI studio for tensor calculation and etc.? > > Thanks! > Youngbin > > -- > Youngbin Kwak M.S. > Ph.D. candidate, Neuroscience Graduate Program > Cognitive Science & Cognitive Neuroscience Program > University of Michigan > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org ________________________________ This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/27cecaed/attachment.html From susumu at mri.jhu.edu Wed May 26 18:59:24 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 26 May 2010 18:59:24 -0400 Subject: [Mristudio-users] dwi images in analyze In-Reply-To: <16D6DA47889FE44BA52573AAAE4493AE2CC920C3@EXMBX10C.crha.bewell.ca> References: <49908.10.16.57.47.1274880852.squirrel@webmail.mristudio.org> <16D6DA47889FE44BA52573AAAE4493AE2CC920C2@EXMBX10C.crha.bewell.ca> <16D6DA47889FE44BA52573AAAE4493AE2CC920C3@EXMBX10C.crha.bewell.ca> Message-ID: Please refer Q15 in https://www.mristudio.org/wiki/faq#head-f499f38374b60cf5e65981924e5f530bb377f958 Hope this will solve your problem. On Wed, May 26, 2010 at 5:35 PM, Lisa Marie Langevin < LisaMarie.Langevin at albertahealthservices.ca> wrote: > If our images load in a different direction than we expect, how do we fix > it? > > In our case, the top right image has anterior toward the bottom of the > screen, instead of anterior oriented toward the top of the screen. > > LM :) > > > Lisa Marie Langevin, Ph.D. > Postdoctoral Research Fellow > Alberta Children's Hospital Research Institute for Child and Maternal > Health > Behavioural Research Unit, Alberta Children's Hospital > Tel: (403) 955-2785, Fax: (403) 955-2772 > Email: lisamarie.langevin at albertahealthservices.ca > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ > susumu at mri.jhu.edu] > *Sent:* May 26, 2010 1:31 PM > > *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support > *Subject:* Re: [Mristudio-users] dwi images in analyze > > When you first time load the Analyze data, or when you reload it as the > raw (REC) file, please go over the pull-down menu in the "image tab" to > inspect all loaded images. Check these; > > >How many images are there? > >Where is the b0 image? > >Do they look correct images? > >The brain positions are all the same? > >what are the image dimensions and how many slices in each data? > > Then when you load the REC file for tensor calculation and specified the > gradient table, check the image dimension, the number of slices, the total > number of gradient orientations, and position of b0 (0, 0, 0). > > They should all match. > > When you got that message, one of these parameters are wrong. > > On Wed, May 26, 2010 at 2:45 PM, Lisa Marie Langevin < > LisaMarie.Langevin at albertahealthservices.ca> wrote: > >> Hi guys, >> >> When I do this, I get an error message saying the file size is smaller >> than the DW-image size. >> >> What am I doing wrong? >> >> LM :) >> >> >> Lisa Marie Langevin, Ph.D. >> Postdoctoral Research Fellow >> Alberta Children's Hospital Research Institute for Child and Maternal >> Health >> Behavioural Research Unit, Alberta Children's Hospital >> Tel: (403) 955-2785, Fax: (403) 955-2772 >> Email: lisamarie.langevin at albertahealthservices.ca >> ________________________________________ >> From: mristudio-users-bounces at mristudio.org [ >> mristudio-users-bounces at mristudio.org] On Behalf Of support at mristudio.org[ >> support at mristudio.org] >> Sent: May 26, 2010 7:34 AM >> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >> Subject: Re: [Mristudio-users] dwi images in analyze >> >> load the images using "File->MriView 3D", re-save them as "RAW" format, >> and then >> use "File->DTI Mapping" for the re-saved file as "Philips REC" format. >> >> >> >> >> >> > Hi all, >> > >> > If we have dwi images in analyze or NIFTI format, how can we load them >> up to >> > DTI studio for tensor calculation and etc.? >> > >> > Thanks! >> > Youngbin >> > >> > -- >> > Youngbin Kwak M.S. >> > Ph.D. candidate, Neuroscience Graduate Program >> > Cognitive Science & Cognitive Neuroscience Program >> > University of Michigan >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> This message and any attached documents are only for the use of the >> intended recipient(s), are confidential and may contain privileged >> information. Any unauthorized review, use, retransmission, or other >> disclosure is strictly prohibited. If you have received this message in >> error, please notify the sender immediately, and then delete the original >> message. Thank you. >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > > > ------------------------------ > This message and any attached documents are only for the use of the > intended recipient(s), are confidential and may contain privileged > information. Any unauthorized review, use, retransmission, or other > disclosure is strictly prohibited. If you have received this message in > error, please notify the sender immediately, and then delete the original > message. Thank you. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/d3227ae2/attachment-0001.html From susumu at mri.jhu.edu Wed May 26 19:21:11 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 26 May 2010 19:21:11 -0400 Subject: [Mristudio-users] gradient table options In-Reply-To: <1274440892.5506.35.camel@fissure.rotman-baycrest.on.ca> References: <1274440892.5506.35.camel@fissure.rotman-baycrest.on.ca> Message-ID: Hi Fred, Here is what we learned about Siemens DICOM so far. The gradient information you can find in Siemens DICOM is always in the patient (image) coordinate; Axial/Coronal/Sagittal. So, if that's true, we don't have to worry anything about oblique angles. So, you SHOULD NOT use "rotate gradient table", as you pointed out. Of course, this assumes that you are using VB15, not VB13 and older. As for why the DICOM gradient information doesn't match the vendor-supplied gradient table, here is my understanding. Suppose you do [1, 0, 0] without any oblique angles. Then it should appear as [1, 0, 0] in DICOM header. However, Siemens actually calculate the exact solution of diffusion weighting including cross terms with imaging and other gradient like slice-selective pulses. For example, in between the two large X diffusion-weighting gradient for [1, 0, 0], there could be crusher gradients and slice-selective gradient along Z. Then you get X-Z cross-terms. If you solve it exactly, you actually can't represent the exact diffusion weighting by simple b-vectors such as [1, 0, 0.1]. You actually need [bxx, byy, bzz, bxy, bxz, byz]. If you look into the DICOM header, you can find this b-matrix. This b-matrix is the exact solution. That means you need a table with 6-element x the number of orientations, not 3-element x the number of orientations. Currently we are trying to incorporate this b-matrix information to DtiStudio. Next question is, then what is the gradient table (3-element x the number of orientation), you can find in DICOM. My understanding is, it is an approximated solution that mimics the exact 6-element table. It's not the exact solution but close. Good thing about this approximation table is that it has the conventional gradient table format and can be used as is without software modification. So I believe the small deviation of the DICOM gradient table you found from the vendor-supplied table is the small contribution of the imaging gradient. I'm not 100% sure about what I said. Once I found out more detail, I'll share the information here. I hope this makes sense for you. Susumu On Fri, May 21, 2010 at 7:21 AM, Fred wrote: > I'm trying to understand better why the "standard" vectors supplied by > the vendor do not match the DICOM header, and what to do about it. I > have read all I can find in the email list archive and the forum. It > makes sense that the DICOM header should contain gradients that are > already adjusted for the oblique acquisition. I believe you on that. > However.... > > I am using Siemens with VB15, mosaic format, and oblique prescription. I > understand from the email list that I should simply click "Get gradient > from DICOM file header" and leave "Rotate gradients if applicable" > *unchecked* because in VB15 the gradient table in the DICOM header is > already rotated. Is that correct? > > What's strange: If my acquisition is straight axial (not oblique), the > gradient table retrieved by DTIStudio from the DICOM header still does > not match the gradient table supplied by Siemens. They are close, but > not close enough to call them equal. Any idea why? > > More discrepancies turn up when comparing dcm2nii and MRIConvert with > DTIStudio (with/without "Rotate gradients if applicable" option), > running them against both straight axial and oblique scans: > > Straight Axial Scan > -------------------- > dcm2nii = mriconvert = dtistudio(read dicom) = dtistudio(read dicom + > rotate) > <> > dtistudio(siemens + rotate) = siemens > > Oblique Scan (T>C30>S20,inplane10) > ----------------------------------- > dcm2nii = dtistudio(read dicom + rotate) > <> > dtistudio(read dicom) = mriconvert > <> > dtistudio(siemens + rotate) > <> > siemens > > Also, none of the gradient tables for the straight axial scan match the > corresponding ones for the oblique scan, so obviously the gradient table > is being adjusted somehow by Siemens before it is stored in the DICOM > header. If that is the case, and we trust the Siemens DICOM field (which > is not clear), we should *not* select the "Rotate gradients if > applicable" option in DTIStudio (and similarly we should not use > dcm2nii) for Siemens VB15, because that would over-rotate the gradient > table. Does this sound reasonable? > > However, if that is true, then dcm2nii should cause problems for other > Siemens users. I have not heard of that happening, although I noticed > one thread on the FSL email list noting the discrepancy. > > What's going on and what should we do about it? > > Thanks in advance for any input, > Fred > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/29da6ccd/attachment.html From susumu at mri.jhu.edu Wed May 26 19:25:51 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 26 May 2010 19:25:51 -0400 Subject: [Mristudio-users] slice rejection In-Reply-To: <4BF55DD7.7030108@sri.utoronto.ca> References: <4BF55DD7.7030108@sri.utoronto.ca> Message-ID: After the calculation is done, go to the "DtiMapping" tab in the lower right corner and click the "Original-ADC-Mean-STD" button at the top right. The rejected images should be crossed out by a large red "X" mark. Susumu On Thu, May 20, 2010 at 12:05 PM, Mojdeh wrote: > Hi again :) > Is there a way to find out which slices have been rejected when using > the "Automatic outlier IMAGE_SLICE rejection" mode for DTI fitting? > thanks, > Mojdeh > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/4fce93ce/attachment.html From ftam-lists at rotman-baycrest.on.ca Wed May 26 21:26:11 2010 From: ftam-lists at rotman-baycrest.on.ca (Fred Tam) Date: Wed, 26 May 2010 21:26:11 -0400 Subject: [Mristudio-users] gradient table options In-Reply-To: References: <1274440892.5506.35.camel@fissure.rotman-baycrest.on.ca> Message-ID: <1274923571.7762.67.camel@fissure.rotman-baycrest.on.ca> Thank you! That makes a lot of sense. Fred On Wed, 2010-05-26 at 19:21 -0400, susumu mori wrote: > Hi Fred, > > Here is what we learned about Siemens DICOM so far. > The gradient information you can find in Siemens DICOM is always in > the patient (image) coordinate; Axial/Coronal/Sagittal. So, if that's > true, we don't have to worry anything about oblique angles. So, you > SHOULD NOT use "rotate gradient table", as you pointed out. Of course, > this assumes that you are using VB15, not VB13 and older. > > As for why the DICOM gradient information doesn't match the > vendor-supplied gradient table, here is my understanding. > > Suppose you do [1, 0, 0] without any oblique angles. Then it should > appear as [1, 0, 0] in DICOM header. However, Siemens actually > calculate the exact solution of diffusion weighting including cross > terms with imaging and other gradient like slice-selective pulses. > > For example, in between the two large X diffusion-weighting gradient > for [1, 0, 0], there could be crusher gradients and slice-selective > gradient along Z. Then you get X-Z cross-terms. If you solve it > exactly, you actually can't represent the exact diffusion weighting > by simple b-vectors such as [1, 0, 0.1]. You actually need [bxx, byy, > bzz, bxy, bxz, byz]. If you look into the DICOM header, you can find > this b-matrix. This b-matrix is the exact solution. That means you > need a table with 6-element x the number of orientations, not > 3-element x the number of orientations. > > Currently we are trying to incorporate this b-matrix information to > DtiStudio. > > Next question is, then what is the gradient table (3-element x the > number of orientation), you can find in DICOM. My understanding is, it > is an approximated solution that mimics the exact 6-element table. > It's not the exact solution but close. Good thing about this > approximation table is that it has the conventional gradient table > format and can be used as is without software modification. > > So I believe the small deviation of the DICOM gradient table you found > from the vendor-supplied table is the small contribution of the > imaging gradient. > > I'm not 100% sure about what I said. Once I found out more detail, > I'll share the information here. > > I hope this makes sense for you. > > Susumu > > On Fri, May 21, 2010 at 7:21 AM, Fred > wrote: > I'm trying to understand better why the "standard" vectors > supplied by > the vendor do not match the DICOM header, and what to do about > it. I > have read all I can find in the email list archive and the > forum. It > makes sense that the DICOM header should contain gradients > that are > already adjusted for the oblique acquisition. I believe you on > that. > However.... > > I am using Siemens with VB15, mosaic format, and oblique > prescription. I > understand from the email list that I should simply click "Get > gradient > from DICOM file header" and leave "Rotate gradients if > applicable" > *unchecked* because in VB15 the gradient table in the DICOM > header is > already rotated. Is that correct? > > What's strange: If my acquisition is straight axial (not > oblique), the > gradient table retrieved by DTIStudio from the DICOM header > still does > not match the gradient table supplied by Siemens. They are > close, but > not close enough to call them equal. Any idea why? > > More discrepancies turn up when comparing dcm2nii and > MRIConvert with > DTIStudio (with/without "Rotate gradients if applicable" > option), > running them against both straight axial and oblique scans: > > Straight Axial Scan > -------------------- > dcm2nii = mriconvert = dtistudio(read dicom) = dtistudio(read > dicom + > rotate) > <> > dtistudio(siemens + rotate) = siemens > > Oblique Scan (T>C30>S20,inplane10) > ----------------------------------- > dcm2nii = dtistudio(read dicom + rotate) > <> > dtistudio(read dicom) = mriconvert > <> > dtistudio(siemens + rotate) > <> > siemens > > Also, none of the gradient tables for the straight axial scan > match the > corresponding ones for the oblique scan, so obviously the > gradient table > is being adjusted somehow by Siemens before it is stored in > the DICOM > header. If that is the case, and we trust the Siemens DICOM > field (which > is not clear), we should *not* select the "Rotate gradients if > applicable" option in DTIStudio (and similarly we should not > use > dcm2nii) for Siemens VB15, because that would over-rotate the > gradient > table. Does this sound reasonable? > > However, if that is true, then dcm2nii should cause problems > for other > Siemens users. I have not heard of that happening, although I > noticed > one thread on the FSL email list noting the discrepancy. > > What's going on and what should we do about it? > > Thanks in advance for any input, > Fred > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Wed May 26 21:55:51 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 26 May 2010 21:55:51 -0400 Subject: [Mristudio-users] image coregistration In-Reply-To: <4BFBEB17.5A9D.002E.1@beaumont.edu> References: <4BFBE9E4.5A9D.002E.1@beaumont.edu> <4BFBEB17.5A9D.002E.1@beaumont.edu> Message-ID: Hi all, We know that the manual is the weakest link of DtiStudio / MriStudio. You can find a manual here (v. 2.10.6, sorry years old) at https://www.mristudio.org/wiki/user_manual. In this page, there is also an online manual, but it is based on this *.doc file. This is for DtiStudio. For DiffeoMap and RoiEditor, there is only the web manuals, which you can also find in the same site. Also, there is videos from my tutorial. http://162.129.247.245/Protocol/DTS/Tutorial/index.htm I hope these are helpful. susumu On Tue, May 25, 2010 at 3:21 PM, Anil Shetty wrote: > Thanks, Youngbin > > anil > > > > > >>> Youngbin Kwak 5/25/2010 3:20 PM >>> > Hi Anil, > > I'm a newby just like you and am feeling quite lost... > I'll let you know if we figure out somewhat standard regime for us.. > > Youngbin > > On Tue, May 25, 2010 at 3:16 PM, Anil Shetty wrote: > > > HI Youngbin > > > > I am the newest one to use the program DTI-Studio. I am having lots of > > problems understanding structure of program steps. Do you have any manual > or > > step by step recipe for doing tractography using Studio. I would greatly > > appreciate your help. > > > > anil shetty > > > > > > > > > > > > Anil N. Shetty, Ph.D. > > Chief, MR Physics > > Diagnostic Radiology > > William Beaumont Hospital > > Clinical Professor, Diagnostic Radiology, Oakland University > > William Beaumont School of Medicine. > > 3601 West 13 Mile Road > > Royal Oak, MI 48073 > > > > Voice: 248-551-1006 > > Fax: 248-551-3521 > > Page: 248-995-3357 > > e-mail: ashetty at beaumont.edu > > > > > > >>> Youngbin Kwak 5/25/2010 2:42 PM >>> > > Hello all, > > > > I'm trying to create an ROI for performing tractography. What I'm > planning > > on is to create an ROI that is defined in a normalized template and then > > convert it to native space. In order to do this, I'd first like to > > coregister a high-resolution anatomical image to the b0 image, so that > > however I create ROI on the anatomy file would parallel the location of > DTI > > images. > > > > In order to do this, I've loaded the anatomical image and selected > > mutual-Info image registration option. I chose b0 image as reference and > > the > > anatomical image as image to be registered and used rigid body > > transformation. However there was an error message saying "RegImgFile.tmp > > was not found". Can someone help me out resolve this issue? > > > > Another question I have is, when I perform AIR registration for all the > dwi > > images, there are new files created labled AIR_filename. > > Does the program know that it should use the newly created files (i.e. > > AIR_filename) to perform tensor calculation and the rest of the step? > > Or should I get rid of the original guys from the image tab and only have > > the new files available before performing tensor calculation? > > > > thanks a bunch! > > > > Youngbin > > > > -- > > Youngbin Kwak M.S. > > Ph.D. candidate, Neuroscience Graduate Program > > Cognitive Science & Cognitive Neuroscience Program > > University of Michigan > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > > > -- > Youngbin Kwak M.S. > Ph.D. candidate, Neuroscience Graduate Program > Cognitive Science & Cognitive Neuroscience Program > University of Michigan > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/fa2f97bb/attachment-0001.html From youngbin at umich.edu Wed May 26 22:24:32 2010 From: youngbin at umich.edu (Youngbin Kwak) Date: Wed, 26 May 2010 22:24:32 -0400 Subject: [Mristudio-users] image coregistration In-Reply-To: References: <4BFBE9E4.5A9D.002E.1@beaumont.edu> <4BFBEB17.5A9D.002E.1@beaumont.edu> Message-ID: Thanks alot! This is really helpful. Youngbin On Wed, May 26, 2010 at 9:55 PM, susumu mori wrote: > Hi all, > > We know that the manual is the weakest link of DtiStudio / MriStudio. > > You can find a manual here (v. 2.10.6, sorry years old) at > https://www.mristudio.org/wiki/user_manual. > > In this page, there is also an online manual, but it is based on this *.doc > file. This is for DtiStudio. > For DiffeoMap and RoiEditor, there is only the web manuals, which you can > also find in the same site. > > Also, there is videos from my tutorial. > > http://162.129.247.245/Protocol/DTS/Tutorial/index.htm > > I hope these are helpful. > > susumu > > > On Tue, May 25, 2010 at 3:21 PM, Anil Shetty wrote: > >> Thanks, Youngbin >> >> anil >> >> >> >> >> >>> Youngbin Kwak 5/25/2010 3:20 PM >>> >> Hi Anil, >> >> I'm a newby just like you and am feeling quite lost... >> I'll let you know if we figure out somewhat standard regime for us.. >> >> Youngbin >> >> On Tue, May 25, 2010 at 3:16 PM, Anil Shetty >> wrote: >> >> > HI Youngbin >> > >> > I am the newest one to use the program DTI-Studio. I am having lots of >> > problems understanding structure of program steps. Do you have any >> manual or >> > step by step recipe for doing tractography using Studio. I would greatly >> > appreciate your help. >> > >> > anil shetty >> > >> > >> > >> > >> > >> > Anil N. Shetty, Ph.D. >> > Chief, MR Physics >> > Diagnostic Radiology >> > William Beaumont Hospital >> > Clinical Professor, Diagnostic Radiology, Oakland University >> > William Beaumont School of Medicine. >> > 3601 West 13 Mile Road >> > Royal Oak, MI 48073 >> > >> > Voice: 248-551-1006 >> > Fax: 248-551-3521 >> > Page: 248-995-3357 >> > e-mail: ashetty at beaumont.edu >> > >> > >> > >>> Youngbin Kwak 5/25/2010 2:42 PM >>> >> > Hello all, >> > >> > I'm trying to create an ROI for performing tractography. What I'm >> planning >> > on is to create an ROI that is defined in a normalized template and then >> > convert it to native space. In order to do this, I'd first like to >> > coregister a high-resolution anatomical image to the b0 image, so that >> > however I create ROI on the anatomy file would parallel the location of >> DTI >> > images. >> > >> > In order to do this, I've loaded the anatomical image and selected >> > mutual-Info image registration option. I chose b0 image as reference and >> > the >> > anatomical image as image to be registered and used rigid body >> > transformation. However there was an error message saying >> "RegImgFile.tmp >> > was not found". Can someone help me out resolve this issue? >> > >> > Another question I have is, when I perform AIR registration for all the >> dwi >> > images, there are new files created labled AIR_filename. >> > Does the program know that it should use the newly created files (i.e. >> > AIR_filename) to perform tensor calculation and the rest of the step? >> > Or should I get rid of the original guys from the image tab and only >> have >> > the new files available before performing tensor calculation? >> > >> > thanks a bunch! >> > >> > Youngbin >> > >> > -- >> > Youngbin Kwak M.S. >> > Ph.D. candidate, Neuroscience Graduate Program >> > Cognitive Science & Cognitive Neuroscience Program >> > University of Michigan >> > >> > >> > _______________________________________________ >> > Mristudio-users mailing list >> > Mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> > Mristudio-users-unsubscribe at mristudio.org >> > >> >> >> >> -- >> Youngbin Kwak M.S. >> Ph.D. candidate, Neuroscience Graduate Program >> Cognitive Science & Cognitive Neuroscience Program >> University of Michigan >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -- Youngbin Kwak M.S. Ph.D. candidate, Neuroscience Graduate Program Cognitive Science & Cognitive Neuroscience Program University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/25ebf725/attachment.html From azhang at psych.uic.edu Thu May 27 14:09:58 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Thu, 27 May 2010 13:09:58 -0500 Subject: [Mristudio-users] AIR registration on single volume Message-ID: <40469184F1D86344A835AB980269681A1696651294@exchange.psych.uic.edu> Dear DTIStudio, Thanks for the wonderful program. I have a simple question, if only one volume for DTI data was obtained, do we need to do the AIR registration of DWIs to B0 images? thanks Aifeng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100527/1d80c45e/attachment.html From susumu at mri.jhu.edu Thu May 27 14:56:14 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 27 May 2010 14:56:14 -0400 Subject: [Mristudio-users] AIR registration on single volume In-Reply-To: <40469184F1D86344A835AB980269681A1696651294@exchange.psych.uic.edu> References: <40469184F1D86344A835AB980269681A1696651294@exchange.psych.uic.edu> Message-ID: Usually so. If you haven't took a look at https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2, it may give you some more information about it. susumu On Thu, May 27, 2010 at 2:09 PM, Zhang, Aifeng wrote: > Dear DTIStudio, > > > > Thanks for the wonderful program. I have a simple question, if only one > volume for DTI data was obtained, do we need to do the AIR registration of > DWIs to B0 images? > > > > thanks > > Aifeng > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100527/6df405c7/attachment.html From susumu at mri.jhu.edu Thu May 27 14:56:14 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 27 May 2010 14:56:14 -0400 Subject: [Mristudio-users] AIR registration on single volume In-Reply-To: <40469184F1D86344A835AB980269681A1696651294@exchange.psych.uic.edu> References: <40469184F1D86344A835AB980269681A1696651294@exchange.psych.uic.edu> Message-ID: Usually so. If you haven't took a look at https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2, it may give you some more information about it. susumu On Thu, May 27, 2010 at 2:09 PM, Zhang, Aifeng wrote: > Dear DTIStudio, > > > > Thanks for the wonderful program. I have a simple question, if only one > volume for DTI data was obtained, do we need to do the AIR registration of > DWIs to B0 images? > > > > thanks > > Aifeng > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100527/6df405c7/attachment-0001.html From azhang at psych.uic.edu Thu May 27 15:12:26 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Thu, 27 May 2010 14:12:26 -0500 Subject: [Mristudio-users] AIR registration on single volume In-Reply-To: References: <40469184F1D86344A835AB980269681A1696651294@exchange.psych.uic.edu> Message-ID: <40469184F1D86344A835AB980269681A16966512CC@exchange.psych.uic.edu> thanks for your prompt response, Dr. Mori. however, I can't open the attachment "Coregistration.pptx" which was downloaded as a Zip file and can't be opened in Powerpoint. Thanks again, Aifeng From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Thursday, May 27, 2010 1:56 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] AIR registration on single volume Usually so. If you haven't took a look at https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2, it may give you some more information about it. susumu On Thu, May 27, 2010 at 2:09 PM, Zhang, Aifeng > wrote: Dear DTIStudio, Thanks for the wonderful program. I have a simple question, if only one volume for DTI data was obtained, do we need to do the AIR registration of DWIs to B0 images? thanks Aifeng _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100527/a1aea5c2/attachment-0001.html From cwber at 126.com Fri May 28 08:34:56 2010 From: cwber at 126.com (cwber) Date: Fri, 28 May 2010 20:34:56 +0800 (CST) Subject: [Mristudio-users] AIR registration on single volume In-Reply-To: <40469184F1D86344A835AB980269681A16966512CC@exchange.psych.uic.edu> References: <40469184F1D86344A835AB980269681A16966512CC@exchange.psych.uic.edu> <40469184F1D86344A835AB980269681A1696651294@exchange.psych.uic.edu> Message-ID: <64759d.f9dc.128dee875d7.Coremail.cwber@126.com> You should use office 2007 to open the file. best wishes! ?2010-05-28 03:12:26?"Zhang, Aifeng" ??? thanks for your prompt response, Dr. Mori. however, I can't open the attachment "Coregistration.pptx" which was downloaded as a Zip file and can't be opened in Powerpoint. Thanks again, Aifeng From:mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Thursday, May 27, 2010 1:56 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] AIR registration on single volume Usually so. If you haven't took a look at https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2, it may give you some more information about it. susumu On Thu, May 27, 2010 at 2:09 PM, Zhang, Aifeng wrote: Dear DTIStudio, Thanks for the wonderful program. I have a simple question, if only one volume for DTI data was obtained, do we need to do the AIR registration of DWIs to B0 images? thanks Aifeng _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100528/01eb1b35/attachment.html From choisj70 at gmail.com Fri May 28 08:49:57 2010 From: choisj70 at gmail.com (Seongjin) Date: Fri, 28 May 2010 08:49:57 -0400 Subject: [Mristudio-users] image coregistration In-Reply-To: References: Message-ID: You can save a set of generated AIR_filenames in a single file with adjusted gradient table. (Gradient table will be changed after the registration. You can find the adjusted gradient file at the end of the saved Airmatrix file.) Then open the save AIR_file with the the adjusted gradient table. The rest of the process is the same as usual process. -SC On Tue, May 25, 2010 at 2:42 PM, Youngbin Kwak wrote: > Hello all, > > I'm trying to create an ROI for performing tractography. What I'm planning > on is to create an ROI that is defined in a normalized template and then > convert it to native space. In order to do this, I'd first like to > coregister a high-resolution anatomical image to the b0 image, so that > however I create ROI on the anatomy file would parallel the location of DTI > images. > > In order to do this, I've loaded the anatomical image and selected > mutual-Info image registration option. I chose b0 image as reference and the > anatomical image as image to be registered and used rigid body > transformation. However there was an error message saying "RegImgFile.tmp > was not found". Can someone help me out resolve this issue? > > Another question I have is, when I perform AIR registration for all the dwi > images, there are new files created labled AIR_filename. > Does the program know that it should use the newly created files (i.e. > AIR_filename) to perform tensor calculation and the rest of the step? > Or should I get rid of the original guys from the image tab and only have > the new files available before performing tensor calculation? > > thanks a bunch! > > Youngbin > > -- > Youngbin Kwak M.S. > Ph.D. candidate, Neuroscience Graduate Program > Cognitive Science & Cognitive Neuroscience Program > University of Michigan > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100528/fa1d9cae/attachment.html From Jan.Tillema at cchmc.org Mon May 31 10:36:29 2010 From: Jan.Tillema at cchmc.org (Jan Tillema) Date: Mon, 31 May 2010 10:36:29 -0400 Subject: [Mristudio-users] using reference for DTI studio & AIR References: <4C038E450200000C0052115D@n6mcgw16.cchmc.org> <4C038E650200000C00521161@n6mcgw16.cchmc.org> <4C03912D0200000C00521165@n6mcgw16.cchmc.org> Message-ID: <4C03912D.D7E9.000C.0@cchmc.org> Using your program, we have completed a brief report that is ready for submission for publication. We want to make sure the references for the methodology used is accurate. Having reviewed the literature, your manuals and the website, there are multiple references floating out there it seems. Do you have any guidance on how you would prefer your software being referred to? This goes for 1) AIR methodology (rigid-body) and the 2) standard/default DTI calculations used, not tractography in this case. We used v.2.4 of DTIstudio & v 1.3 of ROIeditor. Thank you for your help. Sincerely, Jan-Mendelt Tillema, M.D. Resident Pediatric Neurology Cincinnati Children's Hospital Medical Center -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100531/1afe11d3/attachment.html From susumu at mri.jhu.edu Tue Jun 1 08:11:00 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 01 Jun 2010 08:11:00 -0400 Subject: [Mristudio-users] using reference for DTI studio & AIR In-Reply-To: <4C03912D.D7E9.000C.0@cchmc.org> References: <4C038E450200000C0052115D@n6mcgw16.cchmc.org> <4C038E650200000C00521161@n6mcgw16.cchmc.org> <4C03912D0200000C00521165@n6mcgw16.cchmc.org> <4C03912D.D7E9.000C.0@cchmc.org> Message-ID: Hi Jan, AIR is from Roger Woods in UCLA J Comput Assist Tomogr. 1998 Jan-Feb;22(1):139-52 Standard DTI calculation should cite one of Peter Basser's papers in 1996 For DtiStudio, I would appreciate it if you cite; Jiang, H., van Zijl, PCM, Kim J., Pearlson, GD, Mori, S.,?DtiStudio: Resource program for diffusion tensor computation and fiber bundle tracking?, Computer Methods and Programs in Biomedicine, 81, 106-116 (2006) Thanks On Mon, May 31, 2010 at 10:36 AM, Jan Tillema wrote: > Using your program, we have completed a brief report that is ready for > submission for publication. We want to make sure the references for the > methodology used is accurate. Having reviewed the literature, your manuals > and the website, there are multiple references floating out there it seems. > Do you have any guidance on how you would prefer your software being > referred to? This goes for 1) AIR methodology (rigid-body) and the 2) > standard/default DTI calculations used, not tractography in this case. We > used v.2.4 of DTIstudio & v 1.3 of ROIeditor. > > Thank you for your help. > > Sincerely, > > > > > > Jan-Mendelt Tillema, M.D. > Resident Pediatric Neurology > Cincinnati Children's Hospital Medical Center > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100601/43d2fa61/attachment-0001.html From jeongwon at pet.wayne.edu Tue Jun 1 10:18:45 2010 From: jeongwon at pet.wayne.edu (Jeong-Won Jeong) Date: Tue, 01 Jun 2010 10:18:45 -0400 Subject: [Mristudio-users] Anatomical labels of Type II and III WMPM maps Message-ID: <005401cb0195$59b3c6a0$0d1b53e0$@wayne.edu> Hi, Is there anyone to have text files to describe anatomical labels of Type II and III WMPM maps? Oishi's paper lists the labels of Type 1 in Appendix but we need those of Type II and III. Thank you in advance. Jeong-Won. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100601/f132c2c7/attachment.html From xli16 at jhmi.edu Tue Jun 1 10:26:34 2010 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 01 Jun 2010 10:26:34 -0400 Subject: [Mristudio-users] Anatomical labels of Type II and III WMPM maps In-Reply-To: <005401cb0195$59b3c6a0$0d1b53e0$@wayne.edu> References: <005401cb0195$59b3c6a0$0d1b53e0$@wayne.edu> Message-ID: <7250ce5faa37.4c04e05a@johnshopkins.edu> Jeong-Won, If you have the latest version of ROIEditor, please check the folder "\ROIEditor\Images\JHU_MNI_SS". The txt files "JhuMniSSTypeIILabelLookupTable.txt" and "JhuMniSSTypeIIILabelLookupTable.txt" in this folder give the descriptions of the labels of Type II and III WMPM maps. Regards, Xin ----- Original Message ----- From: Jeong-Won Jeong Date: Tuesday, June 1, 2010 10:17 am Subject: [Mristudio-users] Anatomical labels of Type II and III WMPM maps To: mristudio-users at mristudio.org > Hi, > > Is there anyone to have text files to describe anatomical labels of > Type II > and III WMPM maps? > > Oishi's paper lists the labels of Type 1 in Appendix but we need > those of > Type II and III. > > > > Thank you in advance. > > > > Jeong-Won. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From jeongwon at pet.wayne.edu Tue Jun 1 12:41:39 2010 From: jeongwon at pet.wayne.edu (Jeong-Won Jeong) Date: Tue, 01 Jun 2010 12:41:39 -0400 Subject: [Mristudio-users] Anatomical labels of Type II and III WMPM maps In-Reply-To: <7250ce5faa37.4c04e05a@johnshopkins.edu> References: <005401cb0195$59b3c6a0$0d1b53e0$@wayne.edu> <7250ce5faa37.4c04e05a@johnshopkins.edu> Message-ID: <007c01cb01a9$50e978d0$f2bc6a70$@wayne.edu> Thank you, Xin. Jeong-Won. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li Sent: Tuesday, June 01, 2010 10:27 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Anatomical labels of Type II and III WMPM maps Jeong-Won, If you have the latest version of ROIEditor, please check the folder "\ROIEditor\Images\JHU_MNI_SS". The txt files "JhuMniSSTypeIILabelLookupTable.txt" and "JhuMniSSTypeIIILabelLookupTable.txt" in this folder give the descriptions of the labels of Type II and III WMPM maps. Regards, Xin ----- Original Message ----- From: Jeong-Won Jeong Date: Tuesday, June 1, 2010 10:17 am Subject: [Mristudio-users] Anatomical labels of Type II and III WMPM maps To: mristudio-users at mristudio.org > Hi, > > Is there anyone to have text files to describe anatomical labels of > Type II > and III WMPM maps? > > Oishi's paper lists the labels of Type 1 in Appendix but we need > those of > Type II and III. > > > > Thank you in advance. > > > > Jeong-Won. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From akolasny at jhu.edu Tue Jun 1 14:36:42 2010 From: akolasny at jhu.edu (akolasny at jhu.edu) Date: Tue, 01 Jun 2010 14:36:42 -0400 (EDT) Subject: [Mristudio-users] ON JUNE 5th, ALL JHU CLARK HALL COMPUTERS WILL NOT BE ACCESSIBLE. Message-ID: <1233.192.168.2.22.1275417402.squirrel@webmail.cis.jhu.edu> ON JUNE 5th, ALL JHU CLARK HALL COMPUTERS WILL NOT BE ACCESSIBLE. On June 5th, JHU Enterprise Networking will upgrade all networking equipment in Clark Hall. All Clark Hall Computers will not be accessible including DiffeoMap's LDDMM remote processing. The evening of June 4, lddmm jobs will be queued and may not be processed until Monday morning June 7th. DiffeoMap submissions on June 5 will not transfer. If you have any questions, please contact me. Thanks, Anthony ------------------------------------------------------------------- Anthony Kolasny email:akolasny at jhu.edu Center for Imaging Science phone:410.516.4278 Johns Hopkins University FAX:410.516.4594 301 Clark Hall 3400 N. Charles Street Baltimore, Maryland 21218 From choisj70 at gmail.com Tue Jun 1 16:38:54 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 01 Jun 2010 16:38:54 -0400 Subject: [Mristudio-users] using reference for DTI studio & AIR In-Reply-To: References: <4C038E450200000C0052115D@n6mcgw16.cchmc.org> <4C038E650200000C00521161@n6mcgw16.cchmc.org> <4C03912D0200000C00521165@n6mcgw16.cchmc.org> <4C03912D.D7E9.000C.0@cchmc.org> Message-ID: What might be a good reference for the mutual information based registration implemented in latest version of DTI Studio? -SC On Tue, Jun 1, 2010 at 8:11 AM, susumu mori wrote: > Hi Jan, > > AIR is from Roger Woods in UCLA > J Comput Assist Tomogr. 1998 Jan-Feb;22(1):139-52 > > Standard DTI calculation should cite one of Peter Basser's papers in 1996 > > For DtiStudio, I would appreciate it if you cite; > > Jiang, H., van Zijl, PCM, Kim J., Pearlson, GD, Mori, S.,?DtiStudio: > Resource program for diffusion tensor computation and fiber bundle > tracking?, Computer Methods and Programs in Biomedicine, 81, 106-116 (2006) > > > Thanks > > > On Mon, May 31, 2010 at 10:36 AM, Jan Tillema wrote: > >> Using your program, we have completed a brief report that is ready for >> submission for publication. We want to make sure the references for the >> methodology used is accurate. Having reviewed the literature, your manuals >> and the website, there are multiple references floating out there it seems. >> Do you have any guidance on how you would prefer your software being >> referred to? This goes for 1) AIR methodology (rigid-body) and the 2) >> standard/default DTI calculations used, not tractography in this case. We >> used v.2.4 of DTIstudio & v 1.3 of ROIeditor. >> >> Thank you for your help. >> >> Sincerely, >> >> >> >> >> >> Jan-Mendelt Tillema, M.D. >> Resident Pediatric Neurology >> Cincinnati Children's Hospital Medical Center >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100601/f19bf6e9/attachment.html From susumu at mri.jhu.edu Thu Jun 3 12:03:12 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 03 Jun 2010 12:03:12 -0400 Subject: [Mristudio-users] Kirby21 data Message-ID: Hi Jim and Suresh, Question: In Kirby21 data, there are many images with different modalities. Do they all share the same center of FOV and oblique angles? Hangyi, do you know how we can extract information about the FOV location and oblique information from DICOM? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100603/9f0daf86/attachment.html From hzhang84 at asu.edu Tue May 18 18:42:52 2010 From: hzhang84 at asu.edu (Hua Zhang) Date: Tue, 18 May 2010 22:42:52 -0000 Subject: [Mristudio-users] Gradient from bvec can't be used Message-ID: Hi, I have a dti data set of a single subject. The gradient table obtained by dcm2nii is strange and can't get any logical result. Is there some other tools to get the right gradients information. Here I attach the data. Please help. Thanks, Hua Zhang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100518/a467ae1a/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: Big_DTI.rar Type: application/octet-stream Size: 7838023 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100518/a467ae1a/attachment-0001.obj From charpentier.juliette at gmail.com Wed May 26 06:30:25 2010 From: charpentier.juliette at gmail.com (Juliette Charpentier) Date: Wed, 26 May 2010 12:30:25 +0200 Subject: [Mristudio-users] DtiStudio Message-ID: Hello all, In order to use DtiStudio properly, it seems that one needs a gradient table to go along with their data. Our lab is currently using a Philips MR Imaging. Within the dicom header of scanner, under the tag ?DiffusionGradientOrientation?, able to find the x,y,z information but it not seems to be correct. Is there a program that can generate gradient tables to go along with our dicom data, or can it be found on Philips website? Thank you very much for all of your help, it is much appreciated. Sincerely, Juliette Charpentier -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100526/9f6565e1/attachment-0001.html From pekar at jhu.edu Thu Jun 3 12:38:31 2010 From: pekar at jhu.edu (Jim Pekar) Date: Thu, 03 Jun 2010 12:38:31 -0400 Subject: [Mristudio-users] Kirby21 data In-Reply-To: References: Message-ID: <9B312D8C-4AB9-45C0-92B6-81EEB1786926@jhu.edu> Begin forwarded message: > From: Bennett Landman > Date: June 3, 2010 12:36:41 PM EDT > To: , Jim Pekar > Cc: Bennett Landman > Subject: Re: Fwd: Kirby21 data > Reply-To: > > 1. Same FOV/Center - no. We used about 3 different geometries for > the 15 > scans due to the necessities of some of the scan (ex. ventricles > only of > the ASL ref). > > 2. This information is in the anonymized par files under angulation > and > off centre. Example: > > Angulation midslice(ap,fh,rl)[degr]: 0.137 0.788 -8.325 > Off Centre midslice(ap,fh,rl) [mm] : -11.605 -22.643 -5.647 > > The DICOMs have corresponding fields. > > -Bennett > >> dear bennett, >> >> please, might you perchance be able to answer susumu's question 'off >> the top of your head'? >> >> many thanks! >> >> best regards, >> jim >> >> >> >> Begin forwarded message: >> >>> From: susumu mori >>> Date: June 3, 2010 12:03:12 PM EDT >>> To: , ANDREIA FARIA >>> >>> , Hangyi Jiang , Xiaoying Tang , >>> kenichi oishi , ROI Editor Landmarker Questions/ >>> Support DTI Studio >>> Subject: Kirby21 data >>> >>> Hi Jim and Suresh, >>> >>> Question: In Kirby21 data, there are many images with different >>> modalities. Do they all share the same center of FOV and oblique >>> angles? >>> >>> Hangyi, do you know how we can extract information about the FOV >>> location and oblique information from DICOM? >> >> -- >> >> James J. Pekar, Ph.D. >> Associate Professor of Radiology, Johns Hopkins University >> Manager and Research Coordinator, >> F. M. Kirby Research Center for Functional Brain Imaging >> Kennedy Krieger Institute >> 707 North Broadway, Baltimore, Maryland 21205 >> >> mailto:pekar at jhu.edu >> http://godzilla.kennedykrieger.org/~jpekar >> phone: 443.923.9510 fax: 443.923.9505 >> >> >> >> >> Disclaimer: >> The materials in this e-mail are private and may contain Protected >> Health >> Information. Please note that e-mail is not necessarily >> confidential or >> secure. Your use of e-mail constitutes your acknowledgment of these >> confidentiality and security limitations. If you are not the intended >> recipient, be advised that any unauthorized use, disclosure, copying, >> distribution, or the taking of any action in reliance on the >> contents of >> this information is strictly prohibited. If you have received this >> e-mail >> in error, please immediately notify the sender via telephone or >> return >> e-mail. >> > > > ------------------------------------------------------- > Bennett Landman, Ph.D., bennett.landman at vanderbilt.edu > Assistant Professor > Department of Electrical Engineering > Vanderbilt University, School of Engineering > > On Jun 3, 2010, at 12:03 PM, susumu mori wrote: > Hi Jim and Suresh, > > Question: In Kirby21 data, there are many images with different > modalities. Do they all share the same center of FOV and oblique > angles? > > Hangyi, do you know how we can extract information about the FOV > location and oblique information from DICOM? -- James J. Pekar, Ph.D. Associate Professor of Radiology, Johns Hopkins University Manager and Research Coordinator, F. M. Kirby Research Center for Functional Brain Imaging Kennedy Krieger Institute 707 North Broadway, Baltimore, Maryland 21205 mailto:pekar at jhu.edu http://godzilla.kennedykrieger.org/~jpekar phone: 443.923.9510 fax: 443.923.9505 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100603/d5c76bf4/attachment-0001.html From jsadino.queens at gmail.com Mon Jun 7 17:14:28 2010 From: jsadino.queens at gmail.com (Jeff Sadino) Date: Mon, 07 Jun 2010 11:14:28 -1000 Subject: [Mristudio-users] Skull Strip in ROIEditor Message-ID: Aloha DTI experts, I wanted to create a skull stripped image in ROIEditor. I remember reading instructions on it a couple months ago where it said to use intensity thresholding and growing. It was a bit more manual. I see the following message sent on May 20. I wanted to do it the more manual way though. I looked all over the website, but can not find those instructions again. If anyone remembers what I'm referring to, could they please send me the link to where those instructions disappeared to? Thank you very much, Jeff Sadino Open ROIEditor Click folder icon (under File on top toolbar); choose b0 (change parameters according to your image dimensions/type) 1. Scroll down; under TOOL, click button with oval icon (Skull Stripping; last button on right) 1. Choose ?Skull strip the current archive image only.?; click OK 2. Change Segment Downsample (1,2,or 3) to 1; click OK Under IMAGE, click folder icon (Load Image File); choose FA.dat (same image parameters as b0) Under ROI, click icon with +/-/x/? signs (Operation; 1st button) 1. In left box choose SkullStrippedMaskByte_.b0 2. In center pull-down menu choose Multiplication 3. In right box choose FA.dat; click OK Under IMAGE, click disc icon (Save Image File) 1. In left box choose SkullStripped_.b0, click arrow, click OK 2. Save as .b0ss 3. Repeat save, choose Multiply_ SkullStrippedMaskByte_.b0_FA.dat, click arrow, click OK 4. Save as > wrote: >* *>* Could anyone send out a step by step process for skull stripping in *>* ROIeditor? (perhaps using a B0 image?). *>* *>* Thanks, *>* *>* Naama *>* *>* *>* *>* Naama Barnea-Goraly M.D. *>* Instructor *>* Center for Interdisciplinary Brain Sciences Research *>* Stanford University Division of Child and Adolescent Psychiatry *>* 401 Quarry Rd. MC 5795 *>* Stanford University School of Medicine *>* Stanford, CA 94305-5795 *>* Phone: (650) 736-1874, fax: (650) 724-4794 *>* *>* *>* CONFIDENTIALITY NOTICE: This e-mail communication and any attachments *>* may contain confidential information for the use of the designated *>* recipients named above. If you are not the intended recipient, you *>* are hereby notified that you have received this communication in error *>* and that any review, disclosure, dissemination, distribution or *>* copying of it or its contents is prohibited. If you have received *>* this communication in error, please notify Stanford Medical Center *>* immediately by telephone at (650) 725-5722 and destroy all copies of *>* this communication and any attachments. Thank you. * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100607/5cdd795b/attachment-0001.html From susumu at mri.jhu.edu Tue Jun 8 08:56:06 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 08 Jun 2010 08:56:06 -0400 Subject: [Mristudio-users] Skull Strip in ROIEditor In-Reply-To: References: Message-ID: Hi Jeff, There are two ways to do it. One is to use the ROI tools and the other is to use the "skull-strip tool" (the right-most button in the "Tool" section). The former is more manual and the latter is more automated. When you use the automated skull-strip button, you have an access to the overwhelming number of parameters. We haven't tested this function thoroughly. This is a type of region growing tool with which you can control the edge detection and smoothness of the boundary. This is written by Yue Li. Yue, I wonder if you could write a brief summary about which parameter does what. The manual way is the more old-fashioned ROI-based masking. Please do the following to get some idea. 1) Load JHU-MNI-SS-FA from the "Sample atlas" section. 2) Also open b0 and DWI within the same window, so that you have FA/b0/DWI all in one window. Don't open images with "ss", which are already skull stripped. 3) If you look at b0 or DWI, you can find that skull has very low intensity. So they are the best one to remove skull. Let's use b0 for this example. 4) Bring the b0 to the active image displayed. 5) Click "Seed Region Growing" in the "Tool" section 6) set the low threshold to 40, choose 3D, and click the center of the brain 7) you can see the brain is nicely defined by red color. 8) Click "Add" button in "Selection" section 9) The brain boundary is now registered as "object 1". 10) Go to "+.-,/,x" button and combine the FA and Object 1 by "masking". Click OK. 11) You can get a new FA map masked by Object 1. 12) If you want manual touch up, you can modify the Object 1 using the "Pen" tool in "Selection" followed by "Add" or "Remove" button Hope this will help. Susumu On Mon, Jun 7, 2010 at 5:14 PM, Jeff Sadino wrote: > Aloha DTI experts, > > I wanted to create a skull stripped image in ROIEditor. I remember reading instructions on it a couple months ago where it said to use intensity thresholding and growing. It was a bit more manual. I see the following message sent on May 20. I wanted to do it the more manual way though. I looked all over the website, but can not find those instructions again. If anyone remembers what I'm referring to, could they please send me the link to where those instructions disappeared to? > > > Thank you very much, > Jeff Sadino > > Open ROIEditor > Click folder icon (under File on top toolbar); choose b0 (change parameters > according to your image dimensions/type) > 1. Scroll down; under TOOL, click button with oval icon (Skull > > > Stripping; last button on right) > 1. Choose ?Skull strip the current archive image only.?; click OK > 2. Change Segment Downsample (1,2,or 3) to 1; click OK > Under IMAGE, click folder icon (Load Image File); choose FA.dat (same image > > > parameters as b0) > Under ROI, click icon with +/-/x/? signs (Operation; 1st button) > 1. In left box choose SkullStrippedMaskByte_.b0 > 2. In center pull-down menu choose Multiplication > 3. In right box choose FA.dat; click OK > > > Under IMAGE, click disc icon (Save Image File) > 1. In left box choose SkullStripped_.b0, click arrow, click OK > 2. Save as .b0ss > 3. Repeat save, choose Multiply_ > SkullStrippedMaskByte_.b0_FA.dat, click arrow, click OK > > > 4. Save as > Hope this helps, > > Julie > > Julie E. McEntee, MA, CCRP > Senior Research Program Coordinator > Department of Psychiatry- Neuroimaging > Johns Hopkins University School of Medicine > > > 600 N. Wolfe St./Phipps 300 > Baltimore, MD 21287 > Phone: 410-502-0468 > Fax: 410-614-3676 > > > On 5/20/10 3:39 PM, "Naama Barnea-Goraly" > wrote: > > > >* > *>* Could anyone send out a step by step process for skull stripping in > *>* ROIeditor? (perhaps using a B0 image?). > *>* > *>* Thanks, > *>* > *>* Naama > > *>* > *>* > *>* > *>* Naama Barnea-Goraly M.D. > *>* Instructor > *>* Center for Interdisciplinary Brain Sciences Research > *>* Stanford University Division of Child and Adolescent Psychiatry > > *>* 401 Quarry Rd. MC 5795 > *>* Stanford University School of Medicine > *>* Stanford, CA 94305-5795 > *>* Phone: (650) 736-1874, fax: (650) 724-4794 > *>* > *>* > > *>* CONFIDENTIALITY NOTICE: This e-mail communication and any attachments > *>* may contain confidential information for the use of the designated > *>* recipients named above. If you are not the intended recipient, you > > *>* are hereby notified that you have received this communication in error > *>* and that any review, disclosure, dissemination, distribution or > *>* copying of it or its contents is prohibited. If you have received > > *>* this communication in error, please notify Stanford Medical Center > *>* immediately by telephone at (650) 725-5722 and destroy all copies of > *>* this communication and any attachments. Thank you. > > * > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100608/eb8b2070/attachment.html From susumu at mri.jhu.edu Tue Jun 8 11:03:47 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 08 Jun 2010 11:03:47 -0400 Subject: [Mristudio-users] Gradient from bvec can't be used In-Reply-To: References: Message-ID: Hi Hua, We usually do not extract gradient info from any header information because there are many issues related to the gradient table and it is difficult for us to keep track of all different formats especially when the raw MRI data went through other software programs. The only exception is Siemens DICOM after VB15, which is supported by DtiStudio for automated gradient table extraction. If you tell us the type of scanner you used and operating system, we may be able to provide a table. Susumu On Tue, May 18, 2010 at 6:42 PM, Hua Zhang wrote: > Hi, > I have a dti data set of a single subject. The gradient table obtained by > dcm2nii is strange and can't get any logical result. Is there some other > tools to get the right gradients information. Here I attach the data. Please > help. > > Thanks, > Hua Zhang > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100608/140d9d9e/attachment.html From hzhang84 at asu.edu Tue Jun 8 11:18:59 2010 From: hzhang84 at asu.edu (Hua Zhang) Date: Tue, 08 Jun 2010 08:18:59 -0700 Subject: [Mristudio-users] Gradient from bvec can't be used In-Reply-To: References: Message-ID: Dear Professor Susumu Mori, The scanner type is SIEMENS Novus 1.5T ,Series Description=ep2d.diff.DTI 12 Software Version=syngo MR 2002M 4VA22B. Will this information do some help? Best, Hua 2010/6/8 susumu mori > Hi Hua, > > We usually do not extract gradient info from any header information because > there are many issues related to the gradient table and it is difficult for > us to keep track of all different formats especially when the raw MRI data > went through other software programs. The only exception is Siemens DICOM > after VB15, which is supported by DtiStudio for automated gradient table > extraction. > > If you tell us the type of scanner you used and operating system, we may be > able to provide a table. > > Susumu > > On Tue, May 18, 2010 at 6:42 PM, Hua Zhang wrote: > >> Hi, >> I have a dti data set of a single subject. The gradient table obtained by >> dcm2nii is strange and can't get any logical result. Is there some other >> tools to get the right gradients information. Here I attach the data. Please >> help. >> >> Thanks, >> Hua Zhang >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100608/2865bb64/attachment.html From a.v at duke.edu Tue Jun 8 07:59:17 2010 From: a.v at duke.edu (Aravindhan Veerapandiyan) Date: Tue, 08 Jun 2010 07:59:17 -0400 Subject: [Mristudio-users] Gradient from bvec can't be used In-Reply-To: References: Message-ID: hey Zhang, I am new to this Dti studio. I am afraid that I could not be of much help. Thanks Hua Zhang Sent by: mristudio-users-bounces at mristudio.org 06/08/2010 06:50 AM Please respond to "DTI Studio, ROI Editor, DiffeoMap Questions/Support" To Mristudio-users at mristudio.org cc Subject [Mristudio-users] Gradient from bvec can't be used Hi, I have a dti data set of a single subject. The gradient table obtained by dcm2nii is strange and can't get any logical result. Is there some other tools to get the right gradients information. Here I attach the data. Please help. Thanks, Hua Zhang[attachment "Big_DTI.rar" deleted by Aravindhan Veerapandiyan/Pediatrics/mc/Duke] _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100608/f201e792/attachment-0001.html From arthurz.wang at gmail.com Thu Jun 10 08:55:25 2010 From: arthurz.wang at gmail.com (WANG, Zhi(Arthur)) Date: Thu, 10 Jun 2010 20:55:25 +0800 Subject: [Mristudio-users] about the Tutorial.zip Message-ID: Dear all, I found it was very slow to download the tutorial.zip. Can it be divided into several subsections? BR, Zhi From susumu at mri.jhu.edu Thu Jun 10 18:55:59 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 10 Jun 2010 18:55:59 -0400 Subject: [Mristudio-users] Gradient Table Message-ID: Hi all, There are several inquiries about gradient table issues. This is very complicated. In the past, we have tried several times to make it more transparent and we are still trying. In the latest DtiStudio V3.0.2, you might have found a couple of new buttons to get a table relatively easily. However, because there are so many different possibility to get different tables, it is not easy to make it completely automated. Therefore, users need to have some degree of knowledge. There are several ways to notice wrong gradient tables; 1) Totally wrong table: If the table is totally wrong, the color map doesn't make sense. So check color map first. 2) X/Y/Z permutation: If X/Y/Z is miss signed, the color of the color maps doesn't look right. For example, the corpus callosum should look red, not green 3) +/- sign error: Perform tractography. If sign is wrong, it doesn't make any sense. 4) More subtle errors: Look at fitting residual (error) map. There is a file called "DtiStudioUpdate.doc" at https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2. This explains how to get the fitting error maps. 5) Oblique angle: The attached file explains in detail. To make sure everything is right, you can scan a person twice. One in a regular position and one in severe oblique. If everything is working, you should get anatomically comparable tractography results. The attached documents explains the gradient issues. Hope this helps. Susumu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100610/16446c8e/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: Issue of Gradient Table.docx Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document Size: 118760 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100610/16446c8e/attachment-0001.bin From susumu at mri.jhu.edu Thu Jun 10 20:47:01 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 10 Jun 2010 20:47:01 -0400 Subject: [Mristudio-users] about the Tutorial.zip In-Reply-To: References: Message-ID: We'll try. On Thu, Jun 10, 2010 at 8:55 AM, WANG, Zhi(Arthur) wrote: > Dear all, > > I found it was very slow to download the tutorial.zip. Can it be > divided into several subsections? > > BR, > > Zhi > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100610/80f5dea2/attachment.html From hzhang84 at asu.edu Sat Jun 12 14:56:18 2010 From: hzhang84 at asu.edu (Hua Zhang) Date: Sat, 12 Jun 2010 11:56:18 -0700 Subject: [Mristudio-users] Qestion about the scanner verison Message-ID: Dear Professor Susumu Mori, Great thanks for the gradient table document. Here I have a question: how can we know the verison of the scanner is VB13 or VB15? All I do know is the series and tesla number of it. Can we get it from the DICOM files? best, Hua -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100612/415cf63c/attachment.html From azhang at psych.uic.edu Tue Jun 15 19:33:21 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Tue, 15 Jun 2010 18:33:21 -0500 Subject: [Mristudio-users] Saving fiber in data file In-Reply-To: References: <4C038E450200000C0052115D@n6mcgw16.cchmc.org> <4C038E650200000C00521161@n6mcgw16.cchmc.org> <4C03912D0200000C00521165@n6mcgw16.cchmc.org> <4C03912D.D7E9.000C.0@cchmc.org> Message-ID: <40469184F1D86344A835AB980269681A16968C98DC@exchange.psych.uic.edu> Dear DtiStudio, I am trying to save the fiber tracking results into data file for further analysis. The binary file lost the fiber direction information. I am wondering if DtiStudio format keeps the coordinates and direction info for each single fiber. If so, where can I locate the structure of the DtiStudio format? thanks. Sincerely! Aifeng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100615/9561caee/attachment.html From susumu at mri.jhu.edu Tue Jun 15 20:30:58 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 15 Jun 2010 20:30:58 -0400 Subject: [Mristudio-users] Saving fiber in data file In-Reply-To: <40469184F1D86344A835AB980269681A16968C98DC@exchange.psych.uic.edu> References: <4C038E450200000C0052115D@n6mcgw16.cchmc.org> <4C038E650200000C00521161@n6mcgw16.cchmc.org> <4C03912D0200000C00521165@n6mcgw16.cchmc.org> <4C03912D.D7E9.000C.0@cchmc.org> <40469184F1D86344A835AB980269681A16968C98DC@exchange.psych.uic.edu> Message-ID: I hope FAQ#1 (https://www.mristudio.org/wiki/faq) answers the question. susumu On Tue, Jun 15, 2010 at 7:33 PM, Zhang, Aifeng wrote: > Dear DtiStudio, > > > > I am trying to save the fiber tracking results into data file for further > analysis. The binary file lost the fiber direction information. I am > wondering if DtiStudio format keeps the coordinates and direction info for > each single fiber. If so, where can I locate the structure of the DtiStudio > format? thanks. > > > > Sincerely! > > Aifeng > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100615/ea0158ab/attachment.html From NakamaH at dop.hawaii.edu Tue Jun 15 20:31:27 2010 From: NakamaH at dop.hawaii.edu (Nakama, Helenna) Date: Tue, 15 Jun 2010 14:31:27 -1000 Subject: [Mristudio-users] Saving fiber in data file References: <4C038E450200000C0052115D@n6mcgw16.cchmc.org> <4C038E650200000C00521161@n6mcgw16.cchmc.org> <4C03912D0200000C00521165@n6mcgw16.cchmc.org> <4C03912D.D7E9.000C.0@cchmc.org> <40469184F1D86344A835AB980269681A16968C98DC@exchange.psych.uic.edu> Message-ID: <9C9977DB9D84274A9FE2899D6A3692AD012B43A9@dopexch2.dop.hawaii.edu> please remove me from email list. -----Original Message----- From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Tue 6/15/2010 2:30 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Saving fiber in data file I hope FAQ#1 (https://www.mristudio.org/wiki/faq) answers the question. susumu On Tue, Jun 15, 2010 at 7:33 PM, Zhang, Aifeng wrote: > Dear DtiStudio, > > > > I am trying to save the fiber tracking results into data file for further > analysis. The binary file lost the fiber direction information. I am > wondering if DtiStudio format keeps the coordinates and direction info for > each single fiber. If so, where can I locate the structure of the DtiStudio > format? thanks. > > > > Sincerely! > > Aifeng > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3492 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100615/95ff8f60/attachment.bin From fwd9707 at yahoo.com.cn Wed Jun 16 05:32:26 2010 From: fwd9707 at yahoo.com.cn (weidong fang) Date: Wed, 16 Jun 2010 17:32:26 +0800 (CST) Subject: [Mristudio-users] Saving fiber in data file In-Reply-To: <9C9977DB9D84274A9FE2899D6A3692AD012B43A9@dopexch2.dop.hawaii.edu> Message-ID: <544058.61333.qm@web15802.mail.cnb.yahoo.com> thankeyou professer I dont want so much e-mail? to me thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100616/a7133bec/attachment-0001.html From azhang at psych.uic.edu Wed Jun 16 09:33:56 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Wed, 16 Jun 2010 08:33:56 -0500 Subject: [Mristudio-users] Saving fiber in data file In-Reply-To: References: <4C038E450200000C0052115D@n6mcgw16.cchmc.org> <4C038E650200000C00521161@n6mcgw16.cchmc.org> <4C03912D0200000C00521165@n6mcgw16.cchmc.org> <4C03912D.D7E9.000C.0@cchmc.org> <40469184F1D86344A835AB980269681A16968C98DC@exchange.psych.uic.edu> Message-ID: <40469184F1D86344A835AB980269681A16968C991C@exchange.psych.uic.edu> thanks, Dr. Mori! From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Tuesday, June 15, 2010 7:31 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Saving fiber in data file I hope FAQ#1 (https://www.mristudio.org/wiki/faq) answers the question. susumu On Tue, Jun 15, 2010 at 7:33 PM, Zhang, Aifeng > wrote: Dear DtiStudio, I am trying to save the fiber tracking results into data file for further analysis. The binary file lost the fiber direction information. I am wondering if DtiStudio format keeps the coordinates and direction info for each single fiber. If so, where can I locate the structure of the DtiStudio format? thanks. Sincerely! Aifeng _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100616/80cdbb7f/attachment.html From felshahaby at gmail.com Wed Jun 16 16:18:35 2010 From: felshahaby at gmail.com (Fatma ElShahaby) Date: Wed, 16 Jun 2010 16:18:35 -0400 Subject: [Mristudio-users] Questions about Diffeomap and ROIeditor. Message-ID: Dear DtiStudio, I have some questions regarding Diffeomap and ROI editor: 1) I have anatomical images and DTI images, all in DICOM format. And I want to know how to superimpose these two types of images (crop and rescale)?. Here is what I did.I tried to use Diffeomap, I use the "Crop" button to I throw away some axial slices from the anatomical images. Then I use "Resample Image" button, and I enter the dimensions of the DTI image and I get a part of the image (the scaling step was not right? It crops the right and left sides of the image) 2) When I tried to define some ROIs in the ROIeditor and save my ROI data as "binary maps", then try to open this map in DTI Studio, I get a message that tells me *"Unrecognized image-ROI data file!"*. I don't know what this means. 3) Also, can I define the ROIs and the seeds in the anatomical image then transform it to the DTI images? By the way, I can not use the brain Atlas that comes with the software, because I'm not dealing with brain data. Thank you. Fatma. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100616/55e0a7c5/attachment.html From azhang at psych.uic.edu Wed Jun 16 22:49:17 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Wed, 16 Jun 2010 21:49:17 -0500 Subject: [Mristudio-users] Saving fiber in data file In-Reply-To: References: <4C038E450200000C0052115D@n6mcgw16.cchmc.org> <4C038E650200000C00521161@n6mcgw16.cchmc.org> <4C03912D0200000C00521165@n6mcgw16.cchmc.org> <4C03912D.D7E9.000C.0@cchmc.org> <40469184F1D86344A835AB980269681A16968C98DC@exchange.psych.uic.edu> Message-ID: <40469184F1D86344A835AB980269681A1695CAE2C0@exchange.psych.uic.edu> Dr. Mori Does each fiber bundle has an unique RGB FiberColor? Is it the way to identify fiber bundles? and also where can I find the description about the method of grouping fiber bundles? Thanks! Sincerely, Aifeng ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: Tuesday, June 15, 2010 7:30 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Saving fiber in data file I hope FAQ#1 (https://www.mristudio.org/wiki/faq) answers the question. susumu On Tue, Jun 15, 2010 at 7:33 PM, Zhang, Aifeng > wrote: Dear DtiStudio, I am trying to save the fiber tracking results into data file for further analysis. The binary file lost the fiber direction information. I am wondering if DtiStudio format keeps the coordinates and direction info for each single fiber. If so, where can I locate the structure of the DtiStudio format? thanks. Sincerely! Aifeng _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100616/0c0d4866/attachment.html From susumu at mri.jhu.edu Thu Jun 17 08:16:11 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 17 Jun 2010 08:16:11 -0400 Subject: [Mristudio-users] Saving fiber in data file In-Reply-To: <40469184F1D86344A835AB980269681A1695CAE2C0@exchange.psych.uic.edu> References: <4C038E450200000C0052115D@n6mcgw16.cchmc.org> <4C038E650200000C00521161@n6mcgw16.cchmc.org> <4C03912D0200000C00521165@n6mcgw16.cchmc.org> <4C03912D.D7E9.000C.0@cchmc.org> <40469184F1D86344A835AB980269681A16968C98DC@exchange.psych.uic.edu> <40469184F1D86344A835AB980269681A1695CAE2C0@exchange.psych.uic.edu> Message-ID: you can assign a color for each bundle that share the same ROI. For example, you can first choose "red" and draw first ROI. Then all reconstructed streamlines are painted red. Then choose "yellow" and "AND+" tool. Draw another ROI for a portion of the reconstructed streamlines. Those lines penetrates the second ROI becomes yellow while the other lines stay red. You can save this results and the file format is explained in FAQ#1 in www.mristudio.org. Another way is to reconstruct whatever the tracts you want in red and save it. You can reconstruct the second tract independently using yellow and save it. After all the reconstructions are done and saved, you can load them back to DtiStudio. In this way, you can show multiple tracts with different colors. Susumu On Wed, Jun 16, 2010 at 10:49 PM, Zhang, Aifeng wrote: > Dr. Mori > > Does each fiber bundle has an unique RGB FiberColor? Is it the way > to identify fiber bundles? > > and also where can I find the description about the method of > grouping fiber bundles? Thanks! > > Sincerely, > Aifeng > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ > susumu at mri.jhu.edu] > *Sent:* Tuesday, June 15, 2010 7:30 PM > *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support > *Subject:* Re: [Mristudio-users] Saving fiber in data file > > I hope FAQ#1 (https://www.mristudio.org/wiki/faq) answers the question. > > susumu > > On Tue, Jun 15, 2010 at 7:33 PM, Zhang, Aifeng wrote: > >> Dear DtiStudio, >> >> >> >> I am trying to save the fiber tracking results into data file for further >> analysis. The binary file lost the fiber direction information. I am >> wondering if DtiStudio format keeps the coordinates and direction info for >> each single fiber. If so, where can I locate the structure of the DtiStudio >> format? thanks. >> >> >> >> Sincerely! >> >> Aifeng >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100617/0fddbd70/attachment-0001.html From susumu at mri.jhu.edu Thu Jun 17 08:53:38 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 17 Jun 2010 08:53:38 -0400 Subject: [Mristudio-users] Questions about Diffeomap and ROIeditor. In-Reply-To: References: Message-ID: Please see below; > 1) I have anatomical images and DTI images, all in DICOM format. And I want > to know how to superimpose these two types of images (crop and rescale)?. > Here is what I did.I tried to use Diffeomap, I use the "Crop" button to I > throw away some axial slices from the anatomical images. Then I use > "Resample Image" button, and I enter the dimensions of the DTI image and I > get a part of the image (the scaling step was not right? It crops the right > and left sides of the image) > > Crop tool is to prepare two images before submission to non-linear transformation, but not to do resampling. For example, if your image covers only to the level of the midbrain and out atlas is extended to the medulla. Then, non-linear image-matching algorithm (LDDMM) gets confused. In this case, you want to crop the atlas image to the level of the midbrain so that both images covers the same areas of the brains. > You can match the pixel size and matrix size using the "resample image" tool. However, this works only when; 1) the center of FOV is identical (translation) and 2) the orientation of the FOV is identical (rotation). If T1 and DTI were acquired without changing the center of FOV and it's orientation (and also if the subject motion is negligible), you can co-register two images just by the resample tool > If your T1 and DTI were not co-registered when they were acquired, you need post-processing registration. There are 1) theoretical registration and 2) registration tool (AIR) > For theoretical registration, you need to extract information about the center of FOV and oblique (rotation) information from DICOM or other types of header information. Then you can type in these information in the "translation" and "rotation" tools in DiffeoMap. > For registration tool, you need to use "rigid transformation" of AIR. Use DTI (such as b0 or DWI) as a template and register T1 to the template. Here, you can submit T1 image even if the matrix, pixel size, brain positions are different from DTI. The output file has the same dimensions as DTI. This procedure is explained in https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_StepOne_LinearNormalization. As you can see, this could be the easiest way, but please make sure that the output of this automated registration actually worked by carefully inspect the results. If the initial position of the brain in T1 is very different from DTI, it may not work. You many need to use "mutual" registration (it takes much longer) or few-point landmarks (manual but much quicker) for initial alignment or sometimes you need to remove skull intensity. All these operations can be done within DiffeoMap. > 2) When I tried to define some ROIs in the ROIeditor and save my ROI data > as "binary maps", then try to open this map in DTI Studio, I get a message > that tells me *"Unrecognized image-ROI data file!"*. I don't know what > this means. > > please use "binary" not "binary map". To learn what is the "binary map" format, please refer to FAQ#16. You need to save an ROI as "binary" in RoiEditor and open is as "binary" in DtiStudio. If you have only 1 ROI, this is the best way. If you have multiple ROIs and you want to combine them with specific operations such as "OR', "AND", "NOT", then you want to use "binary map". You need to save the ROI files as "binary map" in RoiEditor and load as "binary map". > 3) Also, can I define the ROIs and the seeds in the anatomical image then > transform it to the DTI images? > > Yes, first T1 has to go through DiffeoMap to make sure it is coregistered to DTI and has exactly the same matrix and pixel dimensions (AIR rigid registration could be the easiest way, see above). > Then load the registered T1 to RoiEditor and define ROIs. If you define one ROI, save and load as "binary". If you draw multiple ROIs and combine them for tractography, use "binary map". > By the way, I can not use the brain Atlas that comes with the software, > because I'm not dealing with brain data. Thank you. > > Fatma. > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100617/c5592904/attachment.html From rajagov2 at ccf.org Thu Jun 17 11:16:11 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Thu, 17 Jun 2010 11:16:11 -0400 Subject: [Mristudio-users] Eddy current and motion corrected data set Message-ID: <77A88E90A851594AAEF830450587C39D041831FC@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, I am wondering how to get dti data (all B0 and DW images) after eddy current and motion correction steps or in fact the images which are in same space as FA or other DTI metrics in DTI studio. I need these images in order to register them with anatomical datasets. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100617/0801746b/attachment.html From azhang at psych.uic.edu Thu Jun 17 13:48:49 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Thu, 17 Jun 2010 12:48:49 -0500 Subject: [Mristudio-users] Saving fiber in data file In-Reply-To: References: <4C038E450200000C0052115D@n6mcgw16.cchmc.org> <4C038E650200000C00521161@n6mcgw16.cchmc.org> <4C03912D0200000C00521165@n6mcgw16.cchmc.org> <4C03912D.D7E9.000C.0@cchmc.org> <40469184F1D86344A835AB980269681A16968C98DC@exchange.psych.uic.edu> <40469184F1D86344A835AB980269681A1695CAE2C0@exchange.psych.uic.edu> Message-ID: <40469184F1D86344A835AB980269681A16968C9B1E@exchange.psych.uic.edu> Dear Dr. Mori Thanks a lot for the guidance. Because I am interested in doing further analysis like curvature and torsion on the fiber bundles[1], I am curious about how DtiStudio bundle fibers together. And I found that in the saved fiber tracking results from DtiStudio with the option of Fiber Color as Random, it already assign fibers with RGB colors. Does each bundle assign with unique combination of RGB colors? I am wondering if there is an algorithm that DTIstudio uses to bundle similar fibers together, like the one listed in the following paper. and if the color is the only way to differentiate different bundles? [1] Ding Z, Gore JC, Anderson AW. "Classification and quantification of neuronal fiber pathways using diffusion tensor MRI". Magn Reson Med. 2003 Apr;49(4):716-21. Sincerely, Aifeng From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Thursday, June 17, 2010 7:16 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Saving fiber in data file you can assign a color for each bundle that share the same ROI. For example, you can first choose "red" and draw first ROI. Then all reconstructed streamlines are painted red. Then choose "yellow" and "AND+" tool. Draw another ROI for a portion of the reconstructed streamlines. Those lines penetrates the second ROI becomes yellow while the other lines stay red. You can save this results and the file format is explained in FAQ#1 in www.mristudio.org. Another way is to reconstruct whatever the tracts you want in red and save it. You can reconstruct the second tract independently using yellow and save it. After all the reconstructions are done and saved, you can load them back to DtiStudio. In this way, you can show multiple tracts with different colors. Susumu On Wed, Jun 16, 2010 at 10:49 PM, Zhang, Aifeng > wrote: Dr. Mori Does each fiber bundle has an unique RGB FiberColor? Is it the way to identify fiber bundles? and also where can I find the description about the method of grouping fiber bundles? Thanks! Sincerely, Aifeng ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: Tuesday, June 15, 2010 7:30 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Saving fiber in data file I hope FAQ#1 (https://www.mristudio.org/wiki/faq) answers the question. susumu On Tue, Jun 15, 2010 at 7:33 PM, Zhang, Aifeng > wrote: Dear DtiStudio, I am trying to save the fiber tracking results into data file for further analysis. The binary file lost the fiber direction information. I am wondering if DtiStudio format keeps the coordinates and direction info for each single fiber. If so, where can I locate the structure of the DtiStudio format? thanks. Sincerely! Aifeng _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100617/6c2fb56b/attachment-0001.html From susumu at mri.jhu.edu Thu Jun 17 17:32:50 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 17 Jun 2010 17:32:50 -0400 Subject: [Mristudio-users] Eddy current and motion corrected data set In-Reply-To: <77A88E90A851594AAEF830450587C39D041831FC@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D041831FC@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: In DtiStudio, eddy/motion correction is done simultaneously using AIR affine transformation. The default setting is to create a duplicate data that are AIRed which have AIR_xxx name. So, all b0 and DWIs are duplicated. You can save these images. You can then reload these images to calculate FA and other DTI matrices that are eddy/motion corrected. On Thu, Jun 17, 2010 at 11:16 AM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > Dear All, > > I am wondering how to get dti data (all B0 and DW images) after eddy > current and motion correction steps or in fact the images which are in same > space as FA or other DTI metrics in DTI studio. I need these images in order > to register them with anatomical datasets. > > Thanks > > Venkat > > =================================== > > P Please consider the environment before printing this e-mail > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100617/38c09131/attachment.html From jmcentee at jhmi.edu Thu Jun 17 19:27:03 2010 From: jmcentee at jhmi.edu (Julie McEntee) Date: Thu, 17 Jun 2010 19:27:03 -0400 Subject: [Mristudio-users] theory - registration In-Reply-To: Message-ID: Hi Susumu, I was wondering if you have been able to follow-up on your points in the email to Darren (below). I read the response re: TheoryAir from Hangyi, but it did not indicate whether TheoryAir does a regid or affine transform to answer whether or not it would be able to do eddy current correction-? I am able to do the Pixel rejection using Darren?s method and obtain results with binary mask & no ?Image rejection?; however, I get Image rejection after performing TheoryAir- is that expected? How do you determine the # of iterations to perform with TheoryAir? Lastly, if I want to do TheoryAir and Pixel rejection, would I do TheoryAir, save DWI + b0 images as REC file, re-load into DtiStudio, and then perform Pixel rejection/tensor calculation? Thanks for your help, Julie Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676 On 5/18/10 10:48 AM, "susumu mori" wrote: > Darren, > > You are using the "Pixel rejection" correctly and we have to investigate why > you are getting "Image rejection" results. > > >> 1) Should I run other registration methods such as AIR or MI before >> theory-registratin? Will theory-registration take care of eddy current >> correction? > >> >Theory registration should be used instead of AIR or MI. I have to confirm >> Hangyi if TheoryAIR does rigid or affine. I'll get back to you with this >> respect too. > ? >> >> 2) What images are changed by theory registration? ?The original >> images? It doesn't seem to produce new images such as with mutual >> information or AIR. > >> >Yes, when you use TheoryAIR, you don't get a copy. The original images are >> overwritten. > ? >> >> Thanks, >> Darren >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100617/6e4dc337/attachment.html From choisj70 at gmail.com Thu Jun 17 20:52:47 2010 From: choisj70 at gmail.com (Seongjin) Date: Thu, 17 Jun 2010 20:52:47 -0400 Subject: [Mristudio-users] Digits of ADC and tracer in ROI editor and DTI Studio Message-ID: Digits of ADC and tracer in ROI editor and DTI Studio are different. So measured values for ADC and tracer from ROI Editor using ROI generated in the ROI editor gives out number are somewhat limited. DTI studio give out better digits for ADC and tracer. Is there any method to use the ROI-editor-generated ROI in DTI studio? -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100617/c56cac8b/attachment.html From susumu at mri.jhu.edu Fri Jun 18 10:24:11 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 18 Jun 2010 10:24:11 -0400 Subject: [Mristudio-users] Digits of ADC and tracer in ROI editor and DTI Studio In-Reply-To: References: Message-ID: Thank you for letting us know. We will revise the posted version today so that you can have more digits. On Thu, Jun 17, 2010 at 8:52 PM, [Seongjin] wrote: > Digits of ADC and tracer in ROI editor and DTI Studio are different. > So measured values for ADC and tracer from ROI Editor using ROI generated > in the ROI editor gives out number are somewhat limited. > > DTI studio give out better digits for ADC and tracer. > > Is there any method to use the ROI-editor-generated ROI in DTI studio? > > -SC > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100618/3eb6bd48/attachment.html From choisj70 at gmail.com Fri Jun 18 11:07:39 2010 From: choisj70 at gmail.com (Seongjin) Date: Fri, 18 Jun 2010 11:07:39 -0400 Subject: [Mristudio-users] Digits of ADC and tracer in ROI editor and DTI Studio In-Reply-To: References: Message-ID: It would be great! Would you let us know if the updated ROI-editor is released within today? All the best, -SC On Fri, Jun 18, 2010 at 10:24 AM, susumu mori wrote: > Thank you for letting us know. We will revise the posted version today so > that you can have more digits. > > On Thu, Jun 17, 2010 at 8:52 PM, [Seongjin] wrote: > >> Digits of ADC and tracer in ROI editor and DTI Studio are different. >> So measured values for ADC and tracer from ROI Editor using ROI generated >> in the ROI editor gives out number are somewhat limited. >> >> DTI studio give out better digits for ADC and tracer. >> >> Is there any method to use the ROI-editor-generated ROI in DTI studio? >> >> -SC >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100618/7edd1fb4/attachment-0001.html From rajagov2 at ccf.org Fri Jun 18 11:50:23 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Fri, 18 Jun 2010 11:50:23 -0400 Subject: [Mristudio-users] Eddy current and motion corrected data set References: <77A88E90A851594AAEF830450587C39D041831FC@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D04183206@CCHSCLEXMB56.cc.ad.cchs.net> Sorry Dr.Mori, i don't know whether i have understood you correctly, The default setting is to create a duplicate data that are AIRed which have AIR_xxx name. So, all b0 and DWIs are duplicated. After loading the files and gradient table i click on the Tensor, Colormap tab under calculation tab after this i click on image tab at the bottom right side corner of the DTI studio and then click on the save option where i can find FA, b0 and all the images so these b0 and other dwi images are basically AIRed i.e. corrected for eddy/motion correction. Am i right. Thanks very much venkat ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Thu 6/17/2010 5:32 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Eddy current and motion corrected data set In DtiStudio, eddy/motion correction is done simultaneously using AIR affine transformation. The default setting is to create a duplicate data that are AIRed which have AIR_xxx name. So, all b0 and DWIs are duplicated. You can save these images. You can then reload these images to calculate FA and other DTI matrices that are eddy/motion corrected. On Thu, Jun 17, 2010 at 11:16 AM, Rajagopalan, Venkateswaran wrote: Dear All, I am wondering how to get dti data (all B0 and DW images) after eddy current and motion correction steps or in fact the images which are in same space as FA or other DTI metrics in DTI studio. I need these images in order to register them with anatomical datasets. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100618/d5ef5c28/attachment.html From choisj70 at gmail.com Fri Jun 18 14:33:38 2010 From: choisj70 at gmail.com (Seongjin) Date: Fri, 18 Jun 2010 14:33:38 -0400 Subject: [Mristudio-users] Digits of ADC and tracer in ROI editor and DTI Studio In-Reply-To: References: Message-ID: Thanks very much! It gives out numbers that I need to see. -SC On Fri, Jun 18, 2010 at 10:24 AM, susumu mori wrote: > Thank you for letting us know. We will revise the posted version today so > that you can have more digits. > > On Thu, Jun 17, 2010 at 8:52 PM, [Seongjin] wrote: > >> Digits of ADC and tracer in ROI editor and DTI Studio are different. >> So measured values for ADC and tracer from ROI Editor using ROI generated >> in the ROI editor gives out number are somewhat limited. >> >> DTI studio give out better digits for ADC and tracer. >> >> Is there any method to use the ROI-editor-generated ROI in DTI studio? >> >> -SC >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100618/078d9ad6/attachment.html From susumu at mri.jhu.edu Sat Jun 19 13:45:10 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sat, 19 Jun 2010 13:45:10 -0400 Subject: [Mristudio-users] theory - registration In-Reply-To: References: Message-ID: Hi Julie, Those are all good questions. Our TheoryAIR routine is now being updated to provide more controls over which transformation you want to use (currently Rigid only) and how to combine with outlier rejection (slice rejection or pixel rejection?). Also, currently you can't save TheoryAIRed data. I hope that we can release the revised version in this front in July. As for the iteration, we are still accumulating experiences and want to welcome any information from users. At this point, I would say 5 usually works. DtiStudio provides visual interface to judge the improvement in registration. This is an effective method especially when you have repeated measurements (so that you can see the subtraction of the two to check the registration/correction quality). At this point, you should rely on your visual judgment. As a matter of fact, almost always, difficulty of automated image quality check is how to quantify the improvement by registration/correction schemes. If you can quantify the improvement, we would use such a measure to minimize during the registration and correction process. In the end, our eyeballs are the best method for judgment which we can hardly beat. Susumu On Thu, Jun 17, 2010 at 7:27 PM, Julie McEntee wrote: > Hi Susumu, > > I was wondering if you have been able to follow-up on your points in the > email to Darren (below). > > I read the response re: TheoryAir from Hangyi, but it did not indicate > whether TheoryAir does a regid or affine transform to answer whether or not > it would be able to do eddy current correction-? > > I am able to do the Pixel rejection using Darren?s method and obtain > results with binary mask & no ?Image rejection?; however, I get Image > rejection after performing TheoryAir- is that expected? How do you determine > the # of iterations to perform with TheoryAir? > > Lastly, if I want to do TheoryAir and Pixel rejection, would I do > TheoryAir, save DWI + b0 images as REC file, re-load into DtiStudio, and > then perform Pixel rejection/tensor calculation? > > Thanks for your help, > > Julie > > Julie E. McEntee, MA, CCRP > Senior Research Program Coordinator > Department of Psychiatry- Neuroimaging > Johns Hopkins University School of Medicine > 600 N. Wolfe St./Phipps 300 > Baltimore, MD 21287 > Phone: 410-502-0468 > Fax: 410-614-3676 > > > > On 5/18/10 10:48 AM, "susumu mori" wrote: > > Darren, > > You are using the "Pixel rejection" correctly and we have to investigate > why you are getting "Image rejection" results. > > > 1) Should I run other registration methods such as AIR or MI before > theory-registratin? Will theory-registration take care of eddy current > correction? > > > >Theory registration should be used instead of AIR or MI. I have to confirm > Hangyi if TheoryAIR does rigid or affine. I'll get back to you with this > respect too. > > > > 2) What images are changed by theory registration? The original > images? It doesn't seem to produce new images such as with mutual > information or AIR. > > > >Yes, when you use TheoryAIR, you don't get a copy. The original images are > overwritten. > > > > Thanks, > Darren > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > > ------------------------------ > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100619/f7a6a28b/attachment-0001.html From susumu at mri.jhu.edu Mon Jun 21 15:13:00 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 21 Jun 2010 15:13:00 -0400 Subject: [Mristudio-users] Gradient from bvec can't be used In-Reply-To: References: Message-ID: Sorry for my slow reply. Here are the old and new Siemens 12. You can try both. If you use a wrong one, the color map doesn't make any sense. So you can find which is the correct one for you. Also, Siemens users have to click "rotate if applicable" check box beneath the gradient table input section, if you are using oblique-angle imaging. This automatically read the oblique angle information and rotates the gradient table. You may also check the new button next of the gradient table input section that can extract gradient information from Mosaic file. So no need to specify the table and rotate it. This works for VB15 operating system. Old Siemens 12 0: 0, 0, 0 1: 1, 0, 0.5 2: 0, 0.5, 1 3: 0.5, 1, 0 4: 1, 0.5, 0 5: 0, 1, 0.5 6: 0.5, 0, 1 7: 1, 0, -0.5 8: 0, -0.5, 1 9: -0.5, 1, 0 10: 1, -0.5, 0 11: 0, 1, -0.5 12: -0.5, 0, 1 New Siemens 12 0: 0, 0, 0 1: 1.000000, 0.414250, -0.414250 2: 1.000000, -0.414250, -0.414250 3: 1.000000, -0.414250, 0.414250 4: 1.000000, 0.414250, 0.414250 5: 0.414250, 0.414250, 1.000000 6: 0.414250, 1.000000, 0.414250 7: 0.414250, 1.000000, -0.414250 8: 0.414250, 0.414250, -1.000000 9: 0.414250, -0.414250, -1.000000 10: 0.414250, -1.000000, -0.414250 11: 0.414250, -1.000000, 0.414250 12: 0.414250, -0.414250, 1.000000 On Tue, Jun 8, 2010 at 11:18 AM, Hua Zhang wrote: > Dear Professor Susumu Mori, > > The scanner type is SIEMENS Novus 1.5T ,Series Description=ep2d.diff.DTI 12 > Software Version=syngo MR 2002M 4VA22B. Will this information do some > help? > > Best, > Hua > > 2010/6/8 susumu mori > > Hi Hua, >> >> We usually do not extract gradient info from any header information >> because there are many issues related to the gradient table and it is >> difficult for us to keep track of all different formats especially when the >> raw MRI data went through other software programs. The only exception is >> Siemens DICOM after VB15, which is supported by DtiStudio for automated >> gradient table extraction. >> >> If you tell us the type of scanner you used and operating system, we may >> be able to provide a table. >> >> Susumu >> >> On Tue, May 18, 2010 at 6:42 PM, Hua Zhang wrote: >> >>> Hi, >>> I have a dti data set of a single subject. The gradient table obtained by >>> dcm2nii is strange and can't get any logical result. Is there some other >>> tools to get the right gradients information. Here I attach the data. Please >>> help. >>> >>> Thanks, >>> Hua Zhang >>> >>> _______________________________________________ >>> Mristudio-users mailing list >>> Mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> Mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100621/0365a734/attachment.html From naamab at stanford.edu Tue Jun 22 16:26:43 2010 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Tue, 22 Jun 2010 13:26:43 -0700 Subject: [Mristudio-users] compatibility of dtistudio versions Message-ID: <3820B23D-B351-4A44-8368-8B798B315749@stanford.edu> Is it OK to combine data analyzed in different versions? Is the built- in AIR different than the one that was a standalone program? Thanks, Naama From susumu at mri.jhu.edu Tue Jun 22 16:26:00 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 22 Jun 2010 16:26:00 -0400 Subject: [Mristudio-users] compatibility of dtistudio versions In-Reply-To: <3820B23D-B351-4A44-8368-8B798B315749@stanford.edu> References: <3820B23D-B351-4A44-8368-8B798B315749@stanford.edu> Message-ID: I think that's fine. AIR algorithm itself hasn't changed for a long time. On Tue, Jun 22, 2010 at 4:26 PM, Naama Barnea-Goraly wrote: > > Is it OK to combine data analyzed in different versions? Is the built- > in AIR different than the one that was a standalone program? > > Thanks, > > Naama > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100622/4f82a8b6/attachment.html From felshahaby at gmail.com Wed Jun 23 17:45:10 2010 From: felshahaby at gmail.com (Fatma ElShahaby) Date: Wed, 23 Jun 2010 17:45:10 -0400 Subject: [Mristudio-users] Fibers' colors Message-ID: Hello, I have a question regarding the color of the fibers that we get from the fiber tracking step. Generally, red, green, and blue colors are assigned to right-left, anterior-posterior, and superior-inferior orientations, respectively. Can I assign colors to my fibers in order to meet the above criterion? Actually, the DTIstudio helps me to assign random color or a specific color for the whole fibers within a certain ROI. Thank you Fatma.. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100623/ec6153b7/attachment.html From choisj70 at gmail.com Thu Jun 24 10:24:31 2010 From: choisj70 at gmail.com (Seongjin) Date: Thu, 24 Jun 2010 10:24:31 -0400 Subject: [Mristudio-users] Fibers' colors In-Reply-To: References: Message-ID: As far as I know, directional coloring is not implemented in DTI Studio. -SC On Wed, Jun 23, 2010 at 5:45 PM, Fatma ElShahaby wrote: > Hello, > I have a question regarding the color of the fibers that we get from the > fiber tracking step. Generally, red, green, and blue colors are assigned to > right-left, anterior-posterior, and superior-inferior orientations, > respectively. Can I assign colors to my fibers in order to meet the above > criterion? Actually, the DTIstudio helps me to assign random color or a > specific color for the whole fibers within a certain ROI. Thank you > > Fatma.. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100624/1e307fc5/attachment.html From susumu at mri.jhu.edu Thu Jun 24 10:52:35 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 24 Jun 2010 10:52:35 -0400 Subject: [Mristudio-users] Fibers' colors In-Reply-To: References: Message-ID: SC is correct. We don't have a scheme to color fibers depending on the orientation. On Thu, Jun 24, 2010 at 10:24 AM, [Seongjin] wrote: > As far as I know, directional coloring is not implemented in DTI Studio. > > -SC > > On Wed, Jun 23, 2010 at 5:45 PM, Fatma ElShahaby wrote: > >> Hello, >> I have a question regarding the color of the fibers that we get from the >> fiber tracking step. Generally, red, green, and blue colors are assigned to >> right-left, anterior-posterior, and superior-inferior orientations, >> respectively. Can I assign colors to my fibers in order to meet the above >> criterion? Actually, the DTIstudio helps me to assign random color or a >> specific color for the whole fibers within a certain ROI. Thank you >> >> Fatma.. >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100624/649a11f1/attachment-0001.html From rajagov2 at ccf.org Mon Jun 28 12:07:58 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Mon, 28 Jun 2010 12:07:58 -0400 Subject: [Mristudio-users] Eddy_current_correction Message-ID: <77A88E90A851594AAEF830450587C39D04183232@CCHSCLEXMB56.cc.ad.cchs.net> Hi All, We have diffusion data set acquired with 5 trails/repetitions(in single time point/cross sectional) for each and every subject. This means i have 5 b0(same value) and DW (12 directions) data while doing eddy current correction can i choose for instance b0 from first trail and register all the DW and other b0 images to this or do eddy current correction separately for each and every trail and finally register all of them together say for instance to the first trail. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100628/88cd599b/attachment.html From support at mristudio.org Mon Jun 28 12:24:48 2010 From: support at mristudio.org (support at mristudio.org) Date: Mon, 28 Jun 2010 12:24:48 -0400 (EDT) Subject: [Mristudio-users] Eddy_current_correction In-Reply-To: <77A88E90A851594AAEF830450587C39D04183232@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D04183232@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <40946.10.16.57.47.1277742288.squirrel@webmail.mristudio.org> the 1st method would be fine: use the 1st B0 as a reference and register all others with it. support > > Hi All, > > We have diffusion data set acquired with 5 trails/repetitions(in single time > point/cross sectional) for each and every subject. This means i have 5 b0(same > value) and DW (12 directions) data while doing eddy current correction can i > choose for instance b0 from first trail and register all the DW and other b0 > images to this or do eddy current correction separately for each and every trail > and finally register all of them together say for instance to the first trail. > > Thanks > > venkat > > =================================== > > P Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > From rajagov2 at ccf.org Mon Jun 28 12:51:18 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Mon, 28 Jun 2010 12:51:18 -0400 Subject: [Mristudio-users] Eddy_current_correction References: <77A88E90A851594AAEF830450587C39D04183232@CCHSCLEXMB56.cc.ad.cchs.net> <40946.10.16.57.47.1277742288.squirrel@webmail.mristudio.org> Message-ID: <77A88E90A851594AAEF830450587C39D04183233@CCHSCLEXMB56.cc.ad.cchs.net> Thanks -----Original Message----- From: mristudio-users-bounces at mristudio.org on behalf of support at mristudio.org Sent: Mon 6/28/2010 12:24 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Eddy_current_correction the 1st method would be fine: use the 1st B0 as a reference and register all others with it. support > > Hi All, > > We have diffusion data set acquired with 5 trails/repetitions(in single time > point/cross sectional) for each and every subject. This means i have 5 b0(same > value) and DW (12 directions) data while doing eddy current correction can i > choose for instance b0 from first trail and register all the DW and other b0 > images to this or do eddy current correction separately for each and every trail > and finally register all of them together say for instance to the first trail. > > Thanks > > venkat > > =================================== > > P Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 4002 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100628/a0a7cfba/attachment.bin From minjiewu at gmail.com Mon Jun 28 13:45:45 2010 From: minjiewu at gmail.com (Minjie Wu) Date: Mon, 28 Jun 2010 12:45:45 -0500 Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor Message-ID: Hello All, We need to measure FA in the substantia nigra (SN) in our project. Small ellipse ROIs (4x4) are placed in these area using DTI Studio and ROI Editor respectively. 1. For DTI Studio, the ROI is not placed at the center of the crosshairs, but instead there is an offset. Is there any way to fix or adjust this? 2. For ROI Editor, the ellipsis ROI (4x4) is placed in SN, and the location of the ROI can be adjusted, then added to an object. However once the ellipsis ROI is combined to an object, ellipsis no longer looks like ellipsis. Is there any way to avoid this? Thank you very much. Sincerely, -- Minjie Wu, PhD Department of Neurology Northwestern University 710 N Lake Shore Dr Abbott Hall, 11th floor, Suite 1107 Chicago IL 60611 Phone: 312-503-1522 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100628/5c8fdeb2/attachment.html From xli16 at jhmi.edu Mon Jun 28 14:47:46 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 28 Jun 2010 14:47:46 -0400 Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor In-Reply-To: References: Message-ID: <72109b1124c61.4c28b612@johnshopkins.edu> Hello Minjie, May I ask what you mean about "ellipsis no longer looks like ellipsis"? Xin ----- Original Message ----- From: Minjie Wu Date: Monday, June 28, 2010 1:45 pm Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor To: mristudio-users at mristudio.org > Hello All, > > We need to measure FA in the substantia nigra (SN) in our project. Small > ellipse ROIs (4x4) are placed in these area using DTI Studio and ROI > Editor > respectively. > > 1. For DTI Studio, the ROI is not placed at the center of the crosshairs, > but instead there is an offset. Is there any way to fix or adjust this? > > 2. For ROI Editor, the ellipsis ROI (4x4) is placed in SN, and the location > of the ROI can be adjusted, then added to an object. However once the > ellipsis ROI is combined to an object, ellipsis no longer looks like > ellipsis. Is there any way to avoid this? > > Thank you very much. > > Sincerely, > > -- > Minjie Wu, PhD > Department of Neurology > Northwestern University > 710 N Lake Shore Dr > Abbott Hall, 11th floor, Suite 1107 > Chicago IL 60611 > Phone: 312-503-1522 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From minjiewu at gmail.com Mon Jun 28 15:45:13 2010 From: minjiewu at gmail.com (Minjie Wu) Date: Mon, 28 Jun 2010 14:45:13 -0500 Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor In-Reply-To: <72109b1124c61.4c28b612@johnshopkins.edu> References: <72109b1124c61.4c28b612@johnshopkins.edu> Message-ID: Hello Xin, I have created two ellipsis ROIs of the same size (4x4). The one on the left is added to an object, and the one on the right is not added to an object. The object looks like an arrow instead of an ellipsis. Please see the screenshot through the link. http://picasaweb.google.com/minjiewu/Screenshot#5487912780977013010 Thanks, Minjie On Mon, Jun 28, 2010 at 1:47 PM, Xin Li wrote: > Hello Minjie, > > May I ask what you mean about "ellipsis no longer looks like ellipsis"? > > > Xin > > > ----- Original Message ----- > From: Minjie Wu > Date: Monday, June 28, 2010 1:45 pm > Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor > To: mristudio-users at mristudio.org > > > > Hello All, > > > > We need to measure FA in the substantia nigra (SN) in our project. Small > > ellipse ROIs (4x4) are placed in these area using DTI Studio and ROI > > Editor > > respectively. > > > > 1. For DTI Studio, the ROI is not placed at the center of the > crosshairs, > > but instead there is an offset. Is there any way to fix or adjust this? > > > > 2. For ROI Editor, the ellipsis ROI (4x4) is placed in SN, and the > location > > of the ROI can be adjusted, then added to an object. However once the > > ellipsis ROI is combined to an object, ellipsis no longer looks like > > ellipsis. Is there any way to avoid this? > > > > Thank you very much. > > > > Sincerely, > > > > -- > > Minjie Wu, PhD > > Department of Neurology > > Northwestern University > > 710 N Lake Shore Dr > > Abbott Hall, 11th floor, Suite 1107 > > Chicago IL 60611 > > Phone: 312-503-1522 > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -- Minjie Wu, PhD Department of Neurology Northwestern University 710 N Lake Shore Dr Abbott Hall, 11th floor, Suite 1107 Chicago IL 60611 Phone: 312-503-1522 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100628/92326863/attachment.html From xli16 at jhmi.edu Mon Jun 28 16:37:52 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 28 Jun 2010 16:37:52 -0400 Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor In-Reply-To: References: <72109b1124c61.4c28b612@johnshopkins.edu> Message-ID: <7250979123fe9.4c28cfe0@johnshopkins.edu> Hello Minjie, It is because that the voxel boundary follows the pixel definition. Therefore, even if you draw a round shape, it will still follow the square pixel shape. Regards, Xin ----- Original Message ----- From: Minjie Wu Date: Monday, June 28, 2010 3:45 pm Subject: Re: [Mristudio-users] define ROI in DTI Studio and ROI Editor To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Hello Xin, > > I have created two ellipsis ROIs of the same size (4x4). The one on > the left > is added to an object, and the one on the right is not added to an object. > The object looks like an arrow instead of an ellipsis. Please see the > screenshot through the link. > > > > Thanks, > Minjie > > On Mon, Jun 28, 2010 at 1:47 PM, Xin Li wrote: > > > Hello Minjie, > > > > May I ask what you mean about "ellipsis no longer looks like ellipsis"? > > > > > > Xin > > > > > > ----- Original Message ----- > > From: Minjie Wu > > Date: Monday, June 28, 2010 1:45 pm > > Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor > > To: mristudio-users at mristudio.org > > > > > > > Hello All, > > > > > > We need to measure FA in the substantia nigra (SN) in our > project. Small > > > ellipse ROIs (4x4) are placed in these area using DTI Studio and > ROI > > > Editor > > > respectively. > > > > > > 1. For DTI Studio, the ROI is not placed at the center of the > > crosshairs, > > > but instead there is an offset. Is there any way to fix or > adjust this? > > > > > > 2. For ROI Editor, the ellipsis ROI (4x4) is placed in SN, and the > > location > > > of the ROI can be adjusted, then added to an object. However > once the > > > ellipsis ROI is combined to an object, ellipsis no longer looks > like > > > ellipsis. Is there any way to avoid this? > > > > > > Thank you very much. > > > > > > Sincerely, > > > > > > -- > > > Minjie Wu, PhD > > > Department of Neurology > > > Northwestern University > > > 710 N Lake Shore Dr > > > Abbott Hall, 11th floor, Suite 1107 > > > Chicago IL 60611 > > > Phone: 312-503-1522 > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > > > -- > Minjie Wu, PhD > Department of Neurology > Northwestern University > 710 N Lake Shore Dr > Abbott Hall, 11th floor, Suite 1107 > Chicago IL 60611 > Phone: 312-503-1522 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Mon Jun 28 16:44:13 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 28 Jun 2010 16:44:13 -0400 Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor In-Reply-To: References: <72109b1124c61.4c28b612@johnshopkins.edu> Message-ID: <72b0830e21243.4c28d15d@johnshopkins.edu> Sorry. it should be "the ROI boundary" not "the voxel boundary". Xin ----- Original Message ----- From: Minjie Wu Date: Monday, June 28, 2010 3:45 pm Subject: Re: [Mristudio-users] define ROI in DTI Studio and ROI Editor To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Hello Xin, > > I have created two ellipsis ROIs of the same size (4x4). The one on > the left > is added to an object, and the one on the right is not added to an object. > The object looks like an arrow instead of an ellipsis. Please see the > screenshot through the link. > > > > Thanks, > Minjie > > On Mon, Jun 28, 2010 at 1:47 PM, Xin Li wrote: > > > Hello Minjie, > > > > May I ask what you mean about "ellipsis no longer looks like ellipsis"? > > > > > > Xin > > > > > > ----- Original Message ----- > > From: Minjie Wu > > Date: Monday, June 28, 2010 1:45 pm > > Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor > > To: mristudio-users at mristudio.org > > > > > > > Hello All, > > > > > > We need to measure FA in the substantia nigra (SN) in our > project. Small > > > ellipse ROIs (4x4) are placed in these area using DTI Studio and > ROI > > > Editor > > > respectively. > > > > > > 1. For DTI Studio, the ROI is not placed at the center of the > > crosshairs, > > > but instead there is an offset. Is there any way to fix or > adjust this? > > > > > > 2. For ROI Editor, the ellipsis ROI (4x4) is placed in SN, and the > > location > > > of the ROI can be adjusted, then added to an object. However > once the > > > ellipsis ROI is combined to an object, ellipsis no longer looks > like > > > ellipsis. Is there any way to avoid this? > > > > > > Thank you very much. > > > > > > Sincerely, > > > > > > -- > > > Minjie Wu, PhD > > > Department of Neurology > > > Northwestern University > > > 710 N Lake Shore Dr > > > Abbott Hall, 11th floor, Suite 1107 > > > Chicago IL 60611 > > > Phone: 312-503-1522 > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > > > -- > Minjie Wu, PhD > Department of Neurology > Northwestern University > 710 N Lake Shore Dr > Abbott Hall, 11th floor, Suite 1107 > Chicago IL 60611 > Phone: 312-503-1522 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From minjiewu at gmail.com Mon Jun 28 16:52:05 2010 From: minjiewu at gmail.com (Minjie Wu) Date: Mon, 28 Jun 2010 15:52:05 -0500 Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor In-Reply-To: <72b0830e21243.4c28d15d@johnshopkins.edu> References: <72109b1124c61.4c28b612@johnshopkins.edu> <72b0830e21243.4c28d15d@johnshopkins.edu> Message-ID: Thanks a lot. Appreciate it very much. BTW: Another question in the DTI Studio, is it possible to place the ROI at the center of the crosshairs without offset? Minjie On Mon, Jun 28, 2010 at 3:44 PM, Xin Li wrote: > Sorry. it should be "the ROI boundary" not "the voxel boundary". > > > Xin > > > > ----- Original Message ----- > From: Minjie Wu > Date: Monday, June 28, 2010 3:45 pm > Subject: Re: [Mristudio-users] define ROI in DTI Studio and ROI Editor > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" < > mristudio-users at mristudio.org> > > > > Hello Xin, > > > > I have created two ellipsis ROIs of the same size (4x4). The one on > > the left > > is added to an object, and the one on the right is not added to an > object. > > The object looks like an arrow instead of an ellipsis. Please see the > > screenshot through the link. > > > > > > > > Thanks, > > Minjie > > > > On Mon, Jun 28, 2010 at 1:47 PM, Xin Li wrote: > > > > > Hello Minjie, > > > > > > May I ask what you mean about "ellipsis no longer looks like > ellipsis"? > > > > > > > > > Xin > > > > > > > > > ----- Original Message ----- > > > From: Minjie Wu > > > Date: Monday, June 28, 2010 1:45 pm > > > Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor > > > To: mristudio-users at mristudio.org > > > > > > > > > > Hello All, > > > > > > > > We need to measure FA in the substantia nigra (SN) in our > > project. Small > > > > ellipse ROIs (4x4) are placed in these area using DTI Studio and > > ROI > > > > Editor > > > > respectively. > > > > > > > > 1. For DTI Studio, the ROI is not placed at the center of the > > > crosshairs, > > > > but instead there is an offset. Is there any way to fix or > > adjust this? > > > > > > > > 2. For ROI Editor, the ellipsis ROI (4x4) is placed in SN, and the > > > location > > > > of the ROI can be adjusted, then added to an object. However > > once the > > > > ellipsis ROI is combined to an object, ellipsis no longer looks > > like > > > > ellipsis. Is there any way to avoid this? > > > > > > > > Thank you very much. > > > > > > > > Sincerely, > > > > > > > > -- > > > > Minjie Wu, PhD > > > > Department of Neurology > > > > Northwestern University > > > > 710 N Lake Shore Dr > > > > Abbott Hall, 11th floor, Suite 1107 > > > > Chicago IL 60611 > > > > Phone: 312-503-1522 > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > > > > > > > > > -- > > Minjie Wu, PhD > > Department of Neurology > > Northwestern University > > 710 N Lake Shore Dr > > Abbott Hall, 11th floor, Suite 1107 > > Chicago IL 60611 > > Phone: 312-503-1522 > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100628/42de2c63/attachment-0001.html From Jenifer.Juranek at uth.tmc.edu Mon Jun 28 19:37:18 2010 From: Jenifer.Juranek at uth.tmc.edu (Juranek, Jenifer) Date: Mon, 28 Jun 2010 18:37:18 -0500 Subject: [Mristudio-users] Calculating SNR of DTI data Message-ID: <3A4B564F13D63145AB38101AF6C50FF50B08EACB33@UTHCMS2.uthouston.edu> While the issue of SNR effects on DTI metrics is discussed in the published literature, I have found relatively little information regarding calculating SNR as a screening procedure for image quality. A few authors have reported the SNR range (or cut-off) of their datasets - but not many. I'm curious about the following questions...any responses/opinions would be very helpful. 1) Is calculation of SNR an effective screening tool for image quality in DTI research? 2) Is calculation of SNR helpful for determining the feasibility of pooling 3T DTI data from different scanner platforms (e.g. Siemens and Philips) 3) To what extent do parallel imaging and acceleration factors affect measures of SNR? 4) If calculation of SNR is a "good thing to do and report", then what is the best approach? In particular, datatype for analysis (e.g. b=0, trace, DW) and location "inside the brain" seem to be important things to consider. In terms of datatype, I have seen folks use single non-averaged b=0 for each subject, and a mathematical relation between sequential b=0 images, and some have averaged their b=0 data on the scanner. Many thanks for any feedback, Jenifer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100628/72762515/attachment.html From jsadino.queens at gmail.com Mon Jun 28 19:53:01 2010 From: jsadino.queens at gmail.com (Jeff Sadino) Date: Mon, 28 Jun 2010 13:53:01 -1000 Subject: [Mristudio-users] Kimap, eigenvalues, and longitudinal analysis Message-ID: Hello, Can someone please verify my understanding of how LDDMM works? In the DiffeoMap download, there are template images for B0, FA, etc., but none for the eigenvalues. Is the Kimap only valid for the images used during the LDDMM, or can it be applied to all of the other (scaler) images as well? Can it be applied to the eigenvalue images, or would we have to apply it to a tensor file, load the tensor file into DTIStudio, and then recalculate the eigenvalues? Second, it seems like the more images/channels that are sent to the LDDMM servers for coregistration, the better the Kimap transformation. Is this true? Since we use the B0 image to drive the linear transformation for our FA and Trace maps, which are the values we really are interested in, should we also submit the B0 image to the LDDMM transform, or would that "over-transform" the Kimap? Lastly, is there anything different that we should be doing if we are doing longitudinal analysis, or is the protocol the same as the cross-sectional analysis? Thank you everyone for your continued help and support! Jeff Sadino -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100628/7ab9fd5d/attachment.html From taohaojuan at 163.com Mon Jun 28 23:58:53 2010 From: taohaojuan at 163.com (taohaojuan) Date: Tue, 29 Jun 2010 11:58:53 +0800 (CST) Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor In-Reply-To: References: <72109b1124c61.4c28b612@johnshopkins.edu> <72b0830e21243.4c28d15d@johnshopkins.edu> Message-ID: <60a5f026.4e66.12981db80c3.Coremail.taohaojuan@163.com> At 2010-06-29 04:52:05?"Minjie Wu" wrote: Thanks a lot. Appreciate it very much. BTW: Another question in the DTI Studio, is it possible to place the ROI at the center of the crosshairs without offset? Minjie On Mon, Jun 28, 2010 at 3:44 PM, Xin Li wrote: Sorry. it should be "the ROI boundary" not "the voxel boundary". Xin ----- Original Message ----- From: Minjie Wu Date: Monday, June 28, 2010 3:45 pm Subject: Re: [Mristudio-users] define ROI in DTI Studio and ROI Editor To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Hello Xin, > > I have created two ellipsis ROIs of the same size (4x4). The one on > the left > is added to an object, and the one on the right is not added to an object. > The object looks like an arrow instead of an ellipsis. Please see the > screenshot through the link. > > > > Thanks, > Minjie > > On Mon, Jun 28, 2010 at 1:47 PM, Xin Li wrote: > > > Hello Minjie, > > > > May I ask what you mean about "ellipsis no longer looks like ellipsis"? > > > > > > Xin > > > > > > ----- Original Message ----- > > From: Minjie Wu > > Date: Monday, June 28, 2010 1:45 pm > > Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor > > To: mristudio-users at mristudio.org > > > > > > > Hello All, > > > > > > We need to measure FA in the substantia nigra (SN) in our > project. Small > > > ellipse ROIs (4x4) are placed in these area using DTI Studio and > ROI > > > Editor > > > respectively. > > > > > > 1. For DTI Studio, the ROI is not placed at the center of the > > crosshairs, > > > but instead there is an offset. Is there any way to fix or > adjust this? > > > > > > 2. For ROI Editor, the ellipsis ROI (4x4) is placed in SN, and the > > location > > > of the ROI can be adjusted, then added to an object. However > once the > > > ellipsis ROI is combined to an object, ellipsis no longer looks > like > > > ellipsis. Is there any way to avoid this? > > > > > > Thank you very much. > > > > > > Sincerely, > > > > > > -- > > > Minjie Wu, PhD > > > Department of Neurology > > > Northwestern University > > > 710 N Lake Shore Dr > > > Abbott Hall, 11th floor, Suite 1107 > > > Chicago IL 60611 > > > Phone: 312-503-1522 > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > > > > > -- > Minjie Wu, PhD > Department of Neurology > Northwestern University > 710 N Lake Shore Dr > Abbott Hall, 11th floor, Suite 1107 > Chicago IL 60611 > Phone: 312-503-1522 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100629/2393d02d/attachment-0001.html From choisj70 at gmail.com Tue Jun 29 10:23:43 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 29 Jun 2010 10:23:43 -0400 Subject: [Mristudio-users] Calculating SNR of DTI data In-Reply-To: <3A4B564F13D63145AB38101AF6C50FF50B08EACB33@UTHCMS2.uthouston.edu> References: <3A4B564F13D63145AB38101AF6C50FF50B08EACB33@UTHCMS2.uthouston.edu> Message-ID: My opinions to (3) and (4) (3) In parallel imaging, SNR decreases as acceleration factors increases (R in Philips system). But increased acceleration factors improves geometric distortions (i.e. better shape). You need to find trade off point with your data. In Philips 3T system, I observed significant noise in the images using acceleration factor larger than 3 (R > 3). (4) When you do DTI using parallel imaging, normal SNR methods will not work. You need to have signal image and noise only image. Get the mean signal and noise standard deviation from an ROI then calculate the SNR. You can get noise-only image in RF-off mode. -Seongjin On Mon, Jun 28, 2010 at 7:37 PM, Juranek, Jenifer < Jenifer.Juranek at uth.tmc.edu> wrote: > While the issue of SNR effects on DTI metrics is discussed in the > published literature, I have found relatively little information regarding > calculating SNR as a screening procedure for image quality. A few authors > have reported the SNR range (or cut-off) of their datasets - but not many. > I'm curious about the following questions...any responses/opinions would be > very helpful. > > > > 1) Is calculation of SNR an effective screening tool for image quality in > DTI research? > > 2) Is calculation of SNR helpful for determining the feasibility of pooling > 3T DTI data from different scanner platforms (e.g. Siemens and Philips) > > 3) To what extent do parallel imaging and acceleration factors affect > measures of SNR? > > 4) If calculation of SNR is a "good thing to do and report", then what is > the best approach? > > > > In particular, datatype for analysis (e.g. b=0, trace, DW) and location > "inside the brain" seem to be important things to consider. In terms of > datatype, I have seen folks use single non-averaged b=0 for each subject, > and a mathematical relation between sequential b=0 images, and some have > averaged their b=0 data on the scanner. > > > > Many thanks for any feedback, > > Jenifer > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100629/44f66940/attachment.html From fariaav at gmail.com Tue Jun 29 11:46:03 2010 From: fariaav at gmail.com (Andreia Vaconcellos Faria) Date: Tue, 29 Jun 2010 11:46:03 -0400 Subject: [Mristudio-users] Kimap, eigenvalues, and longitudinal analysis In-Reply-To: References: Message-ID: Hi, Jeff, Q1: Kimap, such as any other matrix or deformation field, will work for any image that is co registered with those you used for the transformation. Since all the DTI (eigenvalues, B0, FA, and also tensors) come from the same file, they are of course coregistered and therefore your Kimap is ?valid? for all of them. The practical advantage of applying Kimap (or any transformation) to the tensors is that, using just this one-step transformation, you can calculate various scalar images (eigenvalues, FA?) from the same ?normalized? tensor file. Also, the tensors are "re-oriented" and there is no lost of the directional information. Q2: The contrasts that drive LDDMM serve as topological information. The most common approach is to use one image with large contrast between brain and ?no-brain? (csf and background), such as B0, adc, trace?; and another channel to provide information about the ?internal? structure, such as FA (that provides contrast within the white matter). The normalization is improved when you use images that provide different kind of information and, theoretically, there is no gain on imputing channels that provide the same kind of information (for example, B0 *AND* trace). The linear transformation and the LDDMM are independent; you can use B0 in both steps if you want. Q3:The idea that drives the imaging process is exactly the same. Of course, you can choose different contrasts (channels), templates and pipelines according the design of your study. I hope it helps. Best, Andreia. On Mon, Jun 28, 2010 at 7:53 PM, Jeff Sadino wrote: > Hello, > > Can someone please verify my understanding of how LDDMM works? In the > DiffeoMap download, there are template images for B0, FA, etc., but none for > the eigenvalues. Is the Kimap only valid for the images used during the > LDDMM, or can it be applied to all of the other (scaler) images as well? > Can it be applied to the eigenvalue images, or would we have to apply it to > a tensor file, load the tensor file into DTIStudio, and then recalculate the > eigenvalues? > > Second, it seems like the more images/channels that are sent to the LDDMM > servers for coregistration, the better the Kimap transformation. Is this > true? Since we use the B0 image to drive the linear transformation for our > FA and Trace maps, which are the values we really are interested in, should > we also submit the B0 image to the LDDMM transform, or would that > "over-transform" the Kimap? > > Lastly, is there anything different that we should be doing if we are doing > longitudinal analysis, or is the protocol the same as the cross-sectional > analysis? > > Thank you everyone for your continued help and support! > Jeff Sadino > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100629/dc8781f2/attachment.html From lana.wassung at gmail.com Tue Jun 29 12:13:48 2010 From: lana.wassung at gmail.com (Lana Wassung, MD) Date: Tue, 29 Jun 2010 18:13:48 +0200 Subject: [Mristudio-users] Please unsubscribe me Message-ID: Please unsubscribe me Lana Vasung, MD, PhD student Croatian Institute for Brain Research School of Medicine, Clinical Hospital Centre Zagreb, University of Zagreb Mob: 00 385 98 993 66 81 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100629/d47c0574/attachment.html From xli16 at jhmi.edu Tue Jun 29 12:16:21 2010 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 29 Jun 2010 12:16:21 -0400 Subject: [Mristudio-users] Please unsubscribe me In-Reply-To: References: Message-ID: <72c0ee2b231cc.4c29e415@johnshopkins.edu> Hello, If you want to unsubscribe, please send a blank email to: Mristudio-users-unsubscribe at mristudio.org Xin ----- Original Message ----- From: "Lana Wassung, MD" Date: Tuesday, June 29, 2010 12:13 pm Subject: [Mristudio-users] Please unsubscribe me To: mristudio-users at mristudio.org > Please unsubscribe me > > > > Lana Vasung, MD, PhD student > Croatian Institute for Brain Research > School of Medicine, > Clinical Hospital Centre Zagreb, > University of Zagreb > Mob: 00 385 98 993 66 81 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From Min.Xu at utsouthwestern.edu Tue Jun 29 12:46:25 2010 From: Min.Xu at utsouthwestern.edu (Min Xu) Date: Tue, 29 Jun 2010 11:46:25 -0500 Subject: [Mristudio-users] Please unsubscribe me. Message-ID: <4C29DD12.0658.0056.0@UTSouthwestern.edu> Please unsubscribe me. From nayanamako at yahoo.co.jp Tue Jun 29 13:34:53 2010 From: nayanamako at yahoo.co.jp (nayanamako at yahoo.co.jp) Date: Wed, 30 Jun 2010 02:34:53 +0900 (JST) Subject: [Mristudio-users] (no subject) Message-ID: <20100629173453.56009.qmail@web2903.mail.tnz.yahoo.co.jp> Please unsubscribe my e-mail adress from the mailing list. Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100630/f6d6b3e8/attachment.html From anathan3 at jhu.edu Tue Jun 29 16:32:13 2010 From: anathan3 at jhu.edu (Alexander Nathan) Date: Tue, 29 Jun 2010 16:32:13 -0400 Subject: [Mristudio-users] Please unsubscribe me Message-ID: <72f09e742ad19.4c2a200d@johnshopkins.edu> Please unsubscribe me From xyou001 at fiu.edu Tue Jun 29 17:08:27 2010 From: xyou001 at fiu.edu (Xiaozhen (Jane)) Date: Tue, 29 Jun 2010 17:08:27 -0400 Subject: [Mristudio-users] Please unsubscribe me Message-ID: Thanks! Xiaozhen From ansgar.furst at gmail.com Tue Jun 29 19:59:16 2010 From: ansgar.furst at gmail.com (Ansgar Furst) Date: Tue, 29 Jun 2010 16:59:16 -0700 Subject: [Mristudio-users] Please unsubscribe me In-Reply-To: References: Message-ID: Hi everybody, Given the number of daily emails it would be preferable to have a weekly digest versiont. Would that be possible to implement? Thanks, Ansgar On Tue, Jun 29, 2010 at 2:08 PM, Xiaozhen (Jane) wrote: > Thanks! > > Xiaozhen > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100629/2c6970a4/attachment.html From choisj70 at gmail.com Tue Jun 29 21:12:06 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 29 Jun 2010 21:12:06 -0400 Subject: [Mristudio-users] Vector info in ROI editor Message-ID: I have two questions on DTI studio and ROI editor. 1. How can I use ROIs generated in ROI editor in DTI studio? Using the ROI in the fiber tracking is OK but it cannot be loaded in the ROI drawing (in the second section). 2. In ROI editor, how can I get the vector information using ROIs generated in the ROI editor? I tried but it gave me warning " Not available." Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100629/1dbc2a14/attachment.html From bjqin at sjtu.edu.cn Tue Jun 29 21:22:39 2010 From: bjqin at sjtu.edu.cn (Binjie Qin) Date: Wed, 30 Jun 2010 09:22:39 +0800 Subject: [Mristudio-users] please remove my email address from maillist In-Reply-To: References: Message-ID: On Wed, 30 Jun 2010 09:12:06 +0800, [Seongjin] wrote: > I have two questions on DTI studio and ROI editor. > > 1. How can I use ROIs generated in ROI editor in DTI studio? > Using the ROI in the fiber tracking is OK but it cannot be loaded in > the > ROI drawing (in the second section). > > 2. In ROI editor, how can I get the vector information using ROIs > generated > in the ROI editor? > I tried but it gave me warning " Not available." > > Thanks in advance. > > -SC > > > > __________ Information from ESET NOD32 Antivirus, version of virus > signature database 5238 (20100629) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > -- Binjie Qin, Ph.D. Associate Professor Dept. of Biomedical Engineering Shanghai Jiao Tong University 800 Dongchuan Road, Min Hang Shanghai, P. R. China, 200240 Phone: 86-21-34204382,86-138-1635-5349 Fax: 86-21-34205709 Email:bjqin at sjtu.edu.cn From susumu at mri.jhu.edu Wed Jun 30 02:20:15 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 30 Jun 2010 02:20:15 -0400 Subject: [Mristudio-users] define ROI in DTI Studio and ROI Editor In-Reply-To: References: Message-ID: Hi Minjie, 1: DtiStudio ROI drawing capability is limited and we recommend to use RoiEditor. 2: When you draw an ellipse, the line is defined by your monitor resolution. However, when RoiEditor registers your input as an object, it has to translate the line to image pixel dimension. However it is difficult to draw a circle with 4x4 pixels, which is the source of the problem. I agree with you that we should do better job to come up with at least a more symmetric ROI. We'll look into this problem to see what we can do. Susumu On Mon, Jun 28, 2010 at 1:45 PM, Minjie Wu wrote: > Hello All, > > We need to measure FA in the substantia nigra (SN) in our project. Small > ellipse ROIs (4x4) are placed in these area using DTI Studio and ROI Editor > respectively. > > 1. For DTI Studio, the ROI is not placed at the center of the crosshairs, > but instead there is an offset. Is there any way to fix or adjust this? > > 2. For ROI Editor, the ellipsis ROI (4x4) is placed in SN, and the location > of the ROI can be adjusted, then added to an object. However once the > ellipsis ROI is combined to an object, ellipsis no longer looks like > ellipsis. Is there any way to avoid this? > > Thank you very much. > > Sincerely, > > -- > Minjie Wu, PhD > Department of Neurology > Northwestern University > 710 N Lake Shore Dr > Abbott Hall, 11th floor, Suite 1107 > Chicago IL 60611 > Phone: 312-503-1522 > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100630/72f95d31/attachment.html From mgnosti at gmail.com Wed Jun 30 03:44:52 2010 From: mgnosti at gmail.com (=?ISO-8859-1?Q?Mar=EDa_Gonz=E1lez?=) Date: Wed, 30 Jun 2010 09:44:52 +0200 Subject: [Mristudio-users] Please unsubscribe me In-Reply-To: References: Message-ID: Please unsubscribe me -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100630/9556a159/attachment.html From yonghong.shi at fudan.edu.cn Wed Jun 30 03:50:15 2010 From: yonghong.shi at fudan.edu.cn (SHI-YongHong) Date: Wed, 30 Jun 2010 15:50:15 +0800 Subject: [Mristudio-users] please unsubscribe me Message-ID: <201006301550144718494@fudan.edu.cn> please unsubscribe me. Thanks! 2010-06-30 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100630/a1411ebe/attachment.html From Inga.Koerte at med.uni-muenchen.de Wed Jun 30 04:07:30 2010 From: Inga.Koerte at med.uni-muenchen.de (=?iso-8859-1?Q?K=F6rte=2C_Inga_Dr=2Emed=2E?=) Date: Wed, 30 Jun 2010 10:07:30 +0200 Subject: [Mristudio-users] please unsubscribe me In-Reply-To: <201006301550144718494@fudan.edu.cn> References: <201006301550144718494@fudan.edu.cn> Message-ID: <8BCCEE5D134DD04DA80BE0992303279B01B589ECB0@MITEX02N.helios.med.uni-muenchen.de> Please unsubscribe me. Thank you! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100630/6d569d32/attachment-0001.html From akolasny at jhu.edu Wed Jun 30 05:16:50 2010 From: akolasny at jhu.edu (akolasny at jhu.edu) Date: Wed, 30 Jun 2010 05:16:50 -0400 (EDT) Subject: [Mristudio-users] MAILING LIST SUBSCRIPTION OPTIONS/FEATURES Message-ID: <53430.68.50.209.72.1277889410.squirrel@webmail.cis.jhu.edu> The MRI Studio mailing list is using the 'GNU mailman' software. There are many features that you may not be aware of including how to automatically the digest messages and unsubscribe to the mailing list without posting to the group. If you know your username and password, you may modify your settings at: https://lists.mristudio.org/mailman/options/mristudio-users If you do not know your password, send an email message to: TO: mristudio-users-request at mristudio.org SUBJECT: password This will return an email with your password and you may then make changes to your settings. If you want to make other changes via email, the help option provides the instructions. To get all the help information, the email should look like: TO: mristudio-users-request at mristudio.org SUBJECT: help TO: mristudio-users-request at mristudio.org SUBJECT: set help From mmarins at crcamp.com.br Wed Jun 30 07:01:48 2010 From: mmarins at crcamp.com.br (marcos marins) Date: Wed, 30 Jun 2010 08:01:48 -0300 Subject: [Mristudio-users] MAILING LIST SUBSCRIPTION OPTIONS/FEATURES In-Reply-To: <53430.68.50.209.72.1277889410.squirrel@webmail.cis.jhu.edu> References: <53430.68.50.209.72.1277889410.squirrel@webmail.cis.jhu.edu> Message-ID: I tried to unsubscribe at least five times. And I still get the email from the group. Please help me unsubscribe. Thanks On Wed, Jun 30, 2010 at 6:16 AM, wrote: > The MRI Studio mailing list is using the 'GNU mailman' software. > > There are many features that you may not be aware of including > how to automatically the digest messages and unsubscribe to the > mailing list without posting to the group. > > If you know your username and password, you may modify your > settings at: > > https://lists.mristudio.org/mailman/options/mristudio-users > > If you do not know your password, send an email message to: > > TO: mristudio-users-request at mristudio.org > SUBJECT: password > > This will return an email with your password and you may then make > changes to your settings. > > If you want to make other changes via email, the help option provides the > instructions. To get all the help information, the email should look > like: > > TO: mristudio-users-request at mristudio.org > SUBJECT: help > > TO: mristudio-users-request at mristudio.org > SUBJECT: set help > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100630/24ecde06/attachment.html From jsadino.queens at gmail.com Tue Jun 15 16:48:22 2010 From: jsadino.queens at gmail.com (Jeff Sadino) Date: Tue, 15 Jun 2010 10:48:22 -1000 Subject: [Mristudio-users] LDDMM Age Range Message-ID: Hello, Thank you to Dr. Mori for his instructions on how to manually do skull stripping within ROIEditor. It was exactly what I was looking for. I have a question on how old a subject has to be in order for LDDMM to be accurate. We have a study group that is in the 4-7 year old age range and we are using the JHU_MNI_SS template. Is it ok to apply DiffeoMap's Linear Transformation and LDDMM Transformation to these subjects using this template? Best regards for your help, Jeff Sadino -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100615/cce124d9/attachment.html From Seyede.Ghazal.Mohades at vub.ac.be Tue Jun 29 06:19:18 2010 From: Seyede.Ghazal.Mohades at vub.ac.be (Seyede Ghazal Mohades) Date: Tue, 29 Jun 2010 12:19:18 +0200 Subject: [Mristudio-users] Eddy_current_correction Message-ID: <80624c29c8a6539a4@wm-srv.ulb.ac.be> >Dear all I have a completely basic question when I try to load Philips Rec images in DTI studio I can do it, however the same set file (which is a DTI ss-EPI sequence )gives the following error when I try to do DTI mapping : the file is Bigger (and sometimes it says smaller)than a DWI sequence! where is the problem? regards Ghazal >Thanks > >-----Original Message----- >From: mristudio-users-bounces at mristudio.org on behalf of support at mristudio.org >Sent: Mon 6/28/2010 12:24 PM >To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >Subject: Re: [Mristudio-users] Eddy_current_correction > >the 1st method would be fine: use the 1st B0 as a reference and register all >others with it. > >support > > > >> >> Hi All, >> >> We have diffusion data set acquired with 5 trails/repetitions(in single time >> point/cross sectional) for each and every subject. This means i have 5 b0(same >> value) and DW (12 directions) data while doing eddy current correction can i >> choose for instance b0 from first trail and register all the DW and other b0 >> images to this or do eddy current correction separately for each and every trail >> and finally register all of them together say for instance to the first trail. >> >> Thanks >> >> venkat >> >> =================================== >> >> P Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked one of the top hospitals >> in America by U.S.News & World Report (2009). >> Visit us online at http://www.clevelandclinic.org for >> a complete listing of our services, staff and >> locations. >> >> >> Confidentiality Note: This message is intended for use >> only by the individual or entity to which it is addressed >> and may contain information that is privileged, >> confidential, and exempt from disclosure under applicable >> law. If the reader of this message is not the intended >> recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are >> hereby notified that any dissemination, distribution or >> copying of this communication is strictly prohibited. If >> you have received this communication in error, please >> contact the sender immediately and destroy the material in >> its entirety, whether electronic or hard copy. Thank you. >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> > > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > >=================================== > >P Please consider the environment before printing this e-mail > >Cleveland Clinic is ranked one of the top hospitals >in America by U.S.News & World Report (2009). >Visit us online at http://www.clevelandclinic.org for >a complete listing of our services, staff and >locations. > > >Confidentiality Note: This message is intended for use >only by the individual or entity to which it is addressed >and may contain information that is privileged, >confidential, and exempt from disclosure under applicable >law. If the reader of this message is not the intended >recipient or the employee or agent responsible for >delivering the message to the intended recipient, you are >hereby notified that any dissemination, distribution or >copying of this communication is strictly prohibited. If >you have received this communication in error, please >contact the sender immediately and destroy the material in >its entirety, whether electronic or hard copy. Thank you. > > From fariaav at gmail.com Wed Jun 30 11:59:58 2010 From: fariaav at gmail.com (Andreia Vaconcellos Faria) Date: Wed, 30 Jun 2010 11:59:58 -0400 Subject: [Mristudio-users] LDDMM Age Range In-Reply-To: References: Message-ID: Hi, Jeff, In a previous study (Neuroimage. 2010 Aug 15;52(2):415-28) we showed that the JHU_MNI_SS template works for normal subjects after 2 years-old. However, we always recommend you test the normalization results in your particular population. best, Andreia On Tue, Jun 15, 2010 at 4:48 PM, Jeff Sadino wrote: > Hello, > > Thank you to Dr. Mori for his instructions on how to manually do skull > stripping within ROIEditor. It was exactly what I was looking for. > > I have a question on how old a subject has to be in order for LDDMM to be > accurate. We have a study group that is in the 4-7 year old age range and > we are using the JHU_MNI_SS template. Is it ok to apply DiffeoMap's Linear > Transformation and LDDMM Transformation to these subjects using this > template? > > Best regards for your help, > Jeff Sadino > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100630/066f959c/attachment.html From xli16 at jhmi.edu Wed Jun 30 12:13:20 2010 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 30 Jun 2010 12:13:20 -0400 Subject: [Mristudio-users] Vector info in ROI editor In-Reply-To: References: Message-ID: <711090d4281ab.4c2b34e0@johnshopkins.edu> Hello, If you right click a ROI object in the ROI object list of ROIEditor, you will see an option "Export Pixel Value". You may use it to get the vector information. Regards, Xin ----- Original Message ----- From: "[Seongjin]" Date: Tuesday, June 29, 2010 9:12 pm Subject: [Mristudio-users] Vector info in ROI editor To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > I have two questions on DTI studio and ROI editor. > > 1. How can I use ROIs generated in ROI editor in DTI studio? > Using the ROI in the fiber tracking is OK but it cannot be loaded > in the > ROI drawing (in the second section). > > 2. In ROI editor, how can I get the vector information using ROIs generated > in the ROI editor? > I tried but it gave me warning " Not available." > > Thanks in advance. > > -SC > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org From support at mristudio.org Wed Jun 30 12:20:01 2010 From: support at mristudio.org (support at mristudio.org) Date: Wed, 30 Jun 2010 12:20:01 -0400 (EDT) Subject: [Mristudio-users] how to unsubscribe Message-ID: <4199.10.16.56.34.1277914801.squirrel@webmail.mristudio.org> Hello Mristudio users, If you want to unsubscribe from the user mailing list, please send a blank email to: Mristudio-users-unsubscribe at mristudio.org If you want to unsubscribe from the announcement list, please send a blank email to: Announcements-unsubscribe at mristudio.org MriStudio Support From choisj70 at gmail.com Wed Jun 30 12:20:17 2010 From: choisj70 at gmail.com (Seongjin) Date: Wed, 30 Jun 2010 12:20:17 -0400 Subject: [Mristudio-users] Vector info in ROI editor In-Reply-To: <711090d4281ab.4c2b34e0@johnshopkins.edu> References: <711090d4281ab.4c2b34e0@johnshopkins.edu> Message-ID: Xin, Thanks very much! It works! -Seongjin On Wed, Jun 30, 2010 at 12:13 PM, Xin Li wrote: > Hello, > > If you right click a ROI object in the ROI object list of ROIEditor, you > will see an option "Export Pixel Value". You may use it to get the vector > information. > > > Regards, > > Xin > > > > ----- Original Message ----- > From: "[Seongjin]" > Date: Tuesday, June 29, 2010 9:12 pm > Subject: [Mristudio-users] Vector info in ROI editor > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > > > I have two questions on DTI studio and ROI editor. > > > > 1. How can I use ROIs generated in ROI editor in DTI studio? > > Using the ROI in the fiber tracking is OK but it cannot be loaded > > in the > > ROI drawing (in the second section). > > > > 2. In ROI editor, how can I get the vector information using ROIs > generated > > in the ROI editor? > > I tried but it gave me warning " Not available." > > > > Thanks in advance. > > > > -SC > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100630/4e1bf93b/attachment.html From choisj70 at gmail.com Wed Jun 30 12:27:03 2010 From: choisj70 at gmail.com (Seongjin) Date: Wed, 30 Jun 2010 12:27:03 -0400 Subject: [Mristudio-users] Vector info in ROI editor In-Reply-To: <711090d4281ab.4c2b34e0@johnshopkins.edu> References: <711090d4281ab.4c2b34e0@johnshopkins.edu> Message-ID: Thanks for your reply to my question. By the way, the text file contains three rows for x, y, z. >From the first set of vector components to the last one, if you have any rules show the list of vector components that way? For example, from the first pixel values in the ROI. Then what is the first pixel in the ROI? You might have some rules to order them, I guess. All the best, -Seongjin On Wed, Jun 30, 2010 at 12:13 PM, Xin Li wrote: > Hello, > > If you right click a ROI object in the ROI object list of ROIEditor, you > will see an option "Export Pixel Value". You may use it to get the vector > information. > > > Regards, > > Xin > > > > ----- Original Message ----- > From: "[Seongjin]" > Date: Tuesday, June 29, 2010 9:12 pm > Subject: [Mristudio-users] Vector info in ROI editor > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > mristudio-users at mristudio.org> > > > > I have two questions on DTI studio and ROI editor. > > > > 1. How can I use ROIs generated in ROI editor in DTI studio? > > Using the ROI in the fiber tracking is OK but it cannot be loaded > > in the > > ROI drawing (in the second section). > > > > 2. In ROI editor, how can I get the vector information using ROIs > generated > > in the ROI editor? > > I tried but it gave me warning " Not available." > > > > Thanks in advance. > > > > -SC > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100630/85212d6b/attachment.html From xli16 at jhmi.edu Wed Jun 30 13:01:03 2010 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 30 Jun 2010 13:01:03 -0400 Subject: [Mristudio-users] Vector info in ROI editor In-Reply-To: References: <711090d4281ab.4c2b34e0@johnshopkins.edu> Message-ID: <72a0d433298bf.4c2b400f@johnshopkins.edu> Hello, The ordering of reading the data was first row(width), then column(height) and then slices. Regards, Xin ----- Original Message ----- From: "[Seongjin]" Date: Wednesday, June 30, 2010 12:27 pm Subject: Re: [Mristudio-users] Vector info in ROI editor To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Thanks for your reply to my question. > > By the way, the text file contains three rows for x, y, z. > >From the first set of vector components to the last one, if you have > any > rules show the list of vector components that way? For example, from > the > first pixel values in the ROI. Then what is the first pixel in the > ROI? You > might have some rules to order them, I guess. > > All the best, > -Seongjin > > On Wed, Jun 30, 2010 at 12:13 PM, Xin Li wrote: > > > Hello, > > > > If you right click a ROI object in the ROI object list of > ROIEditor, you > > will see an option "Export Pixel Value". You may use it to get the > vector > > information. > > > > > > Regards, > > > > Xin > > > > > > > > ----- Original Message ----- > > From: "[Seongjin]" > > Date: Tuesday, June 29, 2010 9:12 pm > > Subject: [Mristudio-users] Vector info in ROI editor > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > > mristudio-users at mristudio.org> > > > > > > > I have two questions on DTI studio and ROI editor. > > > > > > 1. How can I use ROIs generated in ROI editor in DTI studio? > > > Using the ROI in the fiber tracking is OK but it cannot be loaded > > > in the > > > ROI drawing (in the second section). > > > > > > 2. In ROI editor, how can I get the vector information using ROIs > > generated > > > in the ROI editor? > > > I tried but it gave me warning " Not available." > > > > > > Thanks in advance. > > > > > > -SC > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > Mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From choisj70 at gmail.com Wed Jun 30 13:33:34 2010 From: choisj70 at gmail.com (Seongjin) Date: Wed, 30 Jun 2010 13:33:34 -0400 Subject: [Mristudio-users] Vector info in ROI editor In-Reply-To: <72a0d433298bf.4c2b400f@johnshopkins.edu> References: <711090d4281ab.4c2b34e0@johnshopkins.edu> <72a0d433298bf.4c2b400f@johnshopkins.edu> Message-ID: Thanks, Xin! On Wed, Jun 30, 2010 at 1:01 PM, Xin Li wrote: > Hello, > > The ordering of reading the data was first row(width), then column(height) > and then slices. > > > Regards, > > Xin > > > > > > > > ----- Original Message ----- > From: "[Seongjin]" > Date: Wednesday, June 30, 2010 12:27 pm > Subject: Re: [Mristudio-users] Vector info in ROI editor > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" < > mristudio-users at mristudio.org> > > > > Thanks for your reply to my question. > > > > By the way, the text file contains three rows for x, y, z. > > >From the first set of vector components to the last one, if you have > > any > > rules show the list of vector components that way? For example, from > > the > > first pixel values in the ROI. Then what is the first pixel in the > > ROI? You > > might have some rules to order them, I guess. > > > > All the best, > > -Seongjin > > > > On Wed, Jun 30, 2010 at 12:13 PM, Xin Li wrote: > > > > > Hello, > > > > > > If you right click a ROI object in the ROI object list of > > ROIEditor, you > > > will see an option "Export Pixel Value". You may use it to get the > > vector > > > information. > > > > > > > > > Regards, > > > > > > Xin > > > > > > > > > > > > ----- Original Message ----- > > > From: "[Seongjin]" > > > Date: Tuesday, June 29, 2010 9:12 pm > > > Subject: [Mristudio-users] Vector info in ROI editor > > > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < > > > mristudio-users at mristudio.org> > > > > > > > > > > I have two questions on DTI studio and ROI editor. > > > > > > > > 1. How can I use ROIs generated in ROI editor in DTI studio? > > > > Using the ROI in the fiber tracking is OK but it cannot be > loaded > > > > in the > > > > ROI drawing (in the second section). > > > > > > > > 2. In ROI editor, how can I get the vector information using ROIs > > > generated > > > > in the ROI editor? > > > > I tried but it gave me warning " Not available." > > > > > > > > Thanks in advance. > > > > > > > > -SC > > > > _______________________________________________ > > > > Mristudio-users mailing list > > > > Mristudio-users at mristudio.org > > > > > > > > Unsubscribe, send a blank email to: > > > Mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > > > mristudio-users mailing list > > > mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > > mristudio-users-unsubscribe at mristudio.org > > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100630/4e54cb6b/attachment-0001.html From susumu at mri.jhu.edu Wed Jun 30 22:32:27 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 30 Jun 2010 22:32:27 -0400 Subject: [Mristudio-users] Eddy_current_correction In-Reply-To: <80624c29c8a6539a4@wm-srv.ulb.ac.be> References: <80624c29c8a6539a4@wm-srv.ulb.ac.be> Message-ID: When you load the REC file using "Mri3DView", make sure how many images are in the file. For example, if you used Philips "High" table, you have 1 b0 + 32 DWI + 1 extra image, total 34 images. The last one is an isotropically-weighted image generated from the DWIs. Then make sure your gradient table. Most likely, the number of images in your REC and the gradient table are not matching. For example, you may have only 33 lines in the table. For the final image, which you don't use, you can add an extra line with 33: 100, 100, 100. The first "33" is the line number (34th table row), and "100, 100, 100" sends a message to DtiStudio "don't use this image". On Tue, Jun 29, 2010 at 6:19 AM, Seyede Ghazal Mohades < Seyede.Ghazal.Mohades at vub.ac.be> wrote: > >Dear all > I have a completely basic question > when I try to load Philips Rec images in DTI studio I can do it, however > the same set file (which is a DTI ss-EPI sequence )gives the following > error when I try to do DTI mapping : > the file is Bigger (and sometimes it says smaller)than a DWI sequence! > where is the problem? > regards > Ghazal > >Thanks > > > >-----Original Message----- > >From: mristudio-users-bounces at mristudio.org on behalf of > support at mristudio.org > >Sent: Mon 6/28/2010 12:24 PM > >To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > >Subject: Re: [Mristudio-users] Eddy_current_correction > > > >the 1st method would be fine: use the 1st B0 as a reference and register > all > >others with it. > > > >support > > > > > > > >> > >> Hi All, > >> > >> We have diffusion data set acquired with 5 trails/repetitions(in single > time > >> point/cross sectional) for each and every subject. This means i have 5 > b0(same > >> value) and DW (12 directions) data while doing eddy current correction > can i > >> choose for instance b0 from first trail and register all the DW and > other b0 > >> images to this or do eddy current correction separately for each and > every trail > >> and finally register all of them together say for instance to the first > trail. > >> > >> Thanks > >> > >> venkat > >> > >> =================================== > >> > >> P Please consider the environment before printing this e-mail > >> > >> Cleveland Clinic is ranked one of the top hospitals > >> in America by U.S.News & World Report (2009). > >> Visit us online at http://www.clevelandclinic.org for > >> a complete listing of our services, staff and > >> locations. > >> > >> > >> Confidentiality Note: This message is intended for use > >> only by the individual or entity to which it is addressed > >> and may contain information that is privileged, > >> confidential, and exempt from disclosure under applicable > >> law. If the reader of this message is not the intended > >> recipient or the employee or agent responsible for > >> delivering the message to the intended recipient, you are > >> hereby notified that any dissemination, distribution or > >> copying of this communication is strictly prohibited. If > >> you have received this communication in error, please > >> contact the sender immediately and destroy the material in > >> its entirety, whether electronic or hard copy. Thank you. > >> _______________________________________________ > >> Mristudio-users mailing list > >> Mristudio-users at mristudio.org > >> http://lists.mristudio.org/mailman/listinfo/ > >> Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > >> > > > > > >_______________________________________________ > >Mristudio-users mailing list > >Mristudio-users at mristudio.org > >http://lists.mristudio.org/mailman/listinfo/ > >Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > > > > >=================================== > > > >P Please consider the environment before printing this e-mail > > > >Cleveland Clinic is ranked one of the top hospitals > >in America by U.S.News & World Report (2009). > >Visit us online at http://www.clevelandclinic.org for > >a complete listing of our services, staff and > >locations. > > > > > >Confidentiality Note: This message is intended for use > >only by the individual or entity to which it is addressed > >and may contain information that is privileged, > >confidential, and exempt from disclosure under applicable > >law. If the reader of this message is not the intended > >recipient or the employee or agent responsible for > >delivering the message to the intended recipient, you are > >hereby notified that any dissemination, distribution or > >copying of this communication is strictly prohibited. If > >you have received this communication in error, please > >contact the sender immediately and destroy the material in > >its entirety, whether electronic or hard copy. Thank you. > > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100630/ecab0478/attachment.html From elenatrincia at libero.it Sun Jul 4 16:23:47 2010 From: elenatrincia at libero.it (elenatrincia at libero.it) Date: Sun, 04 Jul 2010 22:23:47 +0200 (CEST) Subject: [Mristudio-users] please unscribe me Message-ID: <9777538.1076081278275027097.JavaMail.defaultUser@defaultHost> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100704/35ec66b5/attachment.html From jmcentee at jhmi.edu Mon Jul 5 11:42:09 2010 From: jmcentee at jhmi.edu (Julie E McEntee) Date: Mon, 05 Jul 2010 11:42:09 -0400 Subject: [Mristudio-users] position announcement: Research Program Coordinator/MRI Data Analyst Message-ID: <7220cdc5340f.4c31c511@johnshopkins.edu> The Division of Psychiatric Neuroimaging in the Department of Psychiatry, Johns Hopkins University School of Medicine (Baltimore, MD), is seeking a Research Program Coordinator/MRI Data Analyst. The position will oversee all facets of research activities, data management and administrative aspects for research projects involving multimodal imaging (structural, fMRI, DTI, MRS) on the 3 T and 7 T Philips systems at the F. M. Kirby Center for Functional Neuroimaging, imaging systems at JHH, or other imaging systems. Current research projects include studies of Huntington?s Disease, schizophrenia, anorexia nervosa, other neuropsychiatric conditions and healthy control populations. The primary duties and responsibilities include: Assist development of fMRI neuropsychological protocols, recruit and enroll participants, administer clinical neuropsychological tests and research tasks, assist (with MRI technician) in image acquisition, enter research data, conduct data and image analysis. Essential job functions: Maintaining and monitoring supply of testing materials, monitoring the control of data quality and research integrity. The duties also include organizing and maintaining research files and maintaining study databases. Responsible for the development of IRB applications as well as IRB compliance. Master?s degree in psychology, neuroscience or related discipline relevant to imaging is strongly preferred. Advanced experience with personal computers, Windows 7 and Mac OS operating systems and Microsoft Office 2007/2010 applications (particularly Excel and Access) required; experience with UNIX preferred. Knowledge of univariate and multivariate statistics required; experience with statistical analysis software (e.g., SPSS, SAS, Stata) preferred. Knowledge of imaging analysis software (e.g., SPM, FSL, AFNI, FreeSurfer, MIPAV) preferred. Clinical research experience with neuropsychiatric populations and database management required; experience with completing Case Report Forms (CRF?s) and creating source documents a plus. Must be extremely well organized, precise and detail oriented. Must have the excellent interpersonal skills, ability to problem solve and work independently. Please send statement of interest and CV to Julie McEntee at jmcentee at jhmi.edu and Graham Redgrave at gwr at jhmi.edu. Julie E. McEntee, M.A., C.C.R.P. Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./ Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676 From fjnavas2 at gmail.com Mon Jul 5 12:33:01 2010 From: fjnavas2 at gmail.com (Javier Navas) Date: Mon, 05 Jul 2010 18:33:01 +0200 Subject: [Mristudio-users] Spinal cord dti In-Reply-To: References: Message-ID: Hi! I?m doing a study of FA in spinal cord, the aim is to do fiber-tracking with the images, but I have some problems with DTIstudio, specially in the load of the images that I only can obtain 1 sagital slice (I don?t know why because I describe all the parameters of the images). Someone that could help me? If you want I could send you the original Philips DICOMs. Thank you /**********************************************************\ Francisco Javier Navas S?nchez Laboratorio de Imagen M?dica U.M.C.E. Hospital General Universitario Gregorio Mara??n Dr Esquerdo 46, 28007 Madrid, Spain Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 e-mail:jnavas at hggm.es http://image.hggm.es -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100705/9d2267bc/attachment.html From d-gitelman at northwestern.edu Mon Jul 5 13:26:06 2010 From: d-gitelman at northwestern.edu (Darren Gitelman) Date: Mon, 05 Jul 2010 12:26:06 -0500 Subject: [Mristudio-users] Fwd: questions about ROI's In-Reply-To: References: Message-ID: I have several questions about ROIs 1) In both DTIstudio and ROIeditor ROIs of fixed size are placed with reference to the lower right quadrant of the crosshairs. Is there a reason for this or could the ROI be placed centered on the crosshairs? 2) I would like to know how dtistudio and roieditor calculate the values of ROIs. Please see attached picture. On the left, is a 4 voxel diameter circular ROI overlaid on a grid. This is what the ROI looks like when I first draw it in either DTIstudio or ROIeditor. On top of this is a set of brown voxels, which is what the ROI looks like in ROIeditor when I add it to an object. On the right is the 4 voxel circular ROI on top of a 4 voxel square. How do DTIstudio and ROIeditor get the value of an ROI? ?? - Does it perform a weighted average of voxels in the circle (orange part of circle)? ?? - Does it include only the voxels that show up in the brown object.? ?? - Does it include any voxels that touch the circle (i.e., blue square)? Do DTIstudio and ROIeditor do the same thing when determining the value of ROI's? 3) Is there any way to un-associate an ROI from an object so that it can be moved around again or once it's added to an object that's it? 4) Is there any way to save ROIs in DTIstudio? 5) I've noticed in ROIeditor that undo doesn't always undo the last operation. Thanks, Darren -------------- next part -------------- A non-text attachment was scrubbed... Name: ROIexample1.jpg Type: image/jpeg Size: 24658 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100705/a34b8a9d/attachment-0001.jpg From xli16 at jhmi.edu Tue Jul 6 11:41:49 2010 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 06 Jul 2010 11:41:49 -0400 Subject: [Mristudio-users] Fwd: questions about ROI's In-Reply-To: References: Message-ID: <72b089112bb8.4c33167d@johnshopkins.edu> Hello Darren, 1)It may be caused by integer rounding. I am looking into this. 2) ROIEditor displays the contour of a ROI object stored in memory. In your figure, it includes those brown voxels. I am looking into this and try to find a way to let ROIEditor come up with a more symmetric ROI. 3) After you add a ROI to an object, you may use "undo" if it is the last step. 5) "undo" only works for the last step if it is the "add", "subtract", "and" or "replace" operation. Regards, Xin ----- Original Message ----- From: Darren Gitelman Date: Monday, July 5, 2010 1:26 pm Subject: [Mristudio-users] Fwd: questions about ROI's To: mristudio-users > I have several questions about ROIs > > 1) In both DTIstudio and ROIeditor ROIs of fixed size are placed with > reference to the lower right quadrant of the crosshairs. Is there a > reason for this or could the ROI be placed centered on the crosshairs? > > 2) I would like to know how dtistudio and roieditor calculate the > values of ROIs. Please see attached picture. On the left, is a 4 voxel > diameter circular ROI overlaid on a grid. This is what the ROI looks > like when I first draw it in either DTIstudio or ROIeditor. On top of > this is a set of brown voxels, which is what the ROI looks like in > ROIeditor when I add it to an object. On the right is the 4 voxel > circular ROI on top of a 4 voxel square. How do DTIstudio and > ROIeditor get the value of an ROI? > ?? - Does it perform a weighted average of voxels in the circle > (orange part of circle)? > ?? - Does it include only the voxels that show up in the brown object.? > ?? - Does it include any voxels that touch the circle (i.e., blue square)? > > Do DTIstudio and ROIeditor do the same thing when determining the > value of ROI's? > > 3) Is there any way to un-associate an ROI from an object so that it > can be moved around again or once it's added to an object that's it? > > 4) Is there any way to save ROIs in DTIstudio? > > 5) I've noticed in ROIeditor that undo doesn't always undo the last operation. > > Thanks, > Darren > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Tue Jul 6 15:19:39 2010 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 06 Jul 2010 15:19:39 -0400 Subject: [Mristudio-users] Fwd: questions about ROI's In-Reply-To: References: Message-ID: <72b0e2541798.4c33498b@johnshopkins.edu> Hello Darren, For your first question, actually it is because of the MFC method ROIEditor and DtiStudio use to draw ellipses and rectangles with fixed size. The position where the mouse is clicked down (the center of a crosshair) is used as the upper-left corner of the rectangle or the ellipse's bouding rectangle. Regards, Xin ----- Original Message ----- From: Darren Gitelman Date: Monday, July 5, 2010 1:26 pm Subject: [Mristudio-users] Fwd: questions about ROI's To: mristudio-users > I have several questions about ROIs > > 1) In both DTIstudio and ROIeditor ROIs of fixed size are placed with > reference to the lower right quadrant of the crosshairs. Is there a > reason for this or could the ROI be placed centered on the crosshairs? > > 2) I would like to know how dtistudio and roieditor calculate the > values of ROIs. Please see attached picture. On the left, is a 4 voxel > diameter circular ROI overlaid on a grid. This is what the ROI looks > like when I first draw it in either DTIstudio or ROIeditor. On top of > this is a set of brown voxels, which is what the ROI looks like in > ROIeditor when I add it to an object. On the right is the 4 voxel > circular ROI on top of a 4 voxel square. How do DTIstudio and > ROIeditor get the value of an ROI? > ?? - Does it perform a weighted average of voxels in the circle > (orange part of circle)? > ?? - Does it include only the voxels that show up in the brown object.? > ?? - Does it include any voxels that touch the circle (i.e., blue square)? > > Do DTIstudio and ROIeditor do the same thing when determining the > value of ROI's? > > 3) Is there any way to un-associate an ROI from an object so that it > can be moved around again or once it's added to an object that's it? > > 4) Is there any way to save ROIs in DTIstudio? > > 5) I've noticed in ROIeditor that undo doesn't always undo the last operation. > > Thanks, > Darren > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From choisj70 at gmail.com Tue Jul 6 15:30:54 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 06 Jul 2010 15:30:54 -0400 Subject: [Mristudio-users] Questions about ROI saving in DTI Studio Message-ID: I tried couple of trials on ROI saving in DTI Studio. Q1. It can save binary and binary map formats. And those ROIs can be reused in ROI edtior. However, the ROIs saved in DTI studio could not be reused in DTI studio itself. Any solution to this issue? Q2 ROI saving option in DTI studio, I see Graphic Compatible (default) and Bit-Plains options. But this option fails and DTI studio crashes. I would like to know how to save an ROI in DTI studio and reuse the ROI in DTI studio again. Sincerely, -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100706/d25ecb34/attachment.html From azhang at psych.uic.edu Thu Jul 8 20:08:41 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Thu, 08 Jul 2010 19:08:41 -0500 Subject: [Mristudio-users] Eddy_current_correction In-Reply-To: References: <80624c29c8a6539a4@wm-srv.ulb.ac.be> Message-ID: <40469184F1D86344A835AB980269681A16969FC2A1@exchange.psych.uic.edu> Dear DTIStudio, Is coregistration always recommended as the first step, as I saw from articles from your lab? In our case, we only acquired 1 DTI sequence with 32 directions (~4 mins, with SENSE 2.5). thanks. Sincerely, Aifeng From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Wednesday, June 30, 2010 9:32 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Eddy_current_correction When you load the REC file using "Mri3DView", make sure how many images are in the file. For example, if you used Philips "High" table, you have 1 b0 + 32 DWI + 1 extra image, total 34 images. The last one is an isotropically-weighted image generated from the DWIs. Then make sure your gradient table. Most likely, the number of images in your REC and the gradient table are not matching. For example, you may have only 33 lines in the table. For the final image, which you don't use, you can add an extra line with 33: 100, 100, 100. The first "33" is the line number (34th table row), and "100, 100, 100" sends a message to DtiStudio "don't use this image". On Tue, Jun 29, 2010 at 6:19 AM, Seyede Ghazal Mohades > wrote: >Dear all I have a completely basic question when I try to load Philips Rec images in DTI studio I can do it, however the same set file (which is a DTI ss-EPI sequence )gives the following error when I try to do DTI mapping : the file is Bigger (and sometimes it says smaller)than a DWI sequence! where is the problem? regards Ghazal >Thanks > >-----Original Message----- >From: mristudio-users-bounces at mristudio.org on behalf of support at mristudio.org >Sent: Mon 6/28/2010 12:24 PM >To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >Subject: Re: [Mristudio-users] Eddy_current_correction > >the 1st method would be fine: use the 1st B0 as a reference and register all >others with it. > >support > > > >> >> Hi All, >> >> We have diffusion data set acquired with 5 trails/repetitions(in single time >> point/cross sectional) for each and every subject. This means i have 5 b0(same >> value) and DW (12 directions) data while doing eddy current correction can i >> choose for instance b0 from first trail and register all the DW and other b0 >> images to this or do eddy current correction separately for each and every trail >> and finally register all of them together say for instance to the first trail. >> >> Thanks >> >> venkat >> >> =================================== >> >> P Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked one of the top hospitals >> in America by U.S.News & World Report (2009). >> Visit us online at http://www.clevelandclinic.org for >> a complete listing of our services, staff and >> locations. >> >> >> Confidentiality Note: This message is intended for use >> only by the individual or entity to which it is addressed >> and may contain information that is privileged, >> confidential, and exempt from disclosure under applicable >> law. If the reader of this message is not the intended >> recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are >> hereby notified that any dissemination, distribution or >> copying of this communication is strictly prohibited. If >> you have received this communication in error, please >> contact the sender immediately and destroy the material in >> its entirety, whether electronic or hard copy. Thank you. >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> > > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > >=================================== > >P Please consider the environment before printing this e-mail > >Cleveland Clinic is ranked one of the top hospitals >in America by U.S.News & World Report (2009). >Visit us online at http://www.clevelandclinic.org for >a complete listing of our services, staff and >locations. > > >Confidentiality Note: This message is intended for use >only by the individual or entity to which it is addressed >and may contain information that is privileged, >confidential, and exempt from disclosure under applicable >law. If the reader of this message is not the intended >recipient or the employee or agent responsible for >delivering the message to the intended recipient, you are >hereby notified that any dissemination, distribution or >copying of this communication is strictly prohibited. If >you have received this communication in error, please >contact the sender immediately and destroy the material in >its entirety, whether electronic or hard copy. Thank you. > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100708/5f89412d/attachment-0001.html From duggaldti at hotmail.ca Fri Jul 9 09:20:11 2010 From: duggaldti at hotmail.ca (Duggal Lab DTI) Date: Fri, 09 Jul 2010 09:20:11 -0400 Subject: [Mristudio-users] FA Maps Message-ID: Hello, I am having some difficulty getting my FA Maps to work properly. How do you generate them? When I try I get only black and white pixels (0 and 1 anisotropy) with the brain being black. I am using Siemens Mosaic for .IMA files. Thank you, take care, Stuart _________________________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100709/57aa824a/attachment.html From rajagov2 at ccf.org Fri Jul 9 10:33:05 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Fri, 09 Jul 2010 10:33:05 -0400 Subject: [Mristudio-users] b-matrix from dicom header and from techs Message-ID: <77A88E90A851594AAEF830450587C39D0418324E@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, we collect our data from Siemens scanner. I got b-matrix from our MR techs for software version VA25A b matrix is as follows 0: 0.000, 0.000, 0.000 1: 1.000, 0.000, 0.500 2: 0.000, 0.500, 1.000 3: 0.500, 1.000, 0.000 4: 1.000, 0.500, 0.000 5: 0.000, 1.000, 0.500 6: 0.500, 0.000, 1.000 7: 1.000, 0.000, -0.500 8: 0.000, -0.500, 1.000 9: -0.500, 1.000, 0.000 10: 1.000, -0.500, 0.000 11: 0.000, 1.000, -0.500 12: -0.500, 0.000, 1.000 I used dcm2nii software (to convert hem into nifti file for soem other purpose i also gives me bvec and bval files) which gives me the following matrix from the dicom header file 0 0 0 0.89 0 -0.45 0 0.45 -0.89 0.45 0.89 0 0.89 0.45 0 0 0.89 -0.45 0.45 0 -0.89 0.89 0 0.45 0 -0.45 -0.89 -0.45 0.89 0 0.89 -0.45 0 0 0.89 0.45 -0.45 0 -0.89 Since not only the values are different but +/- signs are also different in DW directions. So I am wondering whether any one could tell me which is the correct table to go with. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. 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URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100709/f18bc4e6/attachment.html From azhang at psych.uic.edu Fri Jul 9 16:49:14 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Fri, 09 Jul 2010 15:49:14 -0500 Subject: [Mristudio-users] using T1 image for ROI drawing In-Reply-To: References: <80624c29c8a6539a4@wm-srv.ulb.ac.be> <40469184F1D86344A835AB980269681A16969FC2A1@exchange.psych.uic.edu> <40469184F1D86344A835AB980269681A16969FC2A6@exchange.psych.uic.edu> Message-ID: <40469184F1D86344A835AB980269681A16969FC3ED@exchange.psych.uic.edu> Dear DTIStudio, Just want to double check with you about my procedure with one DTI sequence and one MPRAGE: In DTIStudio: 1) MRI view3D: register MPRAGE image (voxel size 0.83X0.83X1.1mm) to b0 image (0.83X0.83X2.2mm) using affine transformation. 2) DTI Mapping: register all DWIs to b0 using affine too. 3) Fiber-tracking: draw ROI on co-registered MPRAGE images for fiber tracking. in step 2: do you recommend choosing the option of "Adjusting the gradients of the DWI images if applicable"??? thanks for your help! Sincerely, Aifeng From: smoriw at gmail.com [mailto:smoriw at gmail.com] On Behalf Of susumu mori Sent: Thursday, July 08, 2010 8:01 PM To: Zhang, Aifeng Subject: Re: [Mristudio-users] Eddy_current_correction Yes. Usually all DWIs to b0. On Thu, Jul 8, 2010 at 8:37 PM, Zhang, Aifeng > wrote: Dr. Mori, thanks for quick response. So I will register 32 gradients to b0 for all my data. I don't have error message problem. (maybe it's someone else?) thanks! Aifeng From: smoriw at gmail.com [mailto:smoriw at gmail.com] On Behalf Of susumu mori Sent: Thursday, July 08, 2010 7:30 PM To: Zhang, Aifeng Subject: Re: [Mristudio-users] Eddy_current_correction Do you still have the error message problem? Because coregistration smooths the data and SNR changes, it is a good idea to apply it to all data. On Thu, Jul 8, 2010 at 8:08 PM, Zhang, Aifeng > wrote: Dear DTIStudio, Is coregistration always recommended as the first step, as I saw from articles from your lab? In our case, we only acquired 1 DTI sequence with 32 directions (~4 mins, with SENSE 2.5). thanks. Sincerely, Aifeng From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Wednesday, June 30, 2010 9:32 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Eddy_current_correction When you load the REC file using "Mri3DView", make sure how many images are in the file. For example, if you used Philips "High" table, you have 1 b0 + 32 DWI + 1 extra image, total 34 images. The last one is an isotropically-weighted image generated from the DWIs. Then make sure your gradient table. Most likely, the number of images in your REC and the gradient table are not matching. For example, you may have only 33 lines in the table. For the final image, which you don't use, you can add an extra line with 33: 100, 100, 100. The first "33" is the line number (34th table row), and "100, 100, 100" sends a message to DtiStudio "don't use this image". On Tue, Jun 29, 2010 at 6:19 AM, Seyede Ghazal Mohades > wrote: >Dear all I have a completely basic question when I try to load Philips Rec images in DTI studio I can do it, however the same set file (which is a DTI ss-EPI sequence )gives the following error when I try to do DTI mapping : the file is Bigger (and sometimes it says smaller)than a DWI sequence! where is the problem? regards Ghazal >Thanks > >-----Original Message----- >From: mristudio-users-bounces at mristudio.org on behalf of support at mristudio.org >Sent: Mon 6/28/2010 12:24 PM >To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >Subject: Re: [Mristudio-users] Eddy_current_correction > >the 1st method would be fine: use the 1st B0 as a reference and register all >others with it. > >support > > > >> >> Hi All, >> >> We have diffusion data set acquired with 5 trails/repetitions(in single time >> point/cross sectional) for each and every subject. This means i have 5 b0(same >> value) and DW (12 directions) data while doing eddy current correction can i >> choose for instance b0 from first trail and register all the DW and other b0 >> images to this or do eddy current correction separately for each and every trail >> and finally register all of them together say for instance to the first trail. >> >> Thanks >> >> venkat >> >> =================================== >> >> P Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked one of the top hospitals >> in America by U.S.News & World Report (2009). >> Visit us online at http://www.clevelandclinic.org for >> a complete listing of our services, staff and >> locations. >> >> >> Confidentiality Note: This message is intended for use >> only by the individual or entity to which it is addressed >> and may contain information that is privileged, >> confidential, and exempt from disclosure under applicable >> law. If the reader of this message is not the intended >> recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are >> hereby notified that any dissemination, distribution or >> copying of this communication is strictly prohibited. If >> you have received this communication in error, please >> contact the sender immediately and destroy the material in >> its entirety, whether electronic or hard copy. Thank you. >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> > > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > >=================================== > >P Please consider the environment before printing this e-mail > >Cleveland Clinic is ranked one of the top hospitals >in America by U.S.News & World Report (2009). >Visit us online at http://www.clevelandclinic.org for >a complete listing of our services, staff and >locations. > > >Confidentiality Note: This message is intended for use >only by the individual or entity to which it is addressed >and may contain information that is privileged, >confidential, and exempt from disclosure under applicable >law. If the reader of this message is not the intended >recipient or the employee or agent responsible for >delivering the message to the intended recipient, you are >hereby notified that any dissemination, distribution or >copying of this communication is strictly prohibited. If >you have received this communication in error, please >contact the sender immediately and destroy the material in >its entirety, whether electronic or hard copy. Thank you. > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100709/03146655/attachment-0001.html From jsadino.queens at gmail.com Sat Jul 10 22:51:27 2010 From: jsadino.queens at gmail.com (Jeff Sadino) Date: Sat, 10 Jul 2010 21:51:27 -0500 Subject: [Mristudio-users] b-matrix from dicom header and from techs In-Reply-To: <77A88E90A851594AAEF830450587C39D0418324E@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D0418324E@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Hi Venkat, We had the same question on our Siemens VA25A DTIs. The Siemen's tech support recommended a program called MRIConvert ( http://lcni.uoregon.edu/~jolinda/MRIConvert/) to extract the gradients. I don't have our tables in front of me, but the .8, 0, and .4 values seem pretty close to what I remember. Siemens said that they suspected the 1, 0, .5 values were in the scanner direction and the .8, 0, .4 values were in the patient direction, since I think Siemens automatically adjusts for that. Just be careful when using the MRIConvert program to extract gradients, since it flips the y sign for FSL purposes. Cheers, Jeff On Fri, Jul 9, 2010 at 9:33 AM, Rajagopalan, Venkateswaran wrote: > > Dear All, > > we collect our data from Siemens scanner. I got b-matrix from our MR techs > for software version VA25A b matrix is as follows > > 0: 0.000, 0.000, 0.000 > 1: 1.000, 0.000, 0.500 > 2: 0.000, 0.500, 1.000 > 3: 0.500, 1.000, 0.000 > 4: 1.000, 0.500, 0.000 > 5: 0.000, 1.000, 0.500 > 6: 0.500, 0.000, 1.000 > 7: 1.000, 0.000, -0.500 > 8: 0.000, -0.500, 1.000 > 9: -0.500, 1.000, 0.000 > 10: 1.000, -0.500, 0.000 > 11: 0.000, 1.000, -0.500 > 12: -0.500, 0.000, 1.000 > > I used dcm2nii software (to convert hem into nifti file for soem other > purpose i also gives me bvec and bval files) which gives me the following > matrix from the dicom header file > > 0 0 0 > 0.89 0 -0.45 > 0 0.45 -0.89 > 0.45 0.89 0 > 0.89 0.45 0 > 0 0.89 -0.45 > 0.45 0 -0.89 > 0.89 0 0.45 > 0 -0.45 -0.89 > -0.45 0.89 0 > 0.89 -0.45 0 > 0 0.89 0.45 > -0.45 0 -0.89 > > Since not only the values are different but +/- signs are also different in > DW directions. So I am wondering whether any one could tell me which is the > correct table to go with. > > Thanks > > Venkat > > =================================== > > P Please consider the environment before printing this e-mail > > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100710/b4d2b306/attachment.html From hjiang at jhmi.edu Mon Jul 12 09:56:20 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Mon, 12 Jul 2010 09:56:20 -0400 Subject: [Mristudio-users] b-matrix from dicom header and from techs In-Reply-To: References: <77A88E90A851594AAEF830450587C39D0418324E@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <145933A2BE9E4F48AE079A201379BF2F21300EB8EE@RAD-EXCH1.win.ad.jhu.edu> hi, Jeff, if the files are in Mosaic format, DtiDtudio can get the gradients from the header. below, I attached the email I sent to Venkat for your reference. regards, hangyi >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Venkat, this is one of the most confusions to deal with DICOM files. according the DICOM standard and Siemens documentation, the gradients (bvec as you mentioned) in DICOM header should be defined in patient space (or image matrix space), so the one from dcm2nii should be correct for your dataset. the 1st one (from your MR techs) seems that it is the original definition based on scanner's coordinate system. this one should be adjusted dynamically during scanning according to patient position and orientation. by the way, we usually named it as gradient table, not b-matrix. b-matrix has 6 components for each of DWIs. b-matrix can be calculated from the gradient table. as a matter of fact, Siemens also saves adjusted b-matrix in the DICOM header. if you like, you can also use the adjusted b-matrix from the header for tensor calculation. in fact, using adjusted b-matrix is recommended by Siemens since it also considered other factors (like gradient cross-over effects) for image acquisition. hope it helps. hangyi >>>>>>>>>>>>>>>>>>>>>>>>>>>> ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Jeff Sadino [jsadino.queens at gmail.com] Sent: Saturday, July 10, 2010 10:51 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; rajagov2 at ccf.org Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs Hi Venkat, We had the same question on our Siemens VA25A DTIs. The Siemen's tech support recommended a program called MRIConvert (http://lcni.uoregon.edu/~jolinda/MRIConvert/) to extract the gradients. I don't have our tables in front of me, but the .8, 0, and .4 values seem pretty close to what I remember. Siemens said that they suspected the 1, 0, .5 values were in the scanner direction and the .8, 0, .4 values were in the patient direction, since I think Siemens automatically adjusts for that. Just be careful when using the MRIConvert program to extract gradients, since it flips the y sign for FSL purposes. Cheers, Jeff On Fri, Jul 9, 2010 at 9:33 AM, Rajagopalan, Venkateswaran > wrote: Dear All, we collect our data from Siemens scanner. I got b-matrix from our MR techs for software version VA25A b matrix is as follows 0: 0.000, 0.000, 0.000 1: 1.000, 0.000, 0.500 2: 0.000, 0.500, 1.000 3: 0.500, 1.000, 0.000 4: 1.000, 0.500, 0.000 5: 0.000, 1.000, 0.500 6: 0.500, 0.000, 1.000 7: 1.000, 0.000, -0.500 8: 0.000, -0.500, 1.000 9: -0.500, 1.000, 0.000 10: 1.000, -0.500, 0.000 11: 0.000, 1.000, -0.500 12: -0.500, 0.000, 1.000 I used dcm2nii software (to convert hem into nifti file for soem other purpose i also gives me bvec and bval files) which gives me the following matrix from the dicom header file 0 0 0 0.89 0 -0.45 0 0.45 -0.89 0.45 0.89 0 0.89 0.45 0 0 0.89 -0.45 0.45 0 -0.89 0.89 0 0.45 0 -0.45 -0.89 -0.45 0.89 0 0.89 -0.45 0 0 0.89 0.45 -0.45 0 -0.89 Since not only the values are different but +/- signs are also different in DW directions. So I am wondering whether any one could tell me which is the correct table to go with. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From jamike_408 at hotmail.com Mon Jul 12 11:41:49 2010 From: jamike_408 at hotmail.com (michael brown) Date: Mon, 12 Jul 2010 15:41:49 +0000 Subject: [Mristudio-users] (no subject) Message-ID: Hi Mymname is Mike, I've very recently started using mri studio, it seems realy good so far. My problem is that i've got to learn it quickly. I've got a gradient table and dicom images and I need to find the ADC and FA. I can load the table but I don't know what to do next, can you help me please. Mike _________________________________________________________________ http://clk.atdmt.com/UKM/go/195013117/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100712/f4ca5693/attachment.html From susumu at mri.jhu.edu Mon Jul 12 19:59:29 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 12 Jul 2010 19:59:29 -0400 Subject: [Mristudio-users] b-matrix from dicom header and from techs In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F21300EB8EE@RAD-EXCH1.win.ad.jhu.edu> References: <77A88E90A851594AAEF830450587C39D0418324E@CCHSCLEXMB56.cc.ad.cchs.net> <145933A2BE9E4F48AE079A201379BF2F21300EB8EE@RAD-EXCH1.win.ad.jhu.edu> Message-ID: Hi all, For Siemens users, now a new function to extract a gradient table from Mosaic file header is available. The extracted gradient table is usually different from the generic gradient table provided by Siemens from the following points; > X/Y/Z gradient signs (+/-) are dynamically changed based on image protocol (e.g. axial/sagittal/coronal). The extracted tables have correct signs. > The extracted table is more exact because it includes not only the diffusion-weighing gradients but also a small contribution of imaging gradients. The are some mixed information about whether we need to reorient gradient tables when oblique imaging is used (whether we need to check "rotate if applicable" option or not). We are testing it but with the scanner we tested last time (VB17 operating system), we needed to check to this option. We will follow up this issue soon but we strongly recommend you to test your scanner. It can be easily tested by scanning a person twice. Once with a regular axial and one with a strong oblique (30-45 degree). If you are not sure about your results, you can send us your results for check. Susumu On Mon, Jul 12, 2010 at 9:56 AM, Hangyi Jiang wrote: > hi, Jeff, > > if the files are in Mosaic format, DtiDtudio can get the gradients from the > header. > below, I attached the email I sent to Venkat for your reference. > > regards, > > hangyi > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>> > Hi Venkat, > > this is one of the most confusions to deal with DICOM files. > > according the DICOM standard and Siemens documentation, the gradients (bvec > as you mentioned) in DICOM header should be defined in patient space (or > image matrix space), so the one from dcm2nii should be correct for your > dataset. > > the 1st one (from your MR techs) seems that it is the original definition > based on scanner's coordinate system. this one should be adjusted > dynamically during scanning according to patient position and orientation. > by the way, we usually named it as gradient table, not b-matrix. b-matrix > has 6 components for each of DWIs. b-matrix can be calculated from the > gradient table. > > as a matter of fact, Siemens also saves adjusted b-matrix in the DICOM > header. if you like, you can also use the adjusted b-matrix from the header > for tensor calculation. in fact, using adjusted b-matrix is recommended by > Siemens since it also considered other factors (like gradient cross-over > effects) for image acquisition. > > hope it helps. > > hangyi > >>>>>>>>>>>>>>>>>>>>>>>>>>>> > > > > ________________________________________ > From: mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of Jeff Sadino [ > jsadino.queens at gmail.com] > Sent: Saturday, July 10, 2010 10:51 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; rajagov2 at ccf.org > Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs > > Hi Venkat, > > We had the same question on our Siemens VA25A DTIs. The Siemen's tech > support recommended a program called MRIConvert ( > http://lcni.uoregon.edu/~jolinda/MRIConvert/) > to extract the gradients. I don't have our tables in front of me, but the > .8, 0, and .4 values seem pretty close to what I remember. Siemens said > that they suspected the 1, 0, .5 values were in the scanner direction and > the .8, 0, .4 values were in the patient direction, since I think Siemens > automatically adjusts for that. Just be careful when using the MRIConvert > program to extract gradients, since it flips the y sign for FSL purposes. > > Cheers, > Jeff > > On Fri, Jul 9, 2010 at 9:33 AM, Rajagopalan, Venkateswaran < > rajagov2 at ccf.org> wrote: > > > Dear All, > > we collect our data from Siemens scanner. I got b-matrix from our MR techs > for software version VA25A b matrix is as follows > > 0: 0.000, 0.000, 0.000 > 1: 1.000, 0.000, 0.500 > 2: 0.000, 0.500, 1.000 > 3: 0.500, 1.000, 0.000 > 4: 1.000, 0.500, 0.000 > 5: 0.000, 1.000, 0.500 > 6: 0.500, 0.000, 1.000 > 7: 1.000, 0.000, -0.500 > 8: 0.000, -0.500, 1.000 > 9: -0.500, 1.000, 0.000 > 10: 1.000, -0.500, 0.000 > 11: 0.000, 1.000, -0.500 > 12: -0.500, 0.000, 1.000 > > I used dcm2nii software (to convert hem into nifti file for soem other > purpose i also gives me bvec and bval files) which gives me the following > matrix from the dicom header file > > 0 0 0 > 0.89 0 -0.45 > 0 0.45 -0.89 > 0.45 0.89 0 > 0.89 0.45 0 > 0 0.89 -0.45 > 0.45 0 -0.89 > 0.89 0 0.45 > 0 -0.45 -0.89 > -0.45 0.89 0 > 0.89 -0.45 0 > 0 0.89 0.45 > -0.45 0 -0.89 > > Since not only the values are different but +/- signs are also different in > DW directions. So I am wondering whether any one could tell me which is the > correct table to go with. > > Thanks > > Venkat > > > =================================== > > P Please consider the environment before printing this e-mail > > > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org< > http://www.clevelandclinic.org/> for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org mristudio-users-unsubscribe at mristudio.org> > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100712/e01006c8/attachment-0001.html From felshahaby at gmail.com Mon Jul 12 23:41:17 2010 From: felshahaby at gmail.com (Fatma ElShahaby) Date: Mon, 12 Jul 2010 23:41:17 -0400 Subject: [Mristudio-users] b-matrix from dicom header and from techs In-Reply-To: References: <77A88E90A851594AAEF830450587C39D0418324E@CCHSCLEXMB56.cc.ad.cchs.net> <145933A2BE9E4F48AE079A201379BF2F21300EB8EE@RAD-EXCH1.win.ad.jhu.edu> Message-ID: Dear Dr.Mori, I am currently working with Siemens DICOM with software version VB17 with oblique acquisition. I have the following questions: *1) From the DICOM header of the b0 images, the corresponding gradient direction is not (0,0,0). However, it is (0, 0.7,0.7). What does this mean? Which one is the right one to use?* * * *2) You said that we have to use the gradient table from the DICOM header instead of the Manufacturer's table since the former is more accurate. So,does this mean that we do not need to load the predefined tables any more? Is this true for different scanner software versions or for only VB17? * *3) There is one point that is puzzling me. You said previously that we do not need to reorient the gradient table if we are using software version after VB15. However, I do not understand what do you mean exactly by this sentence?* "*The are some mixed information about whether we need to reorient gradient tables when oblique imaging is used (whether we need to check "rotate if applicable" option or not). We are testing it but with the scanner we tested last time (VB17 operating system), we needed to check to this option.* " *Does this mean that we may need to rotate the gradient table in case of oblique acquisition for VB17? *Thank you very much. Fatma. On Mon, Jul 12, 2010 at 7:59 PM, susumu mori wrote: > Hi all, > > For Siemens users, now a new function to extract a gradient table from > Mosaic file header is available. The extracted gradient table is usually > different from the generic gradient table provided by Siemens from the > following points; > > > X/Y/Z gradient signs (+/-) are dynamically changed based on image > protocol (e.g. axial/sagittal/coronal). The extracted tables have correct > signs. > > The extracted table is more exact because it includes not only the > diffusion-weighing gradients but also a small contribution of imaging > gradients. > > The are some mixed information about whether we need to reorient gradient > tables when oblique imaging is used (whether we need to check "rotate if > applicable" option or not). We are testing it but with the scanner we tested > last time (VB17 operating system), we needed to check to this option. > > We will follow up this issue soon but we strongly recommend you to test > your scanner. It can be easily tested by scanning a person twice. Once with > a regular axial and one with a strong oblique (30-45 degree). If you are not > sure about your results, you can send us your results for check. > > Susumu > > > On Mon, Jul 12, 2010 at 9:56 AM, Hangyi Jiang wrote: > >> hi, Jeff, >> >> if the files are in Mosaic format, DtiDtudio can get the gradients from >> the header. >> below, I attached the email I sent to Venkat for your reference. >> >> regards, >> >> hangyi >> >> >> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Hi Venkat, >> >> this is one of the most confusions to deal with DICOM files. >> >> according the DICOM standard and Siemens documentation, the gradients >> (bvec as you mentioned) in DICOM header should be defined in patient space >> (or image matrix space), so the one from dcm2nii should be correct for your >> dataset. >> >> the 1st one (from your MR techs) seems that it is the original definition >> based on scanner's coordinate system. this one should be adjusted >> dynamically during scanning according to patient position and orientation. >> by the way, we usually named it as gradient table, not b-matrix. b-matrix >> has 6 components for each of DWIs. b-matrix can be calculated from the >> gradient table. >> >> as a matter of fact, Siemens also saves adjusted b-matrix in the DICOM >> header. if you like, you can also use the adjusted b-matrix from the header >> for tensor calculation. in fact, using adjusted b-matrix is recommended by >> Siemens since it also considered other factors (like gradient cross-over >> effects) for image acquisition. >> >> hope it helps. >> >> hangyi >> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >> >> >> >> ________________________________________ >> From: mristudio-users-bounces at mristudio.org [ >> mristudio-users-bounces at mristudio.org] On Behalf Of Jeff Sadino [ >> jsadino.queens at gmail.com] >> Sent: Saturday, July 10, 2010 10:51 PM >> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; rajagov2 at ccf.org >> Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs >> >> Hi Venkat, >> >> We had the same question on our Siemens VA25A DTIs. The Siemen's tech >> support recommended a program called MRIConvert ( >> http://lcni.uoregon.edu/~jolinda/MRIConvert/) >> to extract the gradients. I don't have our tables in front of me, but the >> .8, 0, and .4 values seem pretty close to what I remember. Siemens said >> that they suspected the 1, 0, .5 values were in the scanner direction and >> the .8, 0, .4 values were in the patient direction, since I think Siemens >> automatically adjusts for that. Just be careful when using the MRIConvert >> program to extract gradients, since it flips the y sign for FSL purposes. >> >> Cheers, >> Jeff >> >> On Fri, Jul 9, 2010 at 9:33 AM, Rajagopalan, Venkateswaran < >> rajagov2 at ccf.org> wrote: >> >> >> Dear All, >> >> we collect our data from Siemens scanner. I got b-matrix from our MR techs >> for software version VA25A b matrix is as follows >> >> 0: 0.000, 0.000, 0.000 >> 1: 1.000, 0.000, 0.500 >> 2: 0.000, 0.500, 1.000 >> 3: 0.500, 1.000, 0.000 >> 4: 1.000, 0.500, 0.000 >> 5: 0.000, 1.000, 0.500 >> 6: 0.500, 0.000, 1.000 >> 7: 1.000, 0.000, -0.500 >> 8: 0.000, -0.500, 1.000 >> 9: -0.500, 1.000, 0.000 >> 10: 1.000, -0.500, 0.000 >> 11: 0.000, 1.000, -0.500 >> 12: -0.500, 0.000, 1.000 >> >> I used dcm2nii software (to convert hem into nifti file for soem other >> purpose i also gives me bvec and bval files) which gives me the following >> matrix from the dicom header file >> >> 0 0 0 >> 0.89 0 -0.45 >> 0 0.45 -0.89 >> 0.45 0.89 0 >> 0.89 0.45 0 >> 0 0.89 -0.45 >> 0.45 0 -0.89 >> 0.89 0 0.45 >> 0 -0.45 -0.89 >> -0.45 0.89 0 >> 0.89 -0.45 0 >> 0 0.89 0.45 >> -0.45 0 -0.89 >> >> Since not only the values are different but +/- signs are also different >> in DW directions. So I am wondering whether any one could tell me which is >> the correct table to go with. >> >> Thanks >> >> Venkat >> >> >> =================================== >> >> P Please consider the environment before printing this e-mail >> >> >> >> >> Cleveland Clinic is ranked one of the top hospitals >> in America by U.S.News & World Report (2009). >> Visit us online at http://www.clevelandclinic.org< >> http://www.clevelandclinic.org/> for >> a complete listing of our services, staff and >> locations. >> >> >> Confidentiality Note: This message is intended for use >> only by the individual or entity to which it is addressed >> and may contain information that is privileged, >> confidential, and exempt from disclosure under applicable >> law. If the reader of this message is not the intended >> recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are >> hereby notified that any dissemination, distribution or >> copying of this communication is strictly prohibited. If >> you have received this communication in error, please >> contact the sender immediately and destroy the material in >> its entirety, whether electronic or hard copy. Thank you. >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org> mristudio-users-unsubscribe at mristudio.org> >> >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100712/7cc33173/attachment.html From guhuahh at 126.com Tue Jul 13 02:13:16 2010 From: guhuahh at 126.com (guhuahh) Date: Tue, 13 Jul 2010 14:13:16 +0800 (CST) Subject: [Mristudio-users] =?gbk?b?wLTX1Gd1aHVhaGhAMTI2LmNvbbXE08q8/g==?= Message-ID: <192a76f.48fd.129ca6f93b9.Coremail.guhuahh@126.com> Please unsubscribe me. Thank you! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100713/fda3f447/attachment.html From guhuahh at 126.com Tue Jul 13 02:16:56 2010 From: guhuahh at 126.com (guhuahh) Date: Tue, 13 Jul 2010 14:16:56 +0800 (CST) Subject: [Mristudio-users] Please unsubscribe me In-Reply-To: <72c0ee2b231cc.4c29e415@johnshopkins.edu> References: <72c0ee2b231cc.4c29e415@johnshopkins.edu> Message-ID: >Hello, > >If you want to unsubscribe, please send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > >Xin > > > > >----- Original Message ----- >From: "Lana Wassung, MD" >Date: Tuesday, June 29, 2010 12:13 pm >Subject: [Mristudio-users] Please unsubscribe me >To: mristudio-users at mristudio.org > > >> Please unsubscribe me >> >> >> >> Lana Vasung, MD, PhD student >> Croatian Institute for Brain Research >> School of Medicine, >> Clinical Hospital Centre Zagreb, >> University of Zagreb >> Mob: 00 385 98 993 66 81 >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100713/69e4f291/attachment-0001.html From j.houenou at yahoo.fr Tue Jul 13 06:38:47 2010 From: j.houenou at yahoo.fr (Josselin) Date: Tue, 13 Jul 2010 10:38:47 +0000 (GMT) Subject: [Mristudio-users] compiled makeaheader.exe, alignlinear.exe, align_warp.exe and invert_air.exe (AIR) for windows Message-ID: <561163.39347.qm@web25605.mail.ukl.yahoo.com> Dear all, I would like to use DTI studio. I have a problem: I do not manage to compile makeaheader.exe, alignlinear.exe, align_warp.exe and invert_air.exe for windows from AIR. Do anyone of you could email me these files ? thanks Josselin From choisj70 at gmail.com Tue Jul 13 09:11:13 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 13 Jul 2010 09:11:13 -0400 Subject: [Mristudio-users] Mutual Info Registration Message-ID: Dear DTI studio community, I would like to make it sure if I understood correctly. In the registration methods, there are two method implemented in DTI studio. 1. AIR 2. Mutual information based. In both method, two options are provided: Rigid and Affine. In order to reduce both motion and eddy current, we choose Affine option. Is this correct? I see 6 parameters for rigid and 12 parameters for Affine. I wonder if I choose rigid option then only motion would corrected. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100713/5861f67e/attachment.html From duggaldti at hotmail.ca Tue Jul 13 09:51:46 2010 From: duggaldti at hotmail.ca (Duggal Lab DTI) Date: Tue, 13 Jul 2010 09:51:46 -0400 Subject: [Mristudio-users] Co-Register and Normalize Message-ID: Hello, I was wondering if there is a way to co-register the ADC or FA maps with T1 images in DTI Studio? Also, can they then be normalized to a standard brain in the program as well? If DTI Studio can do this how is it done? If not, are there any suggestions for programs to use for this to completment DTI Studio? Thank you for your help, take care, Stuart _________________________________________________________________ Turn down-time into play-time with Messenger games http://go.microsoft.com/?linkid=9734385 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100713/0288f2a0/attachment.html From azhang at psych.uic.edu Tue Jul 13 12:20:50 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Tue, 13 Jul 2010 11:20:50 -0500 Subject: [Mristudio-users] using T1 image for ROI drawing In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F21300EB8F7@RAD-EXCH1.win.ad.jhu.edu> References: <40469184F1D86344A835AB980269681A1695CAE2C5@exchange.psych.uic.edu> <145933A2BE9E4F48AE079A201379BF2F21300EB8EB@RAD-EXCH1.win.ad.jhu.edu> <40469184F1D86344A835AB980269681A16969FC647@exchange.psych.uic.edu> <145933A2BE9E4F48AE079A201379BF2F21300EB8F7@RAD-EXCH1.win.ad.jhu.edu> Message-ID: <40469184F1D86344A835AB980269681A16969FC6F5@exchange.psych.uic.edu> Hi Hangyi So I tried with Mutual-info registration and it works just fine on MPRAGE and aligned well with b0 images. and I also found that the fibers come out better using mutual-info registration on DWIs. So is mutual-info reg a better choice? thanks, Aifeng -----Original Message----- From: Hangyi Jiang [mailto:hjiang at jhmi.edu] Sent: Tuesday, July 13, 2010 9:49 AM To: Zhang, Aifeng Subject: RE: using T1 image for ROI drawing hi, Aifeng, AIRed images will have same FOV and dimensions with that of the reference image. the slices-shifting is the result of the image registration, so the program try to align two images together. it is not the problem, it is the job that AIR supposed to do. however, AIR may not do the job well (that is why image registration is a very active research field). basically, if AIR can correct motion artifacts between the images of same modality very well. since MPRAGE and B0 (and DWIs) are acquired in different ways, the image intensities (or contract) might be different for same anatomical regions, AIR may not work well. that is why we recommend using B0 (not MPRAGE) as a reference to register DWIs. best, hangyi ________________________________________ From: Zhang, Aifeng [azhang at psych.uic.edu] Sent: Monday, July 12, 2010 6:39 PM To: Hangyi Jiang Subject: RE: using T1 image for ROI drawing hi Hangyi, my AIR co-registered MPRAGE(axial) to b0(axial) have couple slices shifted in head-to-toe direction. It seems like the original MPRAGE doesn't have the same FOV and image center. Could you please tell me what procedure can solve this problem when those two sequences have different FOV and image center? Thanks a lot! Sincerely, Aifeng -----Original Message----- From: Hangyi Jiang [mailto:hjiang at jhmi.edu] Sent: Monday, July 12, 2010 8:48 AM To: Zhang, Aifeng Subject: RE: using T1 image for ROI drawing basically, the procedures are right. in step 3, ROIs are mostly defined on color map or FA map, besides on MPRAGE hangyi ________________________________________ From: Zhang, Aifeng [azhang at psych.uic.edu] Sent: Saturday, July 10, 2010 11:39 PM To: Hangyi Jiang Subject: RE: using T1 image for ROI drawing Thanks, so the rest of my procedure is correct? Sincerely, Aifeng Sent from my Windows Mobile(r) phone. -----Original Message----- From: Hangyi Jiang Sent: Saturday, July 10, 2010 8:34 PM To: Zhang, Aifeng Subject: RE: using T1 image for ROI drawing yes, "Adjusting the gradients" is needed. hangyi ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Zhang, Aifeng [azhang at psych.uic.edu] Sent: Friday, July 09, 2010 4:49 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] using T1 image for ROI drawing Dear DTIStudio, Just want to double check with you about my procedure with one DTI sequence and one MPRAGE: In DTIStudio: 1) MRI view3D: register MPRAGE image (voxel size 0.83X0.83X1.1mm) to b0 image (0.83X0.83X2.2mm) using affine transformation. 2) DTI Mapping: register all DWIs to b0 using affine too. 3) Fiber-tracking: draw ROI on co-registered MPRAGE images for fiber tracking. in step 2: do you recommend choosing the option of "Adjusting the gradients of the DWI images if applicable"??? thanks for your help! Sincerely, Aifeng From: smoriw at gmail.com [mailto:smoriw at gmail.com] On Behalf Of susumu mori Sent: Thursday, July 08, 2010 8:01 PM To: Zhang, Aifeng Subject: Re: [Mristudio-users] Eddy_current_correction Yes. Usually all DWIs to b0. On Thu, Jul 8, 2010 at 8:37 PM, Zhang, Aifeng > wrote: Dr. Mori, thanks for quick response. So I will register 32 gradients to b0 for all my data. I don't have error message problem. (maybe it's someone else?) thanks! Aifeng From: smoriw at gmail.com [mailto:smoriw at gmail.com] On Behalf Of susumu mori Sent: Thursday, July 08, 2010 7:30 PM To: Zhang, Aifeng Subject: Re: [Mristudio-users] Eddy_current_correction Do you still have the error message problem? Because coregistration smooths the data and SNR changes, it is a good idea to apply it to all data. On Thu, Jul 8, 2010 at 8:08 PM, Zhang, Aifeng > wrote: Dear DTIStudio, Is coregistration always recommended as the first step, as I saw from articles from your lab? In our case, we only acquired 1 DTI sequence with 32 directions (~4 mins, with SENSE 2.5). thanks. Sincerely, Aifeng From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Wednesday, June 30, 2010 9:32 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Eddy_current_correction When you load the REC file using "Mri3DView", make sure how many images are in the file. For example, if you used Philips "High" table, you have 1 b0 + 32 DWI + 1 extra image, total 34 images. The last one is an isotropically-weighted image generated from the DWIs. Then make sure your gradient table. Most likely, the number of images in your REC and the gradient table are not matching. For example, you may have only 33 lines in the table. For the final image, which you don't use, you can add an extra line with 33: 100, 100, 100. The first "33" is the line number (34th table row), and "100, 100, 100" sends a message to DtiStudio "don't use this image". On Tue, Jun 29, 2010 at 6:19 AM, Seyede Ghazal Mohades > wrote: >Dear all I have a completely basic question when I try to load Philips Rec images in DTI studio I can do it, however the same set file (which is a DTI ss-EPI sequence )gives the following error when I try to do DTI mapping : the file is Bigger (and sometimes it says smaller)than a DWI sequence! where is the problem? regards Ghazal >Thanks > >-----Original Message----- >From: mristudio-users-bounces at mristudio.org on behalf of support at mristudio.org >Sent: Mon 6/28/2010 12:24 PM >To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >Subject: Re: [Mristudio-users] Eddy_current_correction > >the 1st method would be fine: use the 1st B0 as a reference and register all >others with it. > >support > > > >> >> Hi All, >> >> We have diffusion data set acquired with 5 trails/repetitions(in single time >> point/cross sectional) for each and every subject. This means i have 5 b0(same >> value) and DW (12 directions) data while doing eddy current correction can i >> choose for instance b0 from first trail and register all the DW and other b0 >> images to this or do eddy current correction separately for each and every trail >> and finally register all of them together say for instance to the first trail. >> >> Thanks >> >> venkat >> >> =================================== >> >> P Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked one of the top hospitals >> in America by U.S.News & World Report (2009). >> Visit us online at http://www.clevelandclinic.org for >> a complete listing of our services, staff and >> locations. >> >> >> Confidentiality Note: This message is intended for use >> only by the individual or entity to which it is addressed >> and may contain information that is privileged, >> confidential, and exempt from disclosure under applicable >> law. If the reader of this message is not the intended >> recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are >> hereby notified that any dissemination, distribution or >> copying of this communication is strictly prohibited. If >> you have received this communication in error, please >> contact the sender immediately and destroy the material in >> its entirety, whether electronic or hard copy. Thank you. >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org >> > > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/ >Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org > > > >=================================== > >P Please consider the environment before printing this e-mail > >Cleveland Clinic is ranked one of the top hospitals >in America by U.S.News & World Report (2009). >Visit us online at http://www.clevelandclinic.org for >a complete listing of our services, staff and >locations. > > >Confidentiality Note: This message is intended for use >only by the individual or entity to which it is addressed >and may contain information that is privileged, >confidential, and exempt from disclosure under applicable >law. If the reader of this message is not the intended >recipient or the employee or agent responsible for >delivering the message to the intended recipient, you are >hereby notified that any dissemination, distribution or >copying of this communication is strictly prohibited. If >you have received this communication in error, please >contact the sender immediately and destroy the material in >its entirety, whether electronic or hard copy. Thank you. > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From d-gitelman at northwestern.edu Tue Jul 13 17:28:38 2010 From: d-gitelman at northwestern.edu (Darren Gitelman) Date: Tue, 13 Jul 2010 16:28:38 -0500 Subject: [Mristudio-users] crash when saving ROI's Message-ID: Hi I am having problems with DTI studio crashing when trying to save ROI's. This happens after I draw an ROI and click the save button. Then a dialog (ROI File Format) comes up giving a choice of different formats. I choose Graphic Compatible (default). After clicking OK, a crash window comes up a few seconds later. It is labeled MriView3D MFC application. The only technical information I can find is the following. AppName: dtistudio-latest-x86.exe AppVer: 1.0.0.1 ModName: msvcr80.dll ModVer: 8.0.50727.4053 Offset: 00014458 This occurs whether I have drawn 1 or more ROIs. (fixed size ROI, oval). The size of the ROI does not matter (4 voxel or 10 voxel) It occurs with DTI studio x86 and x64. It occurs with versions 3.0.2 and 2.4.1 of DTIstudio. It occurs whether I have a complete dataset loaded 35 directions, or even if I load just 1 image and draw an ROI on it. It occurs on an HP core duo 2 system running Windows XP SP3, and on a redhat linux KVM virtual machine running windows XP x64. Reinstalling vcredist_x86 or vcredist_x64 from the DTIstudio website does not help on any of the systems. Any suggestions on how to fix? Darren -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100713/aef08964/attachment.html From abraham.padua at siemens.com Tue Jul 13 18:08:48 2010 From: abraham.padua at siemens.com (Padua, Abraham (H USA)) Date: Tue, 13 Jul 2010 18:08:48 -0400 Subject: [Mristudio-users] crash when saving ROI's Message-ID: <96A597CAF1F721498717F951CAF875980541B870@USMLVV1EXCTV03.ww005.siemens.net> Hi Darren, I just opened an account with DTI Studio today. I don't know anything yet about this software and its handling. Sorry, but there should be a contact persons from the development group who created this software. Good luck in resolving your problem. Abe -------------------------- Sent from my BlackBerry Wireless Handheld ________________________________ From: mristudio-users-bounces at mristudio.org To: mristudio-users Sent: Tue Jul 13 17:28:38 2010 Subject: [Mristudio-users] crash when saving ROI's Hi I am having problems with DTI studio crashing when trying to save ROI's. This happens after I draw an ROI and click the save button. Then a dialog (ROI File Format) comes up giving a choice of different formats. I choose Graphic Compatible (default). After clicking OK, a crash window comes up a few seconds later. It is labeled MriView3D MFC application. The only technical information I can find is the following. AppName: dtistudio-latest-x86.exe AppVer: 1.0.0.1 ModName: msvcr80.dll ModVer: 8.0.50727.4053 Offset: 00014458 This occurs whether I have drawn 1 or more ROIs. (fixed size ROI, oval). The size of the ROI does not matter (4 voxel or 10 voxel) It occurs with DTI studio x86 and x64. It occurs with versions 3.0.2 and 2.4.1 of DTIstudio. It occurs whether I have a complete dataset loaded 35 directions, or even if I load just 1 image and draw an ROI on it. It occurs on an HP core duo 2 system running Windows XP SP3, and on a redhat linux KVM virtual machine running windows XP x64. Reinstalling vcredist_x86 or vcredist_x64 from the DTIstudio website does not help on any of the systems. Any suggestions on how to fix? Darren ---------------------------------------------------------------------------- This message and any included attachments are from Siemens Medical Solutions and are intended only for the addressee(s). The information contained herein may include trade secrets or privileged or otherwise confidential information. Unauthorized review, forwarding, printing, copying, distributing, or using such information is strictly prohibited and may be unlawful. If you received this message in error, or have reason to believe you are not authorized to receive it, please promptly delete this message and notify the sender by e-mail with a copy to Central.SecurityOffice at siemens.com Thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100713/ebb3f4a5/attachment-0001.html From choisj70 at gmail.com Tue Jul 13 19:44:55 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 13 Jul 2010 19:44:55 -0400 Subject: [Mristudio-users] crash when saving ROI's In-Reply-To: References: Message-ID: Darren, I experienced the similar problem. I wanted to use ROI drawn in ROI panel but it did not work at all. ROI saving and loading functions seem to work in FIBER panel, but not in the ROI panel. If you want to use ROI for DTI metrics such as FA or ADC measurements, I recommend ROIeditor (a companion tool to DTIstudio). That is more powerful. I always process data in DTI studio. Then load all the processed data into ROI editor. Finally, do the measurement with ROI editor. The saved ROIs can be reused in the DTI studio for fiber tracking. However, again, the ROIs could not be used in ROI panel of the DTI studio on my computers (home computer, laptop, and office computer). I hope this experience might be a bit of help for your problem in using DTI studio. -SC On Tue, Jul 13, 2010 at 5:28 PM, Darren Gitelman < d-gitelman at northwestern.edu> wrote: > Hi > > I am having problems with DTI studio crashing when trying to save ROI's. > > This happens after I draw an ROI and click the save button. Then a dialog > (ROI File Format) comes up giving a choice of different formats. I choose > Graphic Compatible (default). After clicking OK, a crash window comes up a > few seconds later. It is labeled MriView3D MFC application. The only > technical information I can find is the following. > > AppName: dtistudio-latest-x86.exe AppVer: 1.0.0.1 ModName: > msvcr80.dll > ModVer: 8.0.50727.4053 Offset: 00014458 > > This occurs whether I have drawn 1 or more ROIs. (fixed size ROI, oval). > The size of the ROI does not matter (4 voxel or 10 voxel) > It occurs with DTI studio x86 and x64. > It occurs with versions 3.0.2 and 2.4.1 of DTIstudio. > It occurs whether I have a complete dataset loaded 35 directions, or even > if I load just 1 image and draw an ROI on it. > It occurs on an HP core duo 2 system running Windows XP SP3, and on a > redhat linux KVM virtual machine running windows XP x64. > Reinstalling vcredist_x86 or vcredist_x64 from the DTIstudio website does > not help on any of the systems. > > Any suggestions on how to fix? > > Darren > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100713/e8d0711b/attachment.html From choisj70 at gmail.com Tue Jul 13 19:59:49 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 13 Jul 2010 19:59:49 -0400 Subject: [Mristudio-users] Co-Register and Normalize In-Reply-To: References: Message-ID: It should be Diffeomap. It provides you with various ATLAS images, templates, and normalization functionality. -SC On Tue, Jul 13, 2010 at 9:51 AM, Duggal Lab DTI wrote: > Hello, > > I was wondering if there is a way to co-register the ADC or FA maps with T1 > images in DTI Studio? Also, can they then be normalized to a standard brain > in the program as well? If DTI Studio can do this how is it done? If not, > are there any suggestions for programs to use for this to completment DTI > Studio? Thank you for your help, take care, > > Stuart > > ------------------------------ > Your Photo on Bing.ca: You Could WIN on Canada Day! Submit a Photo Now! > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100713/f16a11f9/attachment.html From choisj70 at gmail.com Tue Jul 13 20:18:41 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 13 Jul 2010 20:18:41 -0400 Subject: [Mristudio-users] compiled makeaheader.exe, alignlinear.exe, align_warp.exe and invert_air.exe (AIR) for windows In-Reply-To: <561163.39347.qm@web25605.mail.ukl.yahoo.com> References: <561163.39347.qm@web25605.mail.ukl.yahoo.com> Message-ID: I tried send you the files but total file size was more than 40kB. So I cannot send them immediately. However, if you provide me with your other e-mail account to choi.test at gmail.com, I will send the filed soon. Best, -SC On Tue, Jul 13, 2010 at 6:38 AM, Josselin wrote: > Dear all, > I would like to use DTI studio. I have a problem: I do not manage to > compile makeaheader.exe, alignlinear.exe, align_warp.exe and invert_air.exe > for windows from AIR. Do anyone of you could email me these files ? > thanks > Josselin > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100713/e20e66da/attachment.html From gmak at poczta.onet.pl Thu Jul 15 03:08:58 2010 From: gmak at poczta.onet.pl (gmak at poczta.onet.pl) Date: Thu, 15 Jul 2010 09:08:58 +0200 Subject: [Mristudio-users] AIR files help Message-ID: <82E2CB54D4454DDF8DE744DC4F475E4E@zxzPC> Hi I have a problem to compile makeaheader.exe, alignlinear.exe, align_warp.exe and invert_air.exe for windows from AIR. Do anyone of you could email me these files? gmak13 at wp.pl thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100715/aacc62ab/attachment.html From salvador.castaneda at med.uni-tuebingen.de Wed Jul 14 06:13:48 2010 From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador) Date: Wed, 14 Jul 2010 12:13:48 +0200 Subject: [Mristudio-users] crash when saving ROI's In-Reply-To: References: Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C603@azex2003.raddiag.med.uni-tuebingen.de> SC Thats exactly what i do, i take the image files from dtistudio and load them in the roi editor. i wanted to upload an anatomical picture to better draw y rois because i work with rats. is it possible to dothis even if the matrix and fov are not the same? thanks ________________________________ Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von [Seongjin] Gesendet: Mittwoch, 14. Juli 2010 01:45 An: DTI Studio, ROI Editor, DiffeoMap Questions/Support Betreff: Re: [Mristudio-users] crash when saving ROI's Darren, I experienced the similar problem. I wanted to use ROI drawn in ROI panel but it did not work at all. ROI saving and loading functions seem to work in FIBER panel, but not in the ROI panel. If you want to use ROI for DTI metrics such as FA or ADC measurements, I recommend ROIeditor (a companion tool to DTIstudio). That is more powerful. I always process data in DTI studio. Then load all the processed data into ROI editor. Finally, do the measurement with ROI editor. The saved ROIs can be reused in the DTI studio for fiber tracking. However, again, the ROIs could not be used in ROI panel of the DTI studio on my computers (home computer, laptop, and office computer). I hope this experience might be a bit of help for your problem in using DTI studio. -SC On Tue, Jul 13, 2010 at 5:28 PM, Darren Gitelman wrote: Hi I am having problems with DTI studio crashing when trying to save ROI's. This happens after I draw an ROI and click the save button. Then a dialog (ROI File Format) comes up giving a choice of different formats. I choose Graphic Compatible (default). After clicking OK, a crash window comes up a few seconds later. It is labeled MriView3D MFC application. The only technical information I can find is the following. AppName: dtistudio-latest-x86.exe AppVer: 1.0.0.1 ModName: msvcr80.dll ModVer: 8.0.50727.4053 Offset: 00014458 This occurs whether I have drawn 1 or more ROIs. (fixed size ROI, oval). The size of the ROI does not matter (4 voxel or 10 voxel) It occurs with DTI studio x86 and x64. It occurs with versions 3.0.2 and 2.4.1 of DTIstudio. It occurs whether I have a complete dataset loaded 35 directions, or even if I load just 1 image and draw an ROI on it. It occurs on an HP core duo 2 system running Windows XP SP3, and on a redhat linux KVM virtual machine running windows XP x64. Reinstalling vcredist_x86 or vcredist_x64 from the DTIstudio website does not help on any of the systems. Any suggestions on how to fix? Darren _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100714/82654bf3/attachment-0001.html From salvador.castaneda at med.uni-tuebingen.de Wed Jul 14 07:09:06 2010 From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador) Date: Wed, 14 Jul 2010 13:09:06 +0200 Subject: [Mristudio-users] crash when saving ROI's In-Reply-To: <0AC64F4CB253074799B64FF8F0772D350126C603@azex2003.raddiag.med.uni-tuebingen.de> References: <0AC64F4CB253074799B64FF8F0772D350126C603@azex2003.raddiag.med.uni-tuebingen.de> Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C604@azex2003.raddiag.med.uni-tuebingen.de> SC Sorry again, Do you know if there is such a big difference between the mutual image registration and the automatic. And what exactly does this do just improve the quality of the image all together or what? thanks in advanced Salvador Castaneda ________________________________ Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von Castaneda, Salvador Gesendet: Mittwoch, 14. Juli 2010 12:14 An: DTI Studio, ROI Editor,DiffeoMap Questions/Support Betreff: Re: [Mristudio-users] crash when saving ROI's SC Thats exactly what i do, i take the image files from dtistudio and load them in the roi editor. i wanted to upload an anatomical picture to better draw y rois because i work with rats. is it possible to dothis even if the matrix and fov are not the same? thanks ________________________________ Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von [Seongjin] Gesendet: Mittwoch, 14. Juli 2010 01:45 An: DTI Studio, ROI Editor, DiffeoMap Questions/Support Betreff: Re: [Mristudio-users] crash when saving ROI's Darren, I experienced the similar problem. I wanted to use ROI drawn in ROI panel but it did not work at all. ROI saving and loading functions seem to work in FIBER panel, but not in the ROI panel. If you want to use ROI for DTI metrics such as FA or ADC measurements, I recommend ROIeditor (a companion tool to DTIstudio). That is more powerful. I always process data in DTI studio. Then load all the processed data into ROI editor. Finally, do the measurement with ROI editor. The saved ROIs can be reused in the DTI studio for fiber tracking. However, again, the ROIs could not be used in ROI panel of the DTI studio on my computers (home computer, laptop, and office computer). I hope this experience might be a bit of help for your problem in using DTI studio. -SC On Tue, Jul 13, 2010 at 5:28 PM, Darren Gitelman wrote: Hi I am having problems with DTI studio crashing when trying to save ROI's. This happens after I draw an ROI and click the save button. Then a dialog (ROI File Format) comes up giving a choice of different formats. I choose Graphic Compatible (default). After clicking OK, a crash window comes up a few seconds later. It is labeled MriView3D MFC application. The only technical information I can find is the following. AppName: dtistudio-latest-x86.exe AppVer: 1.0.0.1 ModName: msvcr80.dll ModVer: 8.0.50727.4053 Offset: 00014458 This occurs whether I have drawn 1 or more ROIs. (fixed size ROI, oval). The size of the ROI does not matter (4 voxel or 10 voxel) It occurs with DTI studio x86 and x64. It occurs with versions 3.0.2 and 2.4.1 of DTIstudio. It occurs whether I have a complete dataset loaded 35 directions, or even if I load just 1 image and draw an ROI on it. It occurs on an HP core duo 2 system running Windows XP SP3, and on a redhat linux KVM virtual machine running windows XP x64. Reinstalling vcredist_x86 or vcredist_x64 from the DTIstudio website does not help on any of the systems. Any suggestions on how to fix? Darren _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100714/6ad874c9/attachment.html From choisj70 at gmail.com Wed Jul 14 08:47:13 2010 From: choisj70 at gmail.com (Seongjin) Date: Wed, 14 Jul 2010 08:47:13 -0400 Subject: [Mristudio-users] crash when saving ROI's In-Reply-To: <0AC64F4CB253074799B64FF8F0772D350126C604@azex2003.raddiag.med.uni-tuebingen.de> References: <0AC64F4CB253074799B64FF8F0772D350126C603@azex2003.raddiag.med.uni-tuebingen.de> <0AC64F4CB253074799B64FF8F0772D350126C604@azex2003.raddiag.med.uni-tuebingen.de> Message-ID: Salvador, What I know about difference between AIR and Mutual info based (MUT) registration, AIR is somewhat sensitive to noise level and has more options to be determined. What I heard from developer group about the noise level in AIR is that the noise level should be determined by empirical way. And it has more options for fitting methods. But which one works better, you should decide after a couple of trial and errors. MUT has less option to be determined by user. MUT is based on information entropy maximization as far as I know. It is one of the good registration methods. But I have no idea about which one is better between AIR or MUT. I prefer to use MUT because less user options, which means it is more automatic. At least, I don't need to play with it to find a proper noise level for AIR. Best, -SC On Wed, Jul 14, 2010 at 7:09 AM, Castaneda, Salvador < salvador.castaneda at med.uni-tuebingen.de> wrote: > SC > > Sorry again, Do you know if there is such a big difference between the > mutual image registration and the automatic. And what exactly does this do > just improve the quality of the image all together or what? > thanks in advanced > > Salvador Castaneda > > ------------------------------ > *Von:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *Im Auftrag von *Castaneda, > Salvador > *Gesendet:* Mittwoch, 14. Juli 2010 12:14 > > *An:* DTI Studio, ROI Editor,DiffeoMap Questions/Support > *Betreff:* Re: [Mristudio-users] crash when saving ROI's > > SC > > Thats exactly what i do, i take the image files from dtistudio and load > them in the roi editor. i wanted to upload an anatomical picture to better > draw y rois because i work with rats. is it possible to dothis even if the > matrix and fov are not the same? > thanks > > > ------------------------------ > *Von:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *Im Auftrag von *[Seongjin] > *Gesendet:* Mittwoch, 14. Juli 2010 01:45 > *An:* DTI Studio, ROI Editor, DiffeoMap Questions/Support > *Betreff:* Re: [Mristudio-users] crash when saving ROI's > > Darren, > > I experienced the similar problem. I wanted to use ROI drawn in ROI panel > but it did not work at all. ROI saving and loading functions seem to work in > FIBER panel, but not in the ROI panel. > > If you want to use ROI for DTI metrics such as FA or ADC measurements, I > recommend ROIeditor (a companion tool to DTIstudio). That is more powerful. > > I always process data in DTI studio. Then load all the processed data into > ROI editor. > Finally, do the measurement with ROI editor. > > The saved ROIs can be reused in the DTI studio for fiber tracking. However, > again, the ROIs could not be used in ROI panel of the DTI studio on my > computers (home computer, laptop, and office computer). > > I hope this experience might be a bit of help for your problem in using DTI > studio. > > -SC > > On Tue, Jul 13, 2010 at 5:28 PM, Darren Gitelman < > d-gitelman at northwestern.edu> wrote: > >> Hi >> >> I am having problems with DTI studio crashing when trying to save ROI's. >> >> This happens after I draw an ROI and click the save button. Then a dialog >> (ROI File Format) comes up giving a choice of different formats. I choose >> Graphic Compatible (default). After clicking OK, a crash window comes up a >> few seconds later. It is labeled MriView3D MFC application. The only >> technical information I can find is the following. >> >> AppName: dtistudio-latest-x86.exe AppVer: 1.0.0.1 ModName: >> msvcr80.dll >> ModVer: 8.0.50727.4053 Offset: 00014458 >> >> This occurs whether I have drawn 1 or more ROIs. (fixed size ROI, oval). >> The size of the ROI does not matter (4 voxel or 10 voxel) >> It occurs with DTI studio x86 and x64. >> It occurs with versions 3.0.2 and 2.4.1 of DTIstudio. >> It occurs whether I have a complete dataset loaded 35 directions, or even >> if I load just 1 image and draw an ROI on it. >> It occurs on an HP core duo 2 system running Windows XP SP3, and on a >> redhat linux KVM virtual machine running windows XP x64. >> Reinstalling vcredist_x86 or vcredist_x64 from the DTIstudio website does >> not help on any of the systems. >> >> Any suggestions on how to fix? >> >> Darren >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100714/c0e2f207/attachment.html From azhang at psych.uic.edu Wed Jul 14 13:02:47 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Wed, 14 Jul 2010 12:02:47 -0500 Subject: [Mristudio-users] Mutual-info registration error In-Reply-To: References: <561163.39347.qm@web25605.mail.ukl.yahoo.com> Message-ID: <40469184F1D86344A835AB980269681A16969FC8CD@exchange.psych.uic.edu> Hi DTIStudio, When I try to use mutual-information registration, sometimes error pops up saying "RegImgFile.tmp was not found". Could you please let me know what is that file for and how to proceed with the registration? thanks! Aifeng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100714/1b853050/attachment-0001.html From gmak at poczta.onet.pl Thu Jul 15 11:55:57 2010 From: gmak at poczta.onet.pl (gmak at poczta.onet.pl) Date: Thu, 15 Jul 2010 17:55:57 +0200 Subject: [Mristudio-users] Thanks for your help Message-ID: <5AA88B54CA0C41C1839040FC4E70C5B0@zxzPC> Thanks for your help ! Thanks everyone for sending me the Air files. You are great ;-) Best regards Grzesiek -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100715/0d6d3784/attachment.html From salvador.castaneda at med.uni-tuebingen.de Thu Jul 15 04:42:00 2010 From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador) Date: Thu, 15 Jul 2010 10:42:00 +0200 Subject: [Mristudio-users] crash when saving ROI's In-Reply-To: References: <0AC64F4CB253074799B64FF8F0772D350126C603@azex2003.raddiag.med.uni-tuebingen.de> <0AC64F4CB253074799B64FF8F0772D350126C604@azex2003.raddiag.med.uni-tuebingen.de> Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C605@azex2003.raddiag.med.uni-tuebingen.de> SC So that sounds good... i am using AIR though because the MUT doesnt do anything it gets stuck.... So i am using AIR and 90 for noise reduction because i heard that's what you have to use for siemens machines.... also affine. tri linear interpolation and standard derivation. So im just changing the affine and the 90 noise reduction. The images look ok... bu then again i cant compare it to the MUT because i cant use it. SC, dont you find it troublesome that when you draw the ROIS in ROIeditor, the roi selected isnt really what the selection ends up to be? I mean When you are selecting your pixels and then choose to add as an object, the object you make is not exactly what you had chosen. Is there anyway to fix this? i tried reducing the pencil diameter or doing a fill in the roi and then adding but it always looks kinda crappy... it's still better than picking the ROIS from dtistudio though... I also heard that you can edit your rois importing the images from Dtistudio into ImageJ but i dont know how to do this. Maybe i would try it because in there you can import the anatomy sequences to draw your rois on top of them. anyway, any input in any of these inquiries would be helpful! best regards Salvador ________________________________ Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von [Seongjin] Gesendet: Mittwoch, 14. Juli 2010 14:47 An: DTI Studio, ROI Editor, DiffeoMap Questions/Support Betreff: Re: [Mristudio-users] crash when saving ROI's Salvador, What I know about difference between AIR and Mutual info based (MUT) registration, AIR is somewhat sensitive to noise level and has more options to be determined. What I heard from developer group about the noise level in AIR is that the noise level should be determined by empirical way. And it has more options for fitting methods. But which one works better, you should decide after a couple of trial and errors. MUT has less option to be determined by user. MUT is based on information entropy maximization as far as I know. It is one of the good registration methods. But I have no idea about which one is better between AIR or MUT. I prefer to use MUT because less user options, which means it is more automatic. At least, I don't need to play with it to find a proper noise level for AIR. Best, -SC On Wed, Jul 14, 2010 at 7:09 AM, Castaneda, Salvador wrote: SC Sorry again, Do you know if there is such a big difference between the mutual image registration and the automatic. And what exactly does this do just improve the quality of the image all together or what? thanks in advanced Salvador Castaneda ________________________________ Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von Castaneda, Salvador Gesendet: Mittwoch, 14. Juli 2010 12:14 An: DTI Studio, ROI Editor,DiffeoMap Questions/Support Betreff: Re: [Mristudio-users] crash when saving ROI's SC Thats exactly what i do, i take the image files from dtistudio and load them in the roi editor. i wanted to upload an anatomical picture to better draw y rois because i work with rats. is it possible to dothis even if the matrix and fov are not the same? thanks ________________________________ Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von [Seongjin] Gesendet: Mittwoch, 14. Juli 2010 01:45 An: DTI Studio, ROI Editor, DiffeoMap Questions/Support Betreff: Re: [Mristudio-users] crash when saving ROI's Darren, I experienced the similar problem. I wanted to use ROI drawn in ROI panel but it did not work at all. ROI saving and loading functions seem to work in FIBER panel, but not in the ROI panel. If you want to use ROI for DTI metrics such as FA or ADC measurements, I recommend ROIeditor (a companion tool to DTIstudio). That is more powerful. I always process data in DTI studio. Then load all the processed data into ROI editor. Finally, do the measurement with ROI editor. The saved ROIs can be reused in the DTI studio for fiber tracking. However, again, the ROIs could not be used in ROI panel of the DTI studio on my computers (home computer, laptop, and office computer). I hope this experience might be a bit of help for your problem in using DTI studio. -SC On Tue, Jul 13, 2010 at 5:28 PM, Darren Gitelman wrote: Hi I am having problems with DTI studio crashing when trying to save ROI's. This happens after I draw an ROI and click the save button. Then a dialog (ROI File Format) comes up giving a choice of different formats. I choose Graphic Compatible (default). After clicking OK, a crash window comes up a few seconds later. It is labeled MriView3D MFC application. The only technical information I can find is the following. AppName: dtistudio-latest-x86.exe AppVer: 1.0.0.1 ModName: msvcr80.dll ModVer: 8.0.50727.4053 Offset: 00014458 This occurs whether I have drawn 1 or more ROIs. (fixed size ROI, oval). The size of the ROI does not matter (4 voxel or 10 voxel) It occurs with DTI studio x86 and x64. It occurs with versions 3.0.2 and 2.4.1 of DTIstudio. It occurs whether I have a complete dataset loaded 35 directions, or even if I load just 1 image and draw an ROI on it. It occurs on an HP core duo 2 system running Windows XP SP3, and on a redhat linux KVM virtual machine running windows XP x64. Reinstalling vcredist_x86 or vcredist_x64 from the DTIstudio website does not help on any of the systems. Any suggestions on how to fix? Darren _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100715/9d119c47/attachment.html From bhaas at stanford.edu Thu Jul 15 17:58:46 2010 From: bhaas at stanford.edu (Brian W. Haas) Date: Thu, 15 Jul 2010 14:58:46 -0700 (PDT) Subject: [Mristudio-users] Using "and" with imported ROIs in DTIstudio Message-ID: <88657818.77554.1279231126160.JavaMail.root@zm07.stanford.edu> Hello DTIstudio users, I am interested in tracking fibers between two ROIs. These two rois have been drawn in a different program and then converted to a binary image to be used in DTI studio. I can use each ROI individually to track fibers that project from it (using "or" function). However, if I then select "and" and then import a second ROI, the "and" function does not work. Specifically, it will import the second ROI and track the fibers projecting from it but disregard the first ROI completely. My understanding, is that DTIstudio can only import a single ROI onto the work space and only import it using the "or" function. Is this correct? If this is not the case, can someone explain how I can track fibers between two imported ROIs? Alternatively, does anyone possibly have a handy work around? thank you very much for your time! Brian -- Brian W. Haas, Ph.D. Center for Interdisciplinary Brain Sciences Research //cibsr.stanford.edu/ //med.stanford.edu/profiles/Brian_Haas/ From choisj70 at gmail.com Thu Jul 15 20:27:35 2010 From: choisj70 at gmail.com (Seongjin) Date: Thu, 15 Jul 2010 20:27:35 -0400 Subject: [Mristudio-users] crash when saving ROI's In-Reply-To: <0AC64F4CB253074799B64FF8F0772D350126C605@azex2003.raddiag.med.uni-tuebingen.de> References: <0AC64F4CB253074799B64FF8F0772D350126C603@azex2003.raddiag.med.uni-tuebingen.de> <0AC64F4CB253074799B64FF8F0772D350126C604@azex2003.raddiag.med.uni-tuebingen.de> <0AC64F4CB253074799B64FF8F0772D350126C605@azex2003.raddiag.med.uni-tuebingen.de> Message-ID: Salvador, Your mouse pointer position is not the center of your ROI. It is top-left corner of your ROI. There is 4-arrow buttons (named move ROI) right-lower part of the ROI editor control panel. Adjust your ROI with the buttons. ROI will move by one pixel unit. The drawn ROI will be pixelized. So if you draw a circular ROI it will have pixelized boundary. For the small ROI, rectangular shape will make more sense. You can define the ROI dimensions (width and hight) with option "fixed size". If you fixed the ROI to the object, the arrow button will not work. Make your that you move the ROI location before pressing the add button. I am not aware of ROI importing between DTI studio and ImageJ, Best, -SC On Thu, Jul 15, 2010 at 4:42 AM, Castaneda, Salvador < salvador.castaneda at med.uni-tuebingen.de> wrote: > SC > > So that sounds good... i am using AIR though because the MUT doesnt do > anything it gets stuck.... So i am using AIR and 90 for noise reduction > because i heard that's what you have to use for siemens machines.... also > affine. tri linear interpolation and standard derivation. So im just > changing the affine and the 90 noise reduction. The images look ok... bu > then again i cant compare it to the MUT because i cant use it. SC, dont you > find it troublesome that when you draw the ROIS in ROIeditor, the roi > selected isnt really what the selection ends up to be? I mean When you are > selecting your pixels and then choose to add as an object, the object you > make is not exactly what you had chosen. Is there anyway to fix this? i > tried reducing the pencil diameter or doing a fill in the roi and then > adding but it always looks kinda crappy... it's still better than picking > the ROIS from dtistudio though... I also heard that you can edit your rois > importing the images from Dtistudio into ImageJ but i dont know how to do > this. Maybe i would try it because in there you can import the anatomy > sequences to draw your rois on top of them. > anyway, any input in any of these inquiries would be helpful! > > best regards > > Salvador > > ------------------------------ > *Von:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *Im Auftrag von *[Seongjin] > *Gesendet:* Mittwoch, 14. Juli 2010 14:47 > > *An:* DTI Studio, ROI Editor, DiffeoMap Questions/Support > *Betreff:* Re: [Mristudio-users] crash when saving ROI's > > Salvador, > > What I know about difference between AIR and Mutual info based (MUT) > registration, AIR is somewhat sensitive to noise level and has more options > to be determined. What I heard from developer group about the noise level in > AIR is that the noise level should be determined by empirical way. And it > has more options for fitting methods. But which one works better, you should > decide after a couple of trial and errors. > MUT has less option to be determined by user. MUT is based on information > entropy maximization as far as I know. It is one of the good registration > methods. But I have no idea about which one is better between AIR or MUT. I > prefer to use MUT because less user options, which means it is more > automatic. At least, I don't need to play with it to find a proper noise > level for AIR. > > Best, > -SC > > On Wed, Jul 14, 2010 at 7:09 AM, Castaneda, Salvador < > salvador.castaneda at med.uni-tuebingen.de> wrote: > >> SC >> >> Sorry again, Do you know if there is such a big difference between the >> mutual image registration and the automatic. And what exactly does this do >> just improve the quality of the image all together or what? >> thanks in advanced >> >> Salvador Castaneda >> >> ------------------------------ >> *Von:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *Im Auftrag von *Castaneda, >> Salvador >> *Gesendet:* Mittwoch, 14. Juli 2010 12:14 >> >> *An:* DTI Studio, ROI Editor,DiffeoMap Questions/Support >> *Betreff:* Re: [Mristudio-users] crash when saving ROI's >> >> SC >> >> Thats exactly what i do, i take the image files from dtistudio and load >> them in the roi editor. i wanted to upload an anatomical picture to better >> draw y rois because i work with rats. is it possible to dothis even if the >> matrix and fov are not the same? >> thanks >> >> >> ------------------------------ >> *Von:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *Im Auftrag von *[Seongjin] >> *Gesendet:* Mittwoch, 14. Juli 2010 01:45 >> *An:* DTI Studio, ROI Editor, DiffeoMap Questions/Support >> *Betreff:* Re: [Mristudio-users] crash when saving ROI's >> >> Darren, >> >> I experienced the similar problem. I wanted to use ROI drawn in ROI panel >> but it did not work at all. ROI saving and loading functions seem to work in >> FIBER panel, but not in the ROI panel. >> >> If you want to use ROI for DTI metrics such as FA or ADC measurements, I >> recommend ROIeditor (a companion tool to DTIstudio). That is more powerful. >> >> I always process data in DTI studio. Then load all the processed data into >> ROI editor. >> Finally, do the measurement with ROI editor. >> >> The saved ROIs can be reused in the DTI studio for fiber tracking. >> However, again, the ROIs could not be used in ROI panel of the DTI studio on >> my computers (home computer, laptop, and office computer). >> >> I hope this experience might be a bit of help for your problem in using >> DTI studio. >> >> -SC >> >> On Tue, Jul 13, 2010 at 5:28 PM, Darren Gitelman < >> d-gitelman at northwestern.edu> wrote: >> >>> Hi >>> >>> I am having problems with DTI studio crashing when trying to save ROI's. >>> >>> This happens after I draw an ROI and click the save button. Then a dialog >>> (ROI File Format) comes up giving a choice of different formats. I choose >>> Graphic Compatible (default). After clicking OK, a crash window comes up a >>> few seconds later. It is labeled MriView3D MFC application. The only >>> technical information I can find is the following. >>> >>> AppName: dtistudio-latest-x86.exe AppVer: 1.0.0.1 ModName: >>> msvcr80.dll >>> ModVer: 8.0.50727.4053 Offset: 00014458 >>> >>> This occurs whether I have drawn 1 or more ROIs. (fixed size ROI, oval). >>> The size of the ROI does not matter (4 voxel or 10 voxel) >>> It occurs with DTI studio x86 and x64. >>> It occurs with versions 3.0.2 and 2.4.1 of DTIstudio. >>> It occurs whether I have a complete dataset loaded 35 directions, or even >>> if I load just 1 image and draw an ROI on it. >>> It occurs on an HP core duo 2 system running Windows XP SP3, and on a >>> redhat linux KVM virtual machine running windows XP x64. >>> Reinstalling vcredist_x86 or vcredist_x64 from the DTIstudio website does >>> not help on any of the systems. >>> >>> Any suggestions on how to fix? >>> >>> Darren >>> >>> _______________________________________________ >>> mristudio-users mailing list >>> mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100715/160f10a1/attachment-0001.html From jmcentee at jhmi.edu Fri Jul 16 00:40:21 2010 From: jmcentee at jhmi.edu (Julie E McEntee) Date: Fri, 16 Jul 2010 00:40:21 -0400 Subject: [Mristudio-users] Using "and" with imported ROIs in DTIstudio In-Reply-To: <88657818.77554.1279231126160.JavaMail.root@zm07.stanford.edu> References: <88657818.77554.1279231126160.JavaMail.root@zm07.stanford.edu> Message-ID: <7120b2391d361.4c3faa75@johnshopkins.edu> Try this bit of code provided to our lab by Kenishi Oishi. I believe a similar .txt file can also be created as explained in FAQ #16 on MRIStudio web site. This particular code/.txt file track-traces between 2 ROIs, in this case created in ROIEditor and saved as ROI, binary map format (when loaded into DtiStudio, binary image format). Just have to change paths in .txt file to location of your ROIs; after fiber-tracking in DtiStudio, under Fiber tab, open .txt file as you would an ROI, binary image format. See bottom of .txt file for definitions of parameters in the code to change options or track-tracing procedure. Hope this helps, Julie Julie E. McEntee, M.A., C.C.R.P. Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./ Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676 ----- Original Message ----- From: "Brian W. Haas" Date: Thursday, July 15, 2010 5:59 pm Subject: [Mristudio-users] Using "and" with imported ROIs in DTIstudio To: mristudio-users at mristudio.org > Hello DTIstudio users, > I am interested in tracking fibers between two ROIs. These two > rois have been drawn in a different program and then converted to a > binary image to be used in DTI studio. I can use each ROI > individually to track fibers that project from it (using "or" > function). However, if I then select "and" and then import a second > ROI, the "and" function does not work. Specifically, it will import > the second ROI and track the fibers projecting from it but disregard > the first ROI completely. My understanding, is that DTIstudio can > only import a single ROI onto the work space and only import it using > the "or" function. Is this correct? If this is not the case, can > someone explain how I can track fibers between two imported ROIs? > Alternatively, does anyone possibly have a handy work around? thank > you very much for your time! Brian > > > > -- > Brian W. Haas, Ph.D. > Center for Interdisciplinary Brain Sciences Research > //cibsr.stanford.edu/ > //med.stanford.edu/profiles/Brian_Haas/ > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: L_frontal_to_L_thalamus_MNI.map.txt Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100716/3a22fd11/attachment.txt From jamike_408 at hotmail.com Fri Jul 16 10:37:07 2010 From: jamike_408 at hotmail.com (michael brown) Date: Fri, 16 Jul 2010 14:37:07 +0000 Subject: [Mristudio-users] bruker dicom Message-ID: Hi there my name is Mike Brown, I'm very new to DTI studio. I would like to ask would DTI support images from a bruker dicom. many thanks Mike _________________________________________________________________ http://clk.atdmt.com/UKM/go/195013117/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100716/56c08af3/attachment.html From shereeda at mail.uc.edu Fri Jul 16 12:22:27 2010 From: shereeda at mail.uc.edu (Shereen, Ahmed (shereeda)) Date: Fri, 16 Jul 2010 16:22:27 +0000 Subject: [Mristudio-users] bruker dicom In-Reply-To: References: Message-ID: <77168E3AAEA5744E88FAECF91EA545FB1B7A28A1@BL2PRD0103MB059.prod.exchangelabs.com> Hello Mike Brown, I've not tried using Bruker dicom, but do know that DTI studio will read the Bruker 2dseq files as Philips raw data. ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of michael brown [jamike_408 at hotmail.com] Sent: Friday, July 16, 2010 10:37 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] bruker dicom Hi there my name is Mike Brown, I'm very new to DTI studio. I would like to ask would DTI support images from a bruker dicom. many thanks Mike ________________________________ Get a free e-mail account with Hotmail. Sign-up now. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100716/ac69aa57/attachment.html From susumu at mri.jhu.edu Fri Jul 16 20:20:55 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 16 Jul 2010 20:20:55 -0400 Subject: [Mristudio-users] bruker dicom In-Reply-To: <77168E3AAEA5744E88FAECF91EA545FB1B7A28A1@BL2PRD0103MB059.prod.exchangelabs.com> References: <77168E3AAEA5744E88FAECF91EA545FB1B7A28A1@BL2PRD0103MB059.prod.exchangelabs.com> Message-ID: Does Bruker have DICOM? As Ahmed mentioned, DtiStudio can read raw 2dseq. If you need to read DICOM and none of the existing DICOM readers in DtiStudio can't read it, please let us know. Susumu On Fri, Jul 16, 2010 at 12:22 PM, Shereen, Ahmed (shereeda) < shereeda at mail.uc.edu> wrote: > Hello Mike Brown, > I've not tried using Bruker dicom, but do know that DTI studio will read > the Bruker 2dseq files as Philips raw data. > > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] on behalf of michael brown [ > jamike_408 at hotmail.com] > *Sent:* Friday, July 16, 2010 10:37 AM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] bruker dicom > > Hi there my name is Mike Brown, > I'm very new to DTI studio. I would like to ask would DTI support images > from a bruker dicom. > many thanks > Mike > > ------------------------------ > Get a free e-mail account with Hotmail. Sign-up now. > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100716/30bc373c/attachment.html From susumu at mri.jhu.edu Fri Jul 16 21:12:14 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 16 Jul 2010 21:12:14 -0400 Subject: [Mristudio-users] crash when saving ROI's In-Reply-To: References: <0AC64F4CB253074799B64FF8F0772D350126C603@azex2003.raddiag.med.uni-tuebingen.de> <0AC64F4CB253074799B64FF8F0772D350126C604@azex2003.raddiag.med.uni-tuebingen.de> <0AC64F4CB253074799B64FF8F0772D350126C605@azex2003.raddiag.med.uni-tuebingen.de> Message-ID: Hi all, Thanks SC to follow the question. I just want to add several points; 1) We are looking into the way RoiEditor draws ROI and hope we can improve the interface. 2) Please note that one of the reason of jagged ROIs in RoiEditor is due to pixel resolution. The ROIs are drawn based on monitor resolution, which is very high and you can draw smooth ROIs. However, when the drawn ROIs are translated into actual ROIs in the images, they have to be converted to image pixel-dimension. This could be one of the reasons why the final ROIs do not look as good. 3) If you have two images, such as anatomical T1/T2 and DTI, which are not co-registered and you want to register them, you can try DiffeoMap. There are two approaches. For animal studies in which you can assume that the head position is stable, you can register them theoretically based on scan parameters such as the locations and sizes of FOV. DiffeoMap has functions to resize and relocate FOV and matrix. If you can't use this approach for some reason, you can use the AIR/MUT options. 4) DtiStudio also has image registration functions, but they are for intra-DTI image registration. If you want cross-modality (e.g. T1 vs DTI) registration, you need to use DiffeoMap. 5) MUT tends to be more accurate and less sensitive to parameters. However, it takes much longer time. Typical 30-orientation DTI may take overnight. If you are using it for cross-modality registration just for 1 image, you should get results within 30 min or so. On Thu, Jul 15, 2010 at 8:27 PM, [Seongjin] wrote: > Salvador, > > Your mouse pointer position is not the center of your ROI. It is top-left > corner of your ROI. There is 4-arrow buttons (named move ROI) right-lower > part of the ROI editor control panel. Adjust your ROI with the buttons. ROI > will move by one pixel unit. > The drawn ROI will be pixelized. So if you draw a circular ROI it will have > pixelized boundary. For the small ROI, rectangular shape will make more > sense. You can define the ROI dimensions (width and hight) with option > "fixed size". > If you fixed the ROI to the object, the arrow button will not work. > Make your that you move the ROI location before pressing the add button. > > I am not aware of ROI importing between DTI studio and ImageJ, > > Best, > -SC > > On Thu, Jul 15, 2010 at 4:42 AM, Castaneda, Salvador < > salvador.castaneda at med.uni-tuebingen.de> wrote: > >> SC >> >> So that sounds good... i am using AIR though because the MUT doesnt do >> anything it gets stuck.... So i am using AIR and 90 for noise reduction >> because i heard that's what you have to use for siemens machines.... also >> affine. tri linear interpolation and standard derivation. So im just >> changing the affine and the 90 noise reduction. The images look ok... bu >> then again i cant compare it to the MUT because i cant use it. SC, dont you >> find it troublesome that when you draw the ROIS in ROIeditor, the roi >> selected isnt really what the selection ends up to be? I mean When you are >> selecting your pixels and then choose to add as an object, the object you >> make is not exactly what you had chosen. Is there anyway to fix this? i >> tried reducing the pencil diameter or doing a fill in the roi and then >> adding but it always looks kinda crappy... it's still better than picking >> the ROIS from dtistudio though... I also heard that you can edit your rois >> importing the images from Dtistudio into ImageJ but i dont know how to do >> this. Maybe i would try it because in there you can import the anatomy >> sequences to draw your rois on top of them. >> anyway, any input in any of these inquiries would be helpful! >> >> best regards >> >> Salvador >> >> ------------------------------ >> *Von:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *Im Auftrag von *[Seongjin] >> *Gesendet:* Mittwoch, 14. Juli 2010 14:47 >> >> *An:* DTI Studio, ROI Editor, DiffeoMap Questions/Support >> *Betreff:* Re: [Mristudio-users] crash when saving ROI's >> >> Salvador, >> >> What I know about difference between AIR and Mutual info based (MUT) >> registration, AIR is somewhat sensitive to noise level and has more options >> to be determined. What I heard from developer group about the noise level in >> AIR is that the noise level should be determined by empirical way. And it >> has more options for fitting methods. But which one works better, you should >> decide after a couple of trial and errors. >> MUT has less option to be determined by user. MUT is based on information >> entropy maximization as far as I know. It is one of the good registration >> methods. But I have no idea about which one is better between AIR or MUT. I >> prefer to use MUT because less user options, which means it is more >> automatic. At least, I don't need to play with it to find a proper noise >> level for AIR. >> >> Best, >> -SC >> >> On Wed, Jul 14, 2010 at 7:09 AM, Castaneda, Salvador < >> salvador.castaneda at med.uni-tuebingen.de> wrote: >> >>> SC >>> >>> Sorry again, Do you know if there is such a big difference between the >>> mutual image registration and the automatic. And what exactly does this do >>> just improve the quality of the image all together or what? >>> thanks in advanced >>> >>> Salvador Castaneda >>> >>> ------------------------------ >>> *Von:* mristudio-users-bounces at mristudio.org [mailto: >>> mristudio-users-bounces at mristudio.org] *Im Auftrag von *Castaneda, >>> Salvador >>> *Gesendet:* Mittwoch, 14. Juli 2010 12:14 >>> >>> *An:* DTI Studio, ROI Editor,DiffeoMap Questions/Support >>> *Betreff:* Re: [Mristudio-users] crash when saving ROI's >>> >>> SC >>> >>> Thats exactly what i do, i take the image files from dtistudio and load >>> them in the roi editor. i wanted to upload an anatomical picture to better >>> draw y rois because i work with rats. is it possible to dothis even if the >>> matrix and fov are not the same? >>> thanks >>> >>> >>> ------------------------------ >>> *Von:* mristudio-users-bounces at mristudio.org [mailto: >>> mristudio-users-bounces at mristudio.org] *Im Auftrag von *[Seongjin] >>> *Gesendet:* Mittwoch, 14. Juli 2010 01:45 >>> *An:* DTI Studio, ROI Editor, DiffeoMap Questions/Support >>> *Betreff:* Re: [Mristudio-users] crash when saving ROI's >>> >>> Darren, >>> >>> I experienced the similar problem. I wanted to use ROI drawn in ROI panel >>> but it did not work at all. ROI saving and loading functions seem to work in >>> FIBER panel, but not in the ROI panel. >>> >>> If you want to use ROI for DTI metrics such as FA or ADC measurements, I >>> recommend ROIeditor (a companion tool to DTIstudio). That is more powerful. >>> >>> I always process data in DTI studio. Then load all the processed data >>> into ROI editor. >>> Finally, do the measurement with ROI editor. >>> >>> The saved ROIs can be reused in the DTI studio for fiber tracking. >>> However, again, the ROIs could not be used in ROI panel of the DTI studio on >>> my computers (home computer, laptop, and office computer). >>> >>> I hope this experience might be a bit of help for your problem in using >>> DTI studio. >>> >>> -SC >>> >>> On Tue, Jul 13, 2010 at 5:28 PM, Darren Gitelman < >>> d-gitelman at northwestern.edu> wrote: >>> >>>> Hi >>>> >>>> I am having problems with DTI studio crashing when trying to save ROI's. >>>> >>>> >>>> This happens after I draw an ROI and click the save button. Then a >>>> dialog (ROI File Format) comes up giving a choice of different formats. I >>>> choose Graphic Compatible (default). After clicking OK, a crash window comes >>>> up a few seconds later. It is labeled MriView3D MFC application. The only >>>> technical information I can find is the following. >>>> >>>> AppName: dtistudio-latest-x86.exe AppVer: 1.0.0.1 ModName: >>>> msvcr80.dll >>>> ModVer: 8.0.50727.4053 Offset: 00014458 >>>> >>>> This occurs whether I have drawn 1 or more ROIs. (fixed size ROI, oval). >>>> The size of the ROI does not matter (4 voxel or 10 voxel) >>>> It occurs with DTI studio x86 and x64. >>>> It occurs with versions 3.0.2 and 2.4.1 of DTIstudio. >>>> It occurs whether I have a complete dataset loaded 35 directions, or >>>> even if I load just 1 image and draw an ROI on it. >>>> It occurs on an HP core duo 2 system running Windows XP SP3, and on a >>>> redhat linux KVM virtual machine running windows XP x64. >>>> Reinstalling vcredist_x86 or vcredist_x64 from the DTIstudio website >>>> does not help on any of the systems. >>>> >>>> Any suggestions on how to fix? >>>> >>>> Darren >>>> >>>> _______________________________________________ >>>> mristudio-users mailing list >>>> mristudio-users at mristudio.org >>>> http://lists.mristudio.org/mailman/listinfo/ >>>> Unsubscribe, send a blank email to: >>>> mristudio-users-unsubscribe at mristudio.org >>>> >>>> >>> >>> _______________________________________________ >>> mristudio-users mailing list >>> mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100716/fd2dce48/attachment-0001.html From susumu at mri.jhu.edu Fri Jul 16 21:36:55 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 16 Jul 2010 21:36:55 -0400 Subject: [Mristudio-users] Co-Register and Normalize In-Reply-To: References: Message-ID: please also see https://www.mristudio.org/wiki/user_manual/diffeomap to learn functionality of DiffeoMap. On Tue, Jul 13, 2010 at 7:59 PM, [Seongjin] wrote: > It should be Diffeomap. > It provides you with various ATLAS images, templates, and normalization > functionality. > > -SC > > > On Tue, Jul 13, 2010 at 9:51 AM, Duggal Lab DTI wrote: > >> Hello, >> >> I was wondering if there is a way to co-register the ADC or FA maps with >> T1 images in DTI Studio? Also, can they then be normalized to a standard >> brain in the program as well? If DTI Studio can do this how is it done? If >> not, are there any suggestions for programs to use for this to completment >> DTI Studio? Thank you for your help, take care, >> >> Stuart >> >> ------------------------------ >> Your Photo on Bing.ca: You Could WIN on Canada Day! Submit a Photo Now! >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100716/23149bba/attachment.html From susumu at mri.jhu.edu Fri Jul 16 21:45:19 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 16 Jul 2010 21:45:19 -0400 Subject: [Mristudio-users] using T1 image for ROI drawing In-Reply-To: <40469184F1D86344A835AB980269681A16969FC3ED@exchange.psych.uic.edu> References: <80624c29c8a6539a4@wm-srv.ulb.ac.be> <40469184F1D86344A835AB980269681A16969FC2A1@exchange.psych.uic.edu> <40469184F1D86344A835AB980269681A16969FC2A6@exchange.psych.uic.edu> <40469184F1D86344A835AB980269681A16969FC3ED@exchange.psych.uic.edu> Message-ID: Hi Aifeng, As I mentioned in another thread, AIR/MUT in DtiStudio is designed for intra-DTI motion correction. Suppose you have 1 b0 and 30 DWIs, all DWIs can be registered to the b0. In your case, you want to do cross-modality (T1 vs DTI) registration. I recommend you to use DiffeoMap for that purpose. This program is designed for intra-subject cross-modality (the same person, different scans) or inter-subject image registration, which you are interested in. The "adjust the gradient ..." option is for intra-DTI registration. If each DWI is not registered and motion-corrected, you need to recalculate the gradient table, strictly speaking. We usually do not use this option, but sometime reviewers ask if you recalculate the table. On Fri, Jul 9, 2010 at 4:49 PM, Zhang, Aifeng wrote: > Dear DTIStudio, > > > > Just want to double check with you about my procedure with one DTI sequence > and one MPRAGE: > > > > In DTIStudio: > > 1) MRI view3D: register MPRAGE image (voxel size 0.83X0.83X1.1mm) to b0 > image (0.83X0.83X2.2mm) using affine transformation. > > 2) DTI Mapping: register all DWIs to b0 using affine too. > > 3) Fiber-tracking: draw ROI on co-registered MPRAGE images for fiber > tracking. > > > > in step 2: do you recommend choosing the option of "Adjusting the > gradients of the DWI images if applicable"??? > > > > thanks for your help! > > > > Sincerely, > > Aifeng > > > > *From:* smoriw at gmail.com [mailto:smoriw at gmail.com] *On Behalf Of *susumu > mori > *Sent:* Thursday, July 08, 2010 8:01 PM > *To:* Zhang, Aifeng > *Subject:* Re: [Mristudio-users] Eddy_current_correction > > > > Yes. Usually all DWIs to b0. > > On Thu, Jul 8, 2010 at 8:37 PM, Zhang, Aifeng > wrote: > > Dr. Mori, > > > > thanks for quick response. So I will register 32 gradients to b0 for all > my data. > > > > I don't have error message problem. (maybe it's someone else?) > > > > thanks! > > Aifeng > > > > *From:* smoriw at gmail.com [mailto:smoriw at gmail.com] *On Behalf Of *susumu > mori > *Sent:* Thursday, July 08, 2010 7:30 PM > *To:* Zhang, Aifeng > > > *Subject:* Re: [Mristudio-users] Eddy_current_correction > > > > Do you still have the error message problem? > Because coregistration smooths the data and SNR changes, it is a good idea > to apply it to all data. > > On Thu, Jul 8, 2010 at 8:08 PM, Zhang, Aifeng > wrote: > > Dear DTIStudio, > > > > Is coregistration always recommended as the first step, as I saw from > articles from your lab? In our case, we only acquired 1 DTI sequence with 32 > directions (~4 mins, with SENSE 2.5). thanks. > > > > Sincerely, > > Aifeng > > > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *susumu mori > *Sent:* Wednesday, June 30, 2010 9:32 PM > > > *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support > *Subject:* Re: [Mristudio-users] Eddy_current_correction > > > > When you load the REC file using "Mri3DView", make sure how many images are > in the file. For example, if you used Philips "High" table, you have 1 b0 + > 32 DWI + 1 extra image, total 34 images. The last one is an > isotropically-weighted image generated from the DWIs. Then make sure your > gradient table. Most likely, the number of images in your REC and the > gradient table are not matching. > > For example, you may have only 33 lines in the table. For the final image, > which you don't use, you can add an extra line with 33: 100, 100, 100. The > first "33" is the line number (34th table row), and "100, 100, 100" sends a > message to DtiStudio "don't use this image". > > On Tue, Jun 29, 2010 at 6:19 AM, Seyede Ghazal Mohades < > Seyede.Ghazal.Mohades at vub.ac.be> wrote: > > >Dear all > I have a completely basic question > when I try to load Philips Rec images in DTI studio I can do it, however > the same set file (which is a DTI ss-EPI sequence )gives the following > error when I try to do DTI mapping : > the file is Bigger (and sometimes it says smaller)than a DWI sequence! > where is the problem? > regards > Ghazal > >Thanks > > > >-----Original Message----- > >From: mristudio-users-bounces at mristudio.org on behalf of > support at mristudio.org > >Sent: Mon 6/28/2010 12:24 PM > >To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > >Subject: Re: [Mristudio-users] Eddy_current_correction > > > >the 1st method would be fine: use the 1st B0 as a reference and register > all > >others with it. > > > >support > > > > > > > >> > >> Hi All, > >> > >> We have diffusion data set acquired with 5 trails/repetitions(in single > time > >> point/cross sectional) for each and every subject. This means i have 5 > b0(same > >> value) and DW (12 directions) data while doing eddy current correction > can i > >> choose for instance b0 from first trail and register all the DW and > other b0 > >> images to this or do eddy current correction separately for each and > every trail > >> and finally register all of them together say for instance to the first > trail. > >> > >> Thanks > >> > >> venkat > >> > >> =================================== > >> > >> P Please consider the environment before printing this e-mail > >> > >> Cleveland Clinic is ranked one of the top hospitals > >> in America by U.S.News & World Report (2009). > >> Visit us online at http://www.clevelandclinic.org for > >> a complete listing of our services, staff and > >> locations. > >> > >> > >> Confidentiality Note: This message is intended for use > >> only by the individual or entity to which it is addressed > >> and may contain information that is privileged, > >> confidential, and exempt from disclosure under applicable > >> law. If the reader of this message is not the intended > >> recipient or the employee or agent responsible for > >> delivering the message to the intended recipient, you are > >> hereby notified that any dissemination, distribution or > >> copying of this communication is strictly prohibited. If > >> you have received this communication in error, please > >> contact the sender immediately and destroy the material in > >> its entirety, whether electronic or hard copy. Thank you. > >> _______________________________________________ > >> Mristudio-users mailing list > >> Mristudio-users at mristudio.org > >> http://lists.mristudio.org/mailman/listinfo/ > >> Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > >> > > > > > >_______________________________________________ > >Mristudio-users mailing list > >Mristudio-users at mristudio.org > >http://lists.mristudio.org/mailman/listinfo/ > >Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > > > > > > >=================================== > > > >P Please consider the environment before printing this e-mail > > > >Cleveland Clinic is ranked one of the top hospitals > >in America by U.S.News & World Report (2009). > >Visit us online at http://www.clevelandclinic.org for > >a complete listing of our services, staff and > >locations. > > > > > >Confidentiality Note: This message is intended for use > >only by the individual or entity to which it is addressed > >and may contain information that is privileged, > >confidential, and exempt from disclosure under applicable > >law. If the reader of this message is not the intended > >recipient or the employee or agent responsible for > >delivering the message to the intended recipient, you are > >hereby notified that any dissemination, distribution or > >copying of this communication is strictly prohibited. If > >you have received this communication in error, please > >contact the sender immediately and destroy the material in > >its entirety, whether electronic or hard copy. Thank you. > > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100716/e3cd3914/attachment-0001.html From susumu at mri.jhu.edu Fri Jul 16 21:50:22 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 16 Jul 2010 21:50:22 -0400 Subject: [Mristudio-users] Mutual Info Registration In-Reply-To: References: Message-ID: Yes, you are correct. If you use Affine, you can claim that you corrected both Eddy and motion. AIR goes much faster but MUT tends to be more accurate. On Tue, Jul 13, 2010 at 9:11 AM, [Seongjin] wrote: > Dear DTI studio community, > > I would like to make it sure if I understood correctly. > > In the registration methods, there are two method implemented in DTI > studio. > 1. AIR > 2. Mutual information based. > > In both method, two options are provided: Rigid and Affine. > > In order to reduce both motion and eddy current, we choose Affine option. > Is this correct? > > I see 6 parameters for rigid and 12 parameters for Affine. > > I wonder if I choose rigid option then only motion would corrected. > > -SC > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100716/f980cda5/attachment.html From susumu at mri.jhu.edu Fri Jul 16 22:43:44 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 16 Jul 2010 22:43:44 -0400 Subject: [Mristudio-users] b-matrix from dicom header and from techs In-Reply-To: References: <77A88E90A851594AAEF830450587C39D0418324E@CCHSCLEXMB56.cc.ad.cchs.net> <145933A2BE9E4F48AE079A201379BF2F21300EB8EE@RAD-EXCH1.win.ad.jhu.edu> Message-ID: > > *1) From the DICOM header of the b0 images, the corresponding gradient > direction is not (0,0,0). However, it is (0, 0.7,0.7). What does this mean? > Which one is the right one to use?* * > * > Could you send me (susumu at mri.jhu.edu) the copy of the extracted table? We can take a look. > * * > *2) You said that we have to use the gradient table from the DICOM header > instead of the Manufacturer's table since the former is more accurate. > So,does this mean that we do not need to load the predefined tables any > more? Is this true for different scanner software versions or for only VB17? > * > > You can use the generic table but it is much easier to extract the gradient information from DICOM headers because the gradient signs are correct and you don't have to do the "flip X" operation after tensor calculation. Also, it is supposed to be a bit more accurate. > If you use the table extraction function, you no longer need the predefined table. > *3) There is one point that is puzzling me. You said previously that we do > not need to reorient the gradient table if we are using software version > after VB15. However, I do not understand what do you mean exactly by this > sentence?* > > "*The are some mixed information about whether we need to reorient > gradient tables when oblique imaging is used (whether we need to check > "rotate if applicable" option or not). We are testing it but with the > scanner we tested last time (VB17 operating system), we needed to check to > this option.* " > > > There is possibility that we misinformed you regarding the necessity of table rotation for VB15. > We are also very puzzled that we recently encountered data that requires gradient rotation. There are two issues; >> Issue 1: is the gradient table rotated with oblique angle? >> Issue 2: what is the coordinate system of the table information in the DICOM header? Is it in the physical X/Y/Z gradient coordinates or image coordinates? These two coordinates are not the same if the imaging plane is rotated. > For your self-defense, I would suggest you to do the following tests. It is difficult for us to test all manufacturers, all versions, and all image protocols. So we would appreciate your help; >> you can scan a person using a plane axial (the brain should look upright). Then rotate FOV by 30-40 degree and scan again. The brain should look tilted in the image. Ask the person to rotate the brain by 30-40 degree and rotate the FOV so that the brain look upright in the image. Scan again. >> Please process these 3 DTI data. >> I would appreciate it if you could send the data to us too. > *Does this mean that we may need to rotate the gradient table in case of > oblique acquisition for VB17? > > *Thank you very much. > > Fatma. > > > On Mon, Jul 12, 2010 at 7:59 PM, susumu mori wrote: > >> Hi all, >> >> For Siemens users, now a new function to extract a gradient table from >> Mosaic file header is available. The extracted gradient table is usually >> different from the generic gradient table provided by Siemens from the >> following points; >> >> > X/Y/Z gradient signs (+/-) are dynamically changed based on image >> protocol (e.g. axial/sagittal/coronal). The extracted tables have correct >> signs. >> > The extracted table is more exact because it includes not only the >> diffusion-weighing gradients but also a small contribution of imaging >> gradients. >> >> The are some mixed information about whether we need to reorient gradient >> tables when oblique imaging is used (whether we need to check "rotate if >> applicable" option or not). We are testing it but with the scanner we tested >> last time (VB17 operating system), we needed to check to this option. >> >> We will follow up this issue soon but we strongly recommend you to test >> your scanner. It can be easily tested by scanning a person twice. Once with >> a regular axial and one with a strong oblique (30-45 degree). If you are not >> sure about your results, you can send us your results for check. >> >> Susumu >> >> >> On Mon, Jul 12, 2010 at 9:56 AM, Hangyi Jiang wrote: >> >>> hi, Jeff, >>> >>> if the files are in Mosaic format, DtiDtudio can get the gradients from >>> the header. >>> below, I attached the email I sent to Venkat for your reference. >>> >>> regards, >>> >>> hangyi >>> >>> >>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Venkat, >>> >>> this is one of the most confusions to deal with DICOM files. >>> >>> according the DICOM standard and Siemens documentation, the gradients >>> (bvec as you mentioned) in DICOM header should be defined in patient space >>> (or image matrix space), so the one from dcm2nii should be correct for your >>> dataset. >>> >>> the 1st one (from your MR techs) seems that it is the original definition >>> based on scanner's coordinate system. this one should be adjusted >>> dynamically during scanning according to patient position and orientation. >>> by the way, we usually named it as gradient table, not b-matrix. b-matrix >>> has 6 components for each of DWIs. b-matrix can be calculated from the >>> gradient table. >>> >>> as a matter of fact, Siemens also saves adjusted b-matrix in the DICOM >>> header. if you like, you can also use the adjusted b-matrix from the header >>> for tensor calculation. in fact, using adjusted b-matrix is recommended by >>> Siemens since it also considered other factors (like gradient cross-over >>> effects) for image acquisition. >>> >>> hope it helps. >>> >>> hangyi >>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> >>> >>> >>> ________________________________________ >>> From: mristudio-users-bounces at mristudio.org [ >>> mristudio-users-bounces at mristudio.org] On Behalf Of Jeff Sadino [ >>> jsadino.queens at gmail.com] >>> Sent: Saturday, July 10, 2010 10:51 PM >>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; >>> rajagov2 at ccf.org >>> Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs >>> >>> Hi Venkat, >>> >>> We had the same question on our Siemens VA25A DTIs. The Siemen's tech >>> support recommended a program called MRIConvert ( >>> http://lcni.uoregon.edu/~jolinda/MRIConvert/) >>> to extract the gradients. I don't have our tables in front of me, but the >>> .8, 0, and .4 values seem pretty close to what I remember. Siemens said >>> that they suspected the 1, 0, .5 values were in the scanner direction and >>> the .8, 0, .4 values were in the patient direction, since I think Siemens >>> automatically adjusts for that. Just be careful when using the MRIConvert >>> program to extract gradients, since it flips the y sign for FSL purposes. >>> >>> Cheers, >>> Jeff >>> >>> On Fri, Jul 9, 2010 at 9:33 AM, Rajagopalan, Venkateswaran < >>> rajagov2 at ccf.org> wrote: >>> >>> >>> Dear All, >>> >>> we collect our data from Siemens scanner. I got b-matrix from our MR >>> techs for software version VA25A b matrix is as follows >>> >>> 0: 0.000, 0.000, 0.000 >>> 1: 1.000, 0.000, 0.500 >>> 2: 0.000, 0.500, 1.000 >>> 3: 0.500, 1.000, 0.000 >>> 4: 1.000, 0.500, 0.000 >>> 5: 0.000, 1.000, 0.500 >>> 6: 0.500, 0.000, 1.000 >>> 7: 1.000, 0.000, -0.500 >>> 8: 0.000, -0.500, 1.000 >>> 9: -0.500, 1.000, 0.000 >>> 10: 1.000, -0.500, 0.000 >>> 11: 0.000, 1.000, -0.500 >>> 12: -0.500, 0.000, 1.000 >>> >>> I used dcm2nii software (to convert hem into nifti file for soem other >>> purpose i also gives me bvec and bval files) which gives me the following >>> matrix from the dicom header file >>> >>> 0 0 0 >>> 0.89 0 -0.45 >>> 0 0.45 -0.89 >>> 0.45 0.89 0 >>> 0.89 0.45 0 >>> 0 0.89 -0.45 >>> 0.45 0 -0.89 >>> 0.89 0 0.45 >>> 0 -0.45 -0.89 >>> -0.45 0.89 0 >>> 0.89 -0.45 0 >>> 0 0.89 0.45 >>> -0.45 0 -0.89 >>> >>> Since not only the values are different but +/- signs are also different >>> in DW directions. So I am wondering whether any one could tell me which is >>> the correct table to go with. >>> >>> Thanks >>> >>> Venkat >>> >>> >>> =================================== >>> >>> P Please consider the environment before printing this e-mail >>> >>> >>> >>> >>> Cleveland Clinic is ranked one of the top hospitals >>> in America by U.S.News & World Report (2009). >>> Visit us online at http://www.clevelandclinic.org< >>> http://www.clevelandclinic.org/> for >>> a complete listing of our services, staff and >>> locations. >>> >>> >>> Confidentiality Note: This message is intended for use >>> only by the individual or entity to which it is addressed >>> and may contain information that is privileged, >>> confidential, and exempt from disclosure under applicable >>> law. If the reader of this message is not the intended >>> recipient or the employee or agent responsible for >>> delivering the message to the intended recipient, you are >>> hereby notified that any dissemination, distribution or >>> copying of this communication is strictly prohibited. If >>> you have received this communication in error, please >>> contact the sender immediately and destroy the material in >>> its entirety, whether electronic or hard copy. Thank you. >>> >>> >>> _______________________________________________ >>> mristudio-users mailing list >>> mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> mristudio-users-unsubscribe at mristudio.org>> mristudio-users-unsubscribe at mristudio.org> >>> >>> >>> >>> _______________________________________________ >>> mristudio-users mailing list >>> mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> mristudio-users-unsubscribe at mristudio.org >>> >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100716/7337bb25/attachment-0001.html From susumu at mri.jhu.edu Fri Jul 16 22:52:43 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 16 Jul 2010 22:52:43 -0400 Subject: [Mristudio-users] (no subject) In-Reply-To: References: Message-ID: here (https://www.mristudio.org/wiki/user_manual) you can find a manual and video tutorial. We also offer hand-on tutorial, if you are interested in. On Mon, Jul 12, 2010 at 11:41 AM, michael brown wrote: > Hi Mymname is Mike, > I've very recently started using mri studio, it seems realy good so far. > My problem is that i've got to learn it quickly. I've got a gradient table > and dicom images and I need to find the ADC and FA. I can load the table but > I don't know what to do next, can you help me please. > Mike > > ------------------------------ > Get a new e-mail account with Hotmail - Free. Sign-up now. > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100716/db9016b0/attachment.html From susumu at mri.jhu.edu Sun Jul 18 02:32:11 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sun, 18 Jul 2010 02:32:11 -0400 Subject: [Mristudio-users] Calculating SNR of DTI data In-Reply-To: References: <3A4B564F13D63145AB38101AF6C50FF50B08EACB33@UTHCMS2.uthouston.edu> Message-ID: As SC mentioned, it is not easy to measure SNR for DTI using parallel imaging. First of all, SNR has spatial dependency; higher at the edge (closer to the coils) and lower in the center. As for your point #2, SNR is important for cross-institution calibration because FA has SNR dependence for low SNR regions; the lower the SNR, the higher the FA. Therefore, you have to make sure that you have a protocol with SNR high enough so that small difference in SNR across institutes won't affect the DTI results that much. Namely, if SNR is high enough, the FA values are stable against SNR difference. We published empirical measurement results of the SNR-FA relationship in; Farrell, JAD, Landman, BA, Jones, CK, Smith, SA, Prince, JL, van Zijl, PCM, *Mori, S. *"Effect of SNR on the accuracy and reproducibility of DTI-derived fractional anisotropy, mean diffusivity, and principal eigenvector measurements at 1.5T", J. Magn. Reson. Imag., 26, 756-767 (2007) Currently we are trying to see if this kind of SNR (scan time) - FA relationship can be used for cross-insitution calibration. This type of measurement may not be enough for calibration, but certainly important. On Tue, Jun 29, 2010 at 10:23 AM, [Seongjin] wrote: > My opinions to (3) and (4) > > (3) In parallel imaging, SNR decreases as acceleration factors increases (R > in Philips system). > But increased acceleration factors improves geometric distortions (i.e. > better shape). > You need to find trade off point with your data. In Philips 3T system, I > observed significant noise in the images using acceleration factor larger > than 3 (R > 3). > > (4) When you do DTI using parallel imaging, normal SNR methods will not > work. You need to have signal image and noise only image. Get the mean > signal and noise standard deviation from an ROI then calculate the SNR. You > can get noise-only image in RF-off mode. > > -Seongjin > > > On Mon, Jun 28, 2010 at 7:37 PM, Juranek, Jenifer < > Jenifer.Juranek at uth.tmc.edu> wrote: > >> While the issue of SNR effects on DTI metrics is discussed in the >> published literature, I have found relatively little information regarding >> calculating SNR as a screening procedure for image quality. A few authors >> have reported the SNR range (or cut-off) of their datasets - but not many. >> I'm curious about the following questions...any responses/opinions would be >> very helpful. >> >> >> >> 1) Is calculation of SNR an effective screening tool for image quality in >> DTI research? >> >> 2) Is calculation of SNR helpful for determining the feasibility of >> pooling 3T DTI data from different scanner platforms (e.g. Siemens and >> Philips) >> >> 3) To what extent do parallel imaging and acceleration factors affect >> measures of SNR? >> >> 4) If calculation of SNR is a "good thing to do and report", then what is >> the best approach? >> >> >> >> In particular, datatype for analysis (e.g. b=0, trace, DW) and location >> "inside the brain" seem to be important things to consider. In terms of >> datatype, I have seen folks use single non-averaged b=0 for each subject, >> and a mathematical relation between sequential b=0 images, and some have >> averaged their b=0 data on the scanner. >> >> >> >> Many thanks for any feedback, >> >> Jenifer >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> Mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > Mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100718/8dfbd5d2/attachment.html From xli16 at jhmi.edu Mon Jul 19 10:33:07 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 19 Jul 2010 10:33:07 -0400 Subject: [Mristudio-users] Mutual-info registration error In-Reply-To: <40469184F1D86344A835AB980269681A16969FC8CD@exchange.psych.uic.edu> References: <561163.39347.qm@web25605.mail.ukl.yahoo.com> <40469184F1D86344A835AB980269681A16969FC8CD@exchange.psych.uic.edu> Message-ID: <7200f8821a834.4c4429e3@johnshopkins.edu> Hello Aifeng, May I know which software you are talking about? Xin ----- Original Message ----- From: "Zhang, Aifeng" Date: Wednesday, July 14, 2010 1:03 pm Subject: [Mristudio-users] Mutual-info registration error To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Hi DTIStudio, > > When I try to use mutual-information registration, sometimes error > pops up saying "RegImgFile.tmp was not found". Could you please let > me know what is that file for and how to proceed with the registration? > > thanks! > Aifeng > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From azhang at psych.uic.edu Mon Jul 19 12:05:39 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Mon, 19 Jul 2010 11:05:39 -0500 Subject: [Mristudio-users] Mutual-info registration error In-Reply-To: <7200f8821a834.4c4429e3@johnshopkins.edu> References: <561163.39347.qm@web25605.mail.ukl.yahoo.com> <40469184F1D86344A835AB980269681A16969FC8CD@exchange.psych.uic.edu> <7200f8821a834.4c4429e3@johnshopkins.edu> Message-ID: <40469184F1D86344A835AB980269681A1696B2FAC5@exchange.psych.uic.edu> Hi Xin I only used DtiStudio for mutual-info registration. thanks, Aifeng -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li Sent: Monday, July 19, 2010 9:33 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Mutual-info registration error Hello Aifeng, May I know which software you are talking about? Xin ----- Original Message ----- From: "Zhang, Aifeng" Date: Wednesday, July 14, 2010 1:03 pm Subject: [Mristudio-users] Mutual-info registration error To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Hi DTIStudio, > > When I try to use mutual-information registration, sometimes error > pops up saying "RegImgFile.tmp was not found". Could you please let > me know what is that file for and how to proceed with the registration? > > thanks! > Aifeng > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Mon Jul 19 13:44:13 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 19 Jul 2010 13:44:13 -0400 Subject: [Mristudio-users] Mutual-info registration error In-Reply-To: <40469184F1D86344A835AB980269681A1696B2FAC5@exchange.psych.uic.edu> References: <561163.39347.qm@web25605.mail.ukl.yahoo.com> <40469184F1D86344A835AB980269681A16969FC8CD@exchange.psych.uic.edu> <7200f8821a834.4c4429e3@johnshopkins.edu> <40469184F1D86344A835AB980269681A1696B2FAC5@exchange.psych.uic.edu> Message-ID: <7230db421e411.4c4456ad@johnshopkins.edu> Hello Aifeng, My colleagues will look into it. Regards, Xin ----- Original Message ----- From: "Zhang, Aifeng" Date: Monday, July 19, 2010 12:05 pm Subject: Re: [Mristudio-users] Mutual-info registration error To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Hi Xin > > I only used DtiStudio for mutual-info registration. > > thanks, > Aifeng > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org [ On Behalf Of Xin Li > Sent: Monday, July 19, 2010 9:33 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] Mutual-info registration error > > Hello Aifeng, > > May I know which software you are talking about? > > > Xin > > ----- Original Message ----- > From: "Zhang, Aifeng" > Date: Wednesday, July 14, 2010 1:03 pm > Subject: [Mristudio-users] Mutual-info registration error > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > > > > Hi DTIStudio, > > > > When I try to use mutual-information registration, sometimes error > > > pops up saying "RegImgFile.tmp was not found". Could you please > let > > me know what is that file for and how to proceed with the registration? > > > > thanks! > > Aifeng > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From j.houenou at yahoo.fr Mon Jul 19 16:20:26 2010 From: j.houenou at yahoo.fr (Josselin) Date: Mon, 19 Jul 2010 20:20:26 +0000 (GMT) Subject: [Mristudio-users] ROI transformation Message-ID: <551233.5373.qm@web25607.mail.ukl.yahoo.com> Dear mristudio developers and users, I have a pretty trivial question but I couldn't find any way to do it. I got for one subject a FA image and a B0 image. My goal is to register the WMPM type II eve atlas onto my FA map such as done in http://www.ncbi.nlm.nih.gov/pubmed/20570617 (paper by Zhang). I therefore used the steps described in https://www.mristudio.org/wiki/user_manual/diffeomap/ I coregistered my FA map and B0 map with air then LDDMM and obtained AIR and LDDDM matrices which seem correct: when I apply Hmap to the file named "JHU_MNI_SS_WMPM_TypeII" then the inverted AIR transformation, it fits perfectly well on my original FA map. Nevertheless, I do not know how to transform the file "JHU_MNI_SS_WMPM_TypeII.dat" which contains the ROI label names. Is there any way to do it ? When I load this file as a "subject" in diffeomap and then try to apply Hmap.vtk onto it I get "Cannot crop the LDDMM map" as an error message. Any suggestion ?? Many thanks, Josselin Houenou From xli16 at jhmi.edu Mon Jul 19 16:57:41 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 19 Jul 2010 16:57:41 -0400 Subject: [Mristudio-users] ROI transformation In-Reply-To: <551233.5373.qm@web25607.mail.ukl.yahoo.com> References: <551233.5373.qm@web25607.mail.ukl.yahoo.com> Message-ID: <70e0852d1cb48.4c448405@johnshopkins.edu> Hello Josselin, "JHU_MNI_SS_WMPM_TypeII.dat" is the same file as "JHU_MNI_SS_WMPM_TypeII". You don't need to apply Hmap to "JHU_MNI_SS_WMPM_TypeII.dat" again. If you want to identify the ROIs, you can use "JhuMniSSTypeIILabelLookupTable.txt" that is available at \ROIEditor\Images\JHU_MNI_SS. Regards, Xin ----- Original Message ----- From: Josselin Date: Monday, July 19, 2010 4:20 pm Subject: [Mristudio-users] ROI transformation To: mristudio-users at mristudio.org > Dear mristudio developers and users, > > I have a pretty trivial question but I couldn't find any way to do it. > > I got for one subject a FA image and a B0 image. My goal is to > register the WMPM type II eve atlas onto my FA map such as done in > (paper by Zhang). > > I therefore used the steps described in > I coregistered my FA map and B0 map with air then LDDMM and obtained > AIR and LDDDM matrices which seem correct: when I apply Hmap to the > file named "JHU_MNI_SS_WMPM_TypeII" then the inverted AIR > transformation, it fits perfectly well on my original FA map. > > Nevertheless, I do not know how to transform the file > "JHU_MNI_SS_WMPM_TypeII.dat" which contains the ROI label names. Is > there any way to do it ? When I load this file as a "subject" in > diffeomap and then try to apply Hmap.vtk onto it I get "Cannot crop > the LDDMM map" as an error message. Any suggestion ?? > > Many thanks, > Josselin Houenou > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From jmcentee at jhmi.edu Mon Jul 19 16:58:54 2010 From: jmcentee at jhmi.edu (Julie McEntee) Date: Mon, 19 Jul 2010 16:58:54 -0400 Subject: [Mristudio-users] ROI transformation In-Reply-To: <551233.5373.qm@web25607.mail.ukl.yahoo.com> Message-ID: Try these steps in DiffeoMap: Go to ?Atlas Sample Images? on top toolbar Place curser over ?JHU_MNI_SS?, click ?JHU_MNI_SS_WMPM_TypeII? Click ?File? on top toolbar; click ?Load Subject?? Navigate to ROIEditor/Images/JHU_MNI_SS; double-click ?JHU_MNI_SS_WMPM_TypeII.dat?; click OK In ?JHU_MNI_SS_WMPM_TypeII.dat ? Subject? window, under Transformation, Automatic Image Registration 1) Click Invert button 2) Click AIR File button; navigate to subject?s folder; double-click ?AlignlinearOutput_.air?; click OK Under ?Volume LDDMM?, ?Remote (Send Data to the Server)?, under ?Single Channel? button; click 1st button on left with blue M and open folder icon (Load Transformation Matrix) 1) Choose LDDMM Matrix (VTK Format) 2) Interpolation: Trilinear 3) Click Browse button and navigate to subject?s folder; click OK 4) Navigate to subject?s ?Results? folder, choose Hmap.vtk; click Open; click OK to change dimensions 5) Result file (visable in drop-down menu under Image): Lddmm_JHU_MNI_SS_WMPM_TypeII.dat Click ?Load Transformation Matrix? button (blue ?M? button) 1) Choose AIR Linear Matrix 2) Interpolation: Nearest Neighbor 3) Click Browse button and navigate to subject?s folder; click OK 4) Choose Invert_AlignlinearOutput_.air; click Open 5) Result file (visable in drop-down menu under Image): Air_Lddmm_JHU_MNI_SS_WMPM_TypeII.dat -Julie Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676 On 7/19/10 4:20 PM, "Josselin" wrote: > Dear mristudio developers and users, > > I have a pretty trivial question but I couldn't find any way to do it. > > I got for one subject a FA image and a B0 image. My goal is to register the > WMPM type II eve atlas onto my FA map such as done in > http://www.ncbi.nlm.nih.gov/pubmed/20570617 (paper by Zhang). > > I therefore used the steps described in > https://www.mristudio.org/wiki/user_manual/diffeomap/ > I coregistered my FA map and B0 map with air then LDDMM and obtained AIR and > LDDDM matrices which seem correct: when I apply Hmap to the file named > "JHU_MNI_SS_WMPM_TypeII" then the inverted AIR transformation, it fits > perfectly well on my original FA map. > > Nevertheless, I do not know how to transform the file > "JHU_MNI_SS_WMPM_TypeII.dat" which contains the ROI label names. Is there any > way to do it ? When I load this file as a "subject" in diffeomap and then try > to apply Hmap.vtk onto it I get "Cannot crop the LDDMM map" as an error > message. Any suggestion ?? > > Many thanks, > Josselin Houenou > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From rajagov2 at ccf.org Mon Jul 19 17:03:30 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Mon, 19 Jul 2010 17:03:30 -0400 Subject: [Mristudio-users] b-matrix from dicom header and from techs References: <77A88E90A851594AAEF830450587C39D0418324E@CCHSCLEXMB56.cc.ad.cchs.net> <145933A2BE9E4F48AE079A201379BF2F21300EB8EE@RAD-EXCH1.win.ad.jhu.edu> Message-ID: <77A88E90A851594AAEF830450587C39D0418325D@CCHSCLEXMB56.cc.ad.cchs.net> Dear Dr.Mori, Sorry to digress little bit but something releveant on the same topic. 1) What is the DICOM header tag for gradient table information, I have Siemens versions from 2004 (VA 25A)and came to know that after 2006 they have CSA header info from where you can extract information regarding Diffusion data. So for versions of 2004 and older where can i find gradient table information. 2) When i use dcm2nii to extract gradient table information for these older software versions it is mentioned by Chris Rorden that he appropriately rotates these gradient tables to conform to NIFTI format (since dicom and NIFTI coordinates are different). I am using FSL for eddy/motion correction and also to rotate bvec after eddy/motion correction. I however convert NIFTI to Analyze format and then to dti "raw" format and do tensor calculation so i am wondering whether this "raw"format has same coordinates as NIFTI. 3) Do you have an option in DTIstudio to open NIFTI files. 4) Last one When i try to run DTIstudio-latest-x86.exe it gives me the following error "This application failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem". Any help on this would be greatly appreciated. Thanks Venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Fri 7/16/2010 10:43 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs 1) From the DICOM header of the b0 images, the corresponding gradient direction is not (0,0,0). However, it is (0, 0.7,0.7). What does this mean? Which one is the right one to use? > Could you send me (susumu at mri.jhu.edu) the copy of the extracted table? We can take a look. 2) You said that we have to use the gradient table from the DICOM header instead of the Manufacturer's table since the former is more accurate. So,does this mean that we do not need to load the predefined tables any more? Is this true for different scanner software versions or for only VB17? > You can use the generic table but it is much easier to extract the gradient information from DICOM headers because the gradient signs are correct and you don't have to do the "flip X" operation after tensor calculation. Also, it is supposed to be a bit more accurate. > If you use the table extraction function, you no longer need the predefined table. 3) There is one point that is puzzling me. You said previously that we do not need to reorient the gradient table if we are using software version after VB15. However, I do not understand what do you mean exactly by this sentence? "The are some mixed information about whether we need to reorient gradient tables when oblique imaging is used (whether we need to check "rotate if applicable" option or not). We are testing it but with the scanner we tested last time (VB17 operating system), we needed to check to this option. " > There is possibility that we misinformed you regarding the necessity of table rotation for VB15. > We are also very puzzled that we recently encountered data that requires gradient rotation. There are two issues; >> Issue 1: is the gradient table rotated with oblique angle? >> Issue 2: what is the coordinate system of the table information in the DICOM header? Is it in the physical X/Y/Z gradient coordinates or image coordinates? These two coordinates are not the same if the imaging plane is rotated. > For your self-defense, I would suggest you to do the following tests. It is difficult for us to test all manufacturers, all versions, and all image protocols. So we would appreciate your help; >> you can scan a person using a plane axial (the brain should look upright). Then rotate FOV by 30-40 degree and scan again. The brain should look tilted in the image. Ask the person to rotate the brain by 30-40 degree and rotate the FOV so that the brain look upright in the image. Scan again. >> Please process these 3 DTI data. >> I would appreciate it if you could send the data to us too. Does this mean that we may need to rotate the gradient table in case of oblique acquisition for VB17? Thank you very much. Fatma. On Mon, Jul 12, 2010 at 7:59 PM, susumu mori wrote: Hi all, For Siemens users, now a new function to extract a gradient table from Mosaic file header is available. The extracted gradient table is usually different from the generic gradient table provided by Siemens from the following points; > X/Y/Z gradient signs (+/-) are dynamically changed based on image protocol (e.g. axial/sagittal/coronal). The extracted tables have correct signs. > The extracted table is more exact because it includes not only the diffusion-weighing gradients but also a small contribution of imaging gradients. The are some mixed information about whether we need to reorient gradient tables when oblique imaging is used (whether we need to check "rotate if applicable" option or not). We are testing it but with the scanner we tested last time (VB17 operating system), we needed to check to this option. We will follow up this issue soon but we strongly recommend you to test your scanner. It can be easily tested by scanning a person twice. Once with a regular axial and one with a strong oblique (30-45 degree). If you are not sure about your results, you can send us your results for check. Susumu On Mon, Jul 12, 2010 at 9:56 AM, Hangyi Jiang wrote: hi, Jeff, if the files are in Mosaic format, DtiDtudio can get the gradients from the header. below, I attached the email I sent to Venkat for your reference. regards, hangyi >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Venkat, this is one of the most confusions to deal with DICOM files. according the DICOM standard and Siemens documentation, the gradients (bvec as you mentioned) in DICOM header should be defined in patient space (or image matrix space), so the one from dcm2nii should be correct for your dataset. the 1st one (from your MR techs) seems that it is the original definition based on scanner's coordinate system. this one should be adjusted dynamically during scanning according to patient position and orientation. by the way, we usually named it as gradient table, not b-matrix. b-matrix has 6 components for each of DWIs. b-matrix can be calculated from the gradient table. as a matter of fact, Siemens also saves adjusted b-matrix in the DICOM header. if you like, you can also use the adjusted b-matrix from the header for tensor calculation. in fact, using adjusted b-matrix is recommended by Siemens since it also considered other factors (like gradient cross-over effects) for image acquisition. hope it helps. hangyi >>>>>>>>>>>>>>>>>>>>>>>>>>>> ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Jeff Sadino [jsadino.queens at gmail.com] Sent: Saturday, July 10, 2010 10:51 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; rajagov2 at ccf.org Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs Hi Venkat, We had the same question on our Siemens VA25A DTIs. The Siemen's tech support recommended a program called MRIConvert (http://lcni.uoregon.edu/~jolinda/MRIConvert/ ) to extract the gradients. I don't have our tables in front of me, but the .8, 0, and .4 values seem pretty close to what I remember. Siemens said that they suspected the 1, 0, .5 values were in the scanner direction and the .8, 0, .4 values were in the patient direction, since I think Siemens automatically adjusts for that. Just be careful when using the MRIConvert program to extract gradients, since it flips the y sign for FSL purposes. Cheers, Jeff On Fri, Jul 9, 2010 at 9:33 AM, Rajagopalan, Venkateswaran > wrote: Dear All, we collect our data from Siemens scanner. I got b-matrix from our MR techs for software version VA25A b matrix is as follows 0: 0.000, 0.000, 0.000 1: 1.000, 0.000, 0.500 2: 0.000, 0.500, 1.000 3: 0.500, 1.000, 0.000 4: 1.000, 0.500, 0.000 5: 0.000, 1.000, 0.500 6: 0.500, 0.000, 1.000 7: 1.000, 0.000, -0.500 8: 0.000, -0.500, 1.000 9: -0.500, 1.000, 0.000 10: 1.000, -0.500, 0.000 11: 0.000, 1.000, -0.500 12: -0.500, 0.000, 1.000 I used dcm2nii software (to convert hem into nifti file for soem other purpose i also gives me bvec and bval files) which gives me the following matrix from the dicom header file 0 0 0 0.89 0 -0.45 0 0.45 -0.89 0.45 0.89 0 0.89 0.45 0 0 0.89 -0.45 0.45 0 -0.89 0.89 0 0.45 0 -0.45 -0.89 -0.45 0.89 0 0.89 -0.45 0 0 0.89 0.45 -0.45 0 -0.89 Since not only the values are different but +/- signs are also different in DW directions. So I am wondering whether any one could tell me which is the correct table to go with. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 14808 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100719/b8bf031d/attachment-0001.bin From xli16 at jhmi.edu Mon Jul 19 17:13:47 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 19 Jul 2010 17:13:47 -0400 Subject: [Mristudio-users] b-matrix from dicom header and from techs In-Reply-To: <77A88E90A851594AAEF830450587C39D0418325D@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D0418324E@CCHSCLEXMB56.cc.ad.cchs.net> <145933A2BE9E4F48AE079A201379BF2F21300EB8EE@RAD-EXCH1.win.ad.jhu.edu> <77A88E90A851594AAEF830450587C39D0418325D@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <7250c3b51a076.4c4487cb@johnshopkins.edu> Hello Venkateswaran, For your fourth question, it may be because that your computer doesn't have the Microscoft Visual Studio redistribution package. Please download vcredist_x86.exe at https://www.mristudio.org/wiki/installation and install it before you run DtiStudio. Hope this will solve the problem. Xin ----- Original Message ----- From: "Rajagopalan, Venkateswaran" Date: Monday, July 19, 2010 5:03 pm Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Dear Dr.Mori, > > Sorry to digress little bit but something releveant on the same topic. > > 1) What is the DICOM header tag for gradient table information, I > have Siemens versions from 2004 (VA 25A)and came to know that after > 2006 they have CSA header info from where you can extract information > regarding Diffusion data. So for versions of 2004 and older where can > i find gradient table information. > > 2) When i use dcm2nii to extract gradient table information for these > older software versions it is mentioned by Chris Rorden that he > appropriately rotates these gradient tables to conform to NIFTI format > (since dicom and NIFTI coordinates are different). I am using FSL for > eddy/motion correction and also to rotate bvec after eddy/motion > correction. I however convert NIFTI to Analyze format and then to dti > "raw" format and do tensor calculation so i am wondering whether this > "raw"format has same coordinates as NIFTI. > > 3) Do you have an option in DTIstudio to open NIFTI files. > > 4) Last one When i try to run DTIstudio-latest-x86.exe it gives me > the following error "This application failed to start because the > application configuration is incorrect. Reinstalling the application > may fix this problem". Any help on this would be greatly appreciated. > > Thanks > > Venkateswaran > > ________________________________ > > From: mristudio-users-bounces at mristudio.org on behalf of susumu mori > Sent: Fri 7/16/2010 10:43 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs > > > > > > 1) From the DICOM header of the b0 images, the corresponding > gradient direction is not (0,0,0). However, it is (0, 0.7,0.7). What > does this mean? Which one is the right one to use? > > > > > Could you send me (susumu at mri.jhu.edu) the copy of the extracted > table? We can take a look. > > > > 2) You said that we have to use the gradient table from the DICOM > header instead of the Manufacturer's table since the former is more > accurate. So,does this mean that we do not need to load the predefined > tables any more? Is this true for different scanner software versions > or for only VB17? > > > > > You can use the generic table but it is much easier to extract the > gradient information from DICOM headers because the gradient signs are > correct and you don't have to do the "flip X" operation after tensor > calculation. Also, it is supposed to be a bit more accurate. > > If you use the table extraction function, you no longer need the > predefined table. > > > > > 3) There is one point that is puzzling me. You said previously that > we do not need to reorient the gradient table if we are using software > version after VB15. However, I do not understand what do you mean > exactly by this sentence? > > "The are some mixed information about whether we need to reorient > gradient tables when oblique imaging is used (whether we need to check > "rotate if applicable" option or not). We are testing it but with the > scanner we tested last time (VB17 operating system), we needed to > check to this option. " > > > > > There is possibility that we misinformed you regarding the > necessity of table rotation for VB15. > > We are also very puzzled that we recently encountered data that > requires gradient rotation. There are two issues; > >> Issue 1: is the gradient table rotated with oblique angle? > >> Issue 2: what is the coordinate system of the table information in > the DICOM header? Is it in the physical X/Y/Z gradient coordinates or > image coordinates? These two coordinates are not the same if the > imaging plane is rotated. > > > For your self-defense, I would suggest you to do the following > tests. It is difficult for us to test all manufacturers, all versions, > and all image protocols. So we would appreciate your help; > >> you can scan a person using a plane axial (the brain should look > upright). Then rotate FOV by 30-40 degree and scan again. The brain > should look tilted in the image. Ask the person to rotate the brain by > 30-40 degree and rotate the FOV so that the brain look upright in the > image. Scan again. > >> Please process these 3 DTI data. > >> I would appreciate it if you could send the data to us too. > > > > Does this mean that we may need to rotate the gradient table in case > of oblique acquisition for VB17? > > Thank you very much. > > Fatma. > > > On Mon, Jul 12, 2010 at 7:59 PM, susumu mori wrote: > > > Hi all, > > For Siemens users, now a new function to extract a gradient > table from Mosaic file header is available. The extracted gradient > table is usually different from the generic gradient table provided by > Siemens from the following points; > > > X/Y/Z gradient signs (+/-) are dynamically changed based > on image protocol (e.g. axial/sagittal/coronal). The extracted tables > have correct signs. > > The extracted table is more exact because it includes not > only the diffusion-weighing gradients but also a small contribution of > imaging gradients. > > The are some mixed information about whether we need to > reorient gradient tables when oblique imaging is used (whether we need > to check "rotate if applicable" option or not). We are testing it but > with the scanner we tested last time (VB17 operating system), we > needed to check to this option. > > We will follow up this issue soon but we strongly recommend > you to test your scanner. It can be easily tested by scanning a person > twice. Once with a regular axial and one with a strong oblique (30-45 > degree). If you are not sure about your results, you can send us your > results for check. > > Susumu > > > On Mon, Jul 12, 2010 at 9:56 AM, Hangyi Jiang > wrote: > > > hi, Jeff, > > if the files are in Mosaic format, DtiDtudio can get > the gradients from the header. > below, I attached the email I sent to Venkat for > your reference. > > regards, > > hangyi > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>> > Hi Venkat, > > this is one of the most confusions to deal with > DICOM files. > > according the DICOM standard and Siemens > documentation, the gradients (bvec as you mentioned) in DICOM header > should be defined in patient space (or image matrix space), so the one > from dcm2nii should be correct for your dataset. > > the 1st one (from your MR techs) seems that it is > the original definition based on scanner's coordinate system. this one > should be adjusted dynamically during scanning according to patient > position and orientation. by the way, we usually named it as gradient > table, not b-matrix. b-matrix has 6 components for each of DWIs. > b-matrix can be calculated from the gradient table. > > as a matter of fact, Siemens also saves adjusted > b-matrix in the DICOM header. if you like, you can also use the > adjusted b-matrix from the header for tensor calculation. in fact, > using adjusted b-matrix is recommended by Siemens since it also > considered other factors (like gradient cross-over effects) for image > acquisition. > > hope it helps. > > hangyi > >>>>>>>>>>>>>>>>>>>>>>>>>>>> > > > > ________________________________________ > From: mristudio-users-bounces at mristudio.org > [mristudio-users-bounces at mristudio.org] On Behalf Of Jeff Sadino [jsadino.queens at gmail.com] > Sent: Saturday, July 10, 2010 10:51 PM > To: DTI Studio, ROI Editor, DiffeoMap > Questions/Support; rajagov2 at ccf.org > Subject: Re: [Mristudio-users] b-matrix from dicom > header and from techs > > > Hi Venkat, > > We had the same question on our Siemens VA25A DTIs. > The Siemen's tech support recommended a program called MRIConvert (> ) > to extract the gradients. I don't have our tables in front of me, but > the .8, 0, and .4 values seem pretty close to what I remember. > Siemens said that they suspected the 1, 0, .5 values were in the > scanner direction and the .8, 0, .4 values were in the patient > direction, since I think Siemens automatically adjusts for that. Just > be careful when using the MRIConvert program to extract gradients, > since it flips the y sign for FSL purposes. > > Cheers, > Jeff > > > On Fri, Jul 9, 2010 at 9:33 AM, Rajagopalan, > Venkateswaran > wrote: > > > Dear All, > > we collect our data from Siemens scanner. I got > b-matrix from our MR techs for software version VA25A b matrix is as follows > > 0: 0.000, 0.000, 0.000 > 1: 1.000, 0.000, 0.500 > 2: 0.000, 0.500, 1.000 > 3: 0.500, 1.000, 0.000 > 4: 1.000, 0.500, 0.000 > 5: 0.000, 1.000, 0.500 > 6: 0.500, 0.000, 1.000 > 7: 1.000, 0.000, -0.500 > 8: 0.000, -0.500, 1.000 > 9: -0.500, 1.000, 0.000 > 10: 1.000, -0.500, 0.000 > 11: 0.000, 1.000, -0.500 > 12: -0.500, 0.000, 1.000 > > I used dcm2nii software (to convert hem into nifti > file for soem other purpose i also gives me bvec and bval files) > which gives me the following matrix from the dicom header file > > 0 0 0 > 0.89 0 -0.45 > 0 0.45 -0.89 > 0.45 0.89 0 > 0.89 0.45 0 > 0 0.89 -0.45 > 0.45 0 -0.89 > 0.89 0 0.45 > 0 -0.45 -0.89 > -0.45 0.89 0 > 0.89 -0.45 0 > 0 0.89 0.45 > -0.45 0 -0.89 > > Since not only the values are different but +/- > signs are also different in DW directions. So I am wondering whether > any one could tell me which is the correct table to go with. > > Thanks > > Venkat > > > =================================== > > P Please consider the environment before printing > this e-mail > > > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > > Visit us online at > for > > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for > use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, > you are > hereby notified that any dissemination, distribution > or > copying of this communication is strictly > prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the > material in > its entirety, whether electronic or hard copy. > Thank you. > > > _______________________________________________ > mristudio-users mailing list > > mristudio-users at mristudio.org<> > > > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<> > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > > > > =================================== > > P Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From j.houenou at yahoo.fr Mon Jul 19 17:29:49 2010 From: j.houenou at yahoo.fr (Josselin) Date: Mon, 19 Jul 2010 21:29:49 +0000 (GMT) Subject: [Mristudio-users] Re : ROI transformation Message-ID: <668471.55756.qm@web25605.mail.ukl.yahoo.com> Thanks Julie. Doing your step "4) Navigate to subject?s ?Results? folder, choose Hmap.vtk; click Open; click OK to change dimensions", I get the following error message: "Cannot crop the LDDMM map" Do you have any idea why ? Thanks, Josselin Houenou From oscott at ualberta.ca Mon Jul 19 17:37:41 2010 From: oscott at ualberta.ca (oscott at ualberta.ca) Date: Mon, 19 Jul 2010 15:37:41 -0600 Subject: [Mristudio-users] problem with newest version of DTI studio Message-ID: <20100719153741.291454b1b2lr4osg@webmail.ualberta.ca> Dear all, Up until a few days ago I worked with one of the old version and everything seemed to be working fine; however, I now downloaded the newest veriso and when I try to calculate "Tensor, Color Map etc" using the same parameters and gradient I used with the old version, I get a strange image where the brain is black and the background is colourful. Does anyone have an idea how to solve this? Thank you! From sandyavenugopal at gmail.com Mon Jul 19 19:54:58 2010 From: sandyavenugopal at gmail.com (sandya venugopal) Date: Mon, 19 Jul 2010 16:54:58 -0700 Subject: [Mristudio-users] problem with newest version of DTI studio In-Reply-To: <20100719153741.291454b1b2lr4osg@webmail.ualberta.ca> References: <20100719153741.291454b1b2lr4osg@webmail.ualberta.ca> Message-ID: I have been having the same problems too. I tried to use a different gradient table as well-no luck. I would like to get this resolved soon too. Thanks. On 19 July 2010 14:37, wrote: > Dear all, > > Up until a few days ago I worked with one of the old version and > everything seemed to be working fine; however, I now downloaded the > newest veriso and when I try to calculate "Tensor, Color Map etc" > using the same parameters and gradient I used with the old version, I > get a strange image where the brain is black and the background is > colourful. Does anyone have an idea how to solve this? > > Thank you! > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100719/02085f4d/attachment-0001.html From susumu at mri.jhu.edu Tue Jul 20 05:58:08 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 20 Jul 2010 05:58:08 -0400 Subject: [Mristudio-users] ROI transformation In-Reply-To: <551233.5373.qm@web25607.mail.ukl.yahoo.com> References: <551233.5373.qm@web25607.mail.ukl.yahoo.com> Message-ID: Hi Josselin, If I understood your question correctly, you are interested in how to keep the label name after transformation. I believe "****TypeII" and "****TypeII.dat" are the same file. They both contains 181x217x181 images. The label is in "****.hdr" file. When you load the image as an ROI file, you need the *.hdr and *.dat file. After you transformed a WMPM map (no extension or *.dat file) and save it (e.g. test.dat), I believe you can just rename the *.hdr file so that you can get both test.dat and test.hdr. Xin and Andrea, correct me if I'm wrong. susumu On Mon, Jul 19, 2010 at 4:20 PM, Josselin wrote: > Dear mristudio developers and users, > > I have a pretty trivial question but I couldn't find any way to do it. > > I got for one subject a FA image and a B0 image. My goal is to register the > WMPM type II eve atlas onto my FA map such as done in > http://www.ncbi.nlm.nih.gov/pubmed/20570617 (paper by Zhang). > > I therefore used the steps described in > https://www.mristudio.org/wiki/user_manual/diffeomap/ > I coregistered my FA map and B0 map with air then LDDMM and obtained AIR > and LDDDM matrices which seem correct: when I apply Hmap to the file named > "JHU_MNI_SS_WMPM_TypeII" then the inverted AIR transformation, it fits > perfectly well on my original FA map. > > Nevertheless, I do not know how to transform the file > "JHU_MNI_SS_WMPM_TypeII.dat" which contains the ROI label names. Is there > any way to do it ? When I load this file as a "subject" in diffeomap and > then try to apply Hmap.vtk onto it I get "Cannot crop the LDDMM map" as an > error message. Any suggestion ?? > > Many thanks, > Josselin Houenou > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100720/df316486/attachment.html From susumu at mri.jhu.edu Tue Jul 20 06:11:02 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 20 Jul 2010 06:11:02 -0400 Subject: [Mristudio-users] b-matrix from dicom header and from techs In-Reply-To: <77A88E90A851594AAEF830450587C39D0418325D@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D0418324E@CCHSCLEXMB56.cc.ad.cchs.net> <145933A2BE9E4F48AE079A201379BF2F21300EB8EE@RAD-EXCH1.win.ad.jhu.edu> <77A88E90A851594AAEF830450587C39D0418325D@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Hi Venkateswaran, I think Hangyi can answer some of the questions, but few comments here; 2) When i use dcm2nii to extract gradient table information for these older > software versions it is mentioned by Chris Rorden that he appropriately > rotates these gradient tables to conform to NIFTI format (since dicom and > NIFTI coordinates are different). I am using FSL for eddy/motion correction > and also to rotate bvec after eddy/motion correction. I however convert > NIFTI to Analyze format and then to dti "raw" format and do tensor > calculation so i am wondering whether this "raw"format has same coordinates > as NIFTI. > I believe the coordinate definition is related to the header, but the "raw" format doesn't have header. So, except for the order of the matrix, there should not be difference between NIFTI and raw for the image matrix section. > > 3) Do you have an option in DTIstudio to open NIFTI files. > The current DtiStudio can read NIFTI but I don't think it can extract gradient information in NIFTI. I'm wondering why you are using NIFTI, not the original DICOM (or MOSAIC) files. If you could orient us in this respect, we may put some effort in supporting header structures other than DICOM in terms of the gradient table information. > > 4) Last one When i try to run DTIstudio-latest-x86.exe it gives me the > following error "This application failed to start because the application > configuration is incorrect. Reinstalling the application may fix this > problem". Any help on this would be greatly appreciated. > Is it a reproducible problem? > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100720/2d9c7c32/attachment.html From susumu at mri.jhu.edu Tue Jul 20 09:10:54 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 20 Jul 2010 09:10:54 -0400 Subject: [Mristudio-users] problem with newest version of DTI studio In-Reply-To: References: <20100719153741.291454b1b2lr4osg@webmail.ualberta.ca> Message-ID: Hi all, It seems there are multiple users experiencing the same problem. We want to take a look at the issue. > Are you using the DtiStudio currently posted? > When you load the data, could you see all DW images properly? > After you click the "tensor, color map, ect" button, did you choose "Standard Linear Fitting"? > If all the above questions are "yes", then, please contact Zhipeng and upload your data. We'll look into it. Thanks, Susumu On Mon, Jul 19, 2010 at 7:54 PM, sandya venugopal wrote: > I have been having the same problems too. I tried to use a different > gradient table as well-no luck. I would like to get this resolved soon too. > Thanks. > > > On 19 July 2010 14:37, wrote: > >> Dear all, >> >> Up until a few days ago I worked with one of the old version and >> everything seemed to be working fine; however, I now downloaded the >> newest veriso and when I try to calculate "Tensor, Color Map etc" >> using the same parameters and gradient I used with the old version, I >> get a strange image where the brain is black and the background is >> colourful. Does anyone have an idea how to solve this? >> >> Thank you! >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100720/485b438b/attachment.html From xli16 at jhmi.edu Tue Jul 20 09:46:07 2010 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 20 Jul 2010 09:46:07 -0400 Subject: [Mristudio-users] ROI transformation In-Reply-To: References: <551233.5373.qm@web25607.mail.ukl.yahoo.com> Message-ID: <6ff0abcb20b53.4c45705f@johnshopkins.edu> Yes. Susumu, you are right. Josselin, please follow the steps as Susumu said. Xin ----- Original Message ----- From: susumu mori Date: Tuesday, July 20, 2010 5:58 am Subject: Re: [Mristudio-users] ROI transformation To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" , Xin Li , ANDREIA FARIA > Hi Josselin, > > If I understood your question correctly, you are interested in how to > keep > the label name after transformation. > > I believe "****TypeII" and "****TypeII.dat" are the same file. They both > contains 181x217x181 images. The label is in "****.hdr" file. When > you load > the image as an ROI file, you need the *.hdr and *.dat file. > > After you transformed a WMPM map (no extension or *.dat file) and > save it > (e.g. test.dat), I believe you can just rename the *.hdr file so that > you > can get both test.dat and test.hdr. > > Xin and Andrea, correct me if I'm wrong. > > susumu > > > > On Mon, Jul 19, 2010 at 4:20 PM, Josselin wrote: > > > Dear mristudio developers and users, > > > > I have a pretty trivial question but I couldn't find any way to do > it. > > > > I got for one subject a FA image and a B0 image. My goal is to > register the > > WMPM type II eve atlas onto my FA map such as done in > > (paper by Zhang). > > > > I therefore used the steps described in > > > > I coregistered my FA map and B0 map with air then LDDMM and > obtained AIR > > and LDDDM matrices which seem correct: when I apply Hmap to the > file named > > "JHU_MNI_SS_WMPM_TypeII" then the inverted AIR transformation, it fits > > perfectly well on my original FA map. > > > > Nevertheless, I do not know how to transform the file > > "JHU_MNI_SS_WMPM_TypeII.dat" which contains the ROI label names. Is > there > > any way to do it ? When I load this file as a "subject" in > diffeomap and > > then try to apply Hmap.vtk onto it I get "Cannot crop the LDDMM > map" as an > > error message. Any suggestion ?? > > > > Many thanks, > > Josselin Houenou > > > > > > > > > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > mristudio-users-unsubscribe at mristudio.org > > From jmcentee at jhmi.edu Tue Jul 20 09:50:04 2010 From: jmcentee at jhmi.edu (Julie McEntee) Date: Tue, 20 Jul 2010 09:50:04 -0400 Subject: [Mristudio-users] Re : ROI transformation In-Reply-To: <668471.55756.qm@web25605.mail.ukl.yahoo.com> Message-ID: The only thing I can think of- do you have permission (i.e., able to write to) re: the Image folder (that comes with ROIEditor) or where its located on your computer? -Julie On 7/19/10 5:29 PM, "Josselin" wrote: > Thanks Julie. Doing your step "4) Navigate to subject?s ?Results? folder, > choose Hmap.vtk; click Open; click OK to change dimensions", I get the > following error message: "Cannot crop the LDDMM map" Do you have any idea why > ? Thanks, Josselin Houenou > _______________________________________________ mristudio-users mailing > list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo > / Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Tue Jul 20 09:58:58 2010 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 20 Jul 2010 09:58:58 -0400 Subject: [Mristudio-users] Re : ROI transformation In-Reply-To: <668471.55756.qm@web25605.mail.ukl.yahoo.com> References: <668471.55756.qm@web25605.mail.ukl.yahoo.com> Message-ID: <6ff0aae723b20.4c457362@johnshopkins.edu> Hello Josselin, "JHU_MNI_SS_WMPM_TypeII" and "JHU_MNI_SS_WMPM_TypeII.dat" are the same image files except the file names are different. Since you have successfully transformed "JHU_MNI_SS_WMPM_TypeII", to transform "JHU_MNI_SS_WMPM_TypeII.dat" should be the same. Xin ----- Original Message ----- From: Josselin Date: Monday, July 19, 2010 5:30 pm Subject: [Mristudio-users] Re : ROI transformation To: mristudio-users at mristudio.org > Thanks Julie. > Doing your step "4) Navigate to subject?s ?Results? folder, > choose Hmap.vtk; click Open; click OK to change dimensions", > I get the following error message: "Cannot crop the LDDMM map" > Do you have any idea why ? > > Thanks, > Josselin Houenou > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From hjiang at jhmi.edu Tue Jul 20 11:32:56 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Tue, 20 Jul 2010 11:32:56 -0400 Subject: [Mristudio-users] problem with newest version of DTI studio In-Reply-To: References: <20100719153741.291454b1b2lr4osg@webmail.ualberta.ca> Message-ID: <145933A2BE9E4F48AE079A201379BF2F21300EB913@RAD-EXCH1.win.ad.jhu.edu> hi, please put the correct B-value in the dialog after "tensor.." button, or put 1 as the b-value if you don't know (or don't care) it. regards, hangyi ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of sandya venugopal [sandyavenugopal at gmail.com] Sent: Monday, July 19, 2010 7:54 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problem with newest version of DTI studio I have been having the same problems too. I tried to use a different gradient table as well-no luck. I would like to get this resolved soon too. Thanks. On 19 July 2010 14:37, > wrote: Dear all, Up until a few days ago I worked with one of the old version and everything seemed to be working fine; however, I now downloaded the newest veriso and when I try to calculate "Tensor, Color Map etc" using the same parameters and gradient I used with the old version, I get a strange image where the brain is black and the background is colourful. Does anyone have an idea how to solve this? Thank you! _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From rajagov2 at ccf.org Tue Jul 20 11:21:47 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Tue, 20 Jul 2010 11:21:47 -0400 Subject: [Mristudio-users] b-matrix from dicom header and from techs References: <77A88E90A851594AAEF830450587C39D0418324E@CCHSCLEXMB56.cc.ad.cchs.net> <145933A2BE9E4F48AE079A201379BF2F21300EB8EE@RAD-EXCH1.win.ad.jhu.edu> <77A88E90A851594AAEF830450587C39D0418325D@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D0418325F@CCHSCLEXMB56.cc.ad.cchs.net> Thanks very much Dr.Mori I'm wondering why you are using NIFTI, not the original DICOM (or MOSAIC) files. If you could orient us in this respect, we may put some effort in supporting header structures other than DICOM in terms of the gradient table information. I am using FSL for eddy current/motion correction and rotating bvecs after eddy current/motion correction. Since FSLview is quite handy to look at the quality of registration and even for some of post processed DTI images I am used to FSL. FSL recommends NIFTI format i am using NIFTI. If you can support NIFTI it would be great. Last one When i try to run DTIstudio-latest-x86.exe it gives me the following error "This application failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem". Any help on this would be greatly appreciated. Is it a reproducible problem? Xin helped me with this, i didn't know that i need to install visual studio/C++ which was available in MRI studio website. Sorry about that. Now problem solved. Thanks Venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Tue 7/20/2010 6:11 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs Hi Venkateswaran, I think Hangyi can answer some of the questions, but few comments here; 2) When i use dcm2nii to extract gradient table information for these older software versions it is mentioned by Chris Rorden that he appropriately rotates these gradient tables to conform to NIFTI format (since dicom and NIFTI coordinates are different). I am using FSL for eddy/motion correction and also to rotate bvec after eddy/motion correction. I however convert NIFTI to Analyze format and then to dti "raw" format and do tensor calculation so i am wondering whether this "raw"format has same coordinates as NIFTI. I believe the coordinate definition is related to the header, but the "raw" format doesn't have header. So, except for the order of the matrix, there should not be difference between NIFTI and raw for the image matrix section. 3) Do you have an option in DTIstudio to open NIFTI files. The current DtiStudio can read NIFTI but I don't think it can extract gradient information in NIFTI. I'm wondering why you are using NIFTI, not the original DICOM (or MOSAIC) files. If you could orient us in this respect, we may put some effort in supporting header structures other than DICOM in terms of the gradient table information. 4) Last one When i try to run DTIstudio-latest-x86.exe it gives me the following error "This application failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem". Any help on this would be greatly appreciated. Is it a reproducible problem? =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6588 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100720/6eebc2af/attachment.bin From oscott at ualberta.ca Tue Jul 20 11:44:55 2010 From: oscott at ualberta.ca (oscott at ualberta.ca) Date: Tue, 20 Jul 2010 09:44:55 -0600 Subject: [Mristudio-users] problem with newest version of DTI studio In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F21300EB913@RAD-EXCH1.win.ad.jhu.edu> References: <20100719153741.291454b1b2lr4osg@webmail.ualberta.ca> <145933A2BE9E4F48AE079A201379BF2F21300EB913@RAD-EXCH1.win.ad.jhu.edu> Message-ID: <20100720094455.72123u44kko8nf6s@webmail.ualberta.ca> Thank you Hangyi, Turns out my b-value was set to -1, so changing it to 1 solved the problem. Thanks again! Ori Quoting "Hangyi Jiang" : > hi, > > please put the correct B-value in the dialog after "tensor.." > button, or put 1 as the b-value if you don't know (or don't care) > it. > > regards, > > hangyi > > > > > > ________________________________________ > From: mristudio-users-bounces at mristudio.org > [mristudio-users-bounces at mristudio.org] On Behalf Of sandya > venugopal [sandyavenugopal at gmail.com] > Sent: Monday, July 19, 2010 7:54 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] problem with newest version of DTI studio > > I have been having the same problems too. I tried to use a different > gradient table as well-no luck. I would like to get this resolved > soon too. Thanks. > > On 19 July 2010 14:37, > wrote: > Dear all, > > Up until a few days ago I worked with one of the old version and > everything seemed to be working fine; however, I now downloaded the > newest veriso and when I try to calculate "Tensor, Color Map etc" > using the same parameters and gradient I used with the old version, I > get a strange image where the brain is black and the background is > colourful. Does anyone have an idea how to solve this? > > Thank you! > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > From j.houenou at yahoo.fr Tue Jul 20 17:42:39 2010 From: j.houenou at yahoo.fr (Josselin) Date: Tue, 20 Jul 2010 21:42:39 +0000 (GMT) Subject: [Mristudio-users] ROI transformation In-Reply-To: Message-ID: <255242.68585.qm@web25604.mail.ukl.yahoo.com> Hi, Your solution seems to works perfectly fine ! Thanks, Josselin --- En date de?: Mar 20.7.10, susumu mori a ?crit?: De: susumu mori Objet: Re: [Mristudio-users] ROI transformation ?: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" , "Xin Li" , "ANDREIA FARIA" Date: Mardi 20 juillet 2010, 11h58 Hi Josselin, If I understood your question correctly, you are interested in how to keep the label name after transformation. I believe "****TypeII" and "****TypeII.dat" are the same file. They both contains 181x217x181 images. The label is in "****.hdr" file. When you load the image as an ROI file, you need the *.hdr and *.dat file. After you transformed a WMPM map (no extension or *.dat file) and save it (e.g. test.dat), I believe you can just rename the *.hdr file so that you can get both test.dat and test.hdr. Xin and Andrea, correct me if I'm wrong. susumu On Mon, Jul 19, 2010 at 4:20 PM, Josselin wrote: Dear mristudio developers and users, I have a pretty trivial question but I couldn't find any way to do it. I got for one subject a FA image and a B0 image. My goal is to register the WMPM type II eve atlas onto my FA map such as done in http://www.ncbi.nlm.nih.gov/pubmed/20570617 (paper by Zhang). I therefore used the steps described in https://www.mristudio.org/wiki/user_manual/diffeomap/ I coregistered my FA map and B0 map with air then LDDMM and obtained AIR and LDDDM matrices which seem correct: when I apply Hmap to the file named "JHU_MNI_SS_WMPM_TypeII" then the inverted AIR transformation, it fits perfectly well on my original FA map. Nevertheless, I do not know how to transform the file "JHU_MNI_SS_WMPM_TypeII.dat" which contains the ROI label names. Is there any way to do it ? When I load this file as a "subject" in diffeomap and then try to apply Hmap.vtk onto it I get "Cannot crop the LDDMM map" as an error message. Any suggestion ?? Many thanks, Josselin Houenou _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -----La pi?ce jointe associ?e suit----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100720/3b94b233/attachment-0001.html From j.houenou at yahoo.fr Tue Jul 20 17:44:41 2010 From: j.houenou at yahoo.fr (Josselin) Date: Tue, 20 Jul 2010 21:44:41 +0000 (GMT) Subject: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss Message-ID: <922192.3336.qm@web25607.mail.ukl.yahoo.com> Hi, In many files provided, some have the letters "_ss" attached to them. What does it mean ? e.g. what's the difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss ? thanks, Josselin From susumu at mri.jhu.edu Wed Jul 21 08:33:33 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 21 Jul 2010 08:33:33 -0400 Subject: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss In-Reply-To: <922192.3336.qm@web25607.mail.ukl.yahoo.com> References: <922192.3336.qm@web25607.mail.ukl.yahoo.com> Message-ID: "SS" means "single-subject", while "ss" means "skull stripped". Sorry for the confusing nomenclature. If your data is skull stripped, you should use "ss" atlas. Usually linear transformation works between non-skull stripped data. However, sometimes some extra signal such as sinus interferes with the registration. In this case, you may need to do registration between skull-stripped images. For LDDMM, it is safe to use skull-stripped images. On Tue, Jul 20, 2010 at 5:44 PM, Josselin wrote: > Hi, > In many files provided, some have the letters "_ss" attached to them. What > does it mean ? e.g. what's the difference between JHU_MNI_SS_FA and > JHU_MNI_SS_FA_ss ? > thanks, > Josselin > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100721/0d2e8d29/attachment.html From risen at kennedykrieger.org Wed Jul 21 10:03:40 2010 From: risen at kennedykrieger.org (Risen, Sarah) Date: Wed, 21 Jul 2010 14:03:40 +0000 Subject: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss In-Reply-To: References: <922192.3336.qm@web25607.mail.ukl.yahoo.com> Message-ID: <314E25B8E180B646B49E73A1B01547F20D3304@kki-gsp-mail2.kki.org> Yesterday at 3 pm we did the initial multichannel LDDMM and typed my email. In the tutorial, they said results are emailed in 30 min - 5 hours. Is this an accurate time frame? Is there a contact if we have not received a reply email in >15 hours? Thank you. sarah From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Wednesday, July 21, 2010 8:34 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss "SS" means "single-subject", while "ss" means "skull stripped". Sorry for the confusing nomenclature. If your data is skull stripped, you should use "ss" atlas. Usually linear transformation works between non-skull stripped data. However, sometimes some extra signal such as sinus interferes with the registration. In this case, you may need to do registration between skull-stripped images. For LDDMM, it is safe to use skull-stripped images. On Tue, Jul 20, 2010 at 5:44 PM, Josselin > wrote: Hi, In many files provided, some have the letters "_ss" attached to them. What does it mean ? e.g. what's the difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss ? thanks, Josselin _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100721/28198854/attachment.html From xli16 at jhmi.edu Wed Jul 21 10:06:43 2010 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 21 Jul 2010 10:06:43 -0400 Subject: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss In-Reply-To: <314E25B8E180B646B49E73A1B01547F20D3304@kki-gsp-mail2.kki.org> References: <922192.3336.qm@web25607.mail.ukl.yahoo.com> <314E25B8E180B646B49E73A1B01547F20D3304@kki-gsp-mail2.kki.org> Message-ID: <6f30d867255f2.4c46c6b3@johnshopkins.edu> Hello Sarah, After you sent the data, did you receive an email that told you the lddmm job is processing? Xin ----- Original Message ----- From: "Risen, Sarah" Date: Wednesday, July 21, 2010 10:03 am Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Yesterday at 3 pm we did the initial multichannel LDDMM and typed my > email. In the tutorial, they said results are emailed in 30 min - 5 > hours. Is this an accurate time frame? Is there a contact if we have > not received a reply email in >15 hours? Thank you. sarah > > From: mristudio-users-bounces at mristudio.org [ On Behalf Of susumu mori > Sent: Wednesday, July 21, 2010 8:34 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > > "SS" means "single-subject", while "ss" means "skull stripped". > > Sorry for the confusing nomenclature. > If your data is skull stripped, you should use "ss" atlas. > Usually linear transformation works between non-skull stripped data. > However, sometimes some extra signal such as sinus interferes with the > registration. In this case, you may need to do registration between > skull-stripped images. > For LDDMM, it is safe to use skull-stripped images. > On Tue, Jul 20, 2010 at 5:44 PM, Josselin > wrote: > Hi, > In many files provided, some have the letters "_ss" attached to them. > What does it mean ? e.g. what's the difference between JHU_MNI_SS_FA > and JHU_MNI_SS_FA_ss ? > thanks, > Josselin > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org<> > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<> > > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected > Health Information. Please note that e-mail is not necessarily > confidential or secure. Your use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying, distribution, or the taking of any action in > reliance on the contents of this information is strictly prohibited. > If you have received this e-mail in error, please immediately notify > the sender via telephone or return e-mail. > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From risen at kennedykrieger.org Wed Jul 21 10:09:24 2010 From: risen at kennedykrieger.org (Risen, Sarah) Date: Wed, 21 Jul 2010 14:09:24 +0000 Subject: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss In-Reply-To: <6f30d867255f2.4c46c6b3@johnshopkins.edu> References: <922192.3336.qm@web25607.mail.ukl.yahoo.com> <314E25B8E180B646B49E73A1B01547F20D3304@kki-gsp-mail2.kki.org> <6f30d867255f2.4c46c6b3@johnshopkins.edu> Message-ID: <314E25B8E180B646B49E73A1B01547F20D3339@kki-gsp-mail2.kki.org> No, So I am guessing that it did not go through? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li Sent: Wednesday, July 21, 2010 10:07 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss Hello Sarah, After you sent the data, did you receive an email that told you the lddmm job is processing? Xin ----- Original Message ----- From: "Risen, Sarah" Date: Wednesday, July 21, 2010 10:03 am Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Yesterday at 3 pm we did the initial multichannel LDDMM and typed my > email. In the tutorial, they said results are emailed in 30 min - 5 > hours. Is this an accurate time frame? Is there a contact if we have > not received a reply email in >15 hours? Thank you. sarah > > From: mristudio-users-bounces at mristudio.org [ On Behalf Of susumu mori > Sent: Wednesday, July 21, 2010 8:34 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > > "SS" means "single-subject", while "ss" means "skull stripped". > > Sorry for the confusing nomenclature. > If your data is skull stripped, you should use "ss" atlas. > Usually linear transformation works between non-skull stripped data. > However, sometimes some extra signal such as sinus interferes with the > registration. In this case, you may need to do registration between > skull-stripped images. > For LDDMM, it is safe to use skull-stripped images. > On Tue, Jul 20, 2010 at 5:44 PM, Josselin > wrote: > Hi, > In many files provided, some have the letters "_ss" attached to them. > What does it mean ? e.g. what's the difference between JHU_MNI_SS_FA > and JHU_MNI_SS_FA_ss ? > thanks, > Josselin > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org<> > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<> > > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected > Health Information. Please note that e-mail is not necessarily > confidential or secure. Your use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying, distribution, or the taking of any action in > reliance on the contents of this information is strictly prohibited. > If you have received this e-mail in error, please immediately notify > the sender via telephone or return e-mail. > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Wed Jul 21 10:12:46 2010 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 21 Jul 2010 10:12:46 -0400 Subject: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss In-Reply-To: <314E25B8E180B646B49E73A1B01547F20D3339@kki-gsp-mail2.kki.org> References: <922192.3336.qm@web25607.mail.ukl.yahoo.com> <314E25B8E180B646B49E73A1B01547F20D3304@kki-gsp-mail2.kki.org> <6f30d867255f2.4c46c6b3@johnshopkins.edu> <314E25B8E180B646B49E73A1B01547F20D3339@kki-gsp-mail2.kki.org> Message-ID: <6f30a1a525ac9.4c46c81e@johnshopkins.edu> After you clicked the "OK" button of DiffeoMap, did you get this popped up message "The image data have been sent to the ftp server successfully."? Xin ----- Original Message ----- From: "Risen, Sarah" Date: Wednesday, July 21, 2010 10:09 am Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > No, So I am guessing that it did not go through? > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org [ On Behalf Of Xin Li > Sent: Wednesday, July 21, 2010 10:07 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > > Hello Sarah, > > After you sent the data, did you receive an email that told you the > lddmm job is processing? > > > Xin > > > > ----- Original Message ----- > From: "Risen, Sarah" > Date: Wednesday, July 21, 2010 10:03 am > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > > > > Yesterday at 3 pm we did the initial multichannel LDDMM and typed > my > > email. In the tutorial, they said results are emailed in 30 min - > 5 > > hours. Is this an accurate time frame? Is there a contact if we > have > > not received a reply email in >15 hours? Thank you. sarah > > > > From: mristudio-users-bounces at mristudio.org [ On Behalf Of susumu > mori > > Sent: Wednesday, July 21, 2010 8:34 AM > > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA > and JHU_MNI_SS_FA_ss > > > > "SS" means "single-subject", while "ss" means "skull stripped". > > > > Sorry for the confusing nomenclature. > > If your data is skull stripped, you should use "ss" atlas. > > Usually linear transformation works between non-skull stripped > data. > > However, sometimes some extra signal such as sinus interferes with > the > > registration. In this case, you may need to do registration between > > > skull-stripped images. > > For LDDMM, it is safe to use skull-stripped images. > > On Tue, Jul 20, 2010 at 5:44 PM, Josselin > wrote: > > Hi, > > In many files provided, some have the letters "_ss" attached to > them. > > What does it mean ? e.g. what's the difference between > JHU_MNI_SS_FA > > and JHU_MNI_SS_FA_ss ? > > thanks, > > Josselin > > > > > > > > > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org<> > > > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<> > > > > > > > > > > Disclaimer: > > The materials in this e-mail are private and may contain Protected > > > Health Information. Please note that e-mail is not necessarily > > confidential or secure. Your use of e-mail constitutes your > > acknowledgment of these confidentiality and security limitations. > If > > you are not the intended recipient, be advised that any > unauthorized > > use, disclosure, copying, distribution, or the taking of any action > in > > reliance on the contents of this information is strictly > prohibited. > > If you have received this e-mail in error, please immediately > notify > > the sender via telephone or return e-mail. > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From risen at kennedykrieger.org Wed Jul 21 10:48:48 2010 From: risen at kennedykrieger.org (Risen, Sarah) Date: Wed, 21 Jul 2010 14:48:48 +0000 Subject: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss In-Reply-To: <6f30a1a525ac9.4c46c81e@johnshopkins.edu> References: <922192.3336.qm@web25607.mail.ukl.yahoo.com> <314E25B8E180B646B49E73A1B01547F20D3304@kki-gsp-mail2.kki.org> <6f30d867255f2.4c46c6b3@johnshopkins.edu> <314E25B8E180B646B49E73A1B01547F20D3339@kki-gsp-mail2.kki.org> <6f30a1a525ac9.4c46c81e@johnshopkins.edu> Message-ID: <314E25B8E180B646B49E73A1B01547F20D33C0@kki-gsp-mail2.kki.org> We did get the pop-up message... -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li Sent: Wednesday, July 21, 2010 10:13 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss After you clicked the "OK" button of DiffeoMap, did you get this popped up message "The image data have been sent to the ftp server successfully."? Xin ----- Original Message ----- From: "Risen, Sarah" Date: Wednesday, July 21, 2010 10:09 am Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > No, So I am guessing that it did not go through? > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org [ On Behalf Of Xin Li > Sent: Wednesday, July 21, 2010 10:07 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > > Hello Sarah, > > After you sent the data, did you receive an email that told you the > lddmm job is processing? > > > Xin > > > > ----- Original Message ----- > From: "Risen, Sarah" > Date: Wednesday, July 21, 2010 10:03 am > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > > > > Yesterday at 3 pm we did the initial multichannel LDDMM and typed > my > > email. In the tutorial, they said results are emailed in 30 min - > 5 > > hours. Is this an accurate time frame? Is there a contact if we > have > > not received a reply email in >15 hours? Thank you. sarah > > > > From: mristudio-users-bounces at mristudio.org [ On Behalf Of susumu > mori > > Sent: Wednesday, July 21, 2010 8:34 AM > > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA > and JHU_MNI_SS_FA_ss > > > > "SS" means "single-subject", while "ss" means "skull stripped". > > > > Sorry for the confusing nomenclature. > > If your data is skull stripped, you should use "ss" atlas. > > Usually linear transformation works between non-skull stripped > data. > > However, sometimes some extra signal such as sinus interferes with > the > > registration. In this case, you may need to do registration between > > > skull-stripped images. > > For LDDMM, it is safe to use skull-stripped images. > > On Tue, Jul 20, 2010 at 5:44 PM, Josselin > wrote: > > Hi, > > In many files provided, some have the letters "_ss" attached to > them. > > What does it mean ? e.g. what's the difference between > JHU_MNI_SS_FA > > and JHU_MNI_SS_FA_ss ? > > thanks, > > Josselin > > > > > > > > > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org<> > > > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<> > > > > > > > > > > Disclaimer: > > The materials in this e-mail are private and may contain Protected > > > Health Information. Please note that e-mail is not necessarily > > confidential or secure. Your use of e-mail constitutes your > > acknowledgment of these confidentiality and security limitations. > If > > you are not the intended recipient, be advised that any > unauthorized > > use, disclosure, copying, distribution, or the taking of any action > in > > reliance on the contents of this information is strictly > prohibited. > > If you have received this e-mail in error, please immediately > notify > > the sender via telephone or return e-mail. > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Wed Jul 21 10:58:27 2010 From: xli16 at jhmi.edu (Xin Li) Date: Wed, 21 Jul 2010 10:58:27 -0400 Subject: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss In-Reply-To: <314E25B8E180B646B49E73A1B01547F20D33C0@kki-gsp-mail2.kki.org> References: <922192.3336.qm@web25607.mail.ukl.yahoo.com> <314E25B8E180B646B49E73A1B01547F20D3304@kki-gsp-mail2.kki.org> <6f30d867255f2.4c46c6b3@johnshopkins.edu> <314E25B8E180B646B49E73A1B01547F20D3339@kki-gsp-mail2.kki.org> <6f30a1a525ac9.4c46c81e@johnshopkins.edu> <314E25B8E180B646B49E73A1B01547F20D33C0@kki-gsp-mail2.kki.org> Message-ID: <6ef0ac9322358.4c46d2d3@johnshopkins.edu> I am going to forward your email to my colleague. He will check for you. Xin ----- Original Message ----- From: "Risen, Sarah" Date: Wednesday, July 21, 2010 10:48 am Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > We did get the pop-up message... > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org [ On Behalf Of Xin Li > Sent: Wednesday, July 21, 2010 10:13 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > > After you clicked the "OK" button of DiffeoMap, did you get this > popped up message "The image data have been sent to the ftp server successfully."? > > > Xin > > ----- Original Message ----- > From: "Risen, Sarah" > Date: Wednesday, July 21, 2010 10:09 am > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > > > > No, So I am guessing that it did not go through? > > > > -----Original Message----- > > From: mristudio-users-bounces at mristudio.org [ On Behalf Of Xin Li > > Sent: Wednesday, July 21, 2010 10:07 AM > > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA > and JHU_MNI_SS_FA_ss > > > > Hello Sarah, > > > > After you sent the data, did you receive an email that told you > the > > lddmm job is processing? > > > > > > Xin > > > > > > > > ----- Original Message ----- > > From: "Risen, Sarah" > > Date: Wednesday, July 21, 2010 10:03 am > > Subject: Re: [Mristudio-users] difference > between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > > > > > > > Yesterday at 3 pm we did the initial multichannel LDDMM and > typed > > my > > > email. In the tutorial, they said results are emailed in 30 min > - > > 5 > > > hours. Is this an accurate time frame? Is there a contact if > we > > have > > > not received a reply email in >15 hours? Thank you. sarah > > > > > > From: mristudio-users-bounces at mristudio.org [ On Behalf Of > susumu > > mori > > > Sent: Wednesday, July 21, 2010 8:34 AM > > > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > > > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA > > > and JHU_MNI_SS_FA_ss > > > > > > "SS" means "single-subject", while "ss" means "skull stripped". > > > > > > Sorry for the confusing nomenclature. > > > If your data is skull stripped, you should use "ss" atlas. > > > Usually linear transformation works between non-skull stripped > > > data. > > > However, sometimes some extra signal such as sinus interferes > with > > the > > > registration. In this case, you may need to do registration > between > > > > > skull-stripped images. > > > For LDDMM, it is safe to use skull-stripped images. > > > On Tue, Jul 20, 2010 at 5:44 PM, Josselin > > wrote: > > > Hi, > > > In many files provided, some have the letters "_ss" attached to > > > them. > > > What does it mean ? e.g. what's the difference between > > JHU_MNI_SS_FA > > > and JHU_MNI_SS_FA_ss ? > > > thanks, > > > Josselin > > > > > > > > > > > > > > > > > > _______________________________________________ > > > mristudio-users mailing list > > > mristudio-users at mristudio.org<> > > > > > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<> > > > > > > > > > > > > > > > Disclaimer: > > > The materials in this e-mail are private and may contain > Protected > > > > > Health Information. Please note that e-mail is not necessarily > > > confidential or secure. Your use of e-mail constitutes your > > > acknowledgment of these confidentiality and security > limitations. > > If > > > you are not the intended recipient, be advised that any > > unauthorized > > > use, disclosure, copying, distribution, or the taking of any > action > > in > > > reliance on the contents of this information is strictly > > prohibited. > > > If you have received this e-mail in error, please immediately > > notify > > > the sender via telephone or return e-mail. > > > _______________________________________________ > > > mristudio-users mailing list > > > mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From risen at kennedykrieger.org Wed Jul 21 10:59:32 2010 From: risen at kennedykrieger.org (Risen, Sarah) Date: Wed, 21 Jul 2010 14:59:32 +0000 Subject: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss In-Reply-To: <6ef0ac9322358.4c46d2d3@johnshopkins.edu> References: <922192.3336.qm@web25607.mail.ukl.yahoo.com> <314E25B8E180B646B49E73A1B01547F20D3304@kki-gsp-mail2.kki.org> <6f30d867255f2.4c46c6b3@johnshopkins.edu> <314E25B8E180B646B49E73A1B01547F20D3339@kki-gsp-mail2.kki.org> <6f30a1a525ac9.4c46c81e@johnshopkins.edu> <314E25B8E180B646B49E73A1B01547F20D33C0@kki-gsp-mail2.kki.org> <6ef0ac9322358.4c46d2d3@johnshopkins.edu> Message-ID: <314E25B8E180B646B49E73A1B01547F20D33F9@kki-gsp-mail2.kki.org> Thank you! I typed in : risen at kennedykrieger.org -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li Sent: Wednesday, July 21, 2010 10:58 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss I am going to forward your email to my colleague. He will check for you. Xin ----- Original Message ----- From: "Risen, Sarah" Date: Wednesday, July 21, 2010 10:48 am Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > We did get the pop-up message... > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org [ On Behalf Of Xin Li > Sent: Wednesday, July 21, 2010 10:13 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > > After you clicked the "OK" button of DiffeoMap, did you get this > popped up message "The image data have been sent to the ftp server successfully."? > > > Xin > > ----- Original Message ----- > From: "Risen, Sarah" > Date: Wednesday, July 21, 2010 10:09 am > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > > > > No, So I am guessing that it did not go through? > > > > -----Original Message----- > > From: mristudio-users-bounces at mristudio.org [ On Behalf Of Xin Li > > Sent: Wednesday, July 21, 2010 10:07 AM > > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA > and JHU_MNI_SS_FA_ss > > > > Hello Sarah, > > > > After you sent the data, did you receive an email that told you > the > > lddmm job is processing? > > > > > > Xin > > > > > > > > ----- Original Message ----- > > From: "Risen, Sarah" > > Date: Wednesday, July 21, 2010 10:03 am > > Subject: Re: [Mristudio-users] difference > between JHU_MNI_SS_FA and JHU_MNI_SS_FA_ss > > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > > > > > > > Yesterday at 3 pm we did the initial multichannel LDDMM and > typed > > my > > > email. In the tutorial, they said results are emailed in 30 min > - > > 5 > > > hours. Is this an accurate time frame? Is there a contact if > we > > have > > > not received a reply email in >15 hours? Thank you. sarah > > > > > > From: mristudio-users-bounces at mristudio.org [ On Behalf Of > susumu > > mori > > > Sent: Wednesday, July 21, 2010 8:34 AM > > > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > > > Subject: Re: [Mristudio-users] difference between JHU_MNI_SS_FA > > > and JHU_MNI_SS_FA_ss > > > > > > "SS" means "single-subject", while "ss" means "skull stripped". > > > > > > Sorry for the confusing nomenclature. > > > If your data is skull stripped, you should use "ss" atlas. > > > Usually linear transformation works between non-skull stripped > > > data. > > > However, sometimes some extra signal such as sinus interferes > with > > the > > > registration. In this case, you may need to do registration > between > > > > > skull-stripped images. > > > For LDDMM, it is safe to use skull-stripped images. > > > On Tue, Jul 20, 2010 at 5:44 PM, Josselin > > wrote: > > > Hi, > > > In many files provided, some have the letters "_ss" attached to > > > them. > > > What does it mean ? e.g. what's the difference between > > JHU_MNI_SS_FA > > > and JHU_MNI_SS_FA_ss ? > > > thanks, > > > Josselin > > > > > > > > > > > > > > > > > > _______________________________________________ > > > mristudio-users mailing list > > > mristudio-users at mristudio.org<> > > > > > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org<> > > > > > > > > > > > > > > > Disclaimer: > > > The materials in this e-mail are private and may contain > Protected > > > > > Health Information. Please note that e-mail is not necessarily > > > confidential or secure. Your use of e-mail constitutes your > > > acknowledgment of these confidentiality and security > limitations. > > If > > > you are not the intended recipient, be advised that any > > unauthorized > > > use, disclosure, copying, distribution, or the taking of any > action > > in > > > reliance on the contents of this information is strictly > > prohibited. > > > If you have received this e-mail in error, please immediately > > notify > > > the sender via telephone or return e-mail. > > > _______________________________________________ > > > mristudio-users mailing list > > > mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From jmcentee at jhmi.edu Thu Jul 22 10:51:39 2010 From: jmcentee at jhmi.edu (Julie McEntee) Date: Thu, 22 Jul 2010 10:51:39 -0400 Subject: [Mristudio-users] mristudio : strange ROI image (my message has not been accepted on the list) In-Reply-To: <373078.55826.qm@web25605.mail.ukl.yahoo.com> Message-ID: HI Josselin, I have encountered the same issue- it seems that, in one of the steps used to transform an ROI template into another space, the ROIs do not remain intact. That is, as your pic shows, some of the pixels within each ROI end up elsewhere in the brain. The only solution I can think of (and I haven?t tried it yet) is to ?clean up? the ROI, that is, use the ROI tools to select and ?subtract? the pixels that are outside the ROI. Perhaps someone else on the list has successfully accomplished creating ?clean? ROIs from a transformed template and can comment/assist. Susumu- I?m wondering if you?ve examined whether the mean FA, other stats obtained from transformed ROI templates are affected by the displaced pixels? Thanks, Julie On 7/22/10 4:54 AM, "Josselin" wrote: > Hello, > > I am sending this email directly to you because the list refused it, probably > because of the joint file. > > Using Diffeomap, I use a WMPM_type_II_atlas and registered it on my native FA > image through LDDMM and Air. First, it looked fine > But when I looked deeper and tried to extract only one ROI (the first one): > here is the result I got: (joint jpg file). The core of the ROI seems ok but > it also includes many alien points. Do you have any idea ? > > thanks, > Josselin Houenou > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100722/17a542f1/attachment.html From j.houenou at yahoo.fr Wed Jul 21 01:15:42 2010 From: j.houenou at yahoo.fr (Josselin) Date: Wed, 21 Jul 2010 05:15:42 +0000 (GMT) Subject: [Mristudio-users] strange ROI image Message-ID: <83607.44087.qm@web25603.mail.ukl.yahoo.com> Hi, I use a WMPM_type_II_atlas and registered it on my native FA image through LDDMM and Air. First, it looked fine But when I look deeper and tried to extract only one ROI (the first one):? here is the result I got: (joint jpg file). The core of the ROI seems ok but it also includes many alien points. Do you have any idea ? thanks, Josselin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100721/f8a308c7/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: roi_1_probleme.jpg Type: image/jpeg Size: 88272 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100721/f8a308c7/attachment-0001.jpg From xli16 at jhmi.edu Thu Jul 22 11:15:54 2010 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 22 Jul 2010 11:15:54 -0400 Subject: [Mristudio-users] strange ROI image In-Reply-To: <83607.44087.qm@web25603.mail.ukl.yahoo.com> References: <83607.44087.qm@web25603.mail.ukl.yahoo.com> Message-ID: <6f50d49b2222f.4c48286a@johnshopkins.edu> Hello Josselin, This problem may be caused by the interpolation method you used when you applied the transformation matrix to WMPM_type_II_atlas. In this step, nearest neighbor should be used instead of trilinear. Regards, Xin ----- Original Message ----- From: Josselin Date: Thursday, July 22, 2010 11:10 am Subject: [Mristudio-users] strange ROI image To: mristudio-users at mristudio.org > Hi, > > I use a WMPM_type_II_atlas and registered it on my native FA > image through LDDMM and Air. First, it looked fine > But when I look > deeper and tried to extract only one ROI (the first one):? here is > the > result I got: (joint jpg file). The core of the ROI seems ok but it also > includes many alien points. Do you have any idea ? > > thanks, > Josselin > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From j.houenou at yahoo.fr Thu Jul 22 13:06:02 2010 From: j.houenou at yahoo.fr (Josselin) Date: Thu, 22 Jul 2010 17:06:02 +0000 (GMT) Subject: [Mristudio-users] strange ROI image In-Reply-To: <6f50d49b2222f.4c48286a@johnshopkins.edu> Message-ID: <427032.89177.qm@web25603.mail.ukl.yahoo.com> Hello Xin, It works !!!!! Thank you for taking so much time answering all our questions ... Josselin --- En date de?: Jeu 22.7.10, Xin Li a ?crit?: > De: Xin Li > Objet: Re: [Mristudio-users] strange ROI image > ?: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Date: Jeudi 22 juillet 2010, 17h15 > Hello Josselin, > > This problem may be caused by the interpolation method you > used when you applied the transformation matrix to > WMPM_type_II_atlas. In this step, nearest neighbor should be > used instead of trilinear. > > > Regards, > > Xin > > > > > > > > > ----- Original Message ----- > From: Josselin > Date: Thursday, July 22, 2010 11:10 am > Subject: [Mristudio-users] strange ROI image > To: mristudio-users at mristudio.org > > > > Hi, > >? > >? I use a WMPM_type_II_atlas and registered it on > my native FA > >? image through LDDMM and Air. First, it looked > fine > >? But when I look > >? deeper and tried to extract only one ROI (the > first one):? here is > > the > >? result I got: (joint jpg file). The core of the > ROI seems ok but it also > >???includes many alien points. Do you > have any idea ? > >? > >? thanks, > >? Josselin > >? > >? > >? ? ? ??? > > _______________________________________________ > >? mristudio-users mailing list > >? mristudio-users at mristudio.org > >? > >? Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > From j.houenou at yahoo.fr Thu Jul 22 14:39:25 2010 From: j.houenou at yahoo.fr (Josselin) Date: Thu, 22 Jul 2010 18:39:25 +0000 (GMT) Subject: [Mristudio-users] how to build the "Frontal" ROI for tracking ? Message-ID: <107522.21613.qm@web25607.mail.ukl.yahoo.com> Hi, I use Diffeomap and ROIeditor to reconstruct automatically tracts like in the Zhang paper (2010). ROI registration on a single subject works now perfectly fine (thanks!). In the Zhang paper, e.g. the IFO is the tract going through regions you named "Frontal" and "Occipital". I assume that these are the whole frontal lobe and the whole occipital lobe (?). Have you drawn them manually ? Or is there another any convenient way for it ? thanks again, Josselin From xli16 at jhmi.edu Thu Jul 22 15:19:24 2010 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 22 Jul 2010 15:19:24 -0400 Subject: [Mristudio-users] how to build the "Frontal" ROI for tracking ? In-Reply-To: <107522.21613.qm@web25607.mail.ukl.yahoo.com> References: <107522.21613.qm@web25607.mail.ukl.yahoo.com> Message-ID: <6f70ca8a22f53.4c48617c@johnshopkins.edu> Hello Josselin, I will forward your email to my colleague Yajing Zhang, the author of the paper. Xin ----- Original Message ----- From: Josselin Date: Thursday, July 22, 2010 2:39 pm Subject: [Mristudio-users] how to build the "Frontal" ROI for tracking ? To: mristudio-users at mristudio.org > Hi, > I use Diffeomap and ROIeditor to reconstruct automatically tracts > like in the Zhang paper (2010). > ROI registration on a single subject works now perfectly fine (thanks!). > In the Zhang paper, e.g. the IFO is the tract going through regions > you named "Frontal" and "Occipital". I assume that these are the whole > frontal lobe and the whole occipital lobe (?). > > Have you drawn them manually ? Or is there another any convenient way > for it ? > > thanks again, > Josselin > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Thu Jul 22 15:41:43 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 22 Jul 2010 15:41:43 -0400 Subject: [Mristudio-users] how to build the "Frontal" ROI for tracking ? In-Reply-To: <6f70ca8a22f53.4c48617c@johnshopkins.edu> References: <107522.21613.qm@web25607.mail.ukl.yahoo.com> <6f70ca8a22f53.4c48617c@johnshopkins.edu> Message-ID: As Xin mentioned, you can request the ROI sets for particular tracts of your interest to Yajing. As a matter of fact, I believe the entire ROI files (TRS: Template ROI Set) are posted somewhere. Yajing should be able to elaborate this. On Thu, Jul 22, 2010 at 3:19 PM, Xin Li wrote: > Hello Josselin, > > I will forward your email to my colleague Yajing Zhang, the author of the > paper. > > > Xin > > > > > > ----- Original Message ----- > From: Josselin > Date: Thursday, July 22, 2010 2:39 pm > Subject: [Mristudio-users] how to build the "Frontal" ROI for tracking ? > To: mristudio-users at mristudio.org > > > > Hi, > > I use Diffeomap and ROIeditor to reconstruct automatically tracts > > like in the Zhang paper (2010). > > ROI registration on a single subject works now perfectly fine (thanks!). > > In the Zhang paper, e.g. the IFO is the tract going through regions > > you named "Frontal" and "Occipital". I assume that these are the whole > > frontal lobe and the whole occipital lobe (?). > > > > Have you drawn them manually ? Or is there another any convenient way > > for it ? > > > > thanks again, > > Josselin > > > > > > > > > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100722/5d6ff545/attachment.html From gmak13 at wp.pl Fri Jul 23 16:14:51 2010 From: gmak13 at wp.pl (gmak13 at wp.pl) Date: Fri, 23 Jul 2010 22:14:51 +0200 Subject: [Mristudio-users] LDDMM email Message-ID: <26AB0360B92A4D3E96B39D04EAED5E48@zxzPC> Hi I have problem with LDDMM. Yesterday I did the multichannel LDDMM -everything like in the manual, but I haven't received any emails ("job is processing" or the results). Today I do it second time, and still waiting.... What shuold I do to receive reply emails? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100723/693f358c/attachment.html From xli16 at jhmi.edu Thu Jul 22 16:23:12 2010 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 22 Jul 2010 16:23:12 -0400 Subject: [Mristudio-users] LDDMM email In-Reply-To: <26AB0360B92A4D3E96B39D04EAED5E48@zxzPC> References: <26AB0360B92A4D3E96B39D04EAED5E48@zxzPC> Message-ID: <7250bdd329576.4c487070@johnshopkins.edu> Hello, Please check the spam folder in your email box. Sometimes the emails are filtered by email servers because they don't like the long md5 strings in the subjects of those emails. Xin ----- Original Message ----- From: gmak13 at wp.pl Date: Thursday, July 22, 2010 4:16 pm Subject: [Mristudio-users] LDDMM email To: mristudio-users at mristudio.org > Hi > > I have problem with LDDMM. > Yesterday I did the multichannel LDDMM -everything like in the > manual, but I haven't received any emails ("job is processing" or the > results). > Today I do it second time, and still waiting.... > What shuold I do to receive reply emails? > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From gmak13 at wp.pl Fri Jul 23 17:35:37 2010 From: gmak13 at wp.pl (gmak13 at wp.pl) Date: Fri, 23 Jul 2010 23:35:37 +0200 Subject: [Mristudio-users] LDDMM email In-Reply-To: <7250bdd329576.4c487070@johnshopkins.edu> References: <26AB0360B92A4D3E96B39D04EAED5E48@zxzPC> <7250bdd329576.4c487070@johnshopkins.edu> Message-ID: <1923E4E977194AB0BB5BC52F8748A083@zxzPC> Hi I check my spam folder and didn't found it. any other ideas? what else may I do? Thanks Grzesiek ----- Original Message ----- From: "Xin Li" To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" Sent: Thursday, July 22, 2010 10:23 PM Subject: Re: [Mristudio-users] LDDMM email > Hello, > > Please check the spam folder in your email box. Sometimes the emails are > filtered by email servers because they don't like the long md5 strings in > the subjects of those emails. > > > Xin > > > > > ----- Original Message ----- > From: gmak13 at wp.pl > Date: Thursday, July 22, 2010 4:16 pm > Subject: [Mristudio-users] LDDMM email > To: mristudio-users at mristudio.org > > >> Hi >> >> I have problem with LDDMM. >> Yesterday I did the multichannel LDDMM -everything like in the >> manual, but I haven't received any emails ("job is processing" or the >> results). >> Today I do it second time, and still waiting.... >> What shuold I do to receive reply emails? >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------------------------------------------------------------------------- Nie znaleziono wirusa w tej wiadomosci przychodzacej. Sprawdzone przez AVG - www.avg.com Wersja: 9.0.851 / Baza danych wirusow: 271.1.1/3021 - Data wydania: 07/22/10 08:36:00 From j.houenou at yahoo.fr Fri Jul 23 17:12:47 2010 From: j.houenou at yahoo.fr (Josselin) Date: Fri, 23 Jul 2010 21:12:47 +0000 (GMT) Subject: [Mristudio-users] skull stripping Message-ID: <283184.82926.qm@web25608.mail.ukl.yahoo.com> Hello, In order to process FA data, you advise to use skull stripped brains. I can't find any tool for it in MRIstudio. Am I wrong ? Which one do you recommend ? thanks, Josselin From j.houenou at yahoo.fr Fri Jul 23 17:14:18 2010 From: j.houenou at yahoo.fr (Josselin) Date: Fri, 23 Jul 2010 21:14:18 +0000 (GMT) Subject: [Mristudio-users] AC/PC and AIR Message-ID: <672133.83679.qm@web25608.mail.ukl.yahoo.com> Hi, I am doing acquisitions in a non AC/PC referential (generally slightly oblique to AC/PC). Do you think that I need to transform my FA/b0 images in a AC/PC referential ? Or is AIR sufficient ? thanks, Josselin From xli16 at jhmi.edu Fri Jul 23 17:19:25 2010 From: xli16 at jhmi.edu (Xin Li) Date: Fri, 23 Jul 2010 17:19:25 -0400 Subject: [Mristudio-users] skull stripping In-Reply-To: <283184.82926.qm@web25608.mail.ukl.yahoo.com> References: <283184.82926.qm@web25608.mail.ukl.yahoo.com> Message-ID: <7300eb847f76.4c49cf1d@johnshopkins.edu> Hello Josselin, ROIEditor has the skull stripped tool. You may try it. Xin ----- Original Message ----- From: Josselin Date: Friday, July 23, 2010 5:13 pm Subject: [Mristudio-users] skull stripping To: mristudio-users at mristudio.org > Hello, > In order to process FA data, you advise to use skull stripped brains. > I can't find any tool for it in MRIstudio. Am I wrong ? Which one do > you recommend ? > thanks, > Josselin > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From fariaav at gmail.com Fri Jul 23 17:25:16 2010 From: fariaav at gmail.com (Andreia Vaconcellos Faria) Date: Fri, 23 Jul 2010 17:25:16 -0400 Subject: [Mristudio-users] AC/PC and AIR In-Reply-To: <672133.83679.qm@web25608.mail.ukl.yahoo.com> References: <672133.83679.qm@web25608.mail.ukl.yahoo.com> Message-ID: Hi, Josselin, Usually air can correct the angle differences. If your results are not good, try a rigid transformation before air (mutual has been done a good job). best, Andreia On Fri, Jul 23, 2010 at 5:14 PM, Josselin wrote: > Hi, > I am doing acquisitions in a non AC/PC referential (generally slightly > oblique to AC/PC). > Do you think that I need to transform my FA/b0 images in a AC/PC > referential ? Or is AIR sufficient ? > thanks, > Josselin > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100723/9983f3dc/attachment.html From j.houenou at yahoo.fr Fri Jul 23 17:32:38 2010 From: j.houenou at yahoo.fr (Josselin) Date: Fri, 23 Jul 2010 21:32:38 +0000 (GMT) Subject: [Mristudio-users] skull stripping In-Reply-To: <7300eb847f76.4c49cf1d@johnshopkins.edu> Message-ID: <988964.92273.qm@web25608.mail.ukl.yahoo.com> Hi, Thanks; I can't find any manual for it (there are many parameters...) Josselin --- En date de?: Ven 23.7.10, Xin Li a ?crit?: > De: Xin Li > Objet: Re: [Mristudio-users] skull stripping > ?: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Date: Vendredi 23 juillet 2010, 23h19 > Hello Josselin, > > ROIEditor has the skull stripped tool. You may try it. > > > Xin > > > > > ----- Original Message ----- > From: Josselin > Date: Friday, July 23, 2010 5:13 pm > Subject: [Mristudio-users] skull stripping > To: mristudio-users at mristudio.org > > > > Hello, > >? In order to process FA data, you advise to use > skull stripped brains. > > I can't find any tool for it in MRIstudio. Am I wrong > ? Which one do > > you recommend ? > >? thanks, > >? Josselin > >? > >? > >? ? ? ? > >? > >? > >? _______________________________________________ > >? mristudio-users mailing list > >? mristudio-users at mristudio.org > >? > >? Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > From fariaav at gmail.com Fri Jul 23 17:41:34 2010 From: fariaav at gmail.com (Andreia Vaconcellos Faria) Date: Fri, 23 Jul 2010 17:41:34 -0400 Subject: [Mristudio-users] skull stripping In-Reply-To: <988964.92273.qm@web25608.mail.ukl.yahoo.com> References: <7300eb847f76.4c49cf1d@johnshopkins.edu> <988964.92273.qm@web25608.mail.ukl.yahoo.com> Message-ID: Hi, Josselin, You can use the default parameters, except for W5. W5 values between 0.8 and 1.3 usually work better. The bigger your W5, the more conservative is your stripping. Andreia. On Fri, Jul 23, 2010 at 5:32 PM, Josselin wrote: > Hi, > Thanks; I can't find any manual for it (there are many parameters...) > Josselin > > --- En date de : Ven 23.7.10, Xin Li a ?crit : > > > De: Xin Li > > Objet: Re: [Mristudio-users] skull stripping > > ?: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" < > mristudio-users at mristudio.org> > > Date: Vendredi 23 juillet 2010, 23h19 > > Hello Josselin, > > > > ROIEditor has the skull stripped tool. You may try it. > > > > > > Xin > > > > > > > > > > ----- Original Message ----- > > From: Josselin > > Date: Friday, July 23, 2010 5:13 pm > > Subject: [Mristudio-users] skull stripping > > To: mristudio-users at mristudio.org > > > > > > > Hello, > > > In order to process FA data, you advise to use > > skull stripped brains. > > > I can't find any tool for it in MRIstudio. Am I wrong > > ? Which one do > > > you recommend ? > > > thanks, > > > Josselin > > > > > > > > > > > > > > > > > > _______________________________________________ > > > mristudio-users mailing list > > > mristudio-users at mristudio.org > > > > > > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100723/440adc16/attachment-0001.html From rajagov2 at ccf.org Fri Jul 23 18:19:13 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Fri, 23 Jul 2010 18:19:13 -0400 Subject: [Mristudio-users] new option save fiber density Message-ID: <77A88E90A851594AAEF830450587C39D04183271@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, I am using DTIstudio_latest_x86.exe after fiber tractography I notices a new option named "save fiber density map" (normalized and non normalized). I am wondering what information does this fiber density map convey and how this information can be used for instance to compare between two groups. How the map is normalized. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100723/d09d094b/attachment.html From susumu at mri.jhu.edu Sat Jul 24 08:56:45 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sat, 24 Jul 2010 08:56:45 -0400 Subject: [Mristudio-users] new option save fiber density In-Reply-To: <77A88E90A851594AAEF830450587C39D04183271@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D04183271@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Hi Venkat, After fiber tracking, it is a common practice to quantify the results. For the quantification, the streamline information of the tractography needs to be converted to pixel information. For this conversion, the simplest way is to use 1/0 binarilzation. If a pixel contains a streamline, it becomes 1 and if not, remains 0. This is basically a masking, which can be applied to, for example, a FA map and get a FA value of the tract. You can also count the number of pixels with "1" and use it as the tract volume. One problem of this simple approach is that even if a pixel contains 10 streamlines, the pixel becomes "1", which is the same as another pixel that contains only 1 streamline. Namely, during the binalization, information about the density of the streamline is lost. I believe (Hangyi, please correct me if I'm wrong) "fiber density map" tells how many streamlines were there in each pixel. You can potentially use it to get, for example, density-weighted FA value, in which pixels that contain more streamlines are more weighted than those contain only 1 streamline. On Fri, Jul 23, 2010 at 6:19 PM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > > Dear All, > > I am using DTIstudio_latest_x86.exe after fiber tractography I notices a > new option named "save fiber density map" (normalized and non normalized). I > am wondering what information does this fiber density map convey and how > this information can be used for instance to compare between two groups. How > the map is normalized. > > Thanks > > Venkat > > =================================== > > P Please consider the environment before printing this e-mail > > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100724/96139905/attachment.html From rajagov2 at ccf.org Sun Jul 25 15:10:58 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Sun, 25 Jul 2010 15:10:58 -0400 Subject: [Mristudio-users] new option save fiber density References: <77A88E90A851594AAEF830450587C39D04183271@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D04183272@CCHSCLEXMB56.cc.ad.cchs.net> Thanks very much Dr.Mori, this indeed will give more information. Thanks Venkat ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Sat 7/24/2010 8:56 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang Subject: Re: [Mristudio-users] new option save fiber density Hi Venkat, After fiber tracking, it is a common practice to quantify the results. For the quantification, the streamline information of the tractography needs to be converted to pixel information. For this conversion, the simplest way is to use 1/0 binarilzation. If a pixel contains a streamline, it becomes 1 and if not, remains 0. This is basically a masking, which can be applied to, for example, a FA map and get a FA value of the tract. You can also count the number of pixels with "1" and use it as the tract volume. One problem of this simple approach is that even if a pixel contains 10 streamlines, the pixel becomes "1", which is the same as another pixel that contains only 1 streamline. Namely, during the binalization, information about the density of the streamline is lost. I believe (Hangyi, please correct me if I'm wrong) "fiber density map" tells how many streamlines were there in each pixel. You can potentially use it to get, for example, density-weighted FA value, in which pixels that contain more streamlines are more weighted than those contain only 1 streamline. On Fri, Jul 23, 2010 at 6:19 PM, Rajagopalan, Venkateswaran wrote: Dear All, I am using DTIstudio_latest_x86.exe after fiber tractography I notices a new option named "save fiber density map" (normalized and non normalized). I am wondering what information does this fiber density map convey and how this information can be used for instance to compare between two groups. How the map is normalized. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6352 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100725/79f8445e/attachment-0001.bin From choisj70 at gmail.com Sun Jul 25 16:14:02 2010 From: choisj70 at gmail.com (Seongjin) Date: Sun, 25 Jul 2010 16:14:02 -0400 Subject: [Mristudio-users] new option save fiber density In-Reply-To: References: <77A88E90A851594AAEF830450587C39D04183271@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Dr. Mory, One of Ventat's question was about the normalization condition for the normalized fiber density map. Could you explain the difference between them? Conceptually, I can understand the normalization, but would like to have more detailed explanation on the difference. -Seongjin On Sat, Jul 24, 2010 at 8:56 AM, susumu mori wrote: > Hi Venkat, > > After fiber tracking, it is a common practice to quantify the results. For > the quantification, the streamline information of the tractography needs to > be converted to pixel information. For this conversion, the simplest way is > to use 1/0 binarilzation. If a pixel contains a streamline, it becomes 1 and > if not, remains 0. This is basically a masking, which can be applied to, for > example, a FA map and get a FA value of the tract. You can also count the > number of pixels with "1" and use it as the tract volume. > > One problem of this simple approach is that even if a pixel contains 10 > streamlines, the pixel becomes "1", which is the same as another pixel that > contains only 1 streamline. Namely, during the binalization, information > about the density of the streamline is lost. I believe (Hangyi, please > correct me if I'm wrong) "fiber density map" tells how many streamlines were > there in each pixel. You can potentially use it to get, for example, > density-weighted FA value, in which pixels that contain more streamlines are > more weighted than those contain only 1 streamline. > > On Fri, Jul 23, 2010 at 6:19 PM, Rajagopalan, Venkateswaran < > rajagov2 at ccf.org> wrote: > >> >> Dear All, >> >> I am using DTIstudio_latest_x86.exe after fiber tractography I notices a >> new option named "save fiber density map" (normalized and non normalized). I >> am wondering what information does this fiber density map convey and how >> this information can be used for instance to compare between two groups. How >> the map is normalized. >> >> Thanks >> >> Venkat >> >> =================================== >> >> P Please consider the environment before printing this e-mail >> >> >> >> >> Cleveland Clinic is ranked one of the top hospitals >> in America by U.S.News & World Report (2009). >> Visit us online at http://www.clevelandclinic.org for >> a complete listing of our services, staff and >> locations. >> >> >> Confidentiality Note: This message is intended for use >> only by the individual or entity to which it is addressed >> and may contain information that is privileged, >> confidential, and exempt from disclosure under applicable >> law. If the reader of this message is not the intended >> recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are >> hereby notified that any dissemination, distribution or >> copying of this communication is strictly prohibited. If >> you have received this communication in error, please >> contact the sender immediately and destroy the material in >> its entirety, whether electronic or hard copy. Thank you. >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100725/48ad4bbb/attachment.html From jamike_408 at hotmail.com Tue Jul 27 05:25:27 2010 From: jamike_408 at hotmail.com (michael brown) Date: Tue, 27 Jul 2010 09:25:27 +0000 Subject: [Mristudio-users] bruker dicom In-Reply-To: <77168E3AAEA5744E88FAECF91EA545FB1B7A28A1@BL2PRD0103MB059.prod.exchangelabs.com> References: <77168E3AAEA5744E88FAECF91EA545FB1B7A28A1@BL2PRD0103MB059.prod.exchangelabs.com> Message-ID: Dear mristudio thank you for replying but I still can't seem to get things to work. I have lots of data and these are just one set. This is the gradient table from the bruker dicom. Could you please let me know if i can get the difussion tensor and the FA etc from this data set using mristudio or am i wasting my time 0.666667 0.333333 0.666667 0.666667 -0.333333 0.666667 0.333333 0.666667 0.666667 -0.333333 0.666667 0.666667 0.666667 0.666667 0.333333 0.666667 0.666667 -0.333333. Many thanks Mike Brown Date: Fri, 16 Jul 2010 16:22:27 +0000 From: shereeda at mail.uc.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] bruker dicom Hello Mike Brown, I've not tried using Bruker dicom, but do know that DTI studio will read the Bruker 2dseq files as Philips raw data. From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of michael brown [jamike_408 at hotmail.com] Sent: Friday, July 16, 2010 10:37 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] bruker dicom Hi there my name is Mike Brown, I'm very new to DTI studio. I would like to ask would DTI support images from a bruker dicom. many thanks Mike Get a free e-mail account with Hotmail. Sign-up now. _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ Do you have a story that started on Hotmail? Tell us now -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100727/288b1e0e/attachment.html From gmak at poczta.onet.pl Thu Jul 29 06:58:21 2010 From: gmak at poczta.onet.pl (gmak at poczta.onet.pl) Date: Thu, 29 Jul 2010 12:58:21 +0200 Subject: [Mristudio-users] PDT- probabilistic DTI Message-ID: <1203629047314497A987CE34AFDD46E6@zxzPC> Hello I want to examine my SCA patients in DTIStudio and among other things use PDT like in: http://www.ncbi.nlm.nih.gov/pubmed/19446636 but I am not sure how to performe PDT in DTI studio. I want to evaluate principally ICP, MCP, SCP May you give me any guidelines? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100729/c82a510d/attachment.html From susumu at mri.jhu.edu Wed Jul 28 07:42:43 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 28 Jul 2010 07:42:43 -0400 Subject: [Mristudio-users] PDT- probabilistic DTI In-Reply-To: <1203629047314497A987CE34AFDD46E6@zxzPC> References: <1203629047314497A987CE34AFDD46E6@zxzPC> Message-ID: DtiStudio currently does not provide probabilistic tractography. 2010/7/29 > Hello > > I want to examine my SCA patients in DTIStudio and among other things use > PDT like in: http://www.ncbi.nlm.nih.gov/pubmed/19446636 > but I am not sure how to performe PDT in DTI studio. > I want to evaluate principally ICP, MCP, SCP > > May you give me any guidelines? > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100728/6adf98e8/attachment.html From rajagov2 at ccf.org Wed Jul 28 14:40:26 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Wed, 28 Jul 2010 14:40:26 -0400 Subject: [Mristudio-users] gradient table rotation for multiple repetition data set Message-ID: <77A88E90A851594AAEF830450587C39D0418327D@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, We have diffusion data set acquired with 5 trails/repetitions(in single time point/cross sectional) for each and every subject. After eddy current correction i would like to do gradient table rotation. I am registering all the 5 trails to the b0 image. Since after eddy/motion correction i have affine matrix for all the 5 trails i.e i have 13*5 affine matrices so I am wondering which set of affine matrices i.e first 13 affine matrices or affine matrices from second trail/repetition should i use to rotate my gradient table. Thanks =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100728/405939f9/attachment-0001.html From susumu at mri.jhu.edu Wed Jul 28 15:23:23 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 28 Jul 2010 15:23:23 -0400 Subject: [Mristudio-users] gradient table rotation for multiple repetition data set In-Reply-To: <77A88E90A851594AAEF830450587C39D0418327D@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D0418327D@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Usually, we first calculate tensor and then register the tensor maps with proper reorientation, rather than register the raw DWIs with rotated gradient tables. It is possible to do your approach, but tensor registration would be easier, I think. On Wed, Jul 28, 2010 at 2:40 PM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > > Dear All, > > We have diffusion data set acquired with 5 trails/repetitions(in single > time point/cross sectional) for each and every subject. After eddy current > correction i would like to do gradient table rotation. I am registering all > the 5 trails to the b0 image. Since after eddy/motion correction i have > affine matrix for all the 5 trails i.e i have 13*5 affine matrices so I am > wondering which set of affine matrices i.e first 13 affine matrices or > affine matrices from second trail/repetition should i use to rotate my > gradient table. > > Thanks > > =================================== > > P Please consider the environment before printing this e-mail > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100728/c20a2188/attachment.html From Jan.Tillema at cchmc.org Wed Jul 28 16:01:52 2010 From: Jan.Tillema at cchmc.org (Jan Tillema) Date: Wed, 28 Jul 2010 16:01:52 -0400 Subject: [Mristudio-users] gradient table rotation for multiplerepetition data set In-Reply-To: References: <77A88E90A851594AAEF830450587C39D0418327D@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <4C505474.D7E9.000C.1@cchmc.org> I have a similar question. We have dataset of subjects before/after intervention, we have 15 dir DTI and 3D T1 data (GE) with same parameters both times, but orientation not exactly the same (clinical protocol). The brains are not normal at baseline with enlarged ventricles that may have changed minimally (due to treatment, e.g. smaller size). Normalization is not a possibility d/t abnormalities on brain to begin with, we just want to compare before/after. We are investigating the effect on white matter and would like to get best approach to compare basic measurement before/after. We have manual (blinded) ROI showing differences before/after, but want to make sure we are in the exact same ROI. To co-register seems the best way, but tricky as the structure of the brain is not exactly the same. Any suggestions? 1) would it be best to co-register DTI to T1 at both time points and then to co-register T1 in time point A to B followed by change of DTI with same matrix? If so, I assume this would have to be done with DiffeoMap, what would be the steps to do so? 2) is co-registration to "dangerous" for bias as there is the possibility that the brain is not exactly the same before and after (ventricle size change) Thanks, JMT >>> susumu mori 7/28/2010 3:23 PM >>> Usually, we first calculate tensor and then register the tensor maps with proper reorientation, rather than register the raw DWIs with rotated gradient tables. It is possible to do your approach, but tensor registration would be easier, I think. On Wed, Jul 28, 2010 at 2:40 PM, Rajagopalan, Venkateswaran wrote: Dear All, We have diffusion data set acquired with 5 trails/repetitions(in single time point/cross sectional) for each and every subject. After eddy current correction i would like to do gradient table rotation. I am registering all the 5 trails to the b0 image. Since after eddy/motion correction i have affine matrix for all the 5 trails i.e i have 13*5 affine matrices so I am wondering which set of affine matrices i.e first 13 affine matrices or affine matrices from second trail/repetition should i use to rotate my gradient table. Thanks =================================== PPlease consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100728/b81729ca/attachment.html From susumu at mri.jhu.edu Wed Jul 28 17:59:03 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 28 Jul 2010 17:59:03 -0400 Subject: [Mristudio-users] gradient table rotation for multiplerepetition data set In-Reply-To: <4C505474.D7E9.000C.1@cchmc.org> References: <77A88E90A851594AAEF830450587C39D0418327D@CCHSCLEXMB56.cc.ad.cchs.net> <4C505474.D7E9.000C.1@cchmc.org> Message-ID: On Wed, Jul 28, 2010 at 4:01 PM, Jan Tillema wrote: > I have a similar question. > We have dataset of subjects before/after intervention, we have 15 dir DTI > and 3D T1 data (GE) with same parameters both times, but orientation not > exactly the same (clinical protocol). The brains are not normal at baseline > with enlarged ventricles that may have changed minimally (due to treatment, > e.g. smaller size). Normalization is not a possibility d/t abnormalities on > brain to begin with, we just want to compare before/after. We are > investigating the effect on white matter and would like to get best approach > to compare basic measurement before/after. We have manual (blinded) ROI > showing differences before/after, but want to make sure we are in the exact > same ROI. To co-register seems the best way, but tricky as the structure of > the brain is not exactly the same. Any suggestions? > > 1) would it be best to co-register DTI to T1 at both time points and then > to co-register T1 in time point A to B followed by change of DTI with same > matrix? If so, I assume this would have to be done with DiffeoMap, what > would be the steps to do so? > Unless there is a reason that you want T1-DTI be registered (e.g. ROI drawn in T1, FA measured in DTI), I think you can directly register DTI to DTI. Yes, DiffeoMap should be able to do it. > 2) is co-registration to "dangerous" for bias as there is the possibility > that the brain is not exactly the same before and after (ventricle size > change) > First you have to decide if you want only linear transformation adjusting the overall head positions or do non-linear to remove the tissue deformation due to the surgery. I suspect you want the former (I think the latter is difficult). Linear transformation is mostly driven by brain boundary. So, you can assume that as long as the tissue deformation is mostly inside the brain and the brain boundary shape remains the same, the linear transformation should be able to match the two brains. However, we have seen not-so-perfect linear registration even between two images from the same person. Reason could be; the initial alignment was way off, there is an intense sinus signal in one of them, etc. In the end, it is your subjective judgment if the linear registration is satisfactory. If there is a good quantitative way to judge the alignment, we would have used such a metric to drive the linear registration. In your case, you may want to try the landmark function of DiffeoMap. You need at least 3 point landmarks to define the corresponding structures between the two images. Unfortunately there are not many point landmarks inside the brain. The exceptions are AC and PC. The third point could be some easy-to-define structures in the brainstem at the mid-sagittal level such as the junction of the pons and midbrain. If you can clearly find these 3 points, place these landmarks in both images and use rigid alignment. Let us know if this approach works. Thanks, > > JMT > > >>> susumu mori 7/28/2010 3:23 PM >>> > > Usually, we first calculate tensor and then register the tensor maps with > proper reorientation, rather than register the raw DWIs with rotated > gradient tables. > > It is possible to do your approach, but tensor registration would be > easier, I think. > > On Wed, Jul 28, 2010 at 2:40 PM, Rajagopalan, Venkateswaran < > rajagov2 at ccf.org> wrote: > >> >> Dear All, >> >> We have diffusion data set acquired with 5 trails/repetitions(in single >> time point/cross sectional) for each and every subject. After eddy current >> correction i would like to do gradient table rotation. I am registering all >> the 5 trails to the b0 image. Since after eddy/motion correction i have >> affine matrix for all the 5 trails i.e i have 13*5 affine matrices so I am >> wondering which set of affine matrices i.e first 13 affine matrices or >> affine matrices from second trail/repetition should i use to rotate my >> gradient table. >> >> Thanks >> >> =================================== >> >> P Please consider the environment before printing this e-mail >> >> >> >> Cleveland Clinic is ranked one of the top hospitals >> in America by U.S.News & World Report (2009). >> Visit us online at http://www.clevelandclinic.org for >> a complete listing of our services, staff and >> locations. >> >> >> Confidentiality Note: This message is intended for use >> only by the individual or entity to which it is addressed >> and may contain information that is privileged, >> confidential, and exempt from disclosure under applicable >> law. If the reader of this message is not the intended >> recipient or the employee or agent responsible for >> delivering the message to the intended recipient, you are >> hereby notified that any dissemination, distribution or >> copying of this communication is strictly prohibited. If >> you have received this communication in error, please >> contact the sender immediately and destroy the material in >> its entirety, whether electronic or hard copy. Thank you. >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100728/f34bf9f8/attachment-0001.html From choisj70 at gmail.com Wed Jul 28 22:57:42 2010 From: choisj70 at gmail.com (Seongjin) Date: Wed, 28 Jul 2010 22:57:42 -0400 Subject: [Mristudio-users] Correction of Oblique image Message-ID: Some images are not well aligned vertically (hence horizontally) in the axial image. DTI studio provides to correct this using oblique operation. I guess I should the oblique operation to correct this after the tensor calculation. Then resulting tensor also need to be corrected by the same angle correction done in the oblique correction. Is there any general advice to do this right (including axial /coronal / sagittal rotation)? -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100728/75715403/attachment.html From fjnavas2 at gmail.com Thu Jul 29 10:04:14 2010 From: fjnavas2 at gmail.com (Javier Navas) Date: Thu, 29 Jul 2010 16:04:14 +0200 Subject: [Mristudio-users] Tensor-Trace image Message-ID: Hi all, anyone knows what is the meaning of "tensor-trace" image that appears in the "image seleccion box"? is the tensor image? or is the trace image? Thanks -- /**********************************************************\ Francisco Javier Navas S?nchez Laboratorio de Imagen M?dica U.M.C.E. Hospital General Universitario Gregorio Mara??n Dr Esquerdo 46, 28007 Madrid, Spain Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 e-mail:jnavas at hggm.es http://image.hggm.es -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100729/51b2aff3/attachment.html From junyiwang2002 at yahoo.com Thu Jul 29 10:40:34 2010 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Thu, 29 Jul 2010 07:40:34 -0700 (PDT) Subject: [Mristudio-users] Tensor-Trace image In-Reply-To: References: Message-ID: <825403.35779.qm@web50507.mail.re2.yahoo.com> It is the trace image derived from the tensor calculation. Jun Yi Wang Postdoctoral Scholar Center for Mind and Brain 202 Cousteau Place, Suite 250 Davis, CA 95618 Lab: 530-747-3808 Fax: 530-297-4603 ________________________________ From: Javier Navas To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Thu, July 29, 2010 7:04:14 AM Subject: [Mristudio-users] Tensor-Trace image Hi all, anyone knows what is the meaning of "tensor-trace" image that appears in the "image seleccion box"? is the tensor image? or is the trace image? Thanks -- /**********************************************************\ Francisco Javier Navas S?nchez Laboratorio de Imagen M?dica U.M.C.E. Hospital General Universitario Gregorio Mara??n Dr Esquerdo 46, 28007 Madrid, Spain Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 e-mail:jnavas at hggm.es http://image.hggm.es -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100729/d3c53ca1/attachment.html From MCMoore at interact.ccsd.net Thu Jul 29 11:57:45 2010 From: MCMoore at interact.ccsd.net (Michael C. Moore) Date: Thu, 29 Jul 2010 08:57:45 -0700 Subject: [Mristudio-users] ADC values Message-ID: Are ADC values for a selected ROI 2D or 3D values? and how can you determine the other? Michael Moore UNLV-Health Physics Amigenics Research Group Las Vegas, NV -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100729/f58179ed/attachment.html From choisj70 at gmail.com Thu Jul 29 12:21:23 2010 From: choisj70 at gmail.com (Seongjin) Date: Thu, 29 Jul 2010 12:21:23 -0400 Subject: [Mristudio-users] Tensor-Trace image In-Reply-To: References: Message-ID: It should be the trace of the tensor that you have. -SC On Thu, Jul 29, 2010 at 10:04 AM, Javier Navas wrote: > Hi all, > anyone knows what is the meaning of "tensor-trace" image that appears in > the "image seleccion box"? > is the tensor image? or is the trace image? > > Thanks > > -- > /**********************************************************\ > Francisco Javier Navas S?nchez > Laboratorio de Imagen M?dica U.M.C.E. > Hospital General Universitario Gregorio Mara??n > Dr Esquerdo 46, 28007 Madrid, Spain > Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 > e-mail:jnavas at hggm.es http://image.hggm.es > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100729/321b90fe/attachment.html From choisj70 at gmail.com Thu Jul 29 12:34:38 2010 From: choisj70 at gmail.com (Seongjin) Date: Thu, 29 Jul 2010 12:34:38 -0400 Subject: [Mristudio-users] ADC values In-Reply-To: References: Message-ID: Hi, Michael, It should depend on how you made the ROI. 1) 2D ROI for an object in ROI editor: 2D You can draw an 2D ROI for an object. Apparently, this is a 2D ROI. 2) Multiple 2D ROIs for an object in ROI editor: 3D You can draw multiple 2D ROIs across multiple slices for an object. Hence this is 3D ROI. 3) ADC value from fiber tracking in DTI studio: 3D in the voxels where fiber tracked. best, -SC On Thu, Jul 29, 2010 at 11:57 AM, Michael C. Moore < MCMoore at interact.ccsd.net> wrote: > Are ADC values for a selected ROI 2D or 3D values? and how can you > determine the other? > > Michael Moore > UNLV-Health Physics > Amigenics Research Group > Las Vegas, NV > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100729/20a2eb5f/attachment.html From susumu at mri.jhu.edu Fri Jul 30 10:25:33 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 30 Jul 2010 10:25:33 -0400 Subject: [Mristudio-users] Tensor-Trace image In-Reply-To: References: Message-ID: That's correct. Tensor trace is the addition of Dxx, Dyy, Dzz. If you divide the value by 3, you get so called mean diffusivity or averaged diffusion constant. On Thu, Jul 29, 2010 at 12:21 PM, [Seongjin] wrote: > It should be the trace of the tensor that you have. > > -SC > > On Thu, Jul 29, 2010 at 10:04 AM, Javier Navas wrote: > >> Hi all, >> anyone knows what is the meaning of "tensor-trace" image that appears in >> the "image seleccion box"? >> is the tensor image? or is the trace image? >> >> Thanks >> >> -- >> /**********************************************************\ >> Francisco Javier Navas S?nchez >> Laboratorio de Imagen M?dica U.M.C.E. >> Hospital General Universitario Gregorio Mara??n >> Dr Esquerdo 46, 28007 Madrid, Spain >> Phone : (+34) 91 426 50 67 Fax: (+34) 91 426 5108 >> e-mail:jnavas at hggm.es http://image.hggm.es >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100730/320eb102/attachment-0001.html From susumu at mri.jhu.edu Fri Jul 30 10:35:48 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 30 Jul 2010 10:35:48 -0400 Subject: [Mristudio-users] Correction of Oblique image In-Reply-To: References: Message-ID: The rotation operation DtiStudio provides is for visualization only and should not be used for any quantification purpose. If you need to reorient you data (including image registration, normalization, standardization, alignment, etc), you should use DiffeoMap, UNLESS you are talking about image registration of intra-DTI dataset As someone asked before, there are several ways to reorient your DTI data; 1) Reorient original DWI before tensor calculation. We do not support this approach. 2) First calculate a tensor and reorient the tensor map. This is possible by DiffeoMap. Please load the tensor map by the "load *.d" button so that DiffeoMap knows that it has to perform tensor reorientation. 3) First calculate a tensor and then FA map. Then reorient the FA map by DiffeoMap. Susumu On Wed, Jul 28, 2010 at 10:57 PM, [Seongjin] wrote: > Some images are not well aligned vertically (hence horizontally) in the > axial image. > DTI studio provides to correct this using oblique operation. > I guess I should the oblique operation to correct this after the tensor > calculation. > Then resulting tensor also need to be corrected by the same angle > correction done in the oblique correction. > > Is there any general advice to do this right (including axial /coronal / > sagittal rotation)? > > -SC > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100730/a373db8b/attachment.html From azhang at psych.uic.edu Mon Aug 2 18:33:06 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Mon, 02 Aug 2010 17:33:06 -0500 Subject: [Mristudio-users] how to build the "Frontal" ROI for tracking ? In-Reply-To: References: <107522.21613.qm@web25607.mail.ukl.yahoo.com> <6f70ca8a22f53.4c48617c@johnshopkins.edu> Message-ID: <40469184F1D86344A835AB980269681A1695CAE2C9@exchange.psych.uic.edu> I would also like to inquire the TRS set from Yajing. I can only find the probabilistic maps online at here: http://lbam.med.jhmi.edu/cmrm/Data_Yajing/projectionFiber.htm thanks, Aifeng ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: Thursday, July 22, 2010 2:41 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Yajing Zhang Subject: Re: [Mristudio-users] how to build the "Frontal" ROI for tracking ? As Xin mentioned, you can request the ROI sets for particular tracts of your interest to Yajing. As a matter of fact, I believe the entire ROI files (TRS: Template ROI Set) are posted somewhere. Yajing should be able to elaborate this. On Thu, Jul 22, 2010 at 3:19 PM, Xin Li > wrote: Hello Josselin, I will forward your email to my colleague Yajing Zhang, the author of the paper. Xin ----- Original Message ----- From: Josselin > Date: Thursday, July 22, 2010 2:39 pm Subject: [Mristudio-users] how to build the "Frontal" ROI for tracking ? To: mristudio-users at mristudio.org > Hi, > I use Diffeomap and ROIeditor to reconstruct automatically tracts > like in the Zhang paper (2010). > ROI registration on a single subject works now perfectly fine (thanks!). > In the Zhang paper, e.g. the IFO is the tract going through regions > you named "Frontal" and "Occipital". I assume that these are the whole > frontal lobe and the whole occipital lobe (?). > > Have you drawn them manually ? Or is there another any convenient way > for it ? > > thanks again, > Josselin > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100802/73b27cf0/attachment.html From JLaMarche at tams.com Mon Aug 2 19:01:16 2010 From: JLaMarche at tams.com (John LaMarche) Date: Mon, 02 Aug 2010 16:01:16 -0700 Subject: [Mristudio-users] John LaMarche is out of the office. Message-ID: I will be out of the office starting 08/01/2010 and will not return until 08/08/2010. I will have limited data and phone service during this peroid. From bangsyang at yahoo.com.cn Mon Aug 2 20:10:47 2010 From: bangsyang at yahoo.com.cn (bangs yang) Date: Tue, 03 Aug 2010 08:10:47 +0800 (CST) Subject: [Mristudio-users] =?utf-8?b?IOWbnuWkje+8miAgSm9obiBMYU1hcmNoZSBp?= =?utf-8?q?s_out_of_the_office=2E?= In-Reply-To: Message-ID: <327033.74128.qm@web15007.mail.cnb.yahoo.com> Good luck and have a fun! --- 10?8?3????, John LaMarche ??? ???: John LaMarche ??: [Mristudio-users] John LaMarche is out of the office. ???: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" ??: 2010?8?3?,??,??7:01 I will be out of the office starting? 08/01/2010 and will not return until 08/08/2010. I will have limited data and phone service during this peroid. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100803/81528dd7/attachment.html From j.houenou at yahoo.fr Wed Aug 4 01:15:11 2010 From: j.houenou at yahoo.fr (Josselin) Date: Wed, 04 Aug 2010 05:15:11 +0000 (GMT) Subject: [Mristudio-users] scripting Message-ID: <448143.29843.qm@web25604.mail.ukl.yahoo.com> Hello, Is there any possibility for us users to write scripts or batches in order to perform automatically some functions with diffeomap such as registration, skull stripping or transformation? thanks Josselin From akolasny at jhu.edu Wed Aug 4 09:27:08 2010 From: akolasny at jhu.edu (akolasny at jhu.edu) Date: Wed, 04 Aug 2010 09:27:08 -0400 (EDT) Subject: [Mristudio-users] August 3rd DiffeoMap Processing may need to be resent Message-ID: <44328.192.168.2.29.1280928428.squirrel@webmail.cis.jhu.edu> August 3rd, the DiffeoMap remote processing file server ran out of space. About 20 jobs could not be processed. If you did not get an email that processing started, please resend your job. Disk space has been freed up. Jobs will only remain on the file server for 15 days. I will work on reserving a larger disk space allocation. I'm sorry for the inconvenience, Anthony ------------------------------------------------------------------- Anthony Kolasny email:akolasny at jhu.edu Center for Imaging Science phone:410.516.4278 Johns Hopkins University FAX:410.516.4594 301 Clark Hall 3400 N. Charles Street Baltimore, Maryland 21218 From RDeShazo at amh.org Wed Aug 4 10:26:17 2010 From: RDeShazo at amh.org (DeShazo, Ronald) Date: Wed, 04 Aug 2010 10:26:17 -0400 Subject: [Mristudio-users] scripting In-Reply-To: <448143.29843.qm@web25604.mail.ukl.yahoo.com> References: <448143.29843.qm@web25604.mail.ukl.yahoo.com> Message-ID: Hello All, I'm a new user and would like to know if there is a way to send Dicom post-processed images in our PACS system? Thanks, Ron -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Josselin Sent: Wednesday, August 04, 2010 1:15 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] scripting Hello, Is there any possibility for us users to write scripts or batches in order to perform automatically some functions with diffeomap such as registration, skull stripping or transformation? thanks Josselin _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org ****************** CONFIDENTIALITY NOTICE ********************** This e-mail contains LEGALLY PRIVILEGED AND CONFIDENTIAL INFORMATION intended only for the use of the recipient named above. If you are not the intended recipient, you are hereby notified that any dissemination or copying of this e-mail is strictly prohibited. If you have received this e-mail in error, please notify the transmitting hospital by telephone or e-mail and delete the original e-mail received in error. THIS INFORMATION HAS BEEN DISCLOSED TO YOU FROM RECORDS WHOSE CONFIDENTIALITY IS PROTECTED BY STATE AND FEDERAL LAW. ANY FURTHER DISCLOSURE, COPYING, DISTRIBUTION OR ACTION TAKEN IN RELIANCE ON THE CONTENTS OF THESE DOCUMENTS WITHOUT THE PRIOR WRITTEN CONSENT OF THE PERSON TO WHOM IT PERTAINS IS PROHIBITED. YOU ARE REQUIRED TO DESTROY THE INFORMATION AFTER THE STATED NEED HAS BEEN FULFILLED. From susumu at mri.jhu.edu Wed Aug 4 18:12:12 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 04 Aug 2010 18:12:12 -0400 Subject: [Mristudio-users] scripting In-Reply-To: <448143.29843.qm@web25604.mail.ukl.yahoo.com> References: <448143.29843.qm@web25604.mail.ukl.yahoo.com> Message-ID: We are currently working on an interface that can specify multiple steps at once. It'll take several more months, I think. At this moment, we are not working on a command-line based approach. On Wed, Aug 4, 2010 at 1:15 AM, Josselin wrote: > Hello, > > Is there any possibility for us users to write scripts or batches in order > to perform automatically some functions with diffeomap such as registration, > skull stripping or transformation? > > thanks > Josselin > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100804/ae07e77a/attachment.html From naamab at stanford.edu Fri Aug 6 17:56:25 2010 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Fri, 06 Aug 2010 14:56:25 -0700 Subject: [Mristudio-users] radial diffusivity Message-ID: <024E94BF-559B-4815-BAB0-897E16568975@stanford.edu> Shouldn't radial diffusivity be (Lamda2+Lamda3)/2? DTI-map options says (Lamda1+Lamda2)/2. Thanks, Naama Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. From susumu at mri.jhu.edu Fri Aug 6 18:00:09 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 06 Aug 2010 18:00:09 -0400 Subject: [Mristudio-users] radial diffusivity In-Reply-To: <024E94BF-559B-4815-BAB0-897E16568975@stanford.edu> References: <024E94BF-559B-4815-BAB0-897E16568975@stanford.edu> Message-ID: Sorry. In DtiStudio, it goes lambda 0, 1, 2. Not 1, 2, 3. I know that it's not a conventional way. On Fri, Aug 6, 2010 at 5:56 PM, Naama Barnea-Goraly wrote: > > Shouldn't radial diffusivity be (Lamda2+Lamda3)/2? DTI-map options > says (Lamda1+Lamda2)/2. > > Thanks, > > Naama > > > > Naama Barnea-Goraly M.D. > Instructor > Center for Interdisciplinary Brain Sciences Research > Stanford University Division of Child and Adolescent Psychiatry > 401 Quarry Rd. MC 5795 > Stanford University School of Medicine > Stanford, CA 94305-5795 > Phone: (650) 736-1874, fax: (650) 724-4794 > > > CONFIDENTIALITY NOTICE: This e-mail communication and any attachments > may contain confidential information for the use of the designated > recipients named above. If you are not the intended recipient, you > are hereby notified that you have received this communication in error > and that any review, disclosure, dissemination, distribution or > copying of it or its contents is prohibited. If you have received > this communication in error, please notify Stanford Medical Center > immediately by telephone at (650) 725-5722 and destroy all copies of > this communication and any attachments. Thank you. > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100806/67565131/attachment.html From Jan.Tillema at cchmc.org Sat Aug 7 12:53:16 2010 From: Jan.Tillema at cchmc.org (Jan Tillema) Date: Sat, 07 Aug 2010 12:53:16 -0400 Subject: [Mristudio-users] co-registration question. Message-ID: <4C5D573C.D7E9.000C.1@cchmc.org> Dr. Mori, Thank you very much for your help on my last questions. In response to your answer on my questions from Jul 28 (regarding DTI data before/after intervention) - see below for details - I have a follow up question: I have only used DTIstudio and ROIEditor, and am not too comfortable with Diffeostudio yet. Since you mentioned to try linear transformation I tried the following using AIR in DTIstudio. - I have all my processed data saved in analyze format - so I loaded these in DTIstudio. - using rigid body transformation with AIR I get really nice results for co-registration of B0 images before & after treatment, but when I use the FA maps and individual val0,1&2 & color maps this (not fully surprising) don't always correlate well. - I saved the AirMatrix.txt file from the B0 transformation My questions: --- How can I transform the other images (FA, val0, val1, val2, color map) using this Matrix??? --- Can this be done using DTIstudio or will that have to be done in Diffeomap --- Is this an acceptable way to do it as long as the B0 images correspond (which they visually do nicely) and is there an easier way to do this using Diffeomap? Thanks JMT On Wed, Jul 28, 2010 at 4:01 PM, Jan Tillema wrote: > I have a similar question. >We have dataset of subjects before/after intervention, we have 15 dir DTI >and 3D T1 data (GE) with same parameters both times, but orientation not >exactly the same (clinical protocol). The brains are not normal at baseline >with enlarged ventricles that may have changed minimally (due to treatment, >e.g. smaller size). Normalization is not a possibility d/t abnormalities on >brain to begin with, we just want to compare before/after. We are >investigating the effect on white matter and would like to get best approach>to compare basic measurement before/after. We have manual (blinded) ROI >showing differences before/after, but want to make sure we are in the exact >same ROI. To co-register seems the best way, but tricky as the structure of >the brain is not exactly the same. Any suggestions? > >1) would it be best to co-register DTI to T1 at both time points and then >to co-register T1 in time point A to B followed by change of DTI with same >matrix? If so, I assume this would have to be done with DiffeoMap, what >would be the steps to do so? > Unless there is a reason that you want T1-DTI be registered (e.g. ROI drawn in T1, FA measured in DTI), I think you can directly register DTI to DTI. Yes, DiffeoMap should be able to do it. >2) is co-registration to "dangerous" for bias as there is the possibility >that the brain is not exactly the same before and after (ventricle size >change) > First you have to decide if you want only linear transformation adjusting the overall head positions or do non-linear to remove the tissue deformation due to the surgery. I suspect you want the former (I think the latter is difficult). Linear transformation is mostly driven by brain boundary. So, you can assume that as long as the tissue deformation is mostly inside the brain and the brain boundary shape remains the same, the linear transformation should be able to match the two brains. However, we have seen not-so-perfect linear registration even between two images from the same person. Reason could be; the initial alignment was way off, there is an intense sinus signal in one of them, etc. In the end, it is your subjective judgment if the linear registration is satisfactory. If there is a good quantitative way to judge the alignment, we would have used such a metric to drive the linear registration. In your case, you may want to try the landmark function of DiffeoMap. You need at least 3 point landmarks to define the corresponding structures between the two images. Unfortunately there are not many point landmarks inside the brain. The exceptions are AC and PC. The third point could be some easy-to-define structures in the brainstem at the mid-sagittal level such as the junction of the pons and midbrain. If you can clearly find these 3 points, place these landmarks in both images and use rigid alignment. Let us know if this approach works. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100807/54cd188b/attachment-0001.html From susumu at mri.jhu.edu Sun Aug 8 14:29:48 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sun, 08 Aug 2010 14:29:48 -0400 Subject: [Mristudio-users] co-registration question. In-Reply-To: <4C5D573C.D7E9.000C.1@cchmc.org> References: <4C5D573C.D7E9.000C.1@cchmc.org> Message-ID: Hi Jan, First of all, please make sure the following point; 1) The AIR (or Mutual information) in DtiStudio is for "intra-subject intra-DTI" image registration. DTI data consists of b0 images and diffusion-weighted images; typically there are tens of images, which need to be all co-registered before tensor calculation. 2) After tensor calculation, b0 and all tensor-derived maps (FA, color, eigenvalues) are all naturally co-registered each other and no further registration by AIR is not needed. 3) For intra-subject inter-contrast (e.g. T2 and b0/DTI) or inter-subject registration, you need to use DiffeoMap. This also include intra-subject but scanned at different time points. 4) In general, cross-contrast registration (e.g. b0 vs T1) is difficult. Now, going back to your question, I'm not sure if you want intra-subject (+intra-DTI) or inter-data registration, but I guess the following steps are what you want; > Get two b0s from subject A and B and load them into DiffeoMap. The first image you open (in this case A) will the the template. > Do image registration by, for example, AIR, save the transformation matrix. > Load FA, trace, and other DTI-derived images of B and apply the transformation matrix. Hope this will help. Susumu On Sat, Aug 7, 2010 at 12:53 PM, Jan Tillema wrote: > Dr. Mori, > > Thank you very much for your help on my last questions. In response to > your answer on my questions from Jul 28 (regarding DTI data before/after > intervention) - see below for details - I have a follow up question: > > I have only used DTIstudio and ROIEditor, and am not too comfortable with > Diffeostudio yet. Since you mentioned to try linear transformation I tried > the following using AIR in DTIstudio. > - I have all my processed data saved in analyze format - so I loaded these > in DTIstudio. > - using rigid body transformation with AIR I get really nice results for > co-registration of B0 images before & after treatment, but when I use the FA > maps and individual val0,1&2 & color maps this (not fully surprising) don't > always correlate well. > - I saved the AirMatrix.txt file from the B0 transformation > My questions: > --- How can I transform the other images (FA, val0, val1, val2, color map) > using this Matrix??? > --- Can this be done using DTIstudio or will that have to be done in > Diffeomap > --- Is this an acceptable way to do it as long as the B0 images correspond > (which they visually do nicely) and is there an easier way to do this using > Diffeomap? > > Thanks > > JMT > > > On Wed, Jul 28, 2010 at 4:01 PM, Jan Tillema > > wrote: > > >* I have a similar question. > *>* We have dataset of subjects before/after intervention, we have 15 dir > DTI > *>* and 3D T1 data (GE) with same parameters both times, but orientation > not > *>* exactly the same (clinical protocol). The brains are not normal at > baseline > *>* with enlarged ventricles that may have changed minimally (due to > treatment, > *>* e.g. smaller size). Normalization is not a possibility d/t > abnormalities on > *>* brain to begin with, we just want to compare before/after. We are > *>* investigating the effect on white matter and would like to get best > approach *>* to compare basic measurement before/after. We have manual > (blinded) ROI > *>* showing differences before/after, but want to make sure we are in the > exact > *>* same ROI. To co-register seems the best way, but tricky as the > structure of > *>* the brain is not exactly the same. Any suggestions? > *>* > *>* 1) would it be best to co-register DTI to T1 at both time points and > then > *>* to co-register T1 in time point A to B followed by change of DTI with > same > *>* matrix? If so, I assume this would have to be done with DiffeoMap, > what > *>* would be the steps to do so? > *>* > * > Unless there is a reason that you want T1-DTI be registered (e.g. ROI drawn > in T1, FA measured in DTI), I think you can directly register DTI to DTI. > Yes, DiffeoMap should be able to do it. > > > >* 2) is co-registration to "dangerous" for bias as there is the > possibility > *>* that the brain is not exactly the same before and after (ventricle > size > *>* change) > *>* > * > First you have to decide if you want only linear transformation adjusting > the overall head positions or do non-linear to remove the tissue > deformation > due to the surgery. I suspect you want the former (I think the latter is > difficult). > > Linear transformation is mostly driven by brain boundary. So, you can > assume > that as long as the tissue deformation is mostly inside the brain and the > brain boundary shape remains the same, the linear transformation should be > able to match the two brains. However, we have seen not-so-perfect linear > registration even between two images from the same person. Reason could be; > the initial alignment was way off, there is an intense sinus signal in one > of them, etc. In the end, it is your subjective judgment if the linear > registration is satisfactory. If there is a good quantitative way to judge > the alignment, we would have used such a metric to drive the linear > registration. > > In your case, you may want to try the landmark function of DiffeoMap. You > need at least 3 point landmarks to define the corresponding structures > between the two images. Unfortunately there are not many point landmarks > inside the brain. The exceptions are AC and PC. The third point could be > some easy-to-define structures in the brainstem at the mid-sagittal level > such as the junction of the pons and midbrain. If you can clearly find > these > 3 points, place these landmarks in both images and use rigid alignment. > > Let us know if this approach works. > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100808/b2cc29f4/attachment.html From Surya.Gnyawali at osumc.edu Tue Aug 10 10:22:05 2010 From: Surya.Gnyawali at osumc.edu (Gnyawali, Surya) Date: Tue, 10 Aug 2010 10:22:05 -0400 Subject: [Mristudio-users] Digits of ADC and tracer in ROI editor andDTI Studio In-Reply-To: References: Message-ID: <88C36278CA264743AFC36FB5C4E8CFF20D054290@EXMBOX-VP01.OSUMC.EDU> Hi, Is it possible to save a text file of Gradient table (the gradient direction) from Bruker DtiEpi sequence so one can encorporate in the sequence later? comprehensive explanation for the process is highly appreciated. Thanks SUrya ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: Friday, June 18, 2010 10:24 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Digits of ADC and tracer in ROI editor andDTI Studio Thank you for letting us know. We will revise the posted version today so that you can have more digits. On Thu, Jun 17, 2010 at 8:52 PM, [Seongjin] > wrote: Digits of ADC and tracer in ROI editor and DTI Studio are different. So measured values for ADC and tracer from ROI Editor using ROI generated in the ROI editor gives out number are somewhat limited. DTI studio give out better digits for ADC and tracer. Is there any method to use the ROI-editor-generated ROI in DTI studio? -SC _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100810/e057c06c/attachment.html From azhang at psych.uic.edu Wed Aug 11 20:49:50 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Wed, 11 Aug 2010 19:49:50 -0500 Subject: [Mristudio-users] LDDMM issue Message-ID: <40469184F1D86344A835AB980269681A1696D0AAD6@exchange.psych.uic.edu> Hi DiffeoMap I am using DiffeoMap to do the LDDMM transformation after I first warp the atlas to my subject space (resolution .83*.03*2.2mm). I received error saying "the subject images should be isotropic image". Does the LDDMM only accepts isotropic data? thanks Aifeng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100811/c049f90b/attachment.html From susumu at mri.jhu.edu Wed Aug 11 21:53:39 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 11 Aug 2010 21:53:39 -0400 Subject: [Mristudio-users] LDDMM issue In-Reply-To: <40469184F1D86344A835AB980269681A1696D0AAD6@exchange.psych.uic.edu> References: <40469184F1D86344A835AB980269681A1696D0AAD6@exchange.psych.uic.edu> Message-ID: Sorry, but yes, LDDMM accepts only isotropic data. You first have to resample your template to in isotropic resolution using the resampling tool in DiffeoMap. On Wed, Aug 11, 2010 at 8:49 PM, Zhang, Aifeng wrote: > Hi DiffeoMap > > > > I am using DiffeoMap to do the LDDMM transformation after I first warp the > atlas to my subject space (resolution .83*.03*2.2mm). I received error > saying "the subject images should be isotropic image". Does the LDDMM only > accepts isotropic data? > > > > thanks > > Aifeng > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100811/f8d264ee/attachment-0001.html From azhang at psych.uic.edu Wed Aug 11 22:27:47 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Wed, 11 Aug 2010 21:27:47 -0500 Subject: [Mristudio-users] LDDMM issue In-Reply-To: References: <40469184F1D86344A835AB980269681A1696D0AAD6@exchange.psych.uic.edu> Message-ID: <40469184F1D86344A835AB980269681A1696D0AAD7@exchange.psych.uic.edu> okay, thanks! Aifeng From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Wednesday, August 11, 2010 8:54 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] LDDMM issue Sorry, but yes, LDDMM accepts only isotropic data. You first have to resample your template to in isotropic resolution using the resampling tool in DiffeoMap. On Wed, Aug 11, 2010 at 8:49 PM, Zhang, Aifeng > wrote: Hi DiffeoMap I am using DiffeoMap to do the LDDMM transformation after I first warp the atlas to my subject space (resolution .83*.03*2.2mm). I received error saying "the subject images should be isotropic image". Does the LDDMM only accepts isotropic data? thanks Aifeng _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100811/836fe14a/attachment.html From lucas_lessa at yahoo.com.br Wed Aug 18 13:47:15 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Wed, 18 Aug 2010 10:47:15 -0700 (PDT) Subject: [Mristudio-users] Compile AIR package in Windows Message-ID: <612959.12794.qm@web110202.mail.gq1.yahoo.com> Dear friends, I need a software (preferentially free and for dummies) to compile the AIR package. I?ve tried some free compilers but I can't create the executable files. I guess I using a wrong software, becase there are C, C++ and other compilers and I don't know how to choose. If someone have the exe files I apreciate too. Thank you. Lucas Lessa. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100818/66f2fdc4/attachment.html From lucas_lessa at yahoo.com.br Wed Aug 18 14:04:15 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Wed, 18 Aug 2010 11:04:15 -0700 (PDT) Subject: [Mristudio-users] Compile AIR Package Message-ID: <9363.23338.qm@web110215.mail.gq1.yahoo.com> Dear friends, I need a software (preferentially free and for dummies) to compile the AIR package. I?ve tried some free compilers but I can't create the executable files. I guess I using a wrong software, becase there are C, C++ and other compilers and I don't know how to choose. If someone have the exe files I apreciate too. Thank you. Lucas Lessa. ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100818/b6047a86/attachment.html From azhang at psych.uic.edu Wed Aug 18 18:08:43 2010 From: azhang at psych.uic.edu (Zhang, Aifeng) Date: Wed, 18 Aug 2010 17:08:43 -0500 Subject: [Mristudio-users] new option save fiber density In-Reply-To: References: <77A88E90A851594AAEF830450587C39D04183271@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <40469184F1D86344A835AB980269681A1696E140A5@exchange.psych.uic.edu> Dear DtiStudio, A further question on this topic: Is the statistics (by clicking the statistics button in DtiStudio) given along the select fibers density-weighted or not? thanks, Aifeng From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Saturday, July 24, 2010 7:57 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang Subject: Re: [Mristudio-users] new option save fiber density Hi Venkat, After fiber tracking, it is a common practice to quantify the results. For the quantification, the streamline information of the tractography needs to be converted to pixel information. For this conversion, the simplest way is to use 1/0 binarilzation. If a pixel contains a streamline, it becomes 1 and if not, remains 0. This is basically a masking, which can be applied to, for example, a FA map and get a FA value of the tract. You can also count the number of pixels with "1" and use it as the tract volume. One problem of this simple approach is that even if a pixel contains 10 streamlines, the pixel becomes "1", which is the same as another pixel that contains only 1 streamline. Namely, during the binalization, information about the density of the streamline is lost. I believe (Hangyi, please correct me if I'm wrong) "fiber density map" tells how many streamlines were there in each pixel. You can potentially use it to get, for example, density-weighted FA value, in which pixels that contain more streamlines are more weighted than those contain only 1 streamline. On Fri, Jul 23, 2010 at 6:19 PM, Rajagopalan, Venkateswaran > wrote: Dear All, I am using DTIstudio_latest_x86.exe after fiber tractography I notices a new option named "save fiber density map" (normalized and non normalized). I am wondering what information does this fiber density map convey and how this information can be used for instance to compare between two groups. How the map is normalized. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100818/0daafada/attachment-0001.html From JLaMarche at tams.com Wed Aug 18 18:18:09 2010 From: JLaMarche at tams.com (John LaMarche) Date: Wed, 18 Aug 2010 15:18:09 -0700 Subject: [Mristudio-users] John LaMarche is out of the office. Message-ID: I will be out of the office starting 08/18/2010 and will not return until 09/01/2010. I will have limited data and phone service during this peroid. From lucas_lessa at yahoo.com.br Thu Aug 19 10:01:28 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Thu, 19 Aug 2010 07:01:28 -0700 (PDT) Subject: [Mristudio-users] Image registratioin problem Message-ID: <337816.60588.qm@web110212.mail.gq1.yahoo.com> Dear friends, I have two sequences that I need to mesure the FA and the MTR. I've alrealdy registrated the images, but the second sequence is different from the first, it has less slices and a bigger resolution. I managed to resize the images in the DiffeoMAP, but I can't use them in the ROIeditor because of the wrong slice numbers. Is it possbile to registrate the images and the volume? Taking off the slices that are only in one of the sequences? Thank you very much. Lucas Lessa. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100819/30b942a6/attachment.html From susumu at mri.jhu.edu Thu Aug 19 10:32:01 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 19 Aug 2010 10:32:01 -0400 Subject: [Mristudio-users] Image registratioin problem In-Reply-To: <337816.60588.qm@web110212.mail.gq1.yahoo.com> References: <337816.60588.qm@web110212.mail.gq1.yahoo.com> Message-ID: when you resize your MTR data using DiffeoMap, make sure that both matrix size and pixel size are completely the same. As long as these two parameters are the same, you should be able to load them to RoiEditor together. On Thu, Aug 19, 2010 at 10:01 AM, Lucas Lessa wrote: > Dear friends, > > I have two sequences that I need to mesure the FA and the MTR. > I've alrealdy registrated the images, but the second sequence is different > from the first, it has less slices and a bigger resolution. > I managed to resize the images in the DiffeoMAP, but I can't use them in > the ROIeditor because of the wrong slice numbers. > Is it possbile to registrate the images and the volume? Taking off the > slices that are only in one of the sequences? > Thank you very much. > > Lucas Lessa. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100819/c311cc4d/attachment.html From Weihong.Yuan at cchmc.org Thu Aug 19 12:20:21 2010 From: Weihong.Yuan at cchmc.org (Weihong Yuan) Date: Thu, 19 Aug 2010 12:20:21 -0400 Subject: [Mristudio-users] quantifying motion and batch job In-Reply-To: <337816.60588.qm@web110212.mail.gq1.yahoo.com> References: <337816.60588.qm@web110212.mail.gq1.yahoo.com> Message-ID: <4C6D2185.42F5.004B.1@cchmc.org> Dear Dr. Mori, I have two questions and am wondering if you can help me and direct me to the right direction 1. After registering the DWIs to b0, is there anyway to get some quantification about the motion?It would be great if we can get the frame by frame motion "magnitude" (rotation, translation, skew) data in the form of a text file. Is there a existing function available in DTIStudio that can allow me to do that? 2. Is there a beta version of the software that can do some batch work? I understand the quality checking for bad frame/slice/pixel always needs human decision, as you have mentioned before. What about batch job for motion/eddy current correction, or other procedure that may not need as much human expertise? Thanks in advance Weihong Weihong Yuan, Ph.D. Research Assistant Professor/McLaurin Fellow Pediatric Neuroimaging Research Consortium Imaging Research Center, Dept. of Radiology Cincinnati Children's Hospital Research Foundation 3333 Burnet Ave. Cincinnati, OH 45229 Phone: 513-636-2862 FAX: 513-636-0434 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100819/6051678a/attachment.html From susumu at mri.jhu.edu Thu Aug 19 13:04:43 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 19 Aug 2010 13:04:43 -0400 Subject: [Mristudio-users] quantifying motion and batch job In-Reply-To: <4C6D2185.42F5.004B.1@cchmc.org> References: <337816.60588.qm@web110212.mail.gq1.yahoo.com> <4C6D2185.42F5.004B.1@cchmc.org> Message-ID: Hi Weihong, 1. After registering the DWIs to b0, is there anyway to get some > quantification about the motion?It would be great if we can get the frame by > frame motion "magnitude" (rotation, translation, skew) data in the form of a > text file. Is there a existing function available in DTIStudio that can > allow me to do that? > Please see https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2. There you can find a *.doc file explaining how you can check the motion correction results. In reality, the cross-contrast registration like b0-DWI is difficult and it is difficult to expect perfect registration. However, as the file explains, mutual information, although it takes longer, tends to perform better. AIR also has a strong dependence on threshold value. We are working on quantitative reporting of the registration results. Currently there is an option to save the transformation matrix in the text format. When you start AIR, at the bottom of the AIR window, there is "Save transformation matrix" in the "Other" section. > 2. Is there a beta version of the software that can do some batch work? I > understand the quality checking for bad frame/slice/pixel always needs human > decision, as you have mentioned before. What about batch job for motion/eddy > current correction, or other procedure that may not need as much human > expertise? > Hangyi has a command-line version of the software. It may not support all the functions, but please contact him. > > Thanks in advance > > Weihong > > > Weihong Yuan, Ph.D. > Research Assistant Professor/McLaurin Fellow > Pediatric Neuroimaging Research Consortium > Imaging Research Center, Dept. of Radiology > Cincinnati Children's Hospital Research Foundation > 3333 Burnet Ave. > Cincinnati, OH 45229 > Phone: 513-636-2862 > FAX: 513-636-0434 > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100819/aac06dac/attachment.html From jsadino.queens at gmail.com Thu Aug 19 19:40:28 2010 From: jsadino.queens at gmail.com (Jeff Sadino) Date: Thu, 19 Aug 2010 13:40:28 -1000 Subject: [Mristudio-users] quantifying motion and batch job In-Reply-To: References: <337816.60588.qm@web110212.mail.gq1.yahoo.com> <4C6D2185.42F5.004B.1@cchmc.org> Message-ID: Hello Hangyi, My apologies for hijacking Weihong's thread, but I would also be very interested in a command line version of the program. Can you please let me know where I can find it. I would be happy to report back bug reports to help improve it. Thank you, Jeff On Thu, Aug 19, 2010 at 7:04 AM, susumu mori wrote: > Hi Weihong, > > > 1. After registering the DWIs to b0, is there anyway to get some >> quantification about the motion?It would be great if we can get the frame by >> frame motion "magnitude" (rotation, translation, skew) data in the form of a >> text file. Is there a existing function available in DTIStudio that can >> allow me to do that? >> > > Please see https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2. There > you can find a *.doc file explaining how you can check the motion correction > results. In reality, the cross-contrast registration like b0-DWI is > difficult and it is difficult to expect perfect registration. However, as > the file explains, mutual information, although it takes longer, tends to > perform better. AIR also has a strong dependence on threshold value. > > We are working on quantitative reporting of the registration results. > Currently there is an option to save the transformation matrix in the text > format. When you start AIR, at the bottom of the AIR window, there is "Save > transformation matrix" in the "Other" section. > > >> 2. Is there a beta version of the software that can do some batch work? I >> understand the quality checking for bad frame/slice/pixel always needs human >> decision, as you have mentioned before. What about batch job for motion/eddy >> current correction, or other procedure that may not need as much human >> expertise? >> > > Hangyi has a command-line version of the software. It may not support all > the functions, but please contact him. > > >> >> Thanks in advance >> >> Weihong >> >> >> Weihong Yuan, Ph.D. >> Research Assistant Professor/McLaurin Fellow >> Pediatric Neuroimaging Research Consortium >> Imaging Research Center, Dept. of Radiology >> Cincinnati Children's Hospital Research Foundation >> 3333 Burnet Ave. >> Cincinnati, OH 45229 >> Phone: 513-636-2862 >> FAX: 513-636-0434 >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100819/da0b25de/attachment-0001.html From susumu at mri.jhu.edu Thu Aug 19 20:50:39 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 19 Aug 2010 20:50:39 -0400 Subject: [Mristudio-users] quantifying motion and batch job In-Reply-To: References: <337816.60588.qm@web110212.mail.gq1.yahoo.com> <4C6D2185.42F5.004B.1@cchmc.org> Message-ID: Hi all, For batch processing, quality control has been the biggest issue for us. We've been investing our time on methods to evaluate many different sources of image deterioration (please see "DtiStudioUpdate.doc" at https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2) and correction. It is only recently we start to feel comfortable to use a fixed pipeline. Currently we are working on quantitative reporting of quality control, which may take several months to deliver. I believe it may pave a way for fully automated processing (command line or single-click). So, please wait for release of the full-feature command-line version. Meanwhile, Hangyi may provide a current command line version, although it may not support some functions. Susumu On Thu, Aug 19, 2010 at 7:40 PM, Jeff Sadino wrote: > Hello Hangyi, > > My apologies for hijacking Weihong's thread, but I would also be very > interested in a command line version of the program. Can you please let me > know where I can find it. I would be happy to report back bug reports to > help improve it. > > Thank you, > Jeff > > On Thu, Aug 19, 2010 at 7:04 AM, susumu mori wrote: > >> Hi Weihong, >> >> >> 1. After registering the DWIs to b0, is there anyway to get some >>> quantification about the motion?It would be great if we can get the frame by >>> frame motion "magnitude" (rotation, translation, skew) data in the form of a >>> text file. Is there a existing function available in DTIStudio that can >>> allow me to do that? >>> >> >> Please see https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2. >> There you can find a *.doc file explaining how you can check the motion >> correction results. In reality, the cross-contrast registration like b0-DWI >> is difficult and it is difficult to expect perfect registration. However, as >> the file explains, mutual information, although it takes longer, tends to >> perform better. AIR also has a strong dependence on threshold value. >> >> We are working on quantitative reporting of the registration results. >> Currently there is an option to save the transformation matrix in the text >> format. When you start AIR, at the bottom of the AIR window, there is "Save >> transformation matrix" in the "Other" section. >> >> >>> 2. Is there a beta version of the software that can do some batch work? I >>> understand the quality checking for bad frame/slice/pixel always needs human >>> decision, as you have mentioned before. What about batch job for motion/eddy >>> current correction, or other procedure that may not need as much human >>> expertise? >>> >> >> Hangyi has a command-line version of the software. It may not support all >> the functions, but please contact him. >> >> >>> >>> Thanks in advance >>> >>> Weihong >>> >>> >>> Weihong Yuan, Ph.D. >>> Research Assistant Professor/McLaurin Fellow >>> Pediatric Neuroimaging Research Consortium >>> Imaging Research Center, Dept. of Radiology >>> Cincinnati Children's Hospital Research Foundation >>> 3333 Burnet Ave. >>> Cincinnati, OH 45229 >>> Phone: 513-636-2862 >>> FAX: 513-636-0434 >>> >>> >>> _______________________________________________ >>> mristudio-users mailing list >>> mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100819/f5aca5b1/attachment.html From rperez at humv.es Fri Aug 20 07:20:47 2010 From: rperez at humv.es (=?iso-8859-1?Q?Roc=EDo_P=E9rez_Iglesias?=) Date: Fri, 20 Aug 2010 13:20:47 +0200 (CEST) Subject: [Mristudio-users] AIR filles problems Message-ID: <38161.194.83.138.212.1282303247.squirrel@imap.humv.es> Dear DtiStudio users: I am using DtiStudio and DiffeoMap, 32 bit version. I am struggling in the last two days to compile the files I need to use AIR with DiffeoMap: makeaheader.exe, alignlinear.exe, align_warp.exe and invert_air.exe. I would be grateful if you could share those .exe files with me. I saw in the archives a couple of links to download those files but they do not work anymore. Thanks, Rocio From rperez at humv.es Fri Aug 20 09:40:42 2010 From: rperez at humv.es (=?iso-8859-1?Q?Roc=EDo_P=E9rez_Iglesias?=) Date: Fri, 20 Aug 2010 15:40:42 +0200 (CEST) Subject: [Mristudio-users] AIR files problems Message-ID: <4184.194.83.143.28.1282311642.squirrel@imap.humv.es> Thank you very much for sending me the files. Rocio From lucas_lessa at yahoo.com.br Fri Aug 20 10:29:45 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Fri, 20 Aug 2010 07:29:45 -0700 (PDT) Subject: [Mristudio-users] Image registratioin problem In-Reply-To: Message-ID: <120398.57755.qm@web110202.mail.gq1.yahoo.com> Dr Susumo Mori, One more time thank you for your help. I can`t make the resize images (MTR) with the same pixel size of my DWI, I don`t know why, but probably the problem is in the parameters of these images. One more question: is it possible to zoon in or out the images for them match with the others (DWI, FA, Color MAP)? Thank you. Lucas Lessa. --- Em qui, 19/8/10, susumu mori escreveu: De: susumu mori Assunto: Re: [Mristudio-users] Image registratioin problem Para: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" Data: Quinta-feira, 19 de Agosto de 2010, 11:32 when you resize your MTR data using DiffeoMap, make sure that both matrix size and pixel size are completely the same. As long as these two parameters are the same, you should be able to load them to RoiEditor together. On Thu, Aug 19, 2010 at 10:01 AM, Lucas Lessa wrote: Dear friends, I have two sequences that I need to mesure the FA and the MTR. I've alrealdy registrated the images, but the second sequence is different from the first, it has less slices and a bigger resolution. I managed to resize the images in the DiffeoMAP, but I can't use them in the ROIeditor because of the wrong slice numbers. Is it possbile to registrate the images and the volume? Taking off the slices that are only in one of the sequences? Thank you very much. Lucas Lessa. ? _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -----Anexo incorporado----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100820/7bf7b8cb/attachment.html From lucas_lessa at yahoo.com.br Fri Aug 20 10:29:45 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Fri, 20 Aug 2010 07:29:45 -0700 (PDT) Subject: [Mristudio-users] Image registratioin problem In-Reply-To: Message-ID: <120398.57755.qm@web110202.mail.gq1.yahoo.com> Dr Susumo Mori, One more time thank you for your help. I can`t make the resize images (MTR) with the same pixel size of my DWI, I don`t know why, but probably the problem is in the parameters of these images. One more question: is it possible to zoon in or out the images for them match with the others (DWI, FA, Color MAP)? Thank you. Lucas Lessa. --- Em qui, 19/8/10, susumu mori escreveu: De: susumu mori Assunto: Re: [Mristudio-users] Image registratioin problem Para: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" Data: Quinta-feira, 19 de Agosto de 2010, 11:32 when you resize your MTR data using DiffeoMap, make sure that both matrix size and pixel size are completely the same. As long as these two parameters are the same, you should be able to load them to RoiEditor together. On Thu, Aug 19, 2010 at 10:01 AM, Lucas Lessa wrote: Dear friends, I have two sequences that I need to mesure the FA and the MTR. I've alrealdy registrated the images, but the second sequence is different from the first, it has less slices and a bigger resolution. I managed to resize the images in the DiffeoMAP, but I can't use them in the ROIeditor because of the wrong slice numbers. Is it possbile to registrate the images and the volume? Taking off the slices that are only in one of the sequences? Thank you very much. Lucas Lessa. ? _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -----Anexo incorporado----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100820/7bf7b8cb/attachment-0003.html From daisondias at terra.com.br Sat Aug 21 07:37:41 2010 From: daisondias at terra.com.br (Dr Daison Nelson Ferreira Dias) Date: Sat, 21 Aug 2010 11:37:41 +0000 Subject: [Mristudio-users] Table of Gradients Message-ID: <47806.1282390661@terra.com.br> Hi all! Anybody have the table of gradients of GE 1.5T MRI? Daison -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100821/75a4602c/attachment.html From Malek.Makki at kispi.uzh.ch Sat Aug 21 10:53:00 2010 From: Malek.Makki at kispi.uzh.ch (Makki Malek) Date: Sat, 21 Aug 2010 16:53:00 +0200 Subject: [Mristudio-users] Table of Gradients References: <47806.1282390661@terra.com.br> Message-ID: Hi On your console go to /usr/g/bin and open the file tensor.dat. It has all the schemes Malek ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of Dr Daison Nelson Ferreira Dias Sent: Sat 8/21/2010 1:37 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Table of Gradients Hi all! Anybody have the table of gradients of GE 1.5T MRI? Daison -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3497 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100821/e3c2af84/attachment.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: PGP.sig Type: application/pgp-signature Size: 489 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100821/e3c2af84/attachment-0001.bin From sonogung at catholic.ac.kr Sun Aug 22 09:08:48 2010 From: sonogung at catholic.ac.kr (=?ks_c_5601-1987?B?vNW/tbnO?=) Date: Sun, 22 Aug 2010 22:08:48 +0900 Subject: [Mristudio-users] Table of Gradients In-Reply-To: References: <47806.1282390661@terra.com.br> Message-ID: <003501cb41fb$28eeda90$7acc8fb0$@ac.kr> ???, ?? ?? ???. ??, ???? ?? abstract? ??? ??? ???, ? ?????. ????? ??. ???, table, figure? ?? ???? ?? ??? ? ???? ??? ??. Legend? ?? ???? ??? ????, ?????, ?? ??? ???, reference? ? ??? ?? ? ?????. ??? ???? ????? ??? ??? ??? ???? ??? ? reference? ?? ?? ?? ???? Endnote? reference?? ?? ?? ???? ?? ????? ? ??? ?? ?? ??? ???. ?? ? ??? ?? ??? ????. ???, ??? ??? ??? ??? ??? ?? ??? ?? ??? ? ??. ?????. ^^ ??? ?? ?? ???? ?? ? ??? ????~. ^^ ??? From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users- bounces at mristudio.org] On Behalf Of Makki Malek Sent: Saturday, August 21, 2010 11:53 PM To: daisondias at terra.com.br; DTI Studio, ROI Editor,DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Table of Gradients Hi On your console go to /usr/g/bin and open the file tensor.dat. It has all the schemes Malek _____ From: mristudio-users-bounces at mristudio.org on behalf of Dr Daison Nelson Ferreira Dias Sent: Sat 8/21/2010 1:37 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Table of Gradients Hi all! Anybody have the table of gradients of GE 1.5T MRI? Daison -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 6870 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100822/48cb9026/attachment.bin From Jeffrey.L.Snyder at Dartmouth.edu Tue Aug 24 16:46:26 2010 From: Jeffrey.L.Snyder at Dartmouth.edu (Jeffrey L. Snyder) Date: Tue, 24 Aug 2010 16:46:26 -0400 Subject: [Mristudio-users] Please unsubscribe me Message-ID: <174826645@newdasher.Dartmouth.EDU> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100824/45d04637/attachment.pl From qiang.yu at student.qut.edu.au Wed Aug 25 23:43:13 2010 From: qiang.yu at student.qut.edu.au (QIANG YU) Date: Thu, 26 Aug 2010 13:43:13 +1000 Subject: [Mristudio-users] how to obtain data just from white matter Message-ID: <0A52784B9330A94A9357569C34E81F5E91AB2A6271@QUTEXMBX03.qut.edu.au> Hi all, Anyone who know how to do tissue segmentation and then obtain the figure of white matter? My aim is to obtain some data just from white matter? Thanks! Qiang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100826/163f1615/attachment-0001.html From katja at bilkent.edu.tr Thu Aug 26 07:44:45 2010 From: katja at bilkent.edu.tr (Katja Doerschner) Date: Thu, 26 Aug 2010 14:44:45 +0300 Subject: [Mristudio-users] Coregistration problem Message-ID: <58C9B8B3-FDE5-4712-B0ED-2509182706E2@bilkent.edu.tr> Dear DTI studio users, I am trying to coregister a 3D anatomical (Siemens, 176 Sagittal slices, y224 z256) to DWI mosaic (Siemens mosaic, 50 axial slices x128 y128). When I am loading each of these data sets into the viewer they look fine, however the coregistered images (using Automatic Image Registration) just look very distorted and the views of the coregistered image are switched i.e. sagittal shows now an axial, coronal a sagittal and axial the coronal view. Has anyone encountered this before? Thank you. Katja -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100826/f364d8aa/attachment.html From bangsyang at yahoo.com.cn Thu Aug 26 08:10:51 2010 From: bangsyang at yahoo.com.cn (bangs yang) Date: Thu, 26 Aug 2010 20:10:51 +0800 (CST) Subject: [Mristudio-users] =?utf-8?b?IOWbnuWkje+8miAgaG93IHRvIG9idGFpbiBk?= =?utf-8?q?ata_just_from_white_matter?= In-Reply-To: <0A52784B9330A94A9357569C34E81F5E91AB2A6271@QUTEXMBX03.qut.edu.au> Message-ID: <965854.50661.qm@web15005.mail.cnb.yahoo.com> I think you should use some software wrote by youself to complish the task, while the current tool SPM you are using can not reach. ? --- 10?8?26????, QIANG YU ??? ???: QIANG YU ??: [Mristudio-users] how to obtain data just from white matter ???: "mristudio-users at mristudio.org" ??: 2010?8?26?,??,??11:43 Hi all, ? ??? Anyone who know how to do tissue segmentation and then obtain the?figure of?white matter? My aim is to obtain some data just from white matter? ??? Thanks! ? Qiang -----???????----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100826/edfbd451/attachment.html From susumu at mri.jhu.edu Fri Aug 27 12:06:05 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 27 Aug 2010 12:06:05 -0400 Subject: [Mristudio-users] Coregistration problem In-Reply-To: <58C9B8B3-FDE5-4712-B0ED-2509182706E2@bilkent.edu.tr> References: <58C9B8B3-FDE5-4712-B0ED-2509182706E2@bilkent.edu.tr> Message-ID: Hi Katja, Are you using DtiStudio or DiffeoMap? Both has AIR but the former should be used only for intra-DTI image registration. In your case, you want inter-scan (anatomical vs DTI) registration, which needs the latter (DiffeoMap). Susumu On Thu, Aug 26, 2010 at 7:44 AM, Katja Doerschner wrote: > Dear DTI studio users, > > I am trying to coregister a 3D anatomical (Siemens, 176 Sagittal slices, > y224 z256) to DWI mosaic (Siemens mosaic, 50 axial slices x128 y128). > > When I am loading each of these data sets into the viewer they look fine, > however the coregistered images (using Automatic Image Registration) just > look very distorted and the views of the coregistered image are switched > i.e. sagittal shows now an axial, coronal a sagittal and axial the coronal > view. > > Has anyone encountered this before? > > Thank you. > > Katja > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100827/338c7634/attachment.html From katja at bilkent.edu.tr Fri Aug 27 12:50:30 2010 From: katja at bilkent.edu.tr (katja doerschner) Date: Fri, 27 Aug 2010 19:50:30 +0300 (EEST) Subject: [Mristudio-users] Coregistration problem In-Reply-To: References: <58C9B8B3-FDE5-4712-B0ED-2509182706E2@bilkent.edu.tr> Message-ID: <41356.139.179.134.36.1282927830.squirrel@webmail.bilkent.edu.tr> Hi Susumu, Yes, ? was using DT? studio. I will try the registration with DiffeoMap. Thank you for the advice. Best, Katja > Hi Katja, > > Are you using DtiStudio or DiffeoMap? Both has AIR but the former should > be > used only for intra-DTI image registration. In your case, you want > inter-scan (anatomical vs DTI) registration, which needs the latter > (DiffeoMap). > > Susumu > > On Thu, Aug 26, 2010 at 7:44 AM, Katja Doerschner > wrote: > >> Dear DTI studio users, >> >> I am trying to coregister a 3D anatomical (Siemens, 176 Sagittal slices, >> y224 z256) to DWI mosaic (Siemens mosaic, 50 axial slices x128 y128). >> >> When I am loading each of these data sets into the viewer they look >> fine, >> however the coregistered images (using Automatic Image Registration) >> just >> look very distorted and the views of the coregistered image are switched >> i.e. sagittal shows now an axial, coronal a sagittal and axial the >> coronal >> view. >> >> Has anyone encountered this before? >> >> Thank you. >> >> Katja >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > From madamson at stanford.edu Fri Aug 27 18:00:55 2010 From: madamson at stanford.edu (Maheen M. Adamson) Date: Fri, 27 Aug 2010 15:00:55 -0700 Subject: [Mristudio-users] diffeomap Byte conversion problems In-Reply-To: References: <47806.1282390661@terra.com.br> Message-ID: <000301cb4633$55661160$00323420$@edu> Hello, There are a few questions we have as we run through the sample data for Diffeomap. We are trying to send the preprocessed sample data through to single channel LDDMM server. We have subject_AIR_FA, subject_AIR_b0 and Subject_AIR_d. We used the small button to change the file format to byte, saved it as Image_Byte_Subject_Air. But every time we hit the send to server button, we get the complaint that the image is not a byte image. It is also complaining that the template has to be binary (which is the atlas_MN_SS file). Also, can you also tell us how to deal with repeat gradients (B0 appears three times when you do repeat gradient tables)? Do we just paste the gradient table (with repeats)? Keeps asking me if I want to forget the B0 field. Thank you Maheen Maheen Mausoof Adamson, PhD Clinical Assistant Professor (affiliated) Psychiatry & Behavioral Sciences Stanford School of Medicine Stanford CA Director of Clinical Neuroscience Deputy Director, Data core War Related Illness and Injury Study Center (WRIISC) Vetarans Affairs, Palo Alto Health Care System Palo Alto, CA Phone: (650) 493-5000 x62179 Fax: (650) 852-3297 Email: madamson at stanford.edu maheen.adamson at va.gov NOTICE: DO NOT SEND ME ANY FORM OF PROTECTED HEALTH INFORMATION (PHI) UNDER ANY CIRCUMSTANCES. -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 5402 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100827/47e1deb6/attachment-0001.bin From susumu at mri.jhu.edu Fri Aug 27 19:12:53 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 27 Aug 2010 19:12:53 -0400 Subject: [Mristudio-users] diffeomap Byte conversion problems In-Reply-To: <000301cb4633$55661160$00323420$@edu> References: <47806.1282390661@terra.com.br> <000301cb4633$55661160$00323420$@edu> Message-ID: Hi Maheen, You said that you are running the single-channel LDDMM. That means you need to submit only one atlas image and one subject image. So, you don't need all FA, b0, and *.d. You have to pick one. After LDDMM, you will receive transformation matrices. You can apply these matrices to any maps co-registered to the one you picked to drive the registration. For DTI, we recommend two-channel LDDMM using b0+FA or Trace+FA. In this case, you have to convert to byte both images. This process is explained in "Getting Started" section of https://www.mristudio.org/wiki/user_manual/diffeomap. As for the byte conversion, please make sure that you converted both template and subject images. If you have repeated b0, your table should look like; 1: 0, 0, 0 2: 0, 0, 0 3: 0, 0, 0 4: 1, 0, 0 and so on, if you have three repeated b0s. Susumu On Fri, Aug 27, 2010 at 6:00 PM, Maheen M. Adamson wrote: > Hello, > > > > There are a few questions we have as we run through the sample data for > Diffeomap. We are trying to send the preprocessed sample data through to > single channel LDDMM server. We have subject_AIR_FA, subject_AIR_b0 and > Subject_AIR_d. We used the small button to change the file format to byte, > saved it as Image_Byte_Subject_Air. But every time we hit the send to > server > button, we get the complaint that the image is not a byte image. It is also > complaining that the template has to be binary (which is the atlas_MN_SS > file). > > > > Also, can you also tell us how to deal with repeat gradients (B0 appears > three times when you do repeat gradient tables)? Do we just paste the > gradient table (with repeats)? Keeps asking me if I want to forget the B0 > field. > > > > Thank you > > Maheen > > > > Maheen Mausoof Adamson, PhD > > > > Clinical Assistant Professor (affiliated) > > Psychiatry & Behavioral Sciences > > Stanford School of Medicine > > Stanford CA > > > > Director of Clinical Neuroscience > > Deputy Director, Data core > > War Related Illness and Injury Study Center (WRIISC) > > Vetarans Affairs, Palo Alto Health Care System > > Palo Alto, CA > > Phone: (650) 493-5000 x62179 > > Fax: (650) 852-3297 > > Email: madamson at stanford.edu > > maheen.adamson at va.gov > > NOTICE: DO NOT SEND ME ANY FORM OF PROTECTED HEALTH INFORMATION (PHI) UNDER > ANY CIRCUMSTANCES. > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100827/a7befb69/attachment.html From nestr007 at umn.edu Sat Aug 28 12:09:52 2010 From: nestr007 at umn.edu (nestr007 at umn.edu) Date: Sat, 28 Aug 2010 11:09:52 -0500 Subject: [Mristudio-users] Windows 7 - launching DTI studio issue Message-ID: Hello Susumu, Hangyi, and all DTI studio friends, I am experiencing troubles to launch DTI studio in the 32-bit Windows 7 version. After downloading DtiStudio_latest-x86.exe I am getting an error that "side-by-side configuration is incorrect" and in the event log I can find this info: Activation context generation failed for "C:\DtiStudio-latest-x86.exe". Dependent Assembly Microsoft.VC80.OpenMP,processorArchitecture="x86",publicKeyToken="1fc8b3b9a1e18e3b",type="win32",version="8.0.50727.762" could not be found. Please use sxstrace.exe for detailed diagnosis. Thank you for your help. Best, Igor From yj3 at duke.edu Sun Aug 29 09:28:44 2010 From: yj3 at duke.edu (Yi Jiang) Date: Sun, 29 Aug 2010 22:28:44 +0900 Subject: [Mristudio-users] How to refer to DiffeoMap In-Reply-To: References: <47806.1282390661@terra.com.br> <000301cb4633$55661160$00323420$@edu> Message-ID: <5ACADE9D-78DA-4BF1-8961-2505D95E6F93@duke.edu> Hello, I would like to refer to DiffeoMap in my paper. What is the right format for its reference? Thank you very much! Best, Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100829/7056fb66/attachment.html From tigerzjs at msn.com Mon Aug 30 02:14:30 2010 From: tigerzjs at msn.com (Jingsheng zhou) Date: Mon, 30 Aug 2010 06:14:30 +0000 Subject: [Mristudio-users] How to refer to DiffeoMap In-Reply-To: <5ACADE9D-78DA-4BF1-8961-2505D95E6F93@duke.edu> References: <47806.1282390661@terra.com.br> <000301cb4633$55661160$00323420$@edu> <5ACADE9D-78DA-4BF1-8961-2505D95E6F93@duke.edu> Message-ID: dear all, please delete my email from list. thanks jingsheng Date: Sun, 29 Aug 2010 22:28:44 +0900 From: yj3 at duke.edu To: mristudio-users at mristudio.org Subject: [Mristudio-users] How to refer to DiffeoMap Hello, I would like to refer to DiffeoMap in my paper. What is the right format for its reference? Thank you very much! Best, Yi _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100830/89d64d15/attachment.html From arabinda.mishra at Vanderbilt.Edu Mon Aug 30 10:54:30 2010 From: arabinda.mishra at Vanderbilt.Edu (Mishra, Arabinda) Date: Mon, 30 Aug 2010 09:54:30 -0500 Subject: [Mristudio-users] How to refer to DiffeoMap In-Reply-To: References: <47806.1282390661@terra.com.br> <000301cb4633$55661160$00323420$@edu> <5ACADE9D-78DA-4BF1-8961-2505D95E6F93@duke.edu> Message-ID: <2B6AB3B9480ABC46B1CE48A26C9D71A006097964AC@ITS-HCWNEM02.ds.Vanderbilt.edu> Dear all. Please delete my email from list please. mishra ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Jingsheng zhou [tigerzjs at msn.com] Sent: Monday, August 30, 2010 1:14 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] How to refer to DiffeoMap dear all, please delete my email from list. thanks jingsheng ________________________________ Date: Sun, 29 Aug 2010 22:28:44 +0900 From: yj3 at duke.edu To: mristudio-users at mristudio.org Subject: [Mristudio-users] How to refer to DiffeoMap Hello, I would like to refer to DiffeoMap in my paper. What is the right format for its reference? Thank you very much! Best, Yi _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100830/80df7cc4/attachment.html From xli16 at jhmi.edu Mon Aug 30 10:58:21 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 30 Aug 2010 10:58:21 -0400 Subject: [Mristudio-users] How to refer to DiffeoMap In-Reply-To: <2B6AB3B9480ABC46B1CE48A26C9D71A006097964AC@ITS-HCWNEM02.ds.Vanderbilt.edu> References: <47806.1282390661@terra.com.br> <000301cb4633$55661160$00323420$@edu> <5ACADE9D-78DA-4BF1-8961-2505D95E6F93@duke.edu> <2B6AB3B9480ABC46B1CE48A26C9D71A006097964AC@ITS-HCWNEM02.ds.Vanderbilt.edu> Message-ID: <7120d3b4613f.4c7b8ecd@johnshopkins.edu> Hello, To unsubscribe, please send a blank email to: mristudio-users-unsubscribe at mristudio.org Xin ----- Original Message ----- From: "Mishra, Arabinda" Date: Monday, August 30, 2010 10:56 am Subject: Re: [Mristudio-users] How to refer to DiffeoMap To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Dear all. Please delete my email from list please. > mishra > > ________________________________ > From: mristudio-users-bounces at mristudio.org > [mristudio-users-bounces at mristudio.org] On Behalf Of Jingsheng zhou [tigerzjs at msn.com] > Sent: Monday, August 30, 2010 1:14 AM > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] How to refer to DiffeoMap > > dear all, > please delete my email from list. > thanks > > jingsheng > > ________________________________ > Date: Sun, 29 Aug 2010 22:28:44 +0900 > From: yj3 at duke.edu > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] How to refer to DiffeoMap > > Hello, > > I would like to refer to DiffeoMap in my paper. What is the right > format for its reference? > > Thank you very much! > > Best, > Yi > > > _______________________________________________ mristudio-users > mailing list mristudio-users at mristudio.org Unsubscribe, send a blank > email to: mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From naamab at stanford.edu Tue Aug 31 18:08:31 2010 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Tue, 31 Aug 2010 15:08:31 -0700 Subject: [Mristudio-users] individual B0's into "mosaic" format? Message-ID: <650ADA61-54D9-4F1B-AFCF-EF6598134438@stanford.edu> Dear MRIstudio experts, I have a series of B0 images (series of dicoms) from a Siemens and I would like to get them in a "mosaic" format so that I can see them all in one image (looks like a montage). The goal is to add those to a mosaic DTI scan as an extra B0 run. Any advice would be appreciated. Thanks, Naama From JZwicker at cw.bc.ca Wed Sep 1 13:46:28 2010 From: JZwicker at cw.bc.ca (Zwicker, Jill) Date: Wed, 01 Sep 2010 10:46:28 -0700 Subject: [Mristudio-users] problems with tensor calc Message-ID: <01150B9F5C05274F8013B909B04790E4D7CC9BCA8B@VEXCCR03.phsabc.ehcnet.ca> Hi DTI Studio users, I am relatively new to DTI studio and have been using successfully to do tractography on infant brain data collected on a Seimens. I am now trying to analyze child brain data collected on a Philips. I can get a clear image, but as soon as I try a tensor calculation, the image quality degrades significantly (no matter what the background noise level I set it to). I made gradient tables from the PAR file (forwards and backwards) and also flipped the z as the tutorial suggests. Any suggestions on how I can solve this problem? Thanks for your help. Jill Zwicker, PhD, OT(C) Postdoctoral Fellow Child & Family Research Institute Developmental Neurosciences & Child Health L408 - 4480 Oak Street Vancouver, BC V6H 3V4 Phone: 604-875-2000 ext 6805 Fax: 604-875-3569 jzwicker at cw.bc.ca -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100901/1dc589c3/attachment.html From choisj70 at gmail.com Wed Sep 1 13:56:01 2010 From: choisj70 at gmail.com (Seongjin) Date: Wed, 01 Sep 2010 13:56:01 -0400 Subject: [Mristudio-users] problems with tensor calc In-Reply-To: <01150B9F5C05274F8013B909B04790E4D7CC9BCA8B@VEXCCR03.phsabc.ehcnet.ca> References: <01150B9F5C05274F8013B909B04790E4D7CC9BCA8B@VEXCCR03.phsabc.ehcnet.ca> Message-ID: Use the following link for the gradient table calculation. You need to get some information required to fill in from Par file of your data. If your data is not in ParRec format, get it first. http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html -SC. On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill wrote: > Hi DTI Studio users, > > I am relatively new to DTI studio and have been using successfully to do > tractography on infant brain data collected on a Seimens. I am now trying to > analyze child brain data collected on a Philips. I can get a clear image, > but as soon as I try a tensor calculation, the image quality degrades > significantly (no matter what the background noise level I set it to). I > made gradient tables from the PAR file (forwards and backwards) and also > flipped the z as the tutorial suggests. Any suggestions on how I can solve > this problem? > > Thanks for your help. > > > > Jill Zwicker, PhD, OT(C) > > Postdoctoral Fellow > > Child & Family Research Institute > > Developmental Neurosciences & Child Health > > L408 - 4480 Oak Street > > Vancouver, BC? V6H 3V4 > > Phone: 604-875-2000 ext 6805 > > Fax: 604-875-3569 > > jzwicker at cw.bc.ca > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > From JZwicker at cw.bc.ca Wed Sep 1 14:55:56 2010 From: JZwicker at cw.bc.ca (Zwicker, Jill) Date: Wed, 01 Sep 2010 11:55:56 -0700 Subject: [Mristudio-users] problems with tensor calc In-Reply-To: References: <01150B9F5C05274F8013B909B04790E4D7CC9BCA8B@VEXCCR03.phsabc.ehcnet.ca> Message-ID: <01150B9F5C05274F8013B909B04790E4D7CC9BCA8D@VEXCCR03.phsabc.ehcnet.ca> Thank you so much! After some trial and error, I figured out the correct gradient table. I can now get a beautiful colour map, but I have a new problem. The program crashes everytime I try to do fibre tracking. Any suggestions? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, September 01, 2010 10:56 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc Use the following link for the gradient table calculation. You need to get some information required to fill in from Par file of your data. If your data is not in ParRec format, get it first. http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html -SC. On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill wrote: > Hi DTI Studio users, > > I am relatively new to DTI studio and have been using successfully to do > tractography on infant brain data collected on a Seimens. I am now trying to > analyze child brain data collected on a Philips. I can get a clear image, > but as soon as I try a tensor calculation, the image quality degrades > significantly (no matter what the background noise level I set it to). I > made gradient tables from the PAR file (forwards and backwards) and also > flipped the z as the tutorial suggests. Any suggestions on how I can solve > this problem? > > Thanks for your help. > > > > Jill Zwicker, PhD, OT(C) > > Postdoctoral Fellow > > Child & Family Research Institute > > Developmental Neurosciences & Child Health > > L408 - 4480 Oak Street > > Vancouver, BC? V6H 3V4 > > Phone: 604-875-2000 ext 6805 > > Fax: 604-875-3569 > > jzwicker at cw.bc.ca > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Wed Sep 1 21:25:47 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 01 Sep 2010 21:25:47 -0400 Subject: [Mristudio-users] problems with tensor calc In-Reply-To: <01150B9F5C05274F8013B909B04790E4D7CC9BCA8D@VEXCCR03.phsabc.ehcnet.ca> References: <01150B9F5C05274F8013B909B04790E4D7CC9BCA8B@VEXCCR03.phsabc.ehcnet.ca> <01150B9F5C05274F8013B909B04790E4D7CC9BCA8D@VEXCCR03.phsabc.ehcnet.ca> Message-ID: I suspect memory problem. Please use stricter threshold (like FA>0.3 and angle <30, for example) to see if it works. If it works, then it's memory problem (I mean, you need more memory). You can also save eigenvector0 and FA, close DtiStudio, and redo fiber tracking using the saved file. If you start from tensor calculation, you have all the raw data in your memory. 32-bit operating system can allocate only 1-1.5GB memory. 64bit is much better. susumu On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill wrote: > Thank you so much! After some trial and error, I figured out the correct > gradient table. I can now get a beautiful colour map, but I have a new > problem. The program crashes everytime I try to do fibre tracking. Any > suggestions? > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] > Sent: Wednesday, September 01, 2010 10:56 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] problems with tensor calc > > Use the following link for the gradient table calculation. > You need to get some information required to fill in from Par file of your > data. > If your data is not in ParRec format, get it first. > > http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html > > -SC. > > On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill wrote: > > Hi DTI Studio users, > > > > I am relatively new to DTI studio and have been using successfully to do > > tractography on infant brain data collected on a Seimens. I am now trying > to > > analyze child brain data collected on a Philips. I can get a clear image, > > but as soon as I try a tensor calculation, the image quality degrades > > significantly (no matter what the background noise level I set it to). I > > made gradient tables from the PAR file (forwards and backwards) and also > > flipped the z as the tutorial suggests. Any suggestions on how I can > solve > > this problem? > > > > Thanks for your help. > > > > > > > > Jill Zwicker, PhD, OT(C) > > > > Postdoctoral Fellow > > > > Child & Family Research Institute > > > > Developmental Neurosciences & Child Health > > > > L408 - 4480 Oak Street > > > > Vancouver, BC V6H 3V4 > > > > Phone: 604-875-2000 ext 6805 > > > > Fax: 604-875-3569 > > > > jzwicker at cw.bc.ca > > > > > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > > mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100901/dfb2d08b/attachment-0001.html From wonrad at gmail.com Tue Sep 7 10:57:58 2010 From: wonrad at gmail.com (Won Sang Jung) Date: Tue, 07 Sep 2010 23:57:58 +0900 Subject: [Mristudio-users] (no subject) Message-ID: Dear DTI studio friends, This is a little off-topic, but I would like to ask everyone about 3T MRI sequences. I am a neuroradiologist at ST. Vincent's Hospital in Suwon, South Korea. Recently the hospital purchased a new 3T MRI machine. I'm interested in optimizing 3T MRI sequences and am curious about what kind of enhanced T1 weighted sequences are being used by yourself or your colleagues. Among Fast spin echo, gradient echo, T1 weighted inversion recovery or MP-RAGE sequences which one do you routinely use? Is there any situation that you would use a certain type of sequence according the the disease being evaluated? I would appreciate any advice that you have to give on this topic. Thank you in advance for your reply. Sincerely, Won Sang Jung, M.D. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100907/2dc6d5c3/attachment.html From susumu at mri.jhu.edu Tue Sep 7 21:12:45 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 07 Sep 2010 21:12:45 -0400 Subject: [Mristudio-users] (no subject) In-Reply-To: References: Message-ID: 1mm MPRAGE is the first choice. We also do 1x1x2mm PD/T2 double-echo FSE for T2 contrast and T2 map On Tue, Sep 7, 2010 at 10:57 AM, Won Sang Jung wrote: > Dear DTI studio friends, > > This is a little off-topic, but I would like to ask everyone about 3T MRI > sequences. > > I am a neuroradiologist at ST. Vincent's Hospital in Suwon, South Korea. > Recently the hospital purchased a new 3T MRI machine. > > I'm interested in optimizing 3T MRI sequences and am curious about what > kind of enhanced T1 weighted sequences are being used by yourself or your > colleagues. > > Among Fast spin echo, gradient echo, T1 weighted inversion recovery or > MP-RAGE sequences which one do you routinely use? Is there any situation > that you would use a certain type of sequence according the the disease > being evaluated? > > I would appreciate any advice that you have to give on this topic. Thank > you in advance for your reply. > > > Sincerely, > > Won Sang Jung, M.D. > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100907/8193c551/attachment.html From lucas_lessa at yahoo.com.br Wed Sep 8 14:56:14 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Wed, 08 Sep 2010 11:56:14 -0700 (PDT) Subject: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images Message-ID: <168318.19342.qm@web110208.mail.gq1.yahoo.com> Dear colleagues, I'm having some problems to read the DICOM images from a Philips Scanner (1,5T), with uses the 2.5 release. I didn't figured out what is, becase the problem is intermitent. I have about 40 exams to process and the majority of them I did. But some exams simply don't open in the DTISTUDIO/DTI module. If I try to open the files in the viewer everything goes ok, but when I try to load the DICOM images from the DTI the software returns an error, sayng that it can't read the info in the files. I have a macbook pro inside the network and I can pull the images directy from the scanner. After that I export the DICOM files and try to process them in the DTISTUDIO. I did exacty the samething in all exams, but I can't process some. Does anybody know why? Thank you. Lucas Lessa. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100908/e4b417af/attachment.html From susumu at mri.jhu.edu Wed Sep 8 21:49:43 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 08 Sep 2010 21:49:43 -0400 Subject: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images In-Reply-To: <168318.19342.qm@web110208.mail.gq1.yahoo.com> References: <168318.19342.qm@web110208.mail.gq1.yahoo.com> Message-ID: When you say "intermittent", do you have irreproducible problems with the same data? Or do you mean you have reproducible problems for a subset of data? If latter is the case, we can take a look at the particular data. On Wed, Sep 8, 2010 at 2:56 PM, Lucas Lessa wrote: > Dear colleagues, > > I'm having some problems to read the DICOM images from a Philips Scanner > (1,5T), with uses the 2.5 release. > I didn't figured out what is, becase the problem is intermitent. > I have about 40 exams to process and the majority of them I did. > But some exams simply don't open in the DTISTUDIO/DTI module. > If I try to open the files in the viewer everything goes ok, but when I try > to load the DICOM images from the DTI the software returns an error, sayng > that it can't read the info in the files. > I have a macbook pro inside the network and I can pull the images directy > from the scanner. > After that I export the DICOM files and try to process them in the > DTISTUDIO. > I did exacty the samething in all exams, but I can't process some. > Does anybody know why? > Thank you. > > Lucas Lessa. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100908/47bfad93/attachment.html From xinrugujing at 126.com Thu Sep 9 10:42:40 2010 From: xinrugujing at 126.com (=?gbk?B?sfn3og==?=) Date: Thu, 09 Sep 2010 22:42:40 +0800 (CST) Subject: [Mristudio-users] REC In-Reply-To: References: <168318.19342.qm@web110208.mail.gq1.yahoo.com> Message-ID: <376db580.1050a.12af6f2c722.Coremail.xinrugujing@126.com> Dear sir, Sorry,my English is not well. I have download '01_020729_31.rec' from 'http://cmrm.med.jhmi.edu/'. I want to import data to matlab,but matlab only have the function named 'dicomread'.How can I convert the REC to DCM? If there is a programer for converting these formats? Can you understand what I say? I must say sorry again for my poor English. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100909/3f6521dc/attachment.html From lucas_lessa at yahoo.com.br Thu Sep 9 17:44:04 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Thu, 09 Sep 2010 14:44:04 -0700 (PDT) Subject: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images Message-ID: <404402.63498.qm@web110213.mail.gq1.yahoo.com> Yes, it's very strange, problably it's something that I'm doing weong, but I don't know what. Take a look in the error (see the attached picture). Thank you. --- Em qua, 8/9/10, Hangyi Jiang escreveu: De: Hangyi Jiang Assunto: RE: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images Para: "lucas_lessa at yahoo.com.br" Data: Quarta-feira, 8 de Setembro de 2010, 16:14 it is strange taht you can view the image (by MriView3D I guess), but cannot load them by DTI Mapping. what is error message?? could you please give me some detail? hangyi ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Lucas Lessa [lucas_lessa at yahoo.com.br] Sent: Wednesday, September 08, 2010 2:56 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images Dear colleagues, I'm having some problems to read the DICOM images from a Philips Scanner (1,5T), with uses the 2.5 release. I didn't figured out what is, becase the problem is intermitent. I have about 40 exams to process and the majority of them I did. But some exams simply don't open in the DTISTUDIO/DTI module. If I try to open the files in the viewer everything goes ok, but when I try to load the DICOM images from the DTI the software returns an error, sayng that it can't read the info in the files. I have a macbook pro inside the network and I can pull the images directy from the scanner. After that I export the DICOM files and try to process them in the DTISTUDIO. I did exacty the samething in all exams, but I can't process some. Does anybody know why? Thank you. Lucas Lessa. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100909/84e4e1b9/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: Parallels Picture.png Type: image/png Size: 15919 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100909/84e4e1b9/attachment-0001.png From lucas_lessa at yahoo.com.br Thu Sep 9 17:47:53 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Thu, 09 Sep 2010 14:47:53 -0700 (PDT) Subject: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images In-Reply-To: Message-ID: <39414.24015.qm@web110208.mail.gq1.yahoo.com> I had about 40 exams and 8 or 9 I can't process ind DTISTUDIO, but these exams I can view using the MRIviewer. I did everything using the same protocol. Please Dr Susumu Mori, can you see the picture with the error in my other message? Thank you very much. Lucas Lessa. --- Em qua, 8/9/10, susumu mori escreveu: De: susumu mori Assunto: Re: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images Para: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" Data: Quarta-feira, 8 de Setembro de 2010, 22:49 When you say "intermittent", do you have irreproducible problems with the same data? Or do you mean you have reproducible problems for a subset of data? If latter is the case, we can take a look at the particular data. On Wed, Sep 8, 2010 at 2:56 PM, Lucas Lessa wrote: Dear colleagues, I'm having some problems to read the DICOM images from a Philips Scanner (1,5T), with uses the 2.5 release. I didn't figured out what is, becase the problem is intermitent. I have about 40 exams to process and the majority of them I did. But some exams simply don't open in the DTISTUDIO/DTI module. If I try to open the files in the viewer everything goes ok, but when I try to load the DICOM images from the DTI the software returns an error, sayng that it can't read the info in the files. I have a macbook pro inside the network and I can pull the images directy from the scanner. After that I export the DICOM files and try to process them in the DTISTUDIO. I did exacty the samething in all exams, but I can't process some. Does anybody know why? Thank you. Lucas Lessa. ? _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -----Anexo incorporado----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100909/890bafe8/attachment.html From lucas_lessa at yahoo.com.br Sat Sep 11 13:58:04 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Sat, 11 Sep 2010 10:58:04 -0700 (PDT) Subject: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images In-Reply-To: Message-ID: <507918.95914.qm@web110215.mail.gq1.yahoo.com> I saw. I uploaded two types of exams, one, that it's working (called working), and another that I'm having problems with the processing (called not_working). If something it's wrong, please tell me. Thank you. --- Em sex, 10/9/10, Zhipeng Hou escreveu: De: Zhipeng Hou Assunto: Re: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images Para: "Hangyi Jiang" , lucas_lessa at yahoo.com.br Data: Sexta-feira, 10 de Setembro de 2010, 12:33 Lucas, I already?create?a folder for you.see ftp://162.129.247.245 Zhipeng On Fri, Sep 10, 2010 at 9:45 AM, Hangyi Jiang wrote: hi, if possible, could you please FTP your dataset to us, I'll take a look. please contact with Zhipeng to set up the FTP site. hangyi ________________________________ From: Lucas Lessa [lucas_lessa at yahoo.com.br] Sent: Thursday, September 09, 2010 5:44 PM To: Hangyi Jiang Cc: MRI Studio Mailing list Subject: RE: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images Yes, it's very strange, problably it's something that I'm doing weong, but I don't know what. Take a look in the error (see the attached picture). Thank you. --- Em qua, 8/9/10, Hangyi Jiang escreveu: De: Hangyi Jiang Assunto: RE: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images Para: "lucas_lessa at yahoo.com.br" Data: Quarta-feira, 8 de Setembro de 2010, 16:14 it is strange taht you can view the image (by MriView3D I guess), but cannot load them by DTI Mapping. what is error message? ?could you please give me some detail? hangyi ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Lucas Lessa [lucas_lessa at yahoo.com.br] Sent: Wednesday, September 08, 2010 2:56 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images Dear colleagues, I'm having some problems to read the DICOM images from a Philips Scanner (1,5T), with uses the 2.5 release. I didn't figured out what is, becase the problem is intermitent. I have about 40 exams to process and the majority of them I did. But some exams simply don't open in the DTISTUDIO/DTI module. If I try to open the files in the viewer everything goes ok, but when I try to load the DICOM images from the DTI the software returns an error, sayng that it can't read the info in the files. I have a macbook pro inside the network and I can pull the images directy from the scanner. After that I export the DICOM files and try to process them in the DTISTUDIO. I did exacty the samething in all exams, but I can't process some. Does anybody know why? Thank you. Lucas Lessa. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100911/182711e8/attachment.html From lucas_lessa at yahoo.com.br Mon Sep 13 15:33:20 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Mon, 13 Sep 2010 12:33:20 -0700 (PDT) Subject: [Mristudio-users] Problem reading Philips Achieva r2.5 DICOM images In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F2440E2D4CE@RAD-EXCH1.win.ad.jhu.edu> Message-ID: <641950.81255.qm@web110202.mail.gq1.yahoo.com> Problem solved. Thank you very much support team. Lucas Lessa Brazil -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100913/f034a4ca/attachment.html From rajagov2 at ccf.org Mon Sep 13 16:20:16 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Mon, 13 Sep 2010 16:20:16 -0400 Subject: [Mristudio-users] Range of RA Message-ID: <77A88E90A851594AAEF830450587C39D041832C2@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, I am using recent version of DTI studio (DTISTUDIO-lates-x86.exe) to process my DTI images. I am wondering whether RA and FA maps are normalized i.e. their values range between 0-1 because in cerebral peduncle (for CST) in some of my subjects (controls) I am getting RA values above 1 and FA values close to 1 which i haven't seen while using earlier versions of DTI studio. Kindly clarify the above. Thanks in advance Venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100913/32d951d8/attachment-0001.html From susumu at mri.jhu.edu Mon Sep 13 19:42:44 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 13 Sep 2010 19:42:44 -0400 Subject: [Mristudio-users] Range of RA In-Reply-To: <77A88E90A851594AAEF830450587C39D041832C2@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D041832C2@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: I have to study a bit about RA, but FA should not be more than 1, although there is possibility if the fitting didn't work properly. For example, depending on the degree of anisotropy, noise, registration artifacts (motion, eddy current), it's possible to get negative diagonal elements, (physically impossible but mathematically possible) and FA becomes more than 1. In other words, by applying diffusion-weighting, signal increases. In DtiStudio, if diagonal elements become less than 0, they are replaced by 0, eliminating most of FA>1. On Mon, Sep 13, 2010 at 4:20 PM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > Dear All, > > I am using recent version of DTI studio (DTISTUDIO-lates-x86.exe) to > process my DTI images. I am wondering whether RA and FA maps are normalized > i.e. their values range between 0-1 because in cerebral peduncle (for CST) > in some of my subjects (controls) I am getting RA values above 1 and FA > values close to 1 which i haven't seen while using earlier versions of DTI > studio. Kindly clarify the above. > > Thanks in advance > > Venkateswaran > > =================================== > > P Please consider the environment before printing this e-mail > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100913/2bbdc2b3/attachment.html From rajagov2 at ccf.org Tue Sep 14 10:16:45 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Tue, 14 Sep 2010 10:16:45 -0400 Subject: [Mristudio-users] Range of RA References: <77A88E90A851594AAEF830450587C39D041832C2@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D041832C3@CCHSCLEXMB56.cc.ad.cchs.net> Thanks very much Dr. Mori and Dr.Hanqyi. Venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Mon 9/13/2010 7:42 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Range of RA I have to study a bit about RA, but FA should not be more than 1, although there is possibility if the fitting didn't work properly. For example, depending on the degree of anisotropy, noise, registration artifacts (motion, eddy current), it's possible to get negative diagonal elements, (physically impossible but mathematically possible) and FA becomes more than 1. In other words, by applying diffusion-weighting, signal increases. In DtiStudio, if diagonal elements become less than 0, they are replaced by 0, eliminating most of FA>1. On Mon, Sep 13, 2010 at 4:20 PM, Rajagopalan, Venkateswaran wrote: Dear All, I am using recent version of DTI studio (DTISTUDIO-lates-x86.exe) to process my DTI images. I am wondering whether RA and FA maps are normalized i.e. their values range between 0-1 because in cerebral peduncle (for CST) in some of my subjects (controls) I am getting RA values above 1 and FA values close to 1 which i haven't seen while using earlier versions of DTI studio. Kindly clarify the above. Thanks in advance Venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 5970 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100914/2416eb5b/attachment.bin From mbonares at gmail.com Tue Sep 14 10:56:18 2010 From: mbonares at gmail.com (Michael Bonares) Date: Tue, 14 Sep 2010 14:56:18 +0000 Subject: [Mristudio-users] Range of RA In-Reply-To: <77A88E90A851594AAEF830450587C39D041832C3@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D041832C2@CCHSCLEXMB56.cc.ad.cchs.net> <77A88E90A851594AAEF830450587C39D041832C3@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <248790977-1284476180-cardhu_decombobulator_blackberry.rim.net-552340259-@bda378.bisx.prod.on.blackberry> It's understandable that you're apprehensive. Sent from my BlackBerry device on the Rogers Wireless Network -----Original Message----- From: "Rajagopalan, Venkateswaran" Sender: mristudio-users-bounces at mristudio.org Date: Tue, 14 Sep 2010 10:16:45 To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Reply-To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" Subject: Re: [Mristudio-users] Range of RA Thanks very much Dr. Mori and Dr.Hanqyi. Venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Mon 9/13/2010 7:42 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Range of RA I have to study a bit about RA, but FA should not be more than 1, although there is possibility if the fitting didn't work properly. For example, depending on the degree of anisotropy, noise, registration artifacts (motion, eddy current), it's possible to get negative diagonal elements, (physically impossible but mathematically possible) and FA becomes more than 1. In other words, by applying diffusion-weighting, signal increases. In DtiStudio, if diagonal elements become less than 0, they are replaced by 0, eliminating most of FA>1. On Mon, Sep 13, 2010 at 4:20 PM, Rajagopalan, Venkateswaran wrote: Dear All, I am using recent version of DTI studio (DTISTUDIO-lates-x86.exe) to process my DTI images. I am wondering whether RA and FA maps are normalized i.e. their values range between 0-1 because in cerebral peduncle (for CST) in some of my subjects (controls) I am getting RA values above 1 and FA values close to 1 which i haven't seen while using earlier versions of DTI studio. Kindly clarify the above. Thanks in advance Venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. From basketballmouse at 163.com Tue Sep 14 11:04:10 2010 From: basketballmouse at 163.com (=?gbk?B?u8a6o8fl?=) Date: Tue, 14 Sep 2010 23:04:10 +0800 (CST) Subject: [Mristudio-users] Different Gradient Table of DTI from Philips Achieva 3T Message-ID: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> Hi, I'm dealing with DTI data from Philips Achieva 3T. I tried two methods to compute the gradient table (32+1). (1) " dcm2nii.exe " with Philips dicom files 0 0 0 1.0000 0 0 0 -1.0000 0 0 0 -1.0000 -0.0424 0.1146 0.9925 0.1749 0.2005 0.9640 0.2323 0.1626 0.9590 0.3675 -0.0261 0.9296 0.1902 -0.3744 0.9076 -0.1168 -0.8334 0.5402 -0.2005 -0.2527 0.9465 -0.4958 -0.1345 0.8580 -0.0141 0.6281 0.7780 -0.7445 0.1477 0.6511 -0.7609 -0.3204 0.5643 -0.1809 -0.9247 0.3351 -0.6796 0.4224 0.5997 0.7771 -0.4707 0.4178 0.9242 0.1036 0.3677 0.4685 0.7674 0.4378 0.8817 0.1893 0.4322 0.6904 -0.7062 0.1569 0.2391 -0.7571 0.6080 -0.0578 -0.9837 -0.1703 -0.5368 -0.8361 0.1135 -0.9918 0.1207 0.0423 -0.9968 -0.0709 0.0379 -0.8724 -0.4781 0.1014 -0.2487 -0.9336 -0.2581 0.1183 -0.9919 0.0471 0.3376 -0.8415 -0.4218 0.5286 -0.8409 -0.1163 0.9969 -0.0550 0.0571 (2) " DTI_gradient_table_creator_Philips_RelX.m " with Philips par/rec files -0.6533 -0.2706 -0.7071 -0.2087 -0.6756 -0.7071 0.0197 -0.7068 -0.7071 0.4212 -0.5679 -0.7071 0.6899 -0.1549 -0.7071 -0.6535 -0.2707 -0.7069 -0.5000 -0.5000 -0.7071 -0.2929 -0.7071 -0.6436 0.2945 -0.7064 -0.6436 0.5150 -0.4861 -0.7061 0.7071 -0.2929 -0.6436 -0.7071 -0.4725 -0.5261 -0.4725 -0.7071 -0.5261 0.5555 -0.6439 -0.5261 0.7071 -0.4725 -0.5261 -0.7071 -0.7071 -0.0002 0.7071 -0.7071 0 -0.7071 -0.4725 0.5261 0.7071 -0.4725 0.5261 0.4725 -0.7071 0.5261 0.7071 -0.4725 0.5261 -0.6364 -0.4252 0.6436 -0.7060 -0.7060 0.0547 -0.2929 -0.7071 0.6436 0.2929 -0.7071 0.6436 0.7071 -0.7071 0.0078 0.7071 -0.2929 0.6436 -0.5847 -0.3977 0.7071 -0.7063 -0.7063 0.0489 0.0347 -0.7063 0.7071 0.7071 -0.7071 0.0115 0.7071 0 0.7071 0 0 0 100.0000 100.0000 100.0000 They seem totally different. So can any person explain this problem? Thank you very much! Haiqing -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100914/c67f3122/attachment.html From leggwork at yahoo.com Tue Sep 14 18:12:08 2010 From: leggwork at yahoo.com (Bruce Leggett) Date: Tue, 14 Sep 2010 15:12:08 -0700 (PDT) Subject: [Mristudio-users] Different Gradient Table of DTI from Philips Achieva 3T In-Reply-To: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> References: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> Message-ID: <879003.20670.qm@web110805.mail.gq1.yahoo.com> might it be Overplus off (1st) vs. Overplus on (2nd one)? thanks, bruce ________________________________ From: ??? To: DTI Studio Sent: Tue, September 14, 2010 9:04:10 AM Subject: [Mristudio-users] Different Gradient Table of DTI from Philips Achieva 3T Hi, I'm dealing with DTI data from Philips Achieva 3T. I tried two methods to compute the gradient table (32+1). (1) " dcm2nii.exe " with Philips dicom files 0 0 0 1.0000 0 0 0 -1.0000 0 0 0 -1.0000 -0.0424 0.1146 0.9925 0.1749 0.2005 0.9640 0.2323 0.1626 0.9590 0.3675 -0.0261 0.9296 0.1902 -0.3744 0.9076 -0.1168 -0.8334 0.5402 -0.2005 -0.2527 0.9465 -0.4958 -0.1345 0.8580 -0.0141 0.6281 0.7780 -0.7445 0.1477 0.6511 -0.7609 -0.3204 0.5643 -0.1809 -0.9247 0.3351 -0.6796 0.4224 0.5997 0.7771 -0.4707 0.4178 0.9242 0.1036 0.3677 0.4685 0.7674 0.4378 0.8817 0.1893 0.4322 0.6904 -0.7062 0.1569 0.2391 -0.7571 0.6080 -0.0578 -0.9837 -0.1703 -0.5368 -0.8361 0.1135 -0.9918 0.1207 0.0423 -0.9968 -0.0709 0.0379 -0.8724 -0.4781 0.1014 -0.2487 -0.9336 -0.2581 0.1183 -0.9919 0.0471 0.3376 -0.8415 -0.4218 0.5286 -0.8409 -0.1163 0.9969 -0.0550 0.0571 (2) " DTI_gradient_table_creator_Philips_RelX.m " with Philips par/rec files -0.6533 -0.2706 -0.7071 -0.2087 -0.6756 -0.7071 0.0197 -0.7068 -0.7071 0.4212 -0.5679 -0.7071 0.6899 -0.1549 -0.7071 -0.6535 -0.2707 -0.7069 -0.5000 -0.5000 -0.7071 -0.2929 -0.7071 -0.6436 0.2945 -0.7064 -0.6436 0.5150 -0.4861 -0.7061 0.7071 -0.2929 -0.6436 -0.7071 -0.4725 -0.5261 -0.4725 -0.7071 -0.5261 0.5555 -0.6439 -0.5261 0.7071 -0.4725 -0.5261 -0.7071 -0.7071 -0.0002 0.7071 -0.7071 0 -0.7071 -0.4725 0.5261 0.7071 -0.4725 0.5261 0.4725 -0.7071 0.5261 0.7071 -0.4725 0.5261 -0.6364 -0.4252 0.6436 -0.7060 -0.7060 0.0547 -0.2929 -0.7071 0.6436 0.2929 -0.7071 0.6436 0.7071 -0.7071 0.0078 0.7071 -0.2929 0.6436 -0.5847 -0.3977 0.7071 -0.7063 -0.7063 0.0489 0.0347 -0.7063 0.7071 0.7071 -0.7071 0.0115 0.7071 0 0.7071 0 0 0 100.0000 100.0000 100.0000 They seem totally different. So can any person explain this problem? Thank you very much! Haiqing ________________________________ ??????????????24??????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100914/a995c47a/attachment.html From susumu at mri.jhu.edu Tue Sep 14 18:14:48 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 14 Sep 2010 18:14:48 -0400 Subject: [Mristudio-users] Different Gradient Table of DTI from Philips Achieva 3T In-Reply-To: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> References: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> Message-ID: Hi Hiquing, It seems that the first table was created by a program not provided from us?? The second table seems to be created from the software obtained from Kriby Center in KKI? Anyway, I can give some generic information. 1) In Philips, you can specify the order of 32+1 images. I believe the default is b0 + 32 DWIs + calculated isotropically weighted image. You can also choose to store 32 DWIs + b0 + calculated. This is one reason of the difference 2) In DtiStudio, we use "100, 100, 100" to exclude images you don't need. That is why the second table has 34 rows and the final raw is "100, 100, 100". Apparently, the second table was created specifically for DtiStudio. The first table has only 33 rows because it ignored the last image. This is the second reason of the difference. 3) Philips has two options of gradient tables; with and without gradient overplus. If this option is "on", the table is designed to always use at least 2 gradients. In this way, you can maximize the b-value efficiency and shorten the echo time (thus higher SNR). Apparently the first table is "off", because there is "1, 0, 0". The second is "on". This is the third reason of the difference. Hope this clarify the question. You need to know exactly what you did for the above three points and grab the correct table. Susumu 2010/9/14 ??? > Hi, > > I'm dealing with DTI data from Philips Achieva 3T. I tried two methods to > compute the gradient table (32+1). > (1) " dcm2nii.exe " with Philips dicom files > 0 0 0 > 1.0000 0 0 > 0 -1.0000 0 > 0 0 -1.0000 > -0.0424 0.1146 0.9925 > 0.1749 0.2005 0.9640 > 0.2323 0.1626 0.9590 > 0.3675 -0.0261 0.9296 > 0.1902 -0.3744 0.9076 > -0.1168 -0.8334 0.5402 > -0.2005 -0.2527 0.9465 > -0.4958 -0.1345 0.8580 > -0.0141 0.6281 0.7780 > -0.7445 0.1477 0.6511 > -0.7609 -0.3204 0.5643 > -0.1809 -0.9247 0.3351 > -0.6796 0.4224 0.5997 > 0.7771 -0.4707 0.4178 > 0.9242 0.1036 0.3677 > 0.4685 0.7674 0.4378 > 0.8817 0.1893 0.4322 > 0.6904 -0.7062 0.1569 > 0.2391 -0.7571 0.6080 > -0.0578 -0.9837 -0.1703 > -0.5368 -0.8361 0.1135 > -0.9918 0.1207 0.0423 > -0.9968 -0.0709 0.0379 > -0.8724 -0.4781 0.1014 > -0.2487 -0.9336 -0.2581 > 0.1183 -0.9919 0.0471 > 0.3376 -0.8415 -0.4218 > 0.5286 -0.8409 -0.1163 > 0.9969 -0.0550 0.0571 > (2) " DTI_gradient_table_creator_Philips_RelX.m " with Philips par/rec > files > -0.6533 -0.2706 -0.7071 > -0.2087 -0.6756 -0.7071 > 0.0197 -0.7068 -0.7071 > 0.4212 -0.5679 -0.7071 > 0.6899 -0.1549 -0.7071 > -0.6535 -0.2707 -0.7069 > -0.5000 -0.5000 -0.7071 > -0.2929 -0.7071 -0.6436 > 0.2945 -0.7064 -0.6436 > 0.5150 -0.4861 -0.7061 > 0.7071 -0.2929 -0.6436 > -0.7071 -0.4725 -0.5261 > -0.4725 -0.7071 -0.5261 > 0.5555 -0.6439 -0.5261 > 0.7071 -0.4725 -0.5261 > -0.7071 -0.7071 -0.0002 > 0.7071 -0.7071 0 > -0.7071 -0.4725 0.5261 > 0.7071 -0.4725 0.5261 > 0.4725 -0.7071 0.5261 > 0.7071 -0.4725 0.5261 > -0.6364 -0.4252 0.6436 > -0.7060 -0.7060 0.0547 > -0.2929 -0.7071 0.6436 > 0.2929 -0.7071 0.6436 > 0.7071 -0.7071 0.0078 > 0.7071 -0.2929 0.6436 > -0.5847 -0.3977 0.7071 > -0.7063 -0.7063 0.0489 > 0.0347 -0.7063 0.7071 > 0.7071 -0.7071 0.0115 > 0.7071 0 0.7071 > 0 0 0 > 100.0000 100.0000 100.0000 > They seem totally different. So can any person explain this problem? Thank > you very much! > > Haiqing > > > ------------------------------ > ??????????????24??????? > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100914/b7ff60c3/attachment-0001.html From rajagov2 at ccf.org Fri Sep 17 18:30:24 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Fri, 17 Sep 2010 18:30:24 -0400 Subject: [Mristudio-users] Difference in DTI metric values between different versions of DTI studio Message-ID: <77A88E90A851594AAEF830450587C39D041832D0@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, I am surpirsed to find that DTI metrics (for instance RA metric) between DTIstudio_3.0_ beta version and DTIstudio_latest which i downloaded recently were very much different. Same options were used like automatic outlier rejection of images >3% also the same CST ROI was superimposed in both the DTI studio beta version and in DTIstudio latest RA values along CST using DTIstudio_3.0_ beta version Slice #_Of_Fibers Max_Val Min_Val Mean_Val Std_Dev 9: 1 0.50 0.50 0.50 0.00 1 1 1 1.00 0.00 10: 61 0.79 0.43 0.69 0.10 10 23 1 7.60 7.41 11: 60 0.85 0.18 0.74 0.14 13 25 1 10.62 8.91 12: 61 0.89 0.34 0.76 0.13 12 30 1 11.42 9.25 13: 61 0.95 0.27 0.75 0.15 11 28 1 12.64 9.83 14: 61 0.74 0.39 0.59 0.10 9 39 1 15.22 12.58 15: 61 0.74 0.32 0.57 0.10 10 45 1 14.40 14.19 16: 60 0.72 0.32 0.56 0.08 9 35 1 11.00 11.85 17: 61 0.68 0.47 0.61 0.06 8 37 2 16.13 12.19 18: 60 0.64 0.57 0.63 0.02 9 39 1 12.22 12.44 19: 61 0.61 0.52 0.59 0.02 9 37 1 15.11 10.87 20: 60 0.45 0.34 0.41 0.03 12 36 1 13.50 11.56 21: 61 0.37 0.20 0.30 0.04 16 42 1 12.94 13.91 22: 60 0.35 0.19 0.28 0.03 RA values along CST using DTIstudio_latest Slice #_Of_Fibers Max_Val Min_Val Mean_Val Std_Dev 9: 1 0.97 0.97 0.97 0.00 1 1 1 1.00 0.00 10: 61 1.04 0.47 0.90 0.19 10 23 1 7.60 7.41 11: 60 1.16 0.11 0.93 0.19 13 25 1 10.62 8.91 12: 61 1.05 0.42 0.89 0.14 12 30 1 11.42 9.25 13: 61 1.13 0.25 0.87 0.14 11 28 1 12.64 9.83 14: 61 0.89 0.48 0.70 0.10 9 39 1 15.22 12.58 15: 61 0.87 0.27 0.65 0.13 10 45 1 14.40 14.19 16: 60 0.79 0.27 0.62 0.10 9 35 1 11.00 11.85 17: 61 0.80 0.47 0.68 0.10 8 37 2 16.13 12.19 18: 60 0.75 0.58 0.64 0.05 9 39 1 12.22 12.44 19: 61 0.70 0.53 0.65 0.04 9 37 1 15.11 10.87 20: 60 0.52 0.36 0.46 0.05 12 36 1 13.50 11.56 21: 61 0.43 0.21 0.32 0.04 16 42 1 12.94 13.91 22: 60 0.40 0.19 0.28 0.04 What am i doing wrong here. Same DTI data was used in both the versions and the processing steps were identical. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100917/02f65e8b/attachment.html From susumu at mri.jhu.edu Fri Sep 17 22:18:06 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 17 Sep 2010 22:18:06 -0400 Subject: [Mristudio-users] Difference in DTI metric values between different versions of DTI studio In-Reply-To: <77A88E90A851594AAEF830450587C39D041832D0@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D041832D0@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Thank you for letting us know this. If you just subtract the two FA maps (or RA maps) by using RoiEditor (without tracking), do you get significant difference? The algorithms of automated rejection are not same between the two versions. If your data has some motion problems and many slices were rejected, it is possible that two different algorithms rejected the different number of slices. You can check which slices were rejected. I would recommend you to use the regular tensor calculation without slice rejection and make sure the results are the same. If so, the difference should come from the rejection scheme. On Fri, Sep 17, 2010 at 6:30 PM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > Dear All, > > I am surpirsed to find that DTI metrics (for instance RA metric) between > DTIstudio_3.0_ beta version and DTIstudio_latest which i downloaded recently > were very much different. > > Same options were used like automatic outlier rejection of images >3% also > the same CST ROI was superimposed in both the DTI studio beta version and > in DTIstudio latest > > > RA values along CST using DTIstudio_3.0_ beta version > > Slice #_Of_Fibers Max_Val Min_Val Mean_Val Std_Dev > 9: 1 0.50 0.50 0.50 0.00 1 1 > 1 1.00 0.00 > 10: 61 0.79 0.43 0.69 0.10 10 23 > 1 7.60 7.41 > 11: 60 0.85 0.18 0.74 0.14 13 25 > 1 10.62 8.91 > 12: 61 0.89 0.34 0.76 0.13 12 30 > 1 11.42 9.25 > 13: 61 0.95 0.27 0.75 0.15 11 28 > 1 12.64 9.83 > 14: 61 0.74 0.39 0.59 0.10 9 39 > 1 15.22 12.58 > 15: 61 0.74 0.32 0.57 0.10 10 45 > 1 14.40 14.19 > 16: 60 0.72 0.32 0.56 0.08 9 35 > 1 11.00 11.85 > 17: 61 0.68 0.47 0.61 0.06 8 37 > 2 16.13 12.19 > 18: 60 0.64 0.57 0.63 0.02 9 39 > 1 12.22 12.44 > 19: 61 0.61 0.52 0.59 0.02 9 37 > 1 15.11 10.87 > 20: 60 0.45 0.34 0.41 0.03 12 36 > 1 13.50 11.56 > 21: 61 0.37 0.20 0.30 0.04 16 42 > 1 12.94 13.91 > 22: 60 0.35 0.19 0.28 0.03 > > RA values along CST using DTIstudio_latest > > Slice #_Of_Fibers Max_Val Min_Val Mean_Val Std_Dev > > 9: 1 0.97 0.97 0.97 0.00 1 1 > 1 1.00 0.00 > 10: 61 1.04 0.47 0.90 0.19 10 23 > 1 7.60 7.41 > 11: 60 1.16 0.11 0.93 0.19 13 25 > 1 10.62 8.91 > 12: 61 1.05 0.42 0.89 0.14 12 30 > 1 11.42 9.25 > 13: 61 1.13 0.25 0.87 0.14 11 28 > 1 12.64 9.83 > 14: 61 0.89 0.48 0.70 0.10 9 39 > 1 15.22 12.58 > 15: 61 0.87 0.27 0.65 0.13 10 45 > 1 14.40 14.19 > 16: 60 0.79 0.27 0.62 0.10 9 35 > 1 11.00 11.85 > 17: 61 0.80 0.47 0.68 0.10 8 37 > 2 16.13 12.19 > 18: 60 0.75 0.58 0.64 0.05 9 39 > 1 12.22 12.44 > 19: 61 0.70 0.53 0.65 0.04 9 37 > 1 15.11 10.87 > 20: 60 0.52 0.36 0.46 0.05 12 36 > 1 13.50 11.56 > 21: 61 0.43 0.21 0.32 0.04 16 42 > 1 12.94 13.91 > 22: 60 0.40 0.19 0.28 0.04 > > What am i doing wrong here. Same DTI data was used in both the versions and > the processing steps were identical. > > Thanks > > Venkat > > > > > =================================== > > P Please consider the environment before printing this e-mail > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100917/ea72fbfc/attachment-0001.html From rajagov2 at ccf.org Sun Sep 19 15:48:53 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Sun, 19 Sep 2010 15:48:53 -0400 Subject: [Mristudio-users] Difference in DTI metric values between different versions of DTI studio References: <77A88E90A851594AAEF830450587C39D041832D0@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D041832D2@CCHSCLEXMB56.cc.ad.cchs.net> Thanks very much Dr.Mori, When I unchecked the automatic outlier option (in both the versions and reran) the results are the same between the two versions, so the difference was contributed by the different automatic rejection algorithms. Thanks again Venkat ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Fri 9/17/2010 10:18 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang Subject: Re: [Mristudio-users] Difference in DTI metric values between different versions of DTI studio Thank you for letting us know this. If you just subtract the two FA maps (or RA maps) by using RoiEditor (without tracking), do you get significant difference? The algorithms of automated rejection are not same between the two versions. If your data has some motion problems and many slices were rejected, it is possible that two different algorithms rejected the different number of slices. You can check which slices were rejected. I would recommend you to use the regular tensor calculation without slice rejection and make sure the results are the same. If so, the difference should come from the rejection scheme. On Fri, Sep 17, 2010 at 6:30 PM, Rajagopalan, Venkateswaran wrote: Dear All, I am surpirsed to find that DTI metrics (for instance RA metric) between DTIstudio_3.0_ beta version and DTIstudio_latest which i downloaded recently were very much different. Same options were used like automatic outlier rejection of images >3% also the same CST ROI was superimposed in both the DTI studio beta version and in DTIstudio latest RA values along CST using DTIstudio_3.0_ beta version Slice #_Of_Fibers Max_Val Min_Val Mean_Val Std_Dev 9: 1 0.50 0.50 0.50 0.00 1 1 1 1.00 0.00 10: 61 0.79 0.43 0.69 0.10 10 23 1 7.60 7.41 11: 60 0.85 0.18 0.74 0.14 13 25 1 10.62 8.91 12: 61 0.89 0.34 0.76 0.13 12 30 1 11.42 9.25 13: 61 0.95 0.27 0.75 0.15 11 28 1 12.64 9.83 14: 61 0.74 0.39 0.59 0.10 9 39 1 15.22 12.58 15: 61 0.74 0.32 0.57 0.10 10 45 1 14.40 14.19 16: 60 0.72 0.32 0.56 0.08 9 35 1 11.00 11.85 17: 61 0.68 0.47 0.61 0.06 8 37 2 16.13 12.19 18: 60 0.64 0.57 0.63 0.02 9 39 1 12.22 12.44 19: 61 0.61 0.52 0.59 0.02 9 37 1 15.11 10.87 20: 60 0.45 0.34 0.41 0.03 12 36 1 13.50 11.56 21: 61 0.37 0.20 0.30 0.04 16 42 1 12.94 13.91 22: 60 0.35 0.19 0.28 0.03 RA values along CST using DTIstudio_latest Slice #_Of_Fibers Max_Val Min_Val Mean_Val Std_Dev 9: 1 0.97 0.97 0.97 0.00 1 1 1 1.00 0.00 10: 61 1.04 0.47 0.90 0.19 10 23 1 7.60 7.41 11: 60 1.16 0.11 0.93 0.19 13 25 1 10.62 8.91 12: 61 1.05 0.42 0.89 0.14 12 30 1 11.42 9.25 13: 61 1.13 0.25 0.87 0.14 11 28 1 12.64 9.83 14: 61 0.89 0.48 0.70 0.10 9 39 1 15.22 12.58 15: 61 0.87 0.27 0.65 0.13 10 45 1 14.40 14.19 16: 60 0.79 0.27 0.62 0.10 9 35 1 11.00 11.85 17: 61 0.80 0.47 0.68 0.10 8 37 2 16.13 12.19 18: 60 0.75 0.58 0.64 0.05 9 39 1 12.22 12.44 19: 61 0.70 0.53 0.65 0.04 9 37 1 15.11 10.87 20: 60 0.52 0.36 0.46 0.05 12 36 1 13.50 11.56 21: 61 0.43 0.21 0.32 0.04 16 42 1 12.94 13.91 22: 60 0.40 0.19 0.28 0.04 What am i doing wrong here. Same DTI data was used in both the versions and the processing steps were identical. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 17007 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100919/5bcf4d58/attachment-0001.bin From susumu at mri.jhu.edu Sun Sep 19 16:46:33 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sun, 19 Sep 2010 16:46:33 -0400 Subject: [Mristudio-users] Difference in DTI metric values between different versions of DTI studio In-Reply-To: <77A88E90A851594AAEF830450587C39D041832D2@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D041832D0@CCHSCLEXMB56.cc.ad.cchs.net> <77A88E90A851594AAEF830450587C39D041832D2@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: you can visually inspect the outlier rejection results (a big red cross in the inspection window) and see which version is performing better. It also depends on the threshold value. I believe the newer version performs better. On Sun, Sep 19, 2010 at 3:48 PM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > Thanks very much Dr.Mori, When I unchecked the automatic outlier option (in > both the versions and reran) the results are the same between the two > versions, so the difference was contributed by the different automatic > rejection algorithms. > > Thanks again > > Venkat > > ________________________________ > > From: mristudio-users-bounces at mristudio.org on behalf of susumu mori > Sent: Fri 9/17/2010 10:18 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang > Subject: Re: [Mristudio-users] Difference in DTI metric values between > different versions of DTI studio > > > Thank you for letting us know this. > If you just subtract the two FA maps (or RA maps) by using RoiEditor > (without tracking), do you get significant difference? The algorithms of > automated rejection are not same between the two versions. If your data has > some motion problems and many slices were rejected, it is possible that two > different algorithms rejected the different number of slices. You can check > which slices were rejected. > > I would recommend you to use the regular tensor calculation without slice > rejection and make sure the results are the same. If so, the difference > should come from the rejection scheme. > > > On Fri, Sep 17, 2010 at 6:30 PM, Rajagopalan, Venkateswaran < > rajagov2 at ccf.org> wrote: > > > Dear All, > > I am surpirsed to find that DTI metrics (for instance RA metric) > between DTIstudio_3.0_ beta version and DTIstudio_latest which i downloaded > recently were very much different. > > Same options were used like automatic outlier rejection of images > >3% also the same CST ROI was superimposed in both the DTI studio beta > version and in DTIstudio latest > > > RA values along CST using DTIstudio_3.0_ beta version > > Slice #_Of_Fibers Max_Val Min_Val Mean_Val Std_Dev > 9: 1 0.50 0.50 0.50 0.00 1 > 1 1 1.00 0.00 > 10: 61 0.79 0.43 0.69 0.10 10 > 23 1 7.60 7.41 > 11: 60 0.85 0.18 0.74 0.14 13 > 25 1 10.62 8.91 > 12: 61 0.89 0.34 0.76 0.13 12 > 30 1 11.42 9.25 > 13: 61 0.95 0.27 0.75 0.15 11 > 28 1 12.64 9.83 > 14: 61 0.74 0.39 0.59 0.10 9 > 39 1 15.22 12.58 > 15: 61 0.74 0.32 0.57 0.10 10 > 45 1 14.40 14.19 > 16: 60 0.72 0.32 0.56 0.08 9 > 35 1 11.00 11.85 > 17: 61 0.68 0.47 0.61 0.06 8 > 37 2 16.13 12.19 > 18: 60 0.64 0.57 0.63 0.02 9 > 39 1 12.22 12.44 > 19: 61 0.61 0.52 0.59 0.02 9 > 37 1 15.11 10.87 > 20: 60 0.45 0.34 0.41 0.03 12 > 36 1 13.50 11.56 > 21: 61 0.37 0.20 0.30 0.04 16 > 42 1 12.94 13.91 > 22: 60 0.35 0.19 0.28 0.03 > > RA values along CST using DTIstudio_latest > > Slice #_Of_Fibers Max_Val Min_Val Mean_Val Std_Dev > > 9: 1 0.97 0.97 0.97 0.00 1 > 1 1 1.00 0.00 > 10: 61 1.04 0.47 0.90 0.19 10 > 23 1 7.60 7.41 > 11: 60 1.16 0.11 0.93 0.19 13 > 25 1 10.62 8.91 > 12: 61 1.05 0.42 0.89 0.14 12 > 30 1 11.42 9.25 > 13: 61 1.13 0.25 0.87 0.14 11 > 28 1 12.64 9.83 > 14: 61 0.89 0.48 0.70 0.10 9 > 39 1 15.22 12.58 > 15: 61 0.87 0.27 0.65 0.13 10 > 45 1 14.40 14.19 > 16: 60 0.79 0.27 0.62 0.10 9 > 35 1 11.00 11.85 > 17: 61 0.80 0.47 0.68 0.10 8 > 37 2 16.13 12.19 > 18: 60 0.75 0.58 0.64 0.05 9 > 39 1 12.22 12.44 > 19: 61 0.70 0.53 0.65 0.04 9 > 37 1 15.11 10.87 > 20: 60 0.52 0.36 0.46 0.05 12 > 36 1 13.50 11.56 > 21: 61 0.43 0.21 0.32 0.04 16 > 42 1 12.94 13.91 > 22: 60 0.40 0.19 0.28 0.04 > > What am i doing wrong here. Same DTI data was used in both the > versions and the processing steps were identical. > > Thanks > > Venkat > > > > > > > =================================== > > P Please consider the environment before printing this e-mail > > > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org < > http://www.clevelandclinic.org/> for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > > > > =================================== > > P Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100919/2694d8ad/attachment.html From rajagov2 at ccf.org Sun Sep 19 17:10:58 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Sun, 19 Sep 2010 17:10:58 -0400 Subject: [Mristudio-users] Difference in DTI metric values between different versions of DTI studio References: <77A88E90A851594AAEF830450587C39D041832D0@CCHSCLEXMB56.cc.ad.cchs.net> <77A88E90A851594AAEF830450587C39D041832D2@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D041832D3@CCHSCLEXMB56.cc.ad.cchs.net> Thanks very much. Venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Sun 9/19/2010 4:46 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Difference in DTI metric values between different versions of DTI studio you can visually inspect the outlier rejection results (a big red cross in the inspection window) and see which version is performing better. It also depends on the threshold value. I believe the newer version performs better. On Sun, Sep 19, 2010 at 3:48 PM, Rajagopalan, Venkateswaran wrote: Thanks very much Dr.Mori, When I unchecked the automatic outlier option (in both the versions and reran) the results are the same between the two versions, so the difference was contributed by the different automatic rejection algorithms. Thanks again Venkat ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Fri 9/17/2010 10:18 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang Subject: Re: [Mristudio-users] Difference in DTI metric values between different versions of DTI studio Thank you for letting us know this. If you just subtract the two FA maps (or RA maps) by using RoiEditor (without tracking), do you get significant difference? The algorithms of automated rejection are not same between the two versions. If your data has some motion problems and many slices were rejected, it is possible that two different algorithms rejected the different number of slices. You can check which slices were rejected. I would recommend you to use the regular tensor calculation without slice rejection and make sure the results are the same. If so, the difference should come from the rejection scheme. On Fri, Sep 17, 2010 at 6:30 PM, Rajagopalan, Venkateswaran wrote: Dear All, I am surpirsed to find that DTI metrics (for instance RA metric) between DTIstudio_3.0_ beta version and DTIstudio_latest which i downloaded recently were very much different. Same options were used like automatic outlier rejection of images >3% also the same CST ROI was superimposed in both the DTI studio beta version and in DTIstudio latest RA values along CST using DTIstudio_3.0_ beta version Slice #_Of_Fibers Max_Val Min_Val Mean_Val Std_Dev 9: 1 0.50 0.50 0.50 0.00 1 1 1 1.00 0.00 10: 61 0.79 0.43 0.69 0.10 10 23 1 7.60 7.41 11: 60 0.85 0.18 0.74 0.14 13 25 1 10.62 8.91 12: 61 0.89 0.34 0.76 0.13 12 30 1 11.42 9.25 13: 61 0.95 0.27 0.75 0.15 11 28 1 12.64 9.83 14: 61 0.74 0.39 0.59 0.10 9 39 1 15.22 12.58 15: 61 0.74 0.32 0.57 0.10 10 45 1 14.40 14.19 16: 60 0.72 0.32 0.56 0.08 9 35 1 11.00 11.85 17: 61 0.68 0.47 0.61 0.06 8 37 2 16.13 12.19 18: 60 0.64 0.57 0.63 0.02 9 39 1 12.22 12.44 19: 61 0.61 0.52 0.59 0.02 9 37 1 15.11 10.87 20: 60 0.45 0.34 0.41 0.03 12 36 1 13.50 11.56 21: 61 0.37 0.20 0.30 0.04 16 42 1 12.94 13.91 22: 60 0.35 0.19 0.28 0.03 RA values along CST using DTIstudio_latest Slice #_Of_Fibers Max_Val Min_Val Mean_Val Std_Dev 9: 1 0.97 0.97 0.97 0.00 1 1 1 1.00 0.00 10: 61 1.04 0.47 0.90 0.19 10 23 1 7.60 7.41 11: 60 1.16 0.11 0.93 0.19 13 25 1 10.62 8.91 12: 61 1.05 0.42 0.89 0.14 12 30 1 11.42 9.25 13: 61 1.13 0.25 0.87 0.14 11 28 1 12.64 9.83 14: 61 0.89 0.48 0.70 0.10 9 39 1 15.22 12.58 15: 61 0.87 0.27 0.65 0.13 10 45 1 14.40 14.19 16: 60 0.79 0.27 0.62 0.10 9 35 1 11.00 11.85 17: 61 0.80 0.47 0.68 0.10 8 37 2 16.13 12.19 18: 60 0.75 0.58 0.64 0.05 9 39 1 12.22 12.44 19: 61 0.70 0.53 0.65 0.04 9 37 1 15.11 10.87 20: 60 0.52 0.36 0.46 0.05 12 36 1 13.50 11.56 21: 61 0.43 0.21 0.32 0.04 16 42 1 12.94 13.91 22: 60 0.40 0.19 0.28 0.04 What am i doing wrong here. Same DTI data was used in both the versions and the processing steps were identical. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 16339 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100919/d5123fac/attachment-0001.bin From rajagov2 at ccf.org Wed Sep 22 11:18:24 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Wed, 22 Sep 2010 11:18:24 -0400 Subject: [Mristudio-users] CST atlas Message-ID: <77A88E90A851594AAEF830450587C39D041832D5@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, I am using CST probability atlas for some calculations (i.e. measuring FA values along CST), since the CST atlas includes probability values ranging from 0 to 1, I want to exclude very low probability values like 0.00002 I tried using Percentile ( since It will not raise concerns when I write an article say I want to retain say between 5% and 95%) however since many voxels have very low probability values this is not working good in the sense for 95 percentile my probability value comes to 0.1745 however the probability values range from 0.0 to 0.578 so all the higher probability values above 0.1745 will get rejected. Any suggestions will be of great help. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100922/76eb989a/attachment.html From susumu at mri.jhu.edu Wed Sep 22 13:58:06 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 22 Sep 2010 13:58:06 -0400 Subject: [Mristudio-users] CST atlas In-Reply-To: <77A88E90A851594AAEF830450587C39D041832D5@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D041832D5@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Hi Venkat, I'm not sure why you want to reject >95 percentile pixels because these pixels are the best representation of the CST (highest probability). Isn't it more reasonable to use the probability threshold like >0.2? When we do FA calculation, FA of each pixel is weighted by probability. So high probability pixels have more weight. If you don't want it, you can convert the probability map to binary (1/0) by applying a threshold using RoiEditor. RoiEditor can also allows to apply a cut-off value for FA measurement. In this case, you can, for example, mask-out all pixels with probability <0.2, and then perform probability-weighted FA measurement for those pixels with >=0.2. Susumu On Wed, Sep 22, 2010 at 11:18 AM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > > Dear All, > > I am using CST probability atlas for some calculations (i.e. measuring FA > values along CST), since the CST atlas includes probability values ranging > from 0 to 1, I want to exclude very low probability values like 0.00002 I > tried using Percentile ( since It will not raise concerns when I write an > article say I want to retain say between 5% and 95%) however since many > voxels have very low probability values this is not working good in the > sense for 95 percentile my probability value comes to 0.1745 however the > probability values range from 0.0 to 0.578 so all the higher probability > values above 0.1745 will get rejected. Any suggestions will be of great > help. > > Thanks > > Venkat > > =================================== > > P Please consider the environment before printing this e-mail > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100922/616a2527/attachment.html From rajagov2 at ccf.org Wed Sep 22 14:35:51 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Wed, 22 Sep 2010 14:35:51 -0400 Subject: [Mristudio-users] CST atlas References: <77A88E90A851594AAEF830450587C39D041832D5@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D041832D6@CCHSCLEXMB56.cc.ad.cchs.net> Dear Dr.Mori, Thanks very much for your kind reply. Actually I don't want to delete high probability tracts as you mentioned these are the more accurate tracts I was trying to find a "acceptable" method (so that this will not be an issue when i submit an article) to threshold the tract probability values since there are lot of pixels whose probability values are close to 0 so I thought of using percentile like in outlier rejection procedure that is why i ended up choosing 5% and 95%. The threshold value you gave me (< 0.2%) looks very good. Can you give me the rationale behind choosing that number since this becomes an important question when I submit manuscripts. Thanks very much Venkat -----Original Message----- From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Wed 9/22/2010 1:58 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] CST atlas Hi Venkat, I'm not sure why you want to reject >95 percentile pixels because these pixels are the best representation of the CST (highest probability). Isn't it more reasonable to use the probability threshold like >0.2? When we do FA calculation, FA of each pixel is weighted by probability. So high probability pixels have more weight. If you don't want it, you can convert the probability map to binary (1/0) by applying a threshold using RoiEditor. RoiEditor can also allows to apply a cut-off value for FA measurement. In this case, you can, for example, mask-out all pixels with probability <0.2, and then perform probability-weighted FA measurement for those pixels with >=0.2. Susumu On Wed, Sep 22, 2010 at 11:18 AM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > > Dear All, > > I am using CST probability atlas for some calculations (i.e. measuring FA > values along CST), since the CST atlas includes probability values ranging > from 0 to 1, I want to exclude very low probability values like 0.00002 I > tried using Percentile ( since It will not raise concerns when I write an > article say I want to retain say between 5% and 95%) however since many > voxels have very low probability values this is not working good in the > sense for 95 percentile my probability value comes to 0.1745 however the > probability values range from 0.0 to 0.578 so all the higher probability > values above 0.1745 will get rejected. Any suggestions will be of great > help. > > Thanks > > Venkat > > =================================== > > P Please consider the environment before printing this e-mail > > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 4716 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100922/c280e292/attachment-0001.bin From susumu at mri.jhu.edu Wed Sep 22 15:29:44 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 22 Sep 2010 15:29:44 -0400 Subject: [Mristudio-users] CST atlas In-Reply-To: <77A88E90A851594AAEF830450587C39D041832D6@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D041832D5@CCHSCLEXMB56.cc.ad.cchs.net> <77A88E90A851594AAEF830450587C39D041832D6@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Well, actually when we set a threshold for image analysis, in many cases, it's arbitrary. One thing you can do is to show the results (either FA values or group difference) is not overly dependent on the threshold of your choice. On Wed, Sep 22, 2010 at 2:35 PM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > > Dear Dr.Mori, > > Thanks very much for your kind reply. Actually I don't want to delete high > probability tracts as you mentioned these are the more accurate tracts I was > trying to find a "acceptable" method (so that this will not be an issue when > i submit an article) to threshold the tract probability values since there > are lot of pixels whose probability values are close to 0 so I thought of > using percentile like in outlier rejection procedure that is why i ended up > choosing 5% and 95%. The threshold value you gave me (< 0.2%) looks very > good. Can you give me the rationale behind choosing that number since this > becomes an important question when I submit manuscripts. > > Thanks very much > > Venkat > > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org on behalf of susumu mori > Sent: Wed 9/22/2010 1:58 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] CST atlas > > Hi Venkat, > > I'm not sure why you want to reject >95 percentile pixels because these > pixels are the best representation of the CST (highest probability). Isn't > it more reasonable to use the probability threshold like >0.2? > > When we do FA calculation, FA of each pixel is weighted by probability. So > high probability pixels have more weight. If you don't want it, you can > convert the probability map to binary (1/0) by applying a threshold using > RoiEditor. > > RoiEditor can also allows to apply a cut-off value for FA measurement. In > this case, you can, for example, mask-out all pixels with probability <0.2, > and then perform probability-weighted FA measurement for those pixels with > >=0.2. > > Susumu > > On Wed, Sep 22, 2010 at 11:18 AM, Rajagopalan, Venkateswaran < > rajagov2 at ccf.org> wrote: > > > > > Dear All, > > > > I am using CST probability atlas for some calculations (i.e. measuring FA > > values along CST), since the CST atlas includes probability values > ranging > > from 0 to 1, I want to exclude very low probability values like 0.00002 I > > tried using Percentile ( since It will not raise concerns when I write an > > article say I want to retain say between 5% and 95%) however since many > > voxels have very low probability values this is not working good in the > > sense for 95 percentile my probability value comes to 0.1745 however the > > probability values range from 0.0 to 0.578 so all the higher probability > > values above 0.1745 will get rejected. Any suggestions will be of great > > help. > > > > Thanks > > > > Venkat > > > > =================================== > > > > P Please consider the environment before printing this e-mail > > > > > > Cleveland Clinic is ranked one of the top hospitals > > in America by U.S.News & World Report (2009). > > Visit us online at http://www.clevelandclinic.org for > > a complete listing of our services, staff and > > locations. > > > > > > Confidentiality Note: This message is intended for use > > only by the individual or entity to which it is addressed > > and may contain information that is privileged, > > confidential, and exempt from disclosure under applicable > > law. If the reader of this message is not the intended > > recipient or the employee or agent responsible for > > delivering the message to the intended recipient, you are > > hereby notified that any dissemination, distribution or > > copying of this communication is strictly prohibited. If > > you have received this communication in error, please > > contact the sender immediately and destroy the material in > > its entirety, whether electronic or hard copy. Thank you. > > > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > > mristudio-users-unsubscribe at mristudio.org > > > > > > > =================================== > > P Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100922/9e57cd1e/attachment.html From rajagov2 at ccf.org Wed Sep 22 15:13:17 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Wed, 22 Sep 2010 15:13:17 -0400 Subject: [Mristudio-users] Unable to open FA images properly in DTIstudio Message-ID: <77A88E90A851594AAEF830450587C39D041832D8@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, I processed DTI images using DTI studio and used the option "Save results" in DTI-map window to save FA and other anisotropy maps, unfortunately when I tried to load them in "MRIview 3D" in DTI studio FA images doesn't open properly in the sense I am not able to see all the 30 slices (that is how it is when loaded using dicom format all 30 slices will appear and I can scroll through them) instead I am seeing only 7 slices with two columns of FA images in the viwer window. I tried to attach snapshot of the problem (my message was rejected due to file size problem If you would like to have a look at it kindly give me an FTP or somewhere I can upload it). While opening using MRIview3D I am checking Raw image and float option to open my FA.dat files. What am i doing wrong here. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100922/c81ff313/attachment.html From rajagov2 at ccf.org Wed Sep 22 15:58:40 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Wed, 22 Sep 2010 15:58:40 -0400 Subject: [Mristudio-users] CST atlas References: <77A88E90A851594AAEF830450587C39D041832D5@CCHSCLEXMB56.cc.ad.cchs.net> <77A88E90A851594AAEF830450587C39D041832D6@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D041832D9@CCHSCLEXMB56.cc.ad.cchs.net> Thanks very much Dr.Mori Venkat -----Original Message----- From: mristudio-users-bounces at mristudio.org on behalf of susumu mori Sent: Wed 9/22/2010 3:29 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] CST atlas Well, actually when we set a threshold for image analysis, in many cases, it's arbitrary. One thing you can do is to show the results (either FA values or group difference) is not overly dependent on the threshold of your choice. On Wed, Sep 22, 2010 at 2:35 PM, Rajagopalan, Venkateswaran < rajagov2 at ccf.org> wrote: > > Dear Dr.Mori, > > Thanks very much for your kind reply. Actually I don't want to delete high > probability tracts as you mentioned these are the more accurate tracts I was > trying to find a "acceptable" method (so that this will not be an issue when > i submit an article) to threshold the tract probability values since there > are lot of pixels whose probability values are close to 0 so I thought of > using percentile like in outlier rejection procedure that is why i ended up > choosing 5% and 95%. The threshold value you gave me (< 0.2%) looks very > good. Can you give me the rationale behind choosing that number since this > becomes an important question when I submit manuscripts. > > Thanks very much > > Venkat > > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org on behalf of susumu mori > Sent: Wed 9/22/2010 1:58 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] CST atlas > > Hi Venkat, > > I'm not sure why you want to reject >95 percentile pixels because these > pixels are the best representation of the CST (highest probability). Isn't > it more reasonable to use the probability threshold like >0.2? > > When we do FA calculation, FA of each pixel is weighted by probability. So > high probability pixels have more weight. If you don't want it, you can > convert the probability map to binary (1/0) by applying a threshold using > RoiEditor. > > RoiEditor can also allows to apply a cut-off value for FA measurement. In > this case, you can, for example, mask-out all pixels with probability <0.2, > and then perform probability-weighted FA measurement for those pixels with > >=0.2. > > Susumu > > On Wed, Sep 22, 2010 at 11:18 AM, Rajagopalan, Venkateswaran < > rajagov2 at ccf.org> wrote: > > > > > Dear All, > > > > I am using CST probability atlas for some calculations (i.e. measuring FA > > values along CST), since the CST atlas includes probability values > ranging > > from 0 to 1, I want to exclude very low probability values like 0.00002 I > > tried using Percentile ( since It will not raise concerns when I write an > > article say I want to retain say between 5% and 95%) however since many > > voxels have very low probability values this is not working good in the > > sense for 95 percentile my probability value comes to 0.1745 however the > > probability values range from 0.0 to 0.578 so all the higher probability > > values above 0.1745 will get rejected. Any suggestions will be of great > > help. > > > > Thanks > > > > Venkat > > > > =================================== > > > > P Please consider the environment before printing this e-mail > > > > > > Cleveland Clinic is ranked one of the top hospitals > > in America by U.S.News & World Report (2009). > > Visit us online at http://www.clevelandclinic.org for > > a complete listing of our services, staff and > > locations. > > > > > > Confidentiality Note: This message is intended for use > > only by the individual or entity to which it is addressed > > and may contain information that is privileged, > > confidential, and exempt from disclosure under applicable > > law. If the reader of this message is not the intended > > recipient or the employee or agent responsible for > > delivering the message to the intended recipient, you are > > hereby notified that any dissemination, distribution or > > copying of this communication is strictly prohibited. If > > you have received this communication in error, please > > contact the sender immediately and destroy the material in > > its entirety, whether electronic or hard copy. Thank you. > > > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > > mristudio-users-unsubscribe at mristudio.org > > > > > > > =================================== > > P Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2009). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use > only by the individual or entity to which it is addressed > and may contain information that is privileged, > confidential, and exempt from disclosure under applicable > law. If the reader of this message is not the intended > recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are > hereby notified that any dissemination, distribution or > copying of this communication is strictly prohibited. If > you have received this communication in error, please > contact the sender immediately and destroy the material in > its entirety, whether electronic or hard copy. Thank you. > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > T =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 5312 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100922/2012bf34/attachment-0001.bin From susumu at mri.jhu.edu Thu Sep 23 08:22:16 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 23 Sep 2010 08:22:16 -0400 Subject: [Mristudio-users] Fw: excluding bad images In-Reply-To: <856807.37839.qm@web120319.mail.ne1.yahoo.com> References: <856807.37839.qm@web120319.mail.ne1.yahoo.com> Message-ID: Getting corrupted images degrade your results no matter what you do. If you include them, your FA values deviate from real value. If you remove it, you loose SNR, which is known to increase FA. You have to judge which is worse. For example, if you acquire 30 DWIs (30 orientation, 15 orientation x 2, 10 orientation x 3, it doesn't matter much) and remove 1 DWI, SNR loss could be minimum. So, you may not have to worry much. If you acquire only 12 DWIs and remove one, the SNR impact may be visible, but if you leave the bad image in the calculation, the impact could be even bigger. I have an impression that removing the bad images (sacrifice SNR) is usually the better choice, but again, once you get corrupted images, you always loose some. Another thing you may want to try is "pixel rejection" instead of "slice rejection". If the image corruption is very localized in a small region, the pixel rejection approach can minimize the impact only in that area. There is a detailed description at https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2 describing different types of artifacts and correction methods. On Thu, Sep 23, 2010 at 7:34 AM, Christopher Latsis wrote: > Dr Mori I sent my question below to the mail list but I guess it did not go > through. I hope you would not mind this direct email to you for this one > time. > Thanks in advance for your time and kind attention. Chris. > > > > > Hi All, > I am trying to understand Dtistudio's quality control window. I understand > that > if an image corruption is found, I can simply click on the bad image and > the > image is not used for subsequent calculation. How would this effect the FA > ? > I am planning on doing a VBA type group analysis. Some datasets have signal > loss > at certain slices/gradients. Can I exclude these bad images, calculate FA > for > these certain subjects and compare them to those with good quality data > with no > signal loss? Any good references you could recommend on this > matter? Thanks very much. Chris. > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100923/a30e296f/attachment.html From Ihssan.Abdulkareem at liverpool.ac.uk Thu Sep 23 08:34:30 2010 From: Ihssan.Abdulkareem at liverpool.ac.uk (Abdul-kareem, Ihssan) Date: Thu, 23 Sep 2010 13:34:30 +0100 Subject: [Mristudio-users] corpus callosum morphometry Message-ID: Dear All, I want to measure the FA values of subregions of the corpus callosum using DTI studio, could you please tell me how to obtain the midline sagittal image of the brain, how to rotate the image? Shall I extract it to another program? Many thanks, ---------------------------------------------------------------------- Dr Ihssan Adeeb Abdul-Kareem MBChB, MSc, MRes, PhD student Directorate of Medical Imaging (Radiodiagnosis) Magnetic Resonance and Image Analysis Research Centre, MARIARC School of Clinical Sciences Faculty of Medicine University of Liverpool Mobile no. 07957101512 E-mail: Ihssan.abdulkareem at liv.ac.uk; ihssan_adeeb at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100923/f96dcff9/attachment.html From rajagov2 at ccf.org Thu Sep 23 10:25:58 2010 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Thu, 23 Sep 2010 10:25:58 -0400 Subject: [Mristudio-users] Unable to open FA images properly in DTIstudio Message-ID: <77A88E90A851594AAEF830450587C39D041832DD@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, I processed DTI images using DTI studio and used the option "Save results" in DTI-map window to save FA and other anisotropy maps, unfortunately when I tried to load them in "MRIview 3D" in DTI studio FA images doesn't open properly in the sense I am not able to see all the 30 slices (that is how it is when loaded using dicom format all 30 slices will appear and I can scroll through them) instead I am seeing only 7 slices with two columns of FA images in the viwer window. I tried to attach snapshot of the problem (my message was rejected due to file size problem If you would like to have a look at it kindly give me an FTP or somewhere I can upload it). While opening using MRIview3D I am checking Raw image and float option to open my FA.dat files. What am i doing wrong here. Thanks Venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100923/507913f3/attachment.html From choisj70 at gmail.com Thu Sep 23 11:46:02 2010 From: choisj70 at gmail.com (Seongjin) Date: Thu, 23 Sep 2010 11:46:02 -0400 Subject: [Mristudio-users] Coordinate system Message-ID: Dear all, Simple question about the coordinate system in the Philips Scanners. I would like to confirm the axis directions in terms of X-Y-Z coordinate system. I guess, the axis directions 1) I-S(foot-to-head, inferior-to-superior) is "negative Z" direction 2) A-P(anterior-to-posterior) is "negative Y" direction 3) R-L(right-to-left) is "positive X" direction. If I knew this incorrectly, please correct my guess. Sincerely, -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100923/c9c316ef/attachment.html From lucas_lessa at yahoo.com.br Thu Sep 23 11:51:40 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Thu, 23 Sep 2010 08:51:40 -0700 (PDT) Subject: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? Message-ID: <875829.50924.qm@web110205.mail.gq1.yahoo.com> Dear friends, I made a new protocol for a GE 1,5T HDX, using 33 directions and 50 slices with 2.2 mm thickness. I did this because the vendor programmed a sequence that uses only 12 directions, 20 slices with 5 mm tichness and 1 NEX. I tried to obtain an isotropic image with more signal. But to to this I've changed the TR to 17000 (the maximum). Is there any problem? And, if is possible, can anyone explain for me the significance of this? Thank you very much. Lucas Lessa. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100923/ca62aea1/attachment.html From hjiang at jhmi.edu Thu Sep 23 12:49:40 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Thu, 23 Sep 2010 12:49:40 -0400 Subject: [Mristudio-users] Coordinate system In-Reply-To: References: Message-ID: <145933A2BE9E4F48AE079A201379BF2F2440E2D4E4@RAD-EXCH1.win.ad.jhu.edu> hi, for axial slicing human brain, the X-Y-Z system is in LPS anatomical direction. or X = R->L, Y=A->P, Z=I->S; hangyi ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] [choisj70 at gmail.com] Sent: Thursday, September 23, 2010 11:46 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Coordinate system Dear all, Simple question about the coordinate system in the Philips Scanners. I would like to confirm the axis directions in terms of X-Y-Z coordinate system. I guess, the axis directions 1) I-S(foot-to-head, inferior-to-superior) is "negative Z" direction 2) A-P(anterior-to-posterior) is "negative Y" direction 3) R-L(right-to-left) is "positive X" direction. If I knew this incorrectly, please correct my guess. Sincerely, -SC From choisj70 at gmail.com Thu Sep 23 13:14:34 2010 From: choisj70 at gmail.com (Seongjin) Date: Thu, 23 Sep 2010 13:14:34 -0400 Subject: [Mristudio-users] Coordinate system In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F2440E2D4E4@RAD-EXCH1.win.ad.jhu.edu> References: <145933A2BE9E4F48AE079A201379BF2F2440E2D4E4@RAD-EXCH1.win.ad.jhu.edu> Message-ID: Thanks for your reply. One question about the I->S in Philips scanners. I heard of that in Philips system +Z direction is S->I. I wonder if I am correct on this. If that so, +X = R->L, +Y = A->P, +Z = S->I in Philips scanners. A bit deviation from LPS system regarding +z direction. Sincerely, -Seongjin On Thu, Sep 23, 2010 at 12:49 PM, Hangyi Jiang wrote: > hi, > > for axial slicing human brain, the X-Y-Z system is in LPS anatomical > direction. or X = R->L, Y=A->P, Z=I->S; > > hangyi > > ________________________________________ > From: mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] [ > choisj70 at gmail.com] > Sent: Thursday, September 23, 2010 11:46 AM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: [Mristudio-users] Coordinate system > > Dear all, > > Simple question about the coordinate system in the Philips Scanners. > I would like to confirm the axis directions in terms of X-Y-Z coordinate > system. > > I guess, the axis directions > 1) I-S(foot-to-head, inferior-to-superior) is "negative Z" direction > 2) A-P(anterior-to-posterior) is "negative Y" direction > 3) R-L(right-to-left) is "positive X" direction. > > If I knew this incorrectly, please correct my guess. > > Sincerely, > -SC > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100923/ddb5068f/attachment.html From susumu at mri.jhu.edu Thu Sep 23 17:28:15 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 23 Sep 2010 17:28:15 -0400 Subject: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? In-Reply-To: <875829.50924.qm@web110205.mail.gq1.yahoo.com> References: <875829.50924.qm@web110205.mail.gq1.yahoo.com> Message-ID: Usually, one-slice single-shot imaging takes less than 150ms, I believe. 50 slices thus should take about 50 x 150ms = 7.5 s. This is the repetition time; within this time you are done with one 3D volume. With 33 directions and 3 b0s, for example, you spend 7.5s x 36 images = 4.5 min. If you use repetition time of 17s, your total imaging time will be 17s x 36 = 10 min. So, I would say, 17s is a bit too long and I recommend you to use the shortest TR, if possible. I noticed that some older GE scanners do not allow to use the minimum TR such as 7.5s probably due to gradient heating. So, if the 17s is the shortest you can do, then, that is your only option. Other than that, 2.2 mm isotropic could be a bit too small for 1.5T with 33 DWIs. The SNR may be a noisy side depending on your coil performance. We do 2.5 mm for 1.5T On Thu, Sep 23, 2010 at 11:51 AM, Lucas Lessa wrote: > Dear friends, > > I made a new protocol for a GE 1,5T HDX, using 33 directions and 50 slices > with 2.2 mm thickness. > I did this because the vendor programmed a sequence that uses only 12 > directions, 20 slices with 5 mm tichness and 1 NEX. > I tried to obtain an isotropic image with more signal. > But to to this I've changed the TR to 17000 (the maximum). > Is there any problem? > And, if is possible, can anyone explain for me the significance of this? > Thank you very much. > > Lucas Lessa. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100923/0c6c5ed2/attachment.html From susumu at mri.jhu.edu Thu Sep 23 17:30:58 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 23 Sep 2010 17:30:58 -0400 Subject: [Mristudio-users] Coordinate system In-Reply-To: References: <145933A2BE9E4F48AE079A201379BF2F2440E2D4E4@RAD-EXCH1.win.ad.jhu.edu> Message-ID: These axis definitions are very confusing. If you are asking to get a correct gradient table, I recommend you to use Jon Farrell's gradient table calculator for Philips scanners. On Thu, Sep 23, 2010 at 1:14 PM, [Seongjin] wrote: > Thanks for your reply. > > One question about the I->S in Philips scanners. > I heard of that in Philips system +Z direction is S->I. > I wonder if I am correct on this. > > If that so, +X = R->L, +Y = A->P, +Z = S->I in Philips scanners. > A bit deviation from LPS system regarding +z direction. > > Sincerely, > -Seongjin > > > > On Thu, Sep 23, 2010 at 12:49 PM, Hangyi Jiang wrote: > >> hi, >> >> for axial slicing human brain, the X-Y-Z system is in LPS anatomical >> direction. or X = R->L, Y=A->P, Z=I->S; >> >> hangyi >> >> ________________________________________ >> From: mristudio-users-bounces at mristudio.org [ >> mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] [ >> choisj70 at gmail.com] >> Sent: Thursday, September 23, 2010 11:46 AM >> To: DTI Studio, ROI Editor, Landmarker Questions/Support >> Subject: [Mristudio-users] Coordinate system >> >> Dear all, >> >> Simple question about the coordinate system in the Philips Scanners. >> I would like to confirm the axis directions in terms of X-Y-Z coordinate >> system. >> >> I guess, the axis directions >> 1) I-S(foot-to-head, inferior-to-superior) is "negative Z" direction >> 2) A-P(anterior-to-posterior) is "negative Y" direction >> 3) R-L(right-to-left) is "positive X" direction. >> >> If I knew this incorrectly, please correct my guess. >> >> Sincerely, >> -SC >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100923/e0cc2f4e/attachment.html From Malek.Makki at kispi.uzh.ch Fri Sep 24 02:27:57 2010 From: Malek.Makki at kispi.uzh.ch (Makki Malek) Date: Fri, 24 Sep 2010 08:27:57 +0200 Subject: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? In-Reply-To: Message-ID: I agree with Susumo however there are some differences between vendors We have similar GE system and I am sure that TR=17s is quite long for 33 directions and 50 slices. Are you using 128x128 matrix? Asset On? optimal TE? These systems do not allow to go below 2.5mm slice thickness with spectral slice excitation. Are you using standard excitation with FatSat which may increase SAR and thus increase the TR to compensate with Con you provide further information about your protocol to figure it out Regards ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Malek I. Makki, PhD Diagnostic Imaging Department MRI Center Kinderspital Zurich Phone. +41(0)44 266 3130 Fax: +41(0)44 266 7153 malek.makki at kispi.uzh.ch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Thursday, September 23, 2010 11:28 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? Usually, one-slice single-shot imaging takes less than 150ms, I believe. 50 slices thus should take about 50 x 150ms = 7.5 s. This is the repetition time; within this time you are done with one 3D volume. With 33 directions and 3 b0s, for example, you spend 7.5s x 36 images = 4.5 min. If you use repetition time of 17s, your total imaging time will be 17s x 36 = 10 min. So, I would say, 17s is a bit too long and I recommend you to use the shortest TR, if possible. I noticed that some older GE scanners do not allow to use the minimum TR such as 7.5s probably due to gradient heating. So, if the 17s is the shortest you can do, then, that is your only option. Other than that, 2.2 mm isotropic could be a bit too small for 1.5T with 33 DWIs. The SNR may be a noisy side depending on your coil performance. We do 2.5 mm for 1.5T On Thu, Sep 23, 2010 at 11:51 AM, Lucas Lessa wrote: Dear friends, I made a new protocol for a GE 1,5T HDX, using 33 directions and 50 slices with 2.2 mm thickness. I did this because the vendor programmed a sequence that uses only 12 directions, 20 slices with 5 mm tichness and 1 NEX. I tried to obtain an isotropic image with more signal. But to to this I've changed the TR to 17000 (the maximum). Is there any problem? And, if is possible, can anyone explain for me the significance of this? Thank you very much. Lucas Lessa. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100924/5b43f001/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: PGP.sig Type: application/pgp-signature Size: 489 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100924/5b43f001/attachment-0001.bin From xinrugujing at 126.com Fri Sep 24 04:19:48 2010 From: xinrugujing at 126.com (=?gbk?B?sfn3og==?=) Date: Fri, 24 Sep 2010 16:19:48 +0800 (CST) Subject: [Mristudio-users] Export FA data from DTIstudio Message-ID: <17823ef.72ac.12b42d3a56d.Coremail.xinrugujing@126.com> Dear All? I have got the eigen values from the REC file through the program which I made by myself with Matlab.Then I got the FA map with the formulas,but which is very different from the FA map calculated by DTIstudio.I have not made image processing and digital processing so that the images are terrible but I want to know my FA data is correct or not first.Thus I try to export the FA 3D_marix from DTIstudio and no button to use. Could you tell me how to obtain the FA data from DTIstudio? Many thanks, Xin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100924/c2c00689/attachment.html From lucas_lessa at yahoo.com.br Sat Sep 25 09:14:08 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Sat, 25 Sep 2010 06:14:08 -0700 (PDT) Subject: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? In-Reply-To: Message-ID: <408525.37170.qm@web110211.mail.gq1.yahoo.com> Good Morning Malek, I'm using a 128x128 matrix, no ASSET, minimum TE and the??standard excitation with FatSat is turned off too.I tried to cover the entire brain, using multiple directions (33) and 2 NEX.?The sequence takes about 10 min and the noise is quite significant.Thank you. --- Em sex, 24/9/10, Makki Malek escreveu: De: Makki Malek Assunto: Re: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? Para: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" Data: Sexta-feira, 24 de Setembro de 2010, 3:27 I agree with Susumo however there are some differences between vendors ? We have similar GE system and I am sure that TR=17s is quite long for 33 directions and 50 slices. ? Are you using 128x128 matrix? Asset On? optimal TE? ? These systems do not allow to go below 2.5mm slice thickness with spectral slice excitation. Are you using standard excitation with FatSat which may increase SAR and thus increase the TR to compensate with ? Con you provide further information about your protocol to figure it out ? Regards ? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Malek I. Makki, PhD Diagnostic Imaging Department MRI Center Kinderspital Zurich ? Phone. +41(0)44 266 3130 Fax:????? +41(0)44 266 7153 malek.makki at kispi.uzh.ch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ? ? ? From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Thursday, September 23, 2010 11:28 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? ? Usually, one-slice single-shot imaging takes less than 150ms, I believe. 50 slices thus should take about 50 x 150ms = 7.5 s. This is the repetition time; within this time you are done with one 3D volume. With 33 directions and 3 b0s, for example, you spend 7.5s x 36 images = 4.5 min. ? If you use repetition time of 17s, your total imaging time will be 17s x 36 = 10 min. ? So, I would say, 17s is a bit too long and I recommend you to use the shortest TR, if possible. I noticed that some older GE scanners do not allow to use the minimum TR such as 7.5s probably due to gradient heating. So, if the 17s is the shortest you can do, then, that is your only option.? ? Other than that, 2.2 mm isotropic could be a bit too small for 1.5T with 33 DWIs. The SNR may be a noisy side depending on your coil performance. We do 2.5 mm for 1.5T On Thu, Sep 23, 2010 at 11:51 AM, Lucas Lessa wrote: Dear friends, I made a new protocol for a GE 1,5T HDX, using 33 directions and 50 slices with 2.2 mm thickness. I did this because the vendor programmed a sequence that uses only 12 directions, 20 slices with 5 mm tichness and 1 NEX. I tried to obtain an isotropic image with more signal. But to to this I've changed the TR to 17000 (the maximum). Is there any problem? And, if is possible, can anyone explain for me the significance of this? Thank you very much. Lucas Lessa. ? _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org ? -----Anexo incorporado----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100925/96291688/attachment.html From Malek.Makki at kispi.uzh.ch Sat Sep 25 13:07:27 2010 From: Malek.Makki at kispi.uzh.ch (Makki Malek) Date: Sat, 25 Sep 2010 19:07:27 +0200 Subject: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? References: <408525.37170.qm@web110211.mail.gq1.yahoo.com> Message-ID: If you are using 2 Nex and no ASSET, than it is normal to take 10 min. It is like acquiring 65 directions + 1 T2w. But I don't understnad the reason of the noise. With standard excitation I expect chemical shift artefact. I recommend ASSET which will reduce the distortion and improve acquistion time. Any reason for not selecting it? Regards ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of Lucas Lessa Sent: Sat 9/25/2010 3:14 PM To: ROI Editor DiffeoMap Questions/SupportDTI Studio Subject: Re: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? Good Morning Malek, I'm using a 128x128 matrix, no ASSET, minimum TE and the standard excitation with FatSat is turned off too. I tried to cover the entire brain, using multiple directions (33) and 2 NEX. The sequence takes about 10 min and the noise is quite significant. Thank you. --- Em sex, 24/9/10, Makki Malek escreveu: De: Makki Malek Assunto: Re: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? Para: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" Data: Sexta-feira, 24 de Setembro de 2010, 3:27 I agree with Susumo however there are some differences between vendors We have similar GE system and I am sure that TR=17s is quite long for 33 directions and 50 slices. Are you using 128x128 matrix? Asset On? optimal TE? These systems do not allow to go below 2.5mm slice thickness with spectral slice excitation. Are you using standard excitation with FatSat which may increase SAR and thus increase the TR to compensate with Con you provide further information about your protocol to figure it out Regards ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Malek I. Makki, PhD Diagnostic Imaging Department MRI Center Kinderspital Zurich Phone. +41(0)44 266 3130 Fax: +41(0)44 266 7153 malek.makki at kispi.uzh.ch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Thursday, September 23, 2010 11:28 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? Usually, one-slice single-shot imaging takes less than 150ms, I believe. 50 slices thus should take about 50 x 150ms = 7.5 s. This is the repetition time; within this time you are done with one 3D volume. With 33 directions and 3 b0s, for example, you spend 7.5s x 36 images = 4.5 min. If you use repetition time of 17s, your total imaging time will be 17s x 36 = 10 min. So, I would say, 17s is a bit too long and I recommend you to use the shortest TR, if possible. I noticed that some older GE scanners do not allow to use the minimum TR such as 7.5s probably due to gradient heating. So, if the 17s is the shortest you can do, then, that is your only option. Other than that, 2.2 mm isotropic could be a bit too small for 1.5T with 33 DWIs. The SNR may be a noisy side depending on your coil performance. We do 2.5 mm for 1.5T On Thu, Sep 23, 2010 at 11:51 AM, Lucas Lessa wrote: Dear friends, I made a new protocol for a GE 1,5T HDX, using 33 directions and 50 slices with 2.2 mm thickness. I did this because the vendor programmed a sequence that uses only 12 directions, 20 slices with 5 mm tichness and 1 NEX. I tried to obtain an isotropic image with more signal. But to to this I've changed the TR to 17000 (the maximum). Is there any problem? And, if is possible, can anyone explain for me the significance of this? Thank you very much. Lucas Lessa. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -----Anexo incorporado----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 11595 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100925/112acdc6/attachment-0002.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: PGP.sig Type: application/pgp-signature Size: 489 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100925/112acdc6/attachment-0003.bin From dr.deepali.saxena at gmail.com Sun Sep 26 08:16:48 2010 From: dr.deepali.saxena at gmail.com (Deepali Saxena (nee Khanna)) Date: Sun, 26 Sep 2010 17:46:48 +0530 Subject: [Mristudio-users] (no subject) Message-ID: Hi all Am a new DTI studio user... n having starting hiccups ! We have a 1.5 T GE signa HDX scanner. Images are acquired 51 directions, with 3 mm sl thk and 0 spacing. The DTI Studio software asks for 1. 'FA map' and 'Vector' values...which am not sure what to fill in 2. If you could tell me how the GE MRI scanner stores the DICOM images, and in which files , I guess I would be able to fill the data. 3. Am i supposed to know the gradient tables and vector maps for tensor calculations.. if so, does anybody know what they are n how to use them in GE scanner ? Any help with this is most appreciated. Thanks Ms. Deepali Saxena -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100926/e80b6eef/attachment.html From Karan.Shukla at uth.tmc.edu Mon Sep 27 10:23:19 2010 From: Karan.Shukla at uth.tmc.edu (Shukla, Karan) Date: Mon, 27 Sep 2010 09:23:19 -0500 Subject: [Mristudio-users] Side-by-Side Configuration Message-ID: <440E0EC90CCF104283C8BF9A9BEE111E06654BBAB9@UTHCMS2.uthouston.edu> I am working on a window 7, 32-bit OS and when trying to install DTI Studio i receive an error saying the side by side configuration is not correct and to please check event log or command line.....Any advice on troubleshooting this problem. Thanks ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Makki Malek [Malek.Makki at kispi.uzh.ch] Sent: Saturday, September 25, 2010 12:07 PM To: DTI Studio, ROI Editor,DiffeoMap Questions/Support Subject: Re: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? If you are using 2 Nex and no ASSET, than it is normal to take 10 min. It is like acquiring 65 directions + 1 T2w. But I don't understnad the reason of the noise. With standard excitation I expect chemical shift artefact. I recommend ASSET which will reduce the distortion and improve acquistion time. Any reason for not selecting it? Regards ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of Lucas Lessa Sent: Sat 9/25/2010 3:14 PM To: ROI Editor DiffeoMap Questions/SupportDTI Studio Subject: Re: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? Good Morning Malek, I'm using a 128x128 matrix, no ASSET, minimum TE and the standard excitation with FatSat is turned off too. I tried to cover the entire brain, using multiple directions (33) and 2 NEX. The sequence takes about 10 min and the noise is quite significant. Thank you. --- Em sex, 24/9/10, Makki Malek escreveu: De: Makki Malek Assunto: Re: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? Para: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" Data: Sexta-feira, 24 de Setembro de 2010, 3:27 I agree with Susumo however there are some differences between vendors We have similar GE system and I am sure that TR=17s is quite long for 33 directions and 50 slices. Are you using 128x128 matrix? Asset On? optimal TE? These systems do not allow to go below 2.5mm slice thickness with spectral slice excitation. Are you using standard excitation with FatSat which may increase SAR and thus increase the TR to compensate with Con you provide further information about your protocol to figure it out Regards ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Malek I. Makki, PhD Diagnostic Imaging Department MRI Center Kinderspital Zurich Phone. +41(0)44 266 3130 Fax: +41(0)44 266 7153 malek.makki at kispi.uzh.ch ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Thursday, September 23, 2010 11:28 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] What is the difference between a TR 7500 and a TR 17000? Usually, one-slice single-shot imaging takes less than 150ms, I believe. 50 slices thus should take about 50 x 150ms = 7.5 s. This is the repetition time; within this time you are done with one 3D volume. With 33 directions and 3 b0s, for example, you spend 7.5s x 36 images = 4.5 min. If you use repetition time of 17s, your total imaging time will be 17s x 36 = 10 min. So, I would say, 17s is a bit too long and I recommend you to use the shortest TR, if possible. I noticed that some older GE scanners do not allow to use the minimum TR such as 7.5s probably due to gradient heating. So, if the 17s is the shortest you can do, then, that is your only option. Other than that, 2.2 mm isotropic could be a bit too small for 1.5T with 33 DWIs. The SNR may be a noisy side depending on your coil performance. We do 2.5 mm for 1.5T On Thu, Sep 23, 2010 at 11:51 AM, Lucas Lessa wrote: Dear friends, I made a new protocol for a GE 1,5T HDX, using 33 directions and 50 slices with 2.2 mm thickness. I did this because the vendor programmed a sequence that uses only 12 directions, 20 slices with 5 mm tichness and 1 NEX. I tried to obtain an isotropic image with more signal. But to to this I've changed the TR to 17000 (the maximum). Is there any problem? And, if is possible, can anyone explain for me the significance of this? Thank you very much. Lucas Lessa. _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -----Anexo incorporado----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Mon Sep 27 11:44:28 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 27 Sep 2010 11:44:28 -0400 Subject: [Mristudio-users] Side-by-Side Configuration In-Reply-To: <440E0EC90CCF104283C8BF9A9BEE111E06654BBAB9@UTHCMS2.uthouston.edu> References: <440E0EC90CCF104283C8BF9A9BEE111E06654BBAB9@UTHCMS2.uthouston.edu> Message-ID: <71d0fd0421772.4ca0839c@johnshopkins.edu> Hello, DtiStudio is a Microsoft Visual Studio application. You need to run the Microsoft Visual Studio Redistribution package "vcredist_x86.exe" before you run DtiStudio. The file "veredist_x86.exe" is available at https://www.mristudio.org/wiki/installation. Regards, Xin ----- Original Message ----- From: "Shukla, Karan" Date: Monday, September 27, 2010 10:25 am Subject: Re: [Mristudio-users] Side-by-Side Configuration To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > I am working on a window 7, 32-bit OS and when trying to install DTI > Studio i receive an error saying the side by side configuration is not > correct and to please check event log or command line.....Any advice > on troubleshooting this problem. > > Thanks > > ________________________________________ > From: mristudio-users-bounces at mristudio.org > [mristudio-users-bounces at mristudio.org] On Behalf Of Makki Malek [Malek.Makki at kispi.uzh.ch] > Sent: Saturday, September 25, 2010 12:07 PM > To: DTI Studio, ROI Editor,DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] What is the difference between a TR > 7500 and a TR 17000? > > If you are using 2 Nex and no ASSET, than it is normal to take 10 > min. It is like acquiring 65 directions + 1 T2w. But I don't > understnad the reason of the noise. With standard excitation I expect > chemical shift artefact. > > I recommend ASSET which will reduce the distortion and improve > acquistion time. Any reason for not selecting it? > > Regards > > > ________________________________ > > From: mristudio-users-bounces at mristudio.org on behalf of Lucas Lessa > Sent: Sat 9/25/2010 3:14 PM > To: ROI Editor DiffeoMap Questions/SupportDTI Studio > Subject: Re: [Mristudio-users] What is the difference between a TR > 7500 and a TR 17000? > > > Good Morning Malek, > > I'm using a 128x128 matrix, no ASSET, minimum TE and the standard > excitation with FatSat is turned off too. > I tried to cover the entire brain, using multiple directions (33) and > 2 NEX. > The sequence takes about 10 min and the noise is quite significant. > Thank you. > > > --- Em sex, 24/9/10, Makki Malek escreveu: > > > > De: Makki Malek > Assunto: Re: [Mristudio-users] What is the difference between > a TR 7500 and a TR 17000? > Para: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" > Data: Sexta-feira, 24 de Setembro de 2010, 3:27 > > > > I agree with Susumo however there are some differences > between vendors > > > > We have similar GE system and I am sure that TR=17s is quite > long for 33 directions and 50 slices. > > > > Are you using 128x128 matrix? Asset On? optimal TE? > > > > These systems do not allow to go below 2.5mm slice thickness > with spectral slice excitation. Are you using standard excitation with > FatSat which may increase SAR and thus increase the TR to compensate with > > > > Con you provide further information about your protocol to > figure it out > > > > Regards > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Malek I. Makki, PhD > > Diagnostic Imaging Department > > MRI Center > > Kinderspital Zurich > > > > Phone. +41(0)44 266 3130 > > Fax: +41(0)44 266 7153 > > malek.makki at kispi.uzh.ch > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > > > > > ________________________________ > > > From: mristudio-users-bounces at mristudio.org [ On Behalf Of > susumu mori > Sent: Thursday, September 23, 2010 11:28 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] What is the difference between > a TR 7500 and a TR 17000? > > > > Usually, one-slice single-shot imaging takes less than 150ms, > I believe. 50 slices thus should take about 50 x 150ms = 7.5 s. > > This is the repetition time; within this time you are done > with one 3D volume. With 33 directions and 3 b0s, for example, you > spend 7.5s x 36 images = 4.5 min. > > > > If you use repetition time of 17s, your total imaging time > will be 17s x 36 = 10 min. > > > > So, I would say, 17s is a bit too long and I recommend you to > use the shortest TR, if possible. > > I noticed that some older GE scanners do not allow to use the > minimum TR such as 7.5s probably due to gradient heating. So, if the > 17s is the shortest you can do, then, that is your only option. > > > > Other than that, 2.2 mm isotropic could be a bit too small > for 1.5T with 33 DWIs. The SNR may be a noisy side depending on your > coil performance. We do 2.5 mm for 1.5T > > On Thu, Sep 23, 2010 at 11:51 AM, Lucas Lessa > wrote: > > Dear friends, > > I made a new protocol for a GE 1,5T HDX, using 33 directions and 50 > slices with 2.2 mm thickness. > I did this because the vendor programmed a sequence that uses only 12 > directions, 20 slices with 5 mm tichness and 1 NEX. > I tried to obtain an isotropic image with more signal. > But to to this I've changed the TR to 17000 (the maximum). > Is there any problem? > And, if is possible, can anyone explain for me the significance of this? > Thank you very much. > > Lucas Lessa. > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > > > -----Anexo incorporado----- > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From Karan.Shukla at uth.tmc.edu Mon Sep 27 13:02:21 2010 From: Karan.Shukla at uth.tmc.edu (Shukla, Karan) Date: Mon, 27 Sep 2010 12:02:21 -0500 Subject: [Mristudio-users] Side-by-Side Configuration In-Reply-To: <71d0fd0421772.4ca0839c@johnshopkins.edu> References: <440E0EC90CCF104283C8BF9A9BEE111E06654BBAB9@UTHCMS2.uthouston.edu> <71d0fd0421772.4ca0839c@johnshopkins.edu> Message-ID: <440E0EC90CCF104283C8BF9A9BEE111E06654BBABA@UTHCMS2.uthouston.edu> THANKS! ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li [xli16 at jhmi.edu] Sent: Monday, September 27, 2010 10:44 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Side-by-Side Configuration Hello, DtiStudio is a Microsoft Visual Studio application. You need to run the Microsoft Visual Studio Redistribution package "vcredist_x86.exe" before you run DtiStudio. The file "veredist_x86.exe" is available at https://www.mristudio.org/wiki/installation. Regards, Xin ----- Original Message ----- From: "Shukla, Karan" Date: Monday, September 27, 2010 10:25 am Subject: Re: [Mristudio-users] Side-by-Side Configuration To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > I am working on a window 7, 32-bit OS and when trying to install DTI > Studio i receive an error saying the side by side configuration is not > correct and to please check event log or command line.....Any advice > on troubleshooting this problem. > > Thanks > > ________________________________________ > From: mristudio-users-bounces at mristudio.org > [mristudio-users-bounces at mristudio.org] On Behalf Of Makki Malek [Malek.Makki at kispi.uzh.ch] > Sent: Saturday, September 25, 2010 12:07 PM > To: DTI Studio, ROI Editor,DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] What is the difference between a TR > 7500 and a TR 17000? > > If you are using 2 Nex and no ASSET, than it is normal to take 10 > min. It is like acquiring 65 directions + 1 T2w. But I don't > understnad the reason of the noise. With standard excitation I expect > chemical shift artefact. > > I recommend ASSET which will reduce the distortion and improve > acquistion time. Any reason for not selecting it? > > Regards > > > ________________________________ > > From: mristudio-users-bounces at mristudio.org on behalf of Lucas Lessa > Sent: Sat 9/25/2010 3:14 PM > To: ROI Editor DiffeoMap Questions/SupportDTI Studio > Subject: Re: [Mristudio-users] What is the difference between a TR > 7500 and a TR 17000? > > > Good Morning Malek, > > I'm using a 128x128 matrix, no ASSET, minimum TE and the standard > excitation with FatSat is turned off too. > I tried to cover the entire brain, using multiple directions (33) and > 2 NEX. > The sequence takes about 10 min and the noise is quite significant. > Thank you. > > > --- Em sex, 24/9/10, Makki Malek escreveu: > > > > De: Makki Malek > Assunto: Re: [Mristudio-users] What is the difference between > a TR 7500 and a TR 17000? > Para: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" > Data: Sexta-feira, 24 de Setembro de 2010, 3:27 > > > > I agree with Susumo however there are some differences > between vendors > > > > We have similar GE system and I am sure that TR=17s is quite > long for 33 directions and 50 slices. > > > > Are you using 128x128 matrix? Asset On? optimal TE? > > > > These systems do not allow to go below 2.5mm slice thickness > with spectral slice excitation. Are you using standard excitation with > FatSat which may increase SAR and thus increase the TR to compensate with > > > > Con you provide further information about your protocol to > figure it out > > > > Regards > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Malek I. Makki, PhD > > Diagnostic Imaging Department > > MRI Center > > Kinderspital Zurich > > > > Phone. +41(0)44 266 3130 > > Fax: +41(0)44 266 7153 > > malek.makki at kispi.uzh.ch > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > > > > > ________________________________ > > > From: mristudio-users-bounces at mristudio.org [ On Behalf Of > susumu mori > Sent: Thursday, September 23, 2010 11:28 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] What is the difference between > a TR 7500 and a TR 17000? > > > > Usually, one-slice single-shot imaging takes less than 150ms, > I believe. 50 slices thus should take about 50 x 150ms = 7.5 s. > > This is the repetition time; within this time you are done > with one 3D volume. With 33 directions and 3 b0s, for example, you > spend 7.5s x 36 images = 4.5 min. > > > > If you use repetition time of 17s, your total imaging time > will be 17s x 36 = 10 min. > > > > So, I would say, 17s is a bit too long and I recommend you to > use the shortest TR, if possible. > > I noticed that some older GE scanners do not allow to use the > minimum TR such as 7.5s probably due to gradient heating. So, if the > 17s is the shortest you can do, then, that is your only option. > > > > Other than that, 2.2 mm isotropic could be a bit too small > for 1.5T with 33 DWIs. The SNR may be a noisy side depending on your > coil performance. We do 2.5 mm for 1.5T > > On Thu, Sep 23, 2010 at 11:51 AM, Lucas Lessa > wrote: > > Dear friends, > > I made a new protocol for a GE 1,5T HDX, using 33 directions and 50 > slices with 2.2 mm thickness. > I did this because the vendor programmed a sequence that uses only 12 > directions, 20 slices with 5 mm tichness and 1 NEX. > I tried to obtain an isotropic image with more signal. > But to to this I've changed the TR to 17000 (the maximum). > Is there any problem? > And, if is possible, can anyone explain for me the significance of this? > Thank you very much. > > Lucas Lessa. > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > > > -----Anexo incorporado----- > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From lucas_lessa at yahoo.com.br Mon Sep 27 13:02:48 2010 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Mon, 27 Sep 2010 10:02:48 -0700 (PDT) Subject: [Mristudio-users] Mesure FA from middle cerebelar peduncles Message-ID: <231953.59705.qm@web110212.mail.gq1.yahoo.com> Good afternoon, I tried to mesure the FA from middle cerebelar peduncles, but I got a significant difference between right and left. Now I want to mesure the FA from the entire middle cerebelar peduncles, not using ROIs as I was doing, but the entire tract. Is it possible? Thank you. Lucas Lessa. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100927/61d8e8a6/attachment-0001.html From arabinda.mishra at Vanderbilt.Edu Mon Sep 27 13:26:46 2010 From: arabinda.mishra at Vanderbilt.Edu (Mishra, Arabinda) Date: Mon, 27 Sep 2010 12:26:46 -0500 Subject: [Mristudio-users] Mesure FA from middle cerebelar peduncles In-Reply-To: <231953.59705.qm@web110212.mail.gq1.yahoo.com> References: <231953.59705.qm@web110212.mail.gq1.yahoo.com> Message-ID: <2B6AB3B9480ABC46B1CE48A26C9D71A0060D68E67B@ITS-HCWNEM02.ds.Vanderbilt.edu> Does anybody know how to take my address off the list. thanks ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Lucas Lessa [lucas_lessa at yahoo.com.br] Sent: Monday, September 27, 2010 12:02 PM To: MRI Studio Mailing list Subject: [Mristudio-users] Mesure FA from middle cerebelar peduncles Good afternoon, I tried to mesure the FA from middle cerebelar peduncles, but I got a significant difference between right and left. Now I want to mesure the FA from the entire middle cerebelar peduncles, not using ROIs as I was doing, but the entire tract. Is it possible? Thank you. Lucas Lessa. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100927/9404dd85/attachment.html From stevie.ray28 at gmail.com Mon Sep 27 18:11:55 2010 From: stevie.ray28 at gmail.com (Stephen Ray) Date: Mon, 27 Sep 2010 16:11:55 -0600 Subject: [Mristudio-users] (no subject) Message-ID: http://capitolbird.org/Nicola.htm From luca.binotto at unipd.it Thu Sep 30 05:20:14 2010 From: luca.binotto at unipd.it (luca.binotto at unipd.it) Date: Thu, 30 Sep 2010 11:20:14 +0200 Subject: [Mristudio-users] makeaheader.exe for DiffeoMap Message-ID: Hello there, I was using DiffeoMap to register images when a message saying "Cannot find makeaheader.exe ...put it in the folder Landmarker" appeared. My air tools are 16-bit compiled both as unsigned and signed. Which should I use? Make any difference ? thanks in advance, Luca From luca.binotto at unipd.it Thu Sep 30 05:20:14 2010 From: luca.binotto at unipd.it (luca.binotto at unipd.it) Date: Thu, 30 Sep 2010 11:20:14 +0200 Subject: [Mristudio-users] makeaheader.exe for DiffeoMap Message-ID: <21ba24422ba160d1ec2a262116b9f1f5.squirrel@webmail.unipd.it> Hello there, I was using DiffeoMap to register images when a message saying "Cannot find makeaheader.exe ...put it in the folder Landmarker" appeared. My air tools are 16-bit compiled both as unsigned and signed. Which should I use? Make any difference ? thanks in advance, Luca From susumu at mri.jhu.edu Thu Sep 30 08:13:48 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 30 Sep 2010 08:13:48 -0400 Subject: [Mristudio-users] Mesure FA from middle cerebelar peduncles In-Reply-To: <231953.59705.qm@web110212.mail.gq1.yahoo.com> References: <231953.59705.qm@web110212.mail.gq1.yahoo.com> Message-ID: In general (not just for the middle cerebellar peduncle), there are several ways for quantification strategy. 1) 2D manual ROI drawing: RoiEditor has very powerful user-interface for ROI drawing. You can define the boundary based on your subjective judgement or using threshold and region growing tools. Please refer to our video tutorial ( https://www.mristudio.org/documentation/video/MristudioTutorialVideo/ROIEditor.htm) about how to use RoiEditor for ROI definition. From somewhere around from 3:30, regular ROI drawing is explained and from around 10:30, strategies to use threshold and region growing tools for more objective definition are explained. 2) 3D manual ROI drawing: The above 2D ROI approach can be easily extended to 3D ROIs using RoiEditor. This is also explained in the video tutorial. 3) Tractography: There are several reasons why you want to use tractography-based tract definition. First, it may save time. Second, it provides an objective way to define a tract, although there is still dependency on ROIs for tract extraction. Third, it has a potential to delineate a tract that can not be done by manual ROIs. For example, the cortico-spinal tract can't be identified discretely at the internal capsule level because it is buried inside it together with many other tracts such as thalamic fibers. By using tractography, you may be able to delineate where is the CST inside the internal capsule with some degree of accuracy. Downside of tractogrpahy is, it could be less reproducible for test-retest and inter-subject, making the standard deviations of normal subjects larger. For tractography-based quantification, please see; https://www.mristudio.org/documentation/video/MristudioTutorialVideo/Fiber.htm At around 15 min, an example of "good protocol" is explained and at 18 min, "CUT" operation is explained, which may be suitable for your quantification purpose. On Mon, Sep 27, 2010 at 1:02 PM, Lucas Lessa wrote: > Good afternoon, > > I tried to mesure the FA from middle cerebelar peduncles, but I got a > significant difference between right and left. > Now I want to mesure the FA from the entire middle cerebelar peduncles, not > using ROIs as I was doing, but the entire tract. > Is it possible? > Thank you. > > Lucas Lessa. > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100930/b58bc872/attachment.html From arthurz.wang at gmail.com Thu Sep 30 09:47:37 2010 From: arthurz.wang at gmail.com (WANG, Zhi(Arthur)) Date: Thu, 30 Sep 2010 21:47:37 +0800 Subject: [Mristudio-users] How to coregister the DTI image with BOLD fMRI image Message-ID: Dear All, Is there anyone who know how to coregister the DTI image with BOLD fMRI image? Is it possible to realise this in DTIstudio? Or I have to use other software, such as AIR? BR -- ?? ??????? ??? Zhi Wang Bejing Hospital From luca.binotto at unipd.it Thu Sep 30 11:18:16 2010 From: luca.binotto at unipd.it (luca.binotto at unipd.it) Date: Thu, 30 Sep 2010 17:18:16 +0200 Subject: [Mristudio-users] makeaheader.exe for DiffeoMap Message-ID: <800ddad5d6abd2bd4d9ee9e24dd4510e.squirrel@webmail.unipd.it> Hello Xin, thanks for the reply. I downloaded it. The file dimensions of the downloaded tools are different from those compiled by my own. Are they modified for matching DiffeoMap needs ? I tried to copy all my compiled AIR tools (signed) on diffeomap folder and now it works, probably it would work also with the unsigned compiled version. I'm a bit confused! Because u suggest them, I'll use the downloaded tools. I didn't find scanair.exe there. Is there an other way to access the trasformation matrix in .air file? thanks, Luca Hello Luca, Please download AIR.zip at http://www.yousendit.com/download/WTNMYURGT01UMFB2Wmc9PQ Unzip this file and you will get four AIR exe files. Please put these four files in the folder "DiffeoMap". Then you should be able to run AIR in DiffeoMap. Regards, Xin ----- Original Message ----- From: luca.binotto at unipd.it Date: Thursday, September 30, 2010 5:20 am Subject: [Mristudio-users] makeaheader.exe for DiffeoMap To: mristudio-users at mristudio.org From susumu at mri.jhu.edu Thu Sep 30 13:06:39 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 30 Sep 2010 13:06:39 -0400 Subject: [Mristudio-users] How to coregister the DTI image with BOLD fMRI image In-Reply-To: References: Message-ID: If you already have fMRI activation map calculated, you can register b0 and raw fMRI EPI image using rigid transformation. In our software family, DiffeoMap can do it. You load b0 in the first window and an fMRI raw image and activation maps in the second window. You can do AIR-based rigid between b0 and fMRI raw image, and then your activation map is also aligned to b0. Please see Getting Started at https://www.mristudio.org/wiki/user_manual/diffeomap for detail. 2010/9/30 WANG, Zhi(Arthur) > Dear All, > Is there anyone who know how to coregister the DTI image with BOLD fMRI > image? > Is it possible to realise this in DTIstudio? Or I have to use > othersoftware, such as AIR? > BR > -- > ????????? ??? > Zhi WangBejing Hospital > _______________________________________________mristudio-users mailing > listmristudio-users at mristudio.orghttp:// > lists.mristudio.org/mailman/listinfo/Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100930/5cfa6826/attachment.html From rosenally at gmail.com Thu Sep 30 13:13:50 2010 From: rosenally at gmail.com (Allyson Rosen) Date: Thu, 30 Sep 2010 10:13:50 -0700 Subject: [Mristudio-users] How to coregister the DTI image with BOLD fMRI image In-Reply-To: References: Message-ID: <00cc01cb60c2$db3c5fc0$91b51f40$@com> Does anyone do correction for partial volume averaging and if so, how do you do it? From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Thursday, September 30, 2010 10:07 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] How to coregister the DTI image with BOLD fMRI image If you already have fMRI activation map calculated, you can register b0 and raw fMRI EPI image using rigid transformation. In our software family, DiffeoMap can do it. You load b0 in the first window and an fMRI raw image and activation maps in the second window. You can do AIR-based rigid between b0 and fMRI raw image, and then your activation map is also aligned to b0. Please see Getting Started at https://www.mristudio.org/wiki/user_manual/diffeomap for detail. 2010/9/30 WANG, Zhi(Arthur) Dear All, Is there anyone who know how to coregister the DTI image with BOLD fMRI image? Is it possible to realise this in DTIstudio? Or I have to use othersoftware, such as AIR? BR -- ????????? ??? Zhi WangBejing Hospital _______________________________________________mristudio-users mailing listmristudio-users at mristudio.orghttp://lists.mristudio.org/mailman/listinfo /Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100930/e22c9159/attachment.html From huxiaopeng1210 at yahoo.com.cn Sat Oct 2 07:57:44 2010 From: huxiaopeng1210 at yahoo.com.cn (=?utf-8?B?6IOh5a2d6bmP?=) Date: Sat, 02 Oct 2010 19:57:44 +0800 (CST) Subject: [Mristudio-users] =?utf-8?b?5ZKo6K+i?= In-Reply-To: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> Message-ID: <694963.97907.qm@web15705.mail.cnb.yahoo.com> ???? ?? ?????DTIstudio??????????????????DTI??????????? ????????????????????? ?? ??????? ??? ???????????? huxiaopeng1210 at yahoo.com.cn --- 10?9?14????, ??? ??? ???: ??? ??: [Mristudio-users] Different Gradient Table of DTI from Philips Achieva 3T ???: "DTI Studio" ??: 2010?9?14?,??,??11:04 Hi, I'm dealing with DTI data from Philips Achieva 3T. I tried two methods to compute the gradient table (32+1). (1) " dcm2nii.exe " with Philips dicom files ???????? 0???????? 0???????? 0 ??? 1.0000???????? 0???????? 0 ???????? 0?? -1.0000???????? 0 ???????? 0???????? 0?? -1.0000 ?? -0.0424??? 0.1146??? 0.9925 ??? 0.1749??? 0.2005??? 0.9640 ??? 0.2323??? 0.1626??? 0.9590 ??? 0.3675?? -0.0261??? 0.9296 ??? 0.1902?? -0.3744??? 0.9076 ?? -0.1168?? -0.8334??? 0.5402 ?? -0.2005?? -0.2527??? 0.9465 ?? -0.4958?? -0.1345??? 0.8580 ?? -0.0141??? 0.6281??? 0.7780 ?? -0.7445??? 0.1477??? 0.6511 ?? -0.7609?? -0.3204??? 0.5643 ?? -0.1809?? -0.9247??? 0.3351 ?? -0.6796??? 0.4224??? 0.5997 ??? 0.7771?? -0.4707??? 0.4178 ??? 0.9242??? 0.1036??? 0.3677 ??? 0.4685??? 0.7674??? 0.4378 ??? 0.8817??? 0.1893??? 0.4322 ??? 0.6904?? -0.7062??? 0.1569 ??? 0.2391?? -0.7571??? 0.6080 ?? -0.0578?? -0.9837?? -0.1703 ?? -0.5368?? -0.8361??? 0.1135 ?? -0.9918??? 0.1207??? 0.0423 ?? -0.9968?? -0.0709??? 0.0379 ?? -0.8724?? -0.4781??? 0.1014 ?? -0.2487?? -0.9336?? -0.2581 ??? 0.1183?? -0.9919??? 0.0471 ??? 0.3376?? -0.8415?? -0.4218 ??? 0.5286?? -0.8409?? -0.1163 ??? 0.9969?? -0.0550??? 0.0571 (2) " DTI_gradient_table_creator_Philips_RelX.m " with Philips par/rec files ?? -0.6533?? -0.2706?? -0.7071 ?? -0.2087?? -0.6756?? -0.7071 ??? 0.0197?? -0.7068?? -0.7071 ??? 0.4212?? -0.5679?? -0.7071 ??? 0.6899?? -0.1549?? -0.7071 ?? -0.6535?? -0.2707?? -0.7069 ?? -0.5000?? -0.5000?? -0.7071 ?? -0.2929?? -0.7071?? -0.6436 ??? 0.2945?? -0.7064?? -0.6436 ??? 0.5150?? -0.4861?? -0.7061 ??? 0.7071?? -0.2929?? -0.6436 ?? -0.7071?? -0.4725?? -0.5261 ?? -0.4725?? -0.7071?? -0.5261 ??? 0.5555?? -0.6439?? -0.5261 ??? 0.7071?? -0.4725?? -0.5261 ?? -0.7071?? -0.7071?? -0.0002 ??? 0.7071?? -0.7071???????? 0 ?? -0.7071?? -0.4725??? 0.5261 ??? 0.7071?? -0.4725??? 0.5261 ??? 0.4725?? -0.7071??? 0.5261 ??? 0.7071?? -0.4725??? 0.5261 ?? -0.6364?? -0.4252??? 0.6436 ?? -0.7060?? -0.7060??? 0.0547 ?? -0.2929?? -0.7071??? 0.6436 ??? 0.2929?? -0.7071??? 0.6436 ??? 0.7071?? -0.7071??? 0.0078 ??? 0.7071?? -0.2929??? 0.6436 ?? -0.5847?? -0.3977??? 0.7071 ?? -0.7063?? -0.7063??? 0.0489 ??? 0.0347?? -0.7063??? 0.7071 ??? 0.7071?? -0.7071??? 0.0115 ??? 0.7071???????? 0??? 0.7071 ???????? 0???????? 0???????? 0 ? 100.0000? 100.0000? 100.0000 They seem totally different. So can any person explain this problem? Thank you very much! Haiqing ??????????????24??????? -----???????----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101002/ddfec6fe/attachment-0001.html From kongyouyong at gmail.com Sat Oct 2 08:01:49 2010 From: kongyouyong at gmail.com (=?GB2312?B?09PTwr/X?=) Date: Sat, 02 Oct 2010 20:01:49 +0800 Subject: [Mristudio-users] =?gb2312?b?18nRrw==?= In-Reply-To: <694963.97907.qm@web15705.mail.cnb.yahoo.com> References: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> <694963.97907.qm@web15705.mail.cnb.yahoo.com> Message-ID: ?????????????????FA??????? ? 2010?10?2? ??7:57???? ??? > > ???? > ?????DTIstudio??????????????????DTI??????????? > ????????????????????? > ??????? > ??? > ???????????? > huxiaopeng1210 at yahoo.com.cn > > --- *10?9?14????, ??? * ??? > > > ???: ??? > ??: [Mristudio-users] Different Gradient Table of DTI from Philips Achieva > 3T > ???: "DTI Studio" > ??: 2010?9?14?,??,??11:04 > > Hi, > > I'm dealing with DTI data from Philips Achieva 3T. I tried two methods to > compute the gradient table (32+1). > (1) " dcm2nii.exe " with Philips dicom files > 0 0 0 > 1.0000 0 0 > 0 -1.0000 0 > 0 0 -1.0000 > -0.0424 0.1146 0.9925 > 0.1749 0.2005 0.9640 > 0.2323 0.1626 0.9590 > 0.3675 -0.0261 0.9296 > 0.1902 -0.3744 0.9076 > -0.1168 -0.8334 0.5402 > -0.2005 -0.2527 0.9465 > -0.4958 -0.1345 0.8580 > -0.0141 0.6281 0.7780 > -0.7445 0.1477 0.6511 > -0.7609 -0.3204 0.5643 > -0.1809 -0.9247 0.3351 > -0.6796 0.4224 0.5997 > 0.7771 -0.4707 0.4178 > 0.9242 0.1036 0.3677 > 0.4685 0.7674 0.4378 > 0.8817 0.1893 0.4322 > 0.6904 -0.7062 0.1569 > 0.2391 -0.7571 0.6080 > -0.0578 -0.9837 -0.1703 > -0.5368 -0.8361 0.1135 > -0.9918 0.1207 0.0423 > -0.9968 -0.0709 0.0379 > -0.8724 -0.4781 0.1014 > -0.2487 -0.9336 -0.2581 > 0.1183 -0.9919 0.0471 > 0.3376 -0.8415 -0.4218 > 0.5286 -0.8409 -0.1163 > 0.9969 -0.0550 0.0571 > (2) " DTI_gradient_table_creator_Philips_RelX.m " with Philips par/rec > files > -0.6533 -0.2706 -0.7071 > -0.2087 -0.6756 -0.7071 > 0.0197 -0.7068 -0.7071 > 0.4212 -0.5679 -0.7071 > 0.6899 -0.1549 -0.7071 > -0.6535 -0.2707 -0.7069 > -0.5000 -0.5000 -0.7071 > -0.2929 -0.7071 -0.6436 > 0.2945 -0.7064 -0.6436 > 0.5150 -0.4861 -0.7061 > 0.7071 -0.2929 -0.6436 > -0.7071 -0.4725 -0.5261 > -0.4725 -0.7071 -0.5261 > 0.5555 -0.6439 -0.5261 > 0.7071 -0.4725 -0.5261 > -0.7071 -0.7071 -0.0002 > 0.7071 -0.7071 0 > -0.7071 -0.4725 0.5261 > 0.7071 -0.4725 0.5261 > 0.4725 -0.7071 0.5261 > 0.7071 -0.4725 0.5261 > -0.6364 -0.4252 0.6436 > -0.7060 -0.7060 0.0547 > -0.2929 -0.7071 0.6436 > 0.2929 -0.7071 0.6436 > 0.7071 -0.7071 0.0078 > 0.7071 -0.2929 0.6436 > -0.5847 -0.3977 0.7071 > -0.7063 -0.7063 0.0489 > 0.0347 -0.7063 0.7071 > 0.7071 -0.7071 0.0115 > 0.7071 0 0.7071 > 0 0 0 > 100.0000 100.0000 100.0000 > They seem totally different. So can any person explain this problem? Thank > you very much! > > Haiqing > > > ------------------------------ > ??????????????24??????? > > -----???????----- > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101002/efa3fb4e/attachment.html From Markus.Gschwind at unige.ch Sat Oct 2 17:11:30 2010 From: Markus.Gschwind at unige.ch (Markus Gschwind) Date: Sat, 02 Oct 2010 23:11:30 +0200 Subject: [Mristudio-users] login and password? Message-ID: Dear administrators, I am a registered membre and I am getting all mails form mristudio.org, but I cannot login. Even when trying to create an account, it asks for a password ;-) What shoud I do, please? Thanks, Markus -- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101002/b33a8161/attachment.html From Shmuel.Miron at sheba.health.gov.il Sun Oct 3 07:49:30 2010 From: Shmuel.Miron at sheba.health.gov.il (Shmuel Miron Dr) Date: Sun, 03 Oct 2010 13:49:30 +0200 Subject: [Mristudio-users] corpus callosum morphometry In-Reply-To: Message-ID: Dear Dr Ihssan I am interested in the same questions in MS patients. To obtain the midline image we first perform a sagittal 3D FSPGR anatomical MRsequence (high resolution-voxel size 1x1x1mm) Now you have 2 possibilities 1. use an axial localizer during EPI acquisition to obtain axial images and the localizer passes through the inferior border of the splenium and rostrum of the corpus callosum. Then, DTI studio recreates the Sagittal view that can be used for further analysis. 2. use a sagittal localizer as in the attached image to obtain sagital EPI axquisition that will give you a good resolution of the CC that will work in DTI studio Do you have a suggestion on how to perform a subregion analysis on DTI studio ? Dr. Samuel Miron Multiple Sclerosis Center -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Abdul-kareem, Ihssan Sent: Thursday, September 23, 2010 2:35 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] corpus callosum morphometry Dear All, I want to measure the FA values of subregions of the corpus callosum using DTI studio, could you please tell me how to obtain the midline sagittal image of the brain, how to rotate the image? Shall I extract it to another program? Many thanks, ---------------------------------------------------------------------- Dr Ihssan Adeeb Abdul-Kareem MBChB, MSc, MRes, PhD student Directorate of Medical Imaging (Radiodiagnosis) Magnetic Resonance and Image Analysis Research Centre, MARIARC School of Clinical Sciences Faculty of Medicine University of Liverpool Mobile no. 07957101512 E-mail: Ihssan.abdulkareem at liv.ac.uk; ihssan_adeeb at yahoo.com ************************************************************************** This email was sent by "SHEBA MEDICAL CENTER" Messaging System. This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed, If you have received this email by mistake please notify the system manager. mailto:Support at Sheba.Health.gov.il -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101003/a4733c97/attachment-0001.html From xuancheng2007 at 163.com Mon Oct 4 02:31:45 2010 From: xuancheng2007 at 163.com (remind) Date: Mon, 04 Oct 2010 14:31:45 +0800 (CST) Subject: [Mristudio-users] =?gbk?b?18nRrw==?= In-Reply-To: References: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> <694963.97907.qm@web15705.mail.cnb.yahoo.com> Message-ID: ??? ??DTI-studio???FA???????????????????????????? ??? ? 2010-10-02 20:01:49?"???" ??? ?????????????????FA??????? ? 2010?10?2? ??7:57??????? ???? ?????DTIstudio??????????????????DTI??????????? ????????????????????? ??????? ??? ???????????? huxiaopeng1210 at yahoo.com.cn ---10?9?14????, ??? ??? ???: ??? ??: [Mristudio-users] Different Gradient Table of DTI from Philips Achieva 3T ???: "DTI Studio" ??: 2010?9?14?,??,??11:04 Hi, I'm dealing with DTI data from Philips Achieva 3T. I tried two methods to compute the gradient table (32+1). (1) " dcm2nii.exe " with Philips dicom files 0 0 0 1.0000 0 0 0 -1.0000 0 0 0 -1.0000 -0.0424 0.1146 0.9925 0.1749 0.2005 0.9640 0.2323 0.1626 0.9590 0.3675 -0.0261 0.9296 0.1902 -0.3744 0.9076 -0.1168 -0.8334 0.5402 -0.2005 -0.2527 0.9465 -0.4958 -0.1345 0.8580 -0.0141 0.6281 0.7780 -0.7445 0.1477 0.6511 -0.7609 -0.3204 0.5643 -0.1809 -0.9247 0.3351 -0.6796 0.4224 0.5997 0.7771 -0.4707 0.4178 0.9242 0.1036 0.3677 0.4685 0.7674 0.4378 0.8817 0.1893 0.4322 0.6904 -0.7062 0.1569 0.2391 -0.7571 0.6080 -0.0578 -0.9837 -0.1703 -0.5368 -0.8361 0.1135 -0.9918 0.1207 0.0423 -0.9968 -0.0709 0.0379 -0.8724 -0.4781 0.1014 -0.2487 -0.9336 -0.2581 0.1183 -0.9919 0.0471 0.3376 -0.8415 -0.4218 0.5286 -0.8409 -0.1163 0.9969 -0.0550 0.0571 (2) " DTI_gradient_table_creator_Philips_RelX.m " with Philips par/rec files -0.6533 -0.2706 -0.7071 -0.2087 -0.6756 -0.7071 0.0197 -0.7068 -0.7071 0.4212 -0.5679 -0.7071 0.6899 -0.1549 -0.7071 -0.6535 -0.2707 -0.7069 -0.5000 -0.5000 -0.7071 -0.2929 -0.7071 -0.6436 0.2945 -0.7064 -0.6436 0.5150 -0.4861 -0.7061 0.7071 -0.2929 -0.6436 -0.7071 -0.4725 -0.5261 -0.4725 -0.7071 -0.5261 0.5555 -0.6439 -0.5261 0.7071 -0.4725 -0.5261 -0.7071 -0.7071 -0.0002 0.7071 -0.7071 0 -0.7071 -0.4725 0.5261 0.7071 -0.4725 0.5261 0.4725 -0.7071 0.5261 0.7071 -0.4725 0.5261 -0.6364 -0.4252 0.6436 -0.7060 -0.7060 0.0547 -0.2929 -0.7071 0.6436 0.2929 -0.7071 0.6436 0.7071 -0.7071 0.0078 0.7071 -0.2929 0.6436 -0.5847 -0.3977 0.7071 -0.7063 -0.7063 0.0489 0.0347 -0.7063 0.7071 0.7071 -0.7071 0.0115 0.7071 0 0.7071 0 0 0 100.0000 100.0000 100.0000 They seem totally different. So can any person explain this problem? Thank you very much! Haiqing ??????????????24??????? -----???????----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to:mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to:mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101004/fa7bb1c0/attachment.html From huxiaopeng1210 at yahoo.com.cn Mon Oct 4 04:31:43 2010 From: huxiaopeng1210 at yahoo.com.cn (=?utf-8?B?6IOh5a2d6bmP?=) Date: Mon, 04 Oct 2010 16:31:43 +0800 (CST) Subject: [Mristudio-users] =?utf-8?b?5ZKo6K+i?= In-Reply-To: Message-ID: <999240.58663.qm@web15705.mail.cnb.yahoo.com> ??????????????3D????????????????????? ??? ???????????? huxiaopeng1210 at yahoo.com.cn --- 10?10?4????, remind ??? ???: remind ??: Re: [Mristudio-users] ?? ???: "DTI Studio, ROI Editor; DiffeoMap Questions/Support" ??: 2010?10?4?,??,??2:31 ??? ??DTI-studio???FA???????????????????????????? ??? ? 2010-10-02 20:01:49?"???"? ??? ?????????????????FA??????? ? 2010?10?2? ??7:57???? ??? ???? ?? ?????DTIstudio??????????????????DTI??????????? ????????????????????? ?? ??????? ??? ???????????? huxiaopeng1210 at yahoo.com.cn --- 10?9?14????, ??? ??? ???: ??? ??: [Mristudio-users] Different Gradient Table of DTI from Philips Achieva 3T ???: "DTI Studio" ??: 2010?9?14?,??,??11:04 Hi, I'm dealing with DTI data from Philips Achieva 3T. I tried two methods to compute the gradient table (32+1). (1) " dcm2nii.exe " with Philips dicom files ???????? 0???????? 0???????? 0 ??? 1.0000???????? 0???????? 0 ???????? 0?? -1.0000???????? 0 ???????? 0???????? 0?? -1.0000 ?? -0.0424??? 0.1146??? 0.9925 ??? 0.1749??? 0.2005??? 0.9640 ??? 0.2323??? 0.1626??? 0.9590 ??? 0.3675?? -0.0261??? 0.9296 ??? 0.1902?? -0.3744??? 0.9076 ?? -0.1168?? -0.8334??? 0.5402 ?? -0.2005?? -0.2527??? 0.9465 ?? -0.4958?? -0.1345??? 0.8580 ?? -0.0141??? 0.6281??? 0.7780 ?? -0.7445??? 0.1477??? 0.6511 ?? -0.7609?? -0.3204??? 0.5643 ?? -0.1809?? -0.9247??? 0.3351 ?? -0.6796??? 0.4224??? 0.5997 ??? 0.7771?? -0.4707??? 0.4178 ??? 0.9242??? 0.1036??? 0.3677 ??? 0.4685??? 0.7674??? 0.4378 ??? 0.8817??? 0.1893??? 0.4322 ??? 0.6904?? -0.7062??? 0.1569 ??? 0.2391?? -0.7571??? 0.6080 ?? -0.0578?? -0.9837?? -0.1703 ?? -0.5368?? -0.8361??? 0.1135 ?? -0.9918??? 0.1207??? 0.0423 ?? -0.9968?? -0.0709??? 0.0379 ?? -0.8724?? -0.4781??? 0.1014 ?? -0.2487?? -0.9336?? -0.2581 ??? 0.1183?? -0.9919??? 0.0471 ??? 0.3376?? -0.8415?? -0.4218 ??? 0.5286?? -0.8409?? -0.1163 ??? 0.9969?? -0.0550??? 0.0571 (2) " DTI_gradient_table_creator_Philips_RelX.m " with Philips par/rec files ?? -0.6533?? -0.2706?? -0.7071 ?? -0.2087?? -0.6756?? -0.7071 ??? 0.0197?? -0.7068?? -0.7071 ??? 0.4212?? -0.5679?? -0.7071 ??? 0.6899?? -0.1549?? -0.7071 ?? -0.6535?? -0.2707?? -0.7069 ?? -0.5000?? -0.5000?? -0.7071 ?? -0.2929?? -0.7071?? -0.6436 ??? 0.2945?? -0.7064?? -0.6436 ??? 0.5150?? -0.4861?? -0.7061 ??? 0.7071?? -0.2929?? -0.6436 ?? -0.7071?? -0.4725?? -0.5261 ?? -0.4725?? -0.7071?? -0.5261 ??? 0.5555?? -0.6439?? -0.5261 ??? 0.7071?? -0.4725?? -0.5261 ?? -0.7071?? -0.7071?? -0.0002 ??? 0.7071?? -0.7071???????? 0 ?? -0.7071?? -0.4725??? 0.5261 ??? 0.7071?? -0.4725??? 0.5261 ??? 0.4725?? -0.7071??? 0.5261 ??? 0.7071?? -0.4725??? 0.5261 ?? -0.6364?? -0.4252??? 0.6436 ?? -0.7060?? -0.7060??? 0.0547 ?? -0.2929?? -0.7071??? 0.6436 ??? 0.2929?? -0.7071??? 0.6436 ??? 0.7071?? -0.7071??? 0.0078 ??? 0.7071?? -0.2929??? 0.6436 ?? -0.5847?? -0.3977??? 0.7071 ?? -0.7063?? -0.7063??? 0.0489 ??? 0.0347?? -0.7063??? 0.7071 ??? 0.7071?? -0.7071??? 0.0115 ??? 0.7071???????? 0??? 0.7071 ???????? 0???????? 0???????? 0 ? 100.0000? 100.0000? 100.0000 They seem totally different. So can any person explain this problem? Thank you very much! Haiqing ??????????????24??????? -----???????----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org ? _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org ??????????????24??????? -----???????----- _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101004/7386686f/attachment-0001.html From xli16 at jhmi.edu Mon Oct 4 09:17:16 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 04 Oct 2010 09:17:16 -0400 Subject: [Mristudio-users] login and password? In-Reply-To: References: Message-ID: <72b0dfc42cfb.4ca99b9c@johnshopkins.edu> Hello Markus, If you go to www.mristudio.org, you will see "Forget password" and "Forget username" in the "Registration" section. Please click them and enter your registered email address. You will get your username and password back. Regards, Xin ----- Original Message ----- From: Markus Gschwind Date: Saturday, October 2, 2010 5:11 pm Subject: [Mristudio-users] login and password? To: mristudio-users at mristudio.org > Dear administrators, > > I am a registered membre and I am getting all mails form > mristudio.org, but > I cannot login. > Even when trying to create an account, it asks for a password ;-) > > What shoud I do, please? > > Thanks, > Markus > > -- > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From Yulin.Ge at nyumc.org Mon Oct 4 09:58:40 2010 From: Yulin.Ge at nyumc.org (Ge, Yulin) Date: Mon, 04 Oct 2010 09:58:40 -0400 Subject: [Mristudio-users] login and password? In-Reply-To: <72b0dfc42cfb.4ca99b9c@johnshopkins.edu> References: <72b0dfc42cfb.4ca99b9c@johnshopkins.edu> Message-ID: Hi Xin, I finished the registration on line, but didn't get further log in info. Can you please let me know what I should do next? Thanks, Yulin ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Yulin Ge, MD Associate Professor of Radiology Department of Radiology/Center for Biomedical Imaging New York University Langone Medical Center 660 First Avenue, Fourth Floor New York, NY 10016 Phone: 212-263-3784 (work) FAX: 212-263-7541 Email: Yulin.Ge at nyumc.org -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li Sent: Monday, October 04, 2010 9:17 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] login and password? Hello Markus, If you go to www.mristudio.org, you will see "Forget password" and "Forget username" in the "Registration" section. Please click them and enter your registered email address. You will get your username and password back. Regards, Xin ----- Original Message ----- From: Markus Gschwind Date: Saturday, October 2, 2010 5:11 pm Subject: [Mristudio-users] login and password? To: mristudio-users at mristudio.org > Dear administrators, > > I am a registered membre and I am getting all mails form > mristudio.org, but > I cannot login. > Even when trying to create an account, it asks for a password ;-) > > What shoud I do, please? > > Thanks, > Markus > > -- > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= From xli16 at jhmi.edu Mon Oct 4 11:26:07 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 04 Oct 2010 11:26:07 -0400 Subject: [Mristudio-users] login and password? In-Reply-To: References: <72b0dfc42cfb.4ca99b9c@johnshopkins.edu> Message-ID: <7240ea38705.4ca9b9cf@johnshopkins.edu> Hello Yulin, After you finished the registration, you should be able to log in using the username and password you created. Let me know if you still cannot log in. Regards, Xin ----- Original Message ----- From: "Ge, Yulin" Date: Monday, October 4, 2010 9:58 am Subject: Re: [Mristudio-users] login and password? To: "'DTI Studio, ROI Editor, DiffeoMap Questions/Support'" > Hi Xin, > > I finished the registration on line, but didn't get further log in > info. Can you please let me know what I should do next? Thanks, > Yulin > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Yulin Ge, MD > Associate Professor of Radiology > Department of Radiology/Center for Biomedical Imaging > New York University Langone Medical Center > 660 First Avenue, Fourth Floor > New York, NY 10016 > Phone: 212-263-3784 (work) > FAX: 212-263-7541 > Email: Yulin.Ge at nyumc.org > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org [ On Behalf Of Xin Li > Sent: Monday, October 04, 2010 9:17 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] login and password? > > Hello Markus, > > If you go to www.mristudio.org, you will see "Forget password" and > "Forget username" in the "Registration" section. Please click them and > enter your registered email address. You will get your username and > password back. > > > Regards, > > Xin > > ----- Original Message ----- > From: Markus Gschwind > Date: Saturday, October 2, 2010 5:11 pm > Subject: [Mristudio-users] login and password? > To: mristudio-users at mristudio.org > > > > Dear administrators, > > > > I am a registered membre and I am getting all mails form > > mristudio.org, but > > I cannot login. > > Even when trying to create an account, it asks for a password ;-) > > > > What shoud I do, please? > > > > Thanks, > > Markus > > > > -- > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > ------------------------------------------------------------ > This email message, including any attachments, is for the sole use of > the intended recipient(s) and may contain information that is > proprietary, confidential, and exempt from disclosure under applicable > law. Any unauthorized review, use, disclosure, or distribution is > prohibited. If you have received this email in error please notify the > sender by return email and delete the original message. Please note, > the recipient should check this email and any attachments for the > presence of viruses. The organization accepts no liability for any > damage caused by any virus transmitted by this email. > ================================= > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From tmsusmaras at suffolk.edu Mon Oct 4 11:26:24 2010 From: tmsusmaras at suffolk.edu (Teresa Susmaras) Date: Mon, 04 Oct 2010 11:26:24 -0400 (EDT) Subject: [Mristudio-users] dti data in 4D and nii formats Message-ID: <20101004112624.CLV12802@mp1.suffolk.edu> Hello, I have DTI data that is in 4D format and DTI Studio will not read it. Is there a way for me to convert this data to 3D? I also have dti data in nii format and I cannot get DTI Studio to read that either. Is there anything I can do? Thank you, Teresa Teresa M. Susmaras, M.A. Doctoral Student of Clinical Psychology (Neuropsychology) Suffolk University, Boston, MA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101004/bb44e241/attachment.html From susumu at mri.jhu.edu Mon Oct 4 11:54:04 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 04 Oct 2010 11:54:04 -0400 Subject: [Mristudio-users] dti data in 4D and nii formats In-Reply-To: <20101004112624.CLV12802@mp1.suffolk.edu> References: <20101004112624.CLV12802@mp1.suffolk.edu> Message-ID: If the 4D data is simple raw images without header and it's integer, you can use REC format. DtiStudio can read and open "nii" files (Mri3DView), but can directly open it for tensor calculation (DtiMapping). I believe you can open all nii files by Mri3DView and save them as one 4D file, which can be loaded to DtiMapping as REC format. Please try. On Mon, Oct 4, 2010 at 11:26 AM, Teresa Susmaras wrote: > Hello, > I have DTI data that is in 4D format and DTI Studio will not read it. Is > there a way for me to convert this data to 3D? I also have dti data in nii > format and I cannot get DTI Studio to read that either. > Is there anything I can do? > Thank you, > Teresa > > Teresa M. Susmaras, M.A. > Doctoral Student of Clinical Psychology (Neuropsychology) > Suffolk University, Boston, MA > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101004/e36e4693/attachment.html From buchmann2 at wisc.edu Mon Oct 4 15:17:47 2010 From: buchmann2 at wisc.edu (Andreas Buchmann) Date: Mon, 04 Oct 2010 13:17:47 -0600 Subject: [Mristudio-users] alignlinear. exe error Message-ID: <0L9S002JK5LPII00@smtpauth3.wiscmail.wisc.edu> Dear Xin, dear Diffeomap experts, i have a similar problem like Peggy this year- when i'm trying linear normalisation of FA images, it says that "cannot find air file", although the 4 required air-Files are in the Diffeomap folders. I tried it also with an older version (Landmarker) and with several different images, and it had the same problem. Any help is appreciated Andreas -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101004/c8912255/attachment.html From ssaksena21 at gmail.com Mon Oct 4 15:20:07 2010 From: ssaksena21 at gmail.com (Saurabh) Date: Mon, 04 Oct 2010 15:20:07 -0400 Subject: [Mristudio-users] dti data in 4D and nii formats In-Reply-To: References: <20101004112624.CLV12802@mp1.suffolk.edu> Message-ID: Dear Mr. Mori, Can you please remove my email id from the distribution list. I will sincerely appreciate your help. Best Regards Sent from my iPhone On Oct 4, 2010, at 11:54 AM, susumu mori wrote: > If the 4D data is simple raw images without header and it's integer, > you can use REC format. > DtiStudio can read and open "nii" files (Mri3DView), but can > directly open it for tensor calculation (DtiMapping). > I believe you can open all nii files by Mri3DView and save them as > one 4D file, which can be loaded to DtiMapping as REC format. Please > try. > > On Mon, Oct 4, 2010 at 11:26 AM, Teresa Susmaras > wrote: > Hello, > I have DTI data that is in 4D format and DTI Studio will not read > it. Is there a way for me to convert this data to 3D? I also have > dti data in nii format and I cannot get DTI Studio to read that > either. > Is there anything I can do? > Thank you, > Teresa > Teresa M. Susmaras, M.A. > Doctoral Student of Clinical Psychology (Neuropsychology) > Suffolk University, Boston, MA > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101004/a4d0659d/attachment-0001.html From cyrou13 at gmail.com Mon Oct 4 15:30:32 2010 From: cyrou13 at gmail.com (Cyril Di Grandi) Date: Mon, 04 Oct 2010 21:30:32 +0200 Subject: [Mristudio-users] Please ramone me Message-ID: <87DF74A9-2E10-48B7-A029-DB88A48CC1B5@gmail.com> >From the mailing list Thanks Envoy? de mon iPhone From xli16 at jhmi.edu Mon Oct 4 15:55:17 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 04 Oct 2010 15:55:17 -0400 Subject: [Mristudio-users] dti data in 4D and nii formats In-Reply-To: References: <20101004112624.CLV12802@mp1.suffolk.edu> Message-ID: <71509f914ec3.4ca9f8e5@johnshopkins.edu> Hello, If you want to unsubscribe, please send a blank email to mristudio-users-unsubscribe at mristudio.org Regards, Xin ----- Original Message ----- From: Saurabh Date: Monday, October 4, 2010 3:22 pm Subject: Re: [Mristudio-users] dti data in 4D and nii formats To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Dear Mr. Mori, > Can you please remove my email id from the distribution list. I will > sincerely appreciate your help. > Best Regards > > Sent from my iPhone > > On Oct 4, 2010, at 11:54 AM, susumu mori wrote: > > >If the 4D data is simple raw images without header and it's integer, > you can use REC format. > >DtiStudio can read and open "nii" files (Mri3DView), but can > directly open it for tensor calculation (DtiMapping). > >I believe you can open all nii files by Mri3DView and save them as > one 4D file, which can be loaded to DtiMapping as REC format. Please try. > > > >On Mon, Oct 4, 2010 at 11:26 AM, Teresa Susmaras > wrote: > >Hello, > >I have DTI data that is in 4D format and DTI Studio will not read > it. Is there a way for me to convert this data to 3D? I also have > dti data in nii format and I cannot get DTI Studio to read that either. > >Is there anything I can do? > >Thank you, > >Teresa > > Teresa M. Susmaras, M.A. > >Doctoral Student of Clinical Psychology (Neuropsychology) > >Suffolk University, Boston, MA > > > > > > > >_______________________________________________ > >mristudio-users mailing list > >mristudio-users at mristudio.org > > > >Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > > > >_______________________________________________ > >mristudio-users mailing list > >mristudio-users at mristudio.org > > > >Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Mon Oct 4 15:56:24 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 04 Oct 2010 15:56:24 -0400 Subject: [Mristudio-users] Please ramone me In-Reply-To: <87DF74A9-2E10-48B7-A029-DB88A48CC1B5@gmail.com> References: <87DF74A9-2E10-48B7-A029-DB88A48CC1B5@gmail.com> Message-ID: <7200d15ba6b.4ca9f928@johnshopkins.edu> Hello, If you want to subscribe, please send a blank email to mristudio-users-unsubscribe at mristudio.org Regards, Xin ----- Original Message ----- From: Cyril Di Grandi Date: Monday, October 4, 2010 3:30 pm Subject: [Mristudio-users] Please ramone me To: "mristudio-users at mristudio.org" > From the mailing list > > Thanks > > Envoy? de mon iPhone > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Mon Oct 4 15:59:04 2010 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 04 Oct 2010 15:59:04 -0400 Subject: [Mristudio-users] alignlinear. exe error In-Reply-To: <0L9S002JK5LPII00@smtpauth3.wiscmail.wisc.edu> References: <0L9S002JK5LPII00@smtpauth3.wiscmail.wisc.edu> Message-ID: <7290bea25272.4ca9f9c8@johnshopkins.edu> Hello Dr. Buchmann, When you ran AIR, DiffeoMap asked you where you would like to save the air file. Could you please tell me where you tried to save the air file? Please give me the whole pathname. Regards, Xin ----- Original Message ----- From: Andreas Buchmann Date: Monday, October 4, 2010 3:18 pm Subject: [Mristudio-users] alignlinear. exe error To: mristudio-users at mristudio.org > Dear Xin, > > dear Diffeomap experts, > > > > i have a similar problem like Peggy this year- when i'm trying linear > normalisation of FA images, it says that "cannot find air file", although > the 4 required air-Files are in the Diffeomap folders. I tried it > also with > an older version (Landmarker) and with several different images, and > it had > the same problem. > > > > Any help is appreciated > > Andreas > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From manojpgi at gmail.com Mon Oct 4 18:37:11 2010 From: manojpgi at gmail.com (manoj verma) Date: Mon, 04 Oct 2010 17:37:11 -0500 Subject: [Mristudio-users] Conversion of Image format Message-ID: Hi every one; I am using DTI studio to convert FA, CL, CP CS and ADC map in to Analyze format and by default it saved in Flot format but I need it as integer format. I will be very grate full to you if any body can help me with this regards. Thanks, -- Manoj K. Verma From darshanp20 at yahoo.com Mon Oct 4 19:09:26 2010 From: darshanp20 at yahoo.com (darshan pai) Date: Mon, 04 Oct 2010 16:09:26 -0700 (PDT) Subject: [Mristudio-users] Conversion of Image format In-Reply-To: References: Message-ID: <273221.58139.qm@web30706.mail.mud.yahoo.com> YOu can use MRIcro to convert it to your specs ----- Original Message ---- From: manoj verma To: mristudio-users at mristudio.org Sent: Mon, October 4, 2010 6:37:11 PM Subject: [Mristudio-users] Conversion of Image format Hi every one; I am using DTI studio to convert FA, CL, CP CS and ADC map in to Analyze format and by default it saved in Flot format but I need it as integer format. I will be very grate full to you if any body can help me with this regards. Thanks, -- Manoj K. Verma _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From Yulin.Ge at nyumc.org Mon Oct 4 19:14:07 2010 From: Yulin.Ge at nyumc.org (Ge, Yulin) Date: Mon, 04 Oct 2010 19:14:07 -0400 Subject: [Mristudio-users] Please ramone me In-Reply-To: <7200d15ba6b.4ca9f928@johnshopkins.edu> References: <87DF74A9-2E10-48B7-A029-DB88A48CC1B5@gmail.com> <7200d15ba6b.4ca9f928@johnshopkins.edu> Message-ID: Hi Xin, I unsubscribed, but it seems to be failed, I still got a lot of emails. Could you please change my work email to my gmail (ygeny2009 at gmail.com) for this subscription? Thanks a lot! Yulin ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Yulin Ge, MD Associate Professor of Radiology Department of Radiology/Center for Biomedical Imaging New York University Langone Medical Center 660 First Avenue, Fourth Floor New York, NY 10016 Phone: 212-263-3784 (work) FAX: 212-263-7541 Email: Yulin.Ge at nyumc.org -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xin Li Sent: Monday, October 04, 2010 3:56 PM To: Cyril Di Grandi; DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Please ramone me Hello, If you want to subscribe, please send a blank email to mristudio-users-unsubscribe at mristudio.org Regards, Xin ----- Original Message ----- From: Cyril Di Grandi Date: Monday, October 4, 2010 3:30 pm Subject: [Mristudio-users] Please ramone me To: "mristudio-users at mristudio.org" > From the mailing list > > Thanks > > Envoy? de mon iPhone > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= From manojpgi at gmail.com Mon Oct 4 19:30:26 2010 From: manojpgi at gmail.com (manoj verma) Date: Mon, 04 Oct 2010 18:30:26 -0500 Subject: [Mristudio-users] Conversion of Image format In-Reply-To: <273221.58139.qm@web30706.mail.mud.yahoo.com> References: <273221.58139.qm@web30706.mail.mud.yahoo.com> Message-ID: Thanks!! I have tried the MRIcro but I did not got it. Can you suggest the how I can open like header information or some other parameter that I have to change. Thanks Manoj On Mon, Oct 4, 2010 at 6:09 PM, darshan pai wrote: > YOu can use MRIcro to convert it to your specs > > > > > ----- Original Message ---- > From: manoj verma > To: mristudio-users at mristudio.org > Sent: Mon, October 4, 2010 6:37:11 PM > Subject: [Mristudio-users] Conversion of Image format > > Hi every one; > > I am using DTI studio to convert FA, CL, CP CS and ADC map in to > Analyze format and by default it saved in Flot format but I need it as > integer format. > I will be very grate full to you if any body can help me with this regards. > > Thanks, > > -- > Manoj K. Verma > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > -- Manoj K. Verma From susumu at mri.jhu.edu Mon Oct 4 19:51:01 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 04 Oct 2010 19:51:01 -0400 Subject: [Mristudio-users] Conversion of Image format In-Reply-To: References: Message-ID: I believe you can do it with DiffeoMap. Please load the images to DiffeoMap and click the "B, F, W" button. There, you can convert the data into another format. Then click the "save" icon and save them as "Analyze" format. Please try. If you have many data, there is the "load command" button. Here I guess you can make a script to perform a repeated operation. If interested, please contact Xin Li. On Mon, Oct 4, 2010 at 6:37 PM, manoj verma wrote: > Hi every one; > > I am using DTI studio to convert FA, CL, CP CS and ADC map in to > Analyze format and by default it saved in Flot format but I need it as > integer format. > I will be very grate full to you if any body can help me with this regards. > > Thanks, > > -- > Manoj K. Verma > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101004/f6eb7d7e/attachment-0001.html From kmanoj at mail.med.upenn.edu Mon Oct 4 21:54:31 2010 From: kmanoj at mail.med.upenn.edu (Manoj Kumar) Date: Mon, 04 Oct 2010 21:54:31 -0400 (EDT) Subject: [Mristudio-users] Conversion of Image format In-Reply-To: Message-ID: <865021017.5100891286243671604.JavaMail.root@zm-mbx-levy.zimbra.upenn.edu> Thanks!! Dr Mori. regards Manoj ----- Original Message ----- From: "susumu mori" To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" , "Xin Li" Sent: Monday, October 4, 2010 6:51:01 PM GMT -06:00 US/Canada Central Subject: Re: [Mristudio-users] Conversion of Image format I believe you can do it with DiffeoMap. Please load the images to DiffeoMap and click the "B, F, W" button. There, you can convert the data into another format. Then click the "save" icon and save them as "Analyze" format. Please try. If you have many data, there is the "load command" button. Here I guess you can make a script to perform a repeated operation. If interested, please contact Xin Li. On Mon, Oct 4, 2010 at 6:37 PM, manoj verma < manojpgi at gmail.com > wrote: Hi every one; I am using DTI studio to convert FA, CL, CP CS and ADC map in to Analyze format and by default it saved in Flot format but I need it as integer format. I will be very grate full to you if any body can help me with this regards. Thanks, -- Manoj K. Verma _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From j.haenggi at psychologie.uzh.ch Tue Oct 5 01:30:29 2010 From: j.haenggi at psychologie.uzh.ch (=?ISO-8859-1?B?SvxyZ2Vu?= =?ISO-8859-1?B?IEjkbmdnaQ==?=) Date: Tue, 05 Oct 2010 07:30:29 +0200 Subject: [Mristudio-users] alignlinear. exe error In-Reply-To: <0L9S002JK5LPII00@smtpauth3.wiscmail.wisc.edu> Message-ID: Hallo Andreas Alles klar bei euch in Amerika? Ich kann dir hier nicht helfen, aber wenn du ein gutes DTI und Traktographie-Programm suchst, welches auch unter Windows l?uft kann ich dir TrackVis (incl. DoffusionToolkit) empfehlen. Da es auf NIFTI Daten beruht, kannst du eine Normalisierung dann auch in SPM machen. Gruss aus der Heimat J?rgen On [DATE], "Andreas Buchmann" <[ADDRESS]> wrote: > Dear Xin, > dear Diffeomap experts, > > i have a similar problem like Peggy this year- when i'm trying linear > normalisation of FA images, it says that "cannot find air file", although the > 4 required air-Files are in the Diffeomap folders. I tried it also with an > older version (Landmarker) and with several different images, and it had the > same problem. > > Any help is appreciated > Andreas > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org ---------------------------------------------------------------------------- J?rgen H?nggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ---------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101005/2a6d9633/attachment.html From cyrou13 at gmail.com Tue Oct 5 03:26:24 2010 From: cyrou13 at gmail.com (Cyril DI GRANDI) Date: Tue, 05 Oct 2010 09:26:24 +0200 Subject: [Mristudio-users] The unsubscription doesn't work Message-ID: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101005/b80a5800/attachment.html From tashimom at gmail.com Tue Oct 5 07:49:22 2010 From: tashimom at gmail.com (Julie Brefczynski-Lewis) Date: Tue, 05 Oct 2010 07:49:22 -0400 Subject: [Mristudio-users] The unsubscription doesn't work In-Reply-To: References: Message-ID: Ditto - kind of frustrating. On Tue, Oct 5, 2010 at 3:26 AM, Cyril DI GRANDI wrote: > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101005/9e0c55cc/attachment.html From buchmann2 at wisc.edu Tue Oct 5 13:28:10 2010 From: buchmann2 at wisc.edu (Andreas Buchmann) Date: Tue, 05 Oct 2010 11:28:10 -0600 Subject: [Mristudio-users] alignlinear. exe error In-Reply-To: <0L9S002JK5LPII00@smtpauth3.wiscmail.wisc.edu> Message-ID: <0L9T00KEUV71Q240@smtpauth3.wiscmail.wisc.edu> Dear Xin, the path of the folder i intended to save the File in was E:\DTI\DTI37dic I have Windows 7. Diffeomap is under C:\Temp\DiffeoMap Thanks a lot Andreas _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Andreas Buchmann Sent: Montag, 4. Oktober 2010 13:18 To: mristudio-users at mristudio.org Subject: [Mristudio-users] alignlinear. exe error Dear Xin, dear Diffeomap experts, i have a similar problem like Peggy this year- when i'm trying linear normalisation of FA images, it says that "cannot find air file", although the 4 required air-Files are in the Diffeomap folders. I tried it also with an older version (Landmarker) and with several different images, and it had the same problem. Any help is appreciated Andreas -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101005/ae6c0047/attachment.html From manojpgi at gmail.com Thu Oct 7 11:48:55 2010 From: manojpgi at gmail.com (manoj verma) Date: Thu, 07 Oct 2010 10:48:55 -0500 Subject: [Mristudio-users] Analyze format and SPM Message-ID: Hi every one, I have DTI map (FA, ADC, CL, and CP) in analyze format which I have generated by using DTIstudio. I want to open these analyze format with SPM for registration but I am unable to open these map properly. Anybody can help me, why it happen and if any one can help me regarding this issue I will be very great full. Thanks -- Manoj K. Verma From katja at bilkent.edu.tr Thu Oct 14 09:38:47 2010 From: katja at bilkent.edu.tr (Katja Doerschner) Date: Thu, 14 Oct 2010 16:38:47 +0300 Subject: [Mristudio-users] DiffeoMap on Parallels Message-ID: <4CEB36A8-2851-49EA-A12C-A3D349879CDC@bilkent.edu.tr> Dear MRI studio users, I am trying to run DiffeoMap-latest-x86.exe on a MAC using Parallels, but Windows seems to recognize the file I downloaded as a zip file (I know it doesn't make sense). Curiously, DTIStudio-latest-x86.exe and vcredist_x86.exe run and work just fine. Has anyone experimented with this and knows how to overcome this problem? Thank you. Katja -- Katja Doerschner Assistant Professor Department of Psychology & National Center for Magnetic Resonance Research (UMRAM) Bilkent University Bilkent Cyberpark, C-Blok, 2. Kat http://www.bilkent.edu.tr/~katja/ office: +90 (312) 290 3004 cell: +90 (530) 640 31 33 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101014/341432a6/attachment.html From xli16 at jhmi.edu Thu Oct 14 10:10:35 2010 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 14 Oct 2010 10:10:35 -0400 Subject: [Mristudio-users] DiffeoMap on Parallels In-Reply-To: <4CEB36A8-2851-49EA-A12C-A3D349879CDC@bilkent.edu.tr> References: <4CEB36A8-2851-49EA-A12C-A3D349879CDC@bilkent.edu.tr> Message-ID: <7250b813579e.4cb6d71b@johnshopkins.edu> Hello Dr. Doerschner, DiffeoMap is a package including several exe files and many atlas images. So this package has to be compressed before it is transferred online. DiffeoMap-latest-x86.exe is a self-extract compressed file. If you double click it, the whole package will be extracted automatically. Regards, Xin ----- Original Message ----- From: Katja Doerschner Date: Thursday, October 14, 2010 9:39 am Subject: [Mristudio-users] DiffeoMap on Parallels To: mristudio-users at mristudio.org > Dear MRI studio users, > > I am trying to run DiffeoMap-latest-x86.exe on a MAC using Parallels, > but Windows seems to recognize the file I downloaded as a zip file (I > know it doesn't make sense). Curiously, DTIStudio-latest-x86.exe and > vcredist_x86.exe run and work just fine. Has anyone experimented with > this and knows how to overcome this problem? > > Thank you. > Katja > -- > > Katja Doerschner > Assistant Professor > Department of Psychology > & National Center for > Magnetic Resonance Research (UMRAM) > Bilkent University > Bilkent Cyberpark, C-Blok, 2. Kat > > office: +90 (312) 290 3004 > cell: +90 (530) 640 31 33 > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From katja at bilkent.edu.tr Thu Oct 14 13:41:28 2010 From: katja at bilkent.edu.tr (katja doerschner) Date: Thu, 14 Oct 2010 20:41:28 +0300 (EEST) Subject: [Mristudio-users] DiffeoMap on Parallels In-Reply-To: <7250b813579e.4cb6d71b@johnshopkins.edu> References: <4CEB36A8-2851-49EA-A12C-A3D349879CDC@bilkent.edu.tr> <7250b813579e.4cb6d71b@johnshopkins.edu> Message-ID: <49203.139.179.135.36.1287078088.squirrel@webmail.bilkent.edu.tr> Thank you very much Xin. Well good thing that my computer is smarter than me :). ? will retry this. Best, k > Hello Dr. Doerschner, > > DiffeoMap is a package including several exe files and many atlas images. > So this package has to be compressed before it is transferred online. > DiffeoMap-latest-x86.exe is a self-extract compressed file. If you double > click it, the whole package will be extracted automatically. > > > Regards, > > > Xin > > > > ----- Original Message ----- > From: Katja Doerschner > Date: Thursday, October 14, 2010 9:39 am > Subject: [Mristudio-users] DiffeoMap on Parallels > To: mristudio-users at mristudio.org > > >> Dear MRI studio users, >> >> I am trying to run DiffeoMap-latest-x86.exe on a MAC using Parallels, >> but Windows seems to recognize the file I downloaded as a zip file (I >> know it doesn't make sense). Curiously, DTIStudio-latest-x86.exe and >> vcredist_x86.exe run and work just fine. Has anyone experimented with >> this and knows how to overcome this problem? >> >> Thank you. >> Katja >> -- >> >> Katja Doerschner >> Assistant Professor >> Department of Psychology >> & National Center for >> Magnetic Resonance Research (UMRAM) >> Bilkent University >> Bilkent Cyberpark, C-Blok, 2. Kat >> >> office: +90 (312) 290 3004 >> cell: +90 (530) 640 31 33 >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > From anqi at cis.jhu.edu Thu Oct 14 16:53:10 2010 From: anqi at cis.jhu.edu (Anqi Qiu) Date: Thu, 14 Oct 2010 16:53:10 -0400 (EDT) Subject: [Mristudio-users] Postdoctoral Fellow position for infant neuroimaging In-Reply-To: <0L9T00KEUV71Q240@smtpauth3.wiscmail.wisc.edu> References: <0L9T00KEUV71Q240@smtpauth3.wiscmail.wisc.edu> Message-ID: <61444.220.255.179.248.1287089590.squirrel@webmail.cis.jhu.edu> Postdoctoral Fellow Position on Infant Neuroimaging Job description: National University of Singapore (NUS) is a leading global university centred in Asia. It offers a global approach to education and research, with a focus on Asian perspectives and expertise. Computation functional anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and cognition studies using neuroimaging techniques. Our group is leading a large-scale infant neuroimaging project in Singapore. The project examines neurocognition using EEG and eye trackers and brain development using diffusion tensor imaging (DTI), resting-state fMRI, and structural MRI. We are looking for a research fellow who is interested in multi-modal MRI studies in infants, especially, who is interested in developing anatomical and functional analysis methods (such as image segmentation) or investigating anatomical and functional connectivity in infants. We offer high salary with medical and other benefits. Requirements: ? Ph. D or MD ? Research background on infant brain is preferable but necessary ? Knowledge in statistical analysis is necessary ? Good communication and writing skills in English language If you are interested in the jobs listed below, please send your CV to Dr. Anqi QIU Division of Bioengineering National University of Singapore Email: bieqa at nus.edu.sg Phone: +(65) 6516 7002 From mbiozl at hotmail.com Fri Oct 15 00:35:39 2010 From: mbiozl at hotmail.com (ZhuangJohnny) Date: Fri, 15 Oct 2010 12:35:39 +0800 Subject: [Mristudio-users] fiber tracking statistics Message-ID: Dear DTI studio experts Currently, I'm using DTIstudio to perform fiber tracking in our sample. The fiber statistics gave me a minimum fiber length of around 2mm in the selected fibre, i'm just wondering if this small value could reflect the true fiber length, or it may result from noise in the DTI data? Many thanks and regards, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101015/f4c9bc03/attachment.html From susumu at mri.jhu.edu Fri Oct 15 07:13:42 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 15 Oct 2010 07:13:42 -0400 Subject: [Mristudio-users] fiber tracking statistics In-Reply-To: References: Message-ID: In DTI-based tractography, there is no "true fiber length", because what we reconstructed in no way represents actual axonal fiber, which has a diameter of few micron, while our pixel size is 2mm. what we reconstruct may reflect the macroscopic configuration of "axonal bundles". Axonal bundles are large enough to visually appreciate it and 2mm pixels are small enough to visualize the large bundles. However, the large bundles we can see and we have named (like the "longitudinal fasciculus") is abstractive and somewhat artifactual concept. They don't have clear boundaries and definitions because at any point, axon (which is the real entity) can merge and exist. So, "the length of the axonal bundles" is often not undefinable. It may contain an axon that goes only 10 mm and also another one with 50 mm length. If our image resolution is 2 mm and tractography gave 6mm fiber length, that simply means there are 3 pixels in row that has similar fiber orientation, pointing each other, with sufficiently high FA. Nothing more than that. It was terminated because of sharp turns or low FA, which could be due to real anatomy or by noise. There is nothing wrong with that; the results are based on our measurements and consistent image analysis algorithm. If there is anything "wrong", it is our interpretation of the results. We often try to connect the measurement and analysis results to real biological entity. It is important but very difficult process. What we are observing is merely water molecule properties, and there is a large disconnection from biological entity. We can still quantify it and compare among different subjects non-invasively and three-dimensionally. We can't do it using histology. The downside is, our observation is disconnected from real biological entity and interpretation, only from MRI observation, is often not possible. Going back to your question, the minimum fiber length is simply set by an arbitrary threshold. Any reconstruction results shorter than that is removed from subsequent analysis. 2010/10/15 ZhuangJohnny > Dear DTI studio experts > > Currently, I'm using DTIstudio to perform fiber tracking in our sample. > The fiber statistics gave me a minimum fiber length of around 2mm in the > selected fibre, i'm just wondering if this small value could reflect the > true fiber length, or it may result from noise in the DTI data? > > Many thanks and regards, > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101015/0b4f5763/attachment-0001.html From mbiozl at hotmail.com Sat Oct 16 20:50:31 2010 From: mbiozl at hotmail.com (ZhuangJohnny) Date: Sun, 17 Oct 2010 08:50:31 +0800 Subject: [Mristudio-users] fiber tracking statistics In-Reply-To: References: Message-ID: Dear Susumu Thank you very much for the informative reply. It's much clearer to me now. Many thanks and regards, Date: Fri, 15 Oct 2010 07:13:42 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] fiber tracking statistics In DTI-based tractography, there is no "true fiber length", because what we reconstructed in no way represents actual axonal fiber, which has a diameter of few micron, while our pixel size is 2mm. what we reconstruct may reflect the macroscopic configuration of "axonal bundles". Axonal bundles are large enough to visually appreciate it and 2mm pixels are small enough to visualize the large bundles. However, the large bundles we can see and we have named (like the "longitudinal fasciculus") is abstractive and somewhat artifactual concept. They don't have clear boundaries and definitions because at any point, axon (which is the real entity) can merge and exist. So, "the length of the axonal bundles" is often not undefinable. It may contain an axon that goes only 10 mm and also another one with 50 mm length. If our image resolution is 2 mm and tractography gave 6mm fiber length, that simply means there are 3 pixels in row that has similar fiber orientation, pointing each other, with sufficiently high FA. Nothing more than that. It was terminated because of sharp turns or low FA, which could be due to real anatomy or by noise. There is nothing wrong with that; the results are based on our measurements and consistent image analysis algorithm. If there is anything "wrong", it is our interpretation of the results. We often try to connect the measurement and analysis results to real biological entity. It is important but very difficult process. What we are observing is merely water molecule properties, and there is a large disconnection from biological entity. We can still quantify it and compare among different subjects non-invasively and three-dimensionally. We can't do it using histology. The downside is, our observation is disconnected from real biological entity and interpretation, only from MRI observation, is often not possible. Going back to your question, the minimum fiber length is simply set by an arbitrary threshold. Any reconstruction results shorter than that is removed from subsequent analysis. 2010/10/15 ZhuangJohnny Dear DTI studio experts Currently, I'm using DTIstudio to perform fiber tracking in our sample. The fiber statistics gave me a minimum fiber length of around 2mm in the selected fibre, i'm just wondering if this small value could reflect the true fiber length, or it may result from noise in the DTI data? Many thanks and regards, _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101017/e6bca64c/attachment.html From gmak at poczta.onet.pl Sun Oct 17 10:45:27 2010 From: gmak at poczta.onet.pl (gmak at poczta.onet.pl) Date: Sun, 17 Oct 2010 16:45:27 +0200 Subject: [Mristudio-users] not valid VTK data File Message-ID: Hi. I have a problem when I try to combine matrices. I have information " The file you want to load is not a valid VTK data file" what may cause this problem? I created two times Kimap and Hmap and there was the same message each time. I correctly combine metrices in 25subjects and this trouble have in 2 subjects. How to solve this problem? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101017/e3d0d749/attachment.html From xli16 at jhmi.edu Tue Oct 19 09:41:47 2010 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 19 Oct 2010 09:41:47 -0400 Subject: [Mristudio-users] not valid VTK data File In-Reply-To: References: Message-ID: <7290befd5e8f.4cbd67db@johnshopkins.edu> Hello, This warning message means that the Kimap and Hamp files you have are not valid VTK files. Did you get these two Kimap and Hmap by running remote LDDMM? The Kimap and Hmap from remote LDDMM are in VTK file format. Xin ----- Original Message ----- From: gmak at poczta.onet.pl Date: Tuesday, October 19, 2010 0:21 am Subject: [Mristudio-users] not valid VTK data File To: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" > Hi. > I have a problem when I try to combine matrices. > I have information " The file you want to load is not a valid VTK > data file" > what may cause this problem? > I created two times Kimap and Hmap and there was the same message > each time. > I correctly combine metrices in 25subjects and this trouble have in 2 > subjects. > How to solve this problem? > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From sabahihadi at yahoo.com Tue Oct 19 10:33:10 2010 From: sabahihadi at yahoo.com (hadi sabahi) Date: Tue, 19 Oct 2010 07:33:10 -0700 (PDT) Subject: [Mristudio-users] question please Message-ID: <927603.69159.qm@web113319.mail.gq1.yahoo.com> Hello, I have problem in launch the dtisudio, when I click the program for running , I get this error : "the application has failed to start beacase its side-by-side configuration is incorrect, please see the application event log for more detail". ? How can I solve this problem ? please. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101019/c23e776e/attachment.html From xli16 at jhmi.edu Tue Oct 19 12:57:08 2010 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 19 Oct 2010 12:57:08 -0400 Subject: [Mristudio-users] question please In-Reply-To: <927603.69159.qm@web113319.mail.gq1.yahoo.com> References: <927603.69159.qm@web113319.mail.gq1.yahoo.com> Message-ID: <7250d5b15430.4cbd95a4@johnshopkins.edu> Hello, The Microsoft Visual Studio Redistribution package needs to be installed on your machine before you run DtiStudio. You can download the redistribution package at https://www.mristudio.org/wiki/installation. If you want to run DtiStudio_latest_x86.exe, please download vcredist_x86.exe. If you want to run DtiStudio_latest_x64.exe, please download vcredist_x64.exe. Xin ----- Original Message ----- From: hadi sabahi Date: Tuesday, October 19, 2010 10:33 am Subject: [Mristudio-users] question please To: mristudio-users at mristudio.org > Hello, I have problem in launch the dtisudio, when I click the program > for running , I get this error : "the application has failed to start > beacase its side-by-side configuration is incorrect, please see the > application event log for more detail". > ? > How can I solve this problem ? please. > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From gmak13 at wp.pl Tue Oct 19 14:29:23 2010 From: gmak13 at wp.pl (gmak13 at wp.pl) Date: Tue, 19 Oct 2010 20:29:23 +0200 Subject: [Mristudio-users] not valid VTK data File In-Reply-To: <7290befd5e8f.4cbd67db@johnshopkins.edu> References: <7290befd5e8f.4cbd67db@johnshopkins.edu> Message-ID: Hi Yes. I get the Kimap and Hmap by running Multichannel remote LDDMM. When I unzip the Result file, the maps seem correct. File name: Hmap.vtk, Kimap.vtk FIle size: Hmap165MB and Kimap 165MB, ca like my other maps when I combine matrices I have message not valid VTK data File and vtkoutputWindow error : "....vtkDataReader.cxx, line 401 vtkStructuredPointsReader [024b4430] Unable to open file...." I run remote LDDMM two times for the same subject and I have the same error massage for two different matrices. ----- Original Message ----- From: "Xin Li" To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" Sent: Tuesday, October 19, 2010 3:41 PM Subject: Re: [Mristudio-users] not valid VTK data File > Hello, > > This warning message means that the Kimap and Hamp files you have are not > valid VTK files. Did you get these two Kimap and Hmap by running remote > LDDMM? The Kimap and Hmap from remote LDDMM are in VTK file format. > > > Xin > > > > ----- Original Message ----- > From: gmak at poczta.onet.pl > Date: Tuesday, October 19, 2010 0:21 am > Subject: [Mristudio-users] not valid VTK data File > To: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" > > > >> Hi. >> I have a problem when I try to combine matrices. >> I have information " The file you want to load is not a valid VTK >> data file" >> what may cause this problem? >> I created two times Kimap and Hmap and there was the same message >> each time. >> I correctly combine metrices in 25subjects and this trouble have in 2 >> subjects. >> How to solve this problem? >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------------------------------------------------------------------------- Nie znaleziono wirusa w tej wiadomosci przychodzacej. Sprawdzone przez AVG - www.avg.com Wersja: 9.0.862 / Baza danych wirusow: 271.1.1/3202 - Data wydania: 10/17/10 08:33:00 From xli16 at jhmi.edu Tue Oct 19 14:36:49 2010 From: xli16 at jhmi.edu (Xin Li) Date: Tue, 19 Oct 2010 14:36:49 -0400 Subject: [Mristudio-users] not valid VTK data File In-Reply-To: References: <7290befd5e8f.4cbd67db@johnshopkins.edu> Message-ID: <7240b9f221b.4cbdad01@johnshopkins.edu> Hello, I cannot tell what is wrong so far. Please send me these two files. I will check them on my machine. Please send them to my email account instead of the mailing list. Xin ----- Original Message ----- From: gmak13 at wp.pl Date: Tuesday, October 19, 2010 2:30 pm Subject: Re: [Mristudio-users] not valid VTK data File To: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" > Hi > Yes. I get the Kimap and Hmap by running Multichannel remote LDDMM. > When I > unzip the Result file, the maps seem correct. > File name: Hmap.vtk, Kimap.vtk > FIle size: Hmap165MB and Kimap 165MB, ca like my other maps > when I combine matrices I have message not valid VTK data File and > vtkoutputWindow error : "....vtkDataReader.cxx, line 401 > vtkStructuredPointsReader [024b4430] Unable to open file...." > I run remote LDDMM two times for the same subject and I have the same > error > massage for two different matrices. > > > > ----- Original Message ----- > From: "Xin Li" > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > > Sent: Tuesday, October 19, 2010 3:41 PM > Subject: Re: [Mristudio-users] not valid VTK data File > > > > Hello, > > > > This warning message means that the Kimap and Hamp files you have > are not > > valid VTK files. Did you get these two Kimap and Hmap by running > remote > > LDDMM? The Kimap and Hmap from remote LDDMM are in VTK file format. > > > > > > Xin > > > > > > > > ----- Original Message ----- > > From: gmak at poczta.onet.pl > > Date: Tuesday, October 19, 2010 0:21 am > > Subject: [Mristudio-users] not valid VTK data File > > To: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" > > > > > > > >> Hi. > >> I have a problem when I try to combine matrices. > >> I have information " The file you want to load is not a valid VTK > >> data file" > >> what may cause this problem? > >> I created two times Kimap and Hmap and there was the same message > >> each time. > >> I correctly combine metrices in 25subjects and this trouble have > in 2 > >> subjects. > >> How to solve this problem? > >> _______________________________________________ > >> mristudio-users mailing list > >> mristudio-users at mristudio.org > >> > >> Unsubscribe, send a blank email to: > >> mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > mristudio-users-unsubscribe at mristudio.org > > > > > -------------------------------------------------------------------------------- > > > > Nie znaleziono wirusa w tej wiadomosci przychodzacej. > Sprawdzone przez AVG - www.avg.com > Wersja: 9.0.862 / Baza danych wirusow: 271.1.1/3202 - Data wydania: > 10/17/10 > 08:33:00 > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From JZwicker at cw.bc.ca Tue Oct 19 16:26:26 2010 From: JZwicker at cw.bc.ca (Zwicker, Jill) Date: Tue, 19 Oct 2010 13:26:26 -0700 Subject: [Mristudio-users] problems with gradients Message-ID: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> Hi Susumu and SC, You previously helped me with a tensor calc issue (see below). I have since used the gradient calculator and obtained more RAM, and have successfully analyzed two scans. However, the remaining scans are not processing properly (i.e., I do not get a proper colour map). In looking at the PAR files, the parameters are the same as the first two scans, with the exception of the rescale and scale slopes, window center and widths, and diffision parameters (nothing that changes what I enter to the online gradient table calculator). Since the gradient table I was using didn't work for successive scans, I took the gradients from the PAR file. This seemed to work, but the colours were reversed, so I switched coloumns around and got a seemingly accurate colour map. However, when I tried to fiber track, the CST seems too short and the values are not consistent with what I obtained in the previous 2 scans. So...I am unsure why the previous gradient table didn't work and I don't think my trial and error method of getting a colour map is accurate. I would be happy to send you the PAR files (off the listserv) if that would help. Thank you in advance for your guidance. Jill ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: September 1, 2010 6:25 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc I suspect memory problem. Please use stricter threshold (like FA>0.3 and angle <30, for example) to see if it works. If it works, then it's memory problem (I mean, you need more memory). You can also save eigenvector0 and FA, close DtiStudio, and redo fiber tracking using the saved file. If you start from tensor calculation, you have all the raw data in your memory. 32-bit operating system can allocate only 1-1.5GB memory. 64bit is much better. susumu On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill > wrote: Thank you so much! After some trial and error, I figured out the correct gradient table. I can now get a beautiful colour map, but I have a new problem. The program crashes everytime I try to do fibre tracking. Any suggestions? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, September 01, 2010 10:56 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc Use the following link for the gradient table calculation. You need to get some information required to fill in from Par file of your data. If your data is not in ParRec format, get it first. http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html -SC. On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill > wrote: > Hi DTI Studio users, > > I am relatively new to DTI studio and have been using successfully to do > tractography on infant brain data collected on a Seimens. I am now trying to > analyze child brain data collected on a Philips. I can get a clear image, > but as soon as I try a tensor calculation, the image quality degrades > significantly (no matter what the background noise level I set it to). I > made gradient tables from the PAR file (forwards and backwards) and also > flipped the z as the tutorial suggests. Any suggestions on how I can solve > this problem? > > Thanks for your help. > > > > Jill Zwicker, PhD, OT(C) > > Postdoctoral Fellow > > Child & Family Research Institute > > Developmental Neurosciences & Child Health > > L408 - 4480 Oak Street > > Vancouver, BC V6H 3V4 > > Phone: 604-875-2000 ext 6805 > > Fax: 604-875-3569 > > jzwicker at cw.bc.ca > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101019/592aa64a/attachment.html From choisj70 at gmail.com Tue Oct 19 16:47:38 2010 From: choisj70 at gmail.com (Seongjin) Date: Tue, 19 Oct 2010 16:47:38 -0400 Subject: [Mristudio-users] problems with gradients In-Reply-To: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> References: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> Message-ID: You may check a few options. 1. Overplus is on or off (make it sure with your examcard if it was on or off.) 2. If b=0 image comes first or last in your DTI acquisition order. 3. DTI input fields are correctly filled out. ... -SC On Tue, Oct 19, 2010 at 4:26 PM, Zwicker, Jill wrote: > Hi Susumu and SC, > You previously helped me with a tensor calc issue (see below). I have since > used the gradient calculator and obtained more RAM, and have successfully > analyzed two scans. However, the remaining scans are not processing properly > (i.e., I do not get a proper colour map). In looking at the PAR files, the > parameters are the same as the first two scans, with the exception of the > rescale and scale slopes, window center and widths, and diffision parameters > (nothing that changes what I enter to the online gradient table calculator). > Since the gradient table I was using didn't work for successive scans, I > took the gradients from the PAR file. This seemed to work, but the colours > were reversed, so I switched coloumns around and got a seemingly accurate > colour map. However, when I tried to fiber track, the CST seems too short > and the values are not consistent with what I obtained in the previous 2 > scans. > So...I am unsure why the previous gradient table didn't work and I don't > think my trial and error method of getting a colour map is accurate. I would > be happy to send you the PAR files (off the listserv) if that would help. > Thank you in advance for your guidance. > Jill > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ > susumu at mri.jhu.edu] > *Sent:* September 1, 2010 6:25 PM > *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support > *Subject:* Re: [Mristudio-users] problems with tensor calc > > I suspect memory problem. > Please use stricter threshold (like FA>0.3 and angle <30, for example) to > see if it works. If it works, then it's memory problem (I mean, you need > more memory). > > You can also save eigenvector0 and FA, close DtiStudio, and redo fiber > tracking using the saved file. If you start from tensor calculation, you > have all the raw data in your memory. > > 32-bit operating system can allocate only 1-1.5GB memory. 64bit is much > better. > > susumu > > On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill wrote: > >> Thank you so much! After some trial and error, I figured out the correct >> gradient table. I can now get a beautiful colour map, but I have a new >> problem. The program crashes everytime I try to do fibre tracking. Any >> suggestions? >> >> -----Original Message----- >> From: mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] >> Sent: Wednesday, September 01, 2010 10:56 AM >> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >> Subject: Re: [Mristudio-users] problems with tensor calc >> >> Use the following link for the gradient table calculation. >> You need to get some information required to fill in from Par file of your >> data. >> If your data is not in ParRec format, get it first. >> >> http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html >> >> -SC. >> >> On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill wrote: >> > Hi DTI Studio users, >> > >> > I am relatively new to DTI studio and have been using successfully to do >> > tractography on infant brain data collected on a Seimens. I am now >> trying to >> > analyze child brain data collected on a Philips. I can get a clear >> image, >> > but as soon as I try a tensor calculation, the image quality degrades >> > significantly (no matter what the background noise level I set it to). I >> > made gradient tables from the PAR file (forwards and backwards) and also >> > flipped the z as the tutorial suggests. Any suggestions on how I can >> solve >> > this problem? >> > >> > Thanks for your help. >> > >> > >> > >> > Jill Zwicker, PhD, OT(C) >> > >> > Postdoctoral Fellow >> > >> > Child & Family Research Institute >> > >> > Developmental Neurosciences & Child Health >> > >> > L408 - 4480 Oak Street >> > >> > Vancouver, BC V6H 3V4 >> > >> > Phone: 604-875-2000 ext 6805 >> > >> > Fax: 604-875-3569 >> > >> > jzwicker at cw.bc.ca >> > >> > >> > >> > _______________________________________________ >> > mristudio-users mailing list >> > mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> > mristudio-users-unsubscribe at mristudio.org >> > >> > >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101019/248fce57/attachment-0001.html From JZwicker at cw.bc.ca Tue Oct 19 16:52:57 2010 From: JZwicker at cw.bc.ca (Zwicker, Jill) Date: Tue, 19 Oct 2010 13:52:57 -0700 Subject: [Mristudio-users] problems with gradients In-Reply-To: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> References: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> Message-ID: <01150B9F5C05274F8013B909B04790E4D7CC9BC5B1@VEXCCR03.phsabc.ehcnet.ca> Further to this message, the ROI values I get are consistent with the previous scans, so it is just the fiber tracking that I am suspicious of... Thanks! ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Zwicker, Jill [JZwicker at cw.bc.ca] Sent: October 19, 2010 1:26 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with gradients Hi Susumu and SC, You previously helped me with a tensor calc issue (see below). I have since used the gradient calculator and obtained more RAM, and have successfully analyzed two scans. However, the remaining scans are not processing properly (i.e., I do not get a proper colour map). In looking at the PAR files, the parameters are the same as the first two scans, with the exception of the rescale and scale slopes, window center and widths, and diffision parameters (nothing that changes what I enter to the online gradient table calculator). Since the gradient table I was using didn't work for successive scans, I took the gradients from the PAR file. This seemed to work, but the colours were reversed, so I switched coloumns around and got a seemingly accurate colour map. However, when I tried to fiber track, the CST seems too short and the values are not consistent with what I obtained in the previous 2 scans. So...I am unsure why the previous gradient table didn't work and I don't think my trial and error method of getting a colour map is accurate. I would be happy to send you the PAR files (off the listserv) if that would help. Thank you in advance for your guidance. Jill ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: September 1, 2010 6:25 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc I suspect memory problem. Please use stricter threshold (like FA>0.3 and angle <30, for example) to see if it works. If it works, then it's memory problem (I mean, you need more memory). You can also save eigenvector0 and FA, close DtiStudio, and redo fiber tracking using the saved file. If you start from tensor calculation, you have all the raw data in your memory. 32-bit operating system can allocate only 1-1.5GB memory. 64bit is much better. susumu On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill > wrote: Thank you so much! After some trial and error, I figured out the correct gradient table. I can now get a beautiful colour map, but I have a new problem. The program crashes everytime I try to do fibre tracking. Any suggestions? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, September 01, 2010 10:56 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc Use the following link for the gradient table calculation. You need to get some information required to fill in from Par file of your data. If your data is not in ParRec format, get it first. http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html -SC. On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill > wrote: > Hi DTI Studio users, > > I am relatively new to DTI studio and have been using successfully to do > tractography on infant brain data collected on a Seimens. I am now trying to > analyze child brain data collected on a Philips. I can get a clear image, > but as soon as I try a tensor calculation, the image quality degrades > significantly (no matter what the background noise level I set it to). I > made gradient tables from the PAR file (forwards and backwards) and also > flipped the z as the tutorial suggests. Any suggestions on how I can solve > this problem? > > Thanks for your help. > > > > Jill Zwicker, PhD, OT(C) > > Postdoctoral Fellow > > Child & Family Research Institute > > Developmental Neurosciences & Child Health > > L408 - 4480 Oak Street > > Vancouver, BC V6H 3V4 > > Phone: 604-875-2000 ext 6805 > > Fax: 604-875-3569 > > jzwicker at cw.bc.ca > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101019/20051db2/attachment.html From jxw73 at psu.edu Wed Oct 20 12:03:23 2010 From: jxw73 at psu.edu (Jianli Wang) Date: Wed, 20 Oct 2010 12:03:23 -0400 Subject: [Mristudio-users] Loading DICOM Message-ID: <58AB69CE563848F1AA827D7436F2442F@df0x5gf1> Hi, DtiStudio experts, I have some trouble loading some Siemens DICOM images in DtiStudio v3.0. When I load the series via the Siemens DICOM option, the DTI images are stretched out in the inferior-superior direction. My DTI data has 65 2-mm slices with 2 averages. After loading, it shows130 2-mm slices. Please let me know how to handle this. Thanks. Jianli -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101020/afed0d86/attachment.html From susumu at mri.jhu.edu Wed Oct 20 22:19:41 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 20 Oct 2010 22:19:41 -0400 Subject: [Mristudio-users] problems with gradients In-Reply-To: <01150B9F5C05274F8013B909B04790E4D7CC9BC5B1@VEXCCR03.phsabc.ehcnet.ca> References: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> <01150B9F5C05274F8013B909B04790E4D7CC9BC5B1@VEXCCR03.phsabc.ehcnet.ca> Message-ID: Hi Jill, I'm second to SC. When you are using Philips, even if you thought that you are using exactly the same parameters, you could end up in two different types of the gradient tables; overplus on and off. This is not recorded in the beginning of PAR file. So my suggestion is, try the "overplus on" option of the table calculator. Also, if you find that you used "overplus on", you have to type in the oblique angle information in the calculator. The angle information is in the PAR file. The reason you didn't get the tractography right is most likely due to "+/-" signs of the gradient table you used. You can test "x/y/z flip" function of the tractography to test it. The best way is to use the gradient calculator, which should be able to sort out all the issues. Susumu On Tue, Oct 19, 2010 at 4:52 PM, Zwicker, Jill wrote: > Further to this message, the ROI values I get are consistent with the > previous scans, so it is just the fiber tracking that I am suspicious of... > Thanks! > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of Zwicker, Jill [ > JZwicker at cw.bc.ca] > *Sent:* October 19, 2010 1:26 PM > > *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support > *Subject:* Re: [Mristudio-users] problems with gradients > > Hi Susumu and SC, > You previously helped me with a tensor calc issue (see below). I have since > used the gradient calculator and obtained more RAM, and have successfully > analyzed two scans. However, the remaining scans are not processing properly > (i.e., I do not get a proper colour map). In looking at the PAR files, the > parameters are the same as the first two scans, with the exception of the > rescale and scale slopes, window center and widths, and diffision parameters > (nothing that changes what I enter to the online gradient table calculator). > Since the gradient table I was using didn't work for successive scans, I > took the gradients from the PAR file. This seemed to work, but the colours > were reversed, so I switched coloumns around and got a seemingly accurate > colour map. However, when I tried to fiber track, the CST seems too short > and the values are not consistent with what I obtained in the previous 2 > scans. > So...I am unsure why the previous gradient table didn't work and I don't > think my trial and error method of getting a colour map is accurate. I would > be happy to send you the PAR files (off the listserv) if that would help. > Thank you in advance for your guidance. > Jill > ------------------------------ > *From:* mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ > susumu at mri.jhu.edu] > *Sent:* September 1, 2010 6:25 PM > *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support > *Subject:* Re: [Mristudio-users] problems with tensor calc > > I suspect memory problem. > Please use stricter threshold (like FA>0.3 and angle <30, for example) to > see if it works. If it works, then it's memory problem (I mean, you need > more memory). > > You can also save eigenvector0 and FA, close DtiStudio, and redo fiber > tracking using the saved file. If you start from tensor calculation, you > have all the raw data in your memory. > > 32-bit operating system can allocate only 1-1.5GB memory. 64bit is much > better. > > susumu > > On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill wrote: > >> Thank you so much! After some trial and error, I figured out the correct >> gradient table. I can now get a beautiful colour map, but I have a new >> problem. The program crashes everytime I try to do fibre tracking. Any >> suggestions? >> >> -----Original Message----- >> From: mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] >> Sent: Wednesday, September 01, 2010 10:56 AM >> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >> Subject: Re: [Mristudio-users] problems with tensor calc >> >> Use the following link for the gradient table calculation. >> You need to get some information required to fill in from Par file of your >> data. >> If your data is not in ParRec format, get it first. >> >> http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html >> >> -SC. >> >> On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill wrote: >> > Hi DTI Studio users, >> > >> > I am relatively new to DTI studio and have been using successfully to do >> > tractography on infant brain data collected on a Seimens. I am now >> trying to >> > analyze child brain data collected on a Philips. I can get a clear >> image, >> > but as soon as I try a tensor calculation, the image quality degrades >> > significantly (no matter what the background noise level I set it to). I >> > made gradient tables from the PAR file (forwards and backwards) and also >> > flipped the z as the tutorial suggests. Any suggestions on how I can >> solve >> > this problem? >> > >> > Thanks for your help. >> > >> > >> > >> > Jill Zwicker, PhD, OT(C) >> > >> > Postdoctoral Fellow >> > >> > Child & Family Research Institute >> > >> > Developmental Neurosciences & Child Health >> > >> > L408 - 4480 Oak Street >> > >> > Vancouver, BC V6H 3V4 >> > >> > Phone: 604-875-2000 ext 6805 >> > >> > Fax: 604-875-3569 >> > >> > jzwicker at cw.bc.ca >> > >> > >> > >> > _______________________________________________ >> > mristudio-users mailing list >> > mristudio-users at mristudio.org >> > http://lists.mristudio.org/mailman/listinfo/ >> > Unsubscribe, send a blank email to: >> > mristudio-users-unsubscribe at mristudio.org >> > >> > >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101020/0b801f69/attachment-0001.html From xuli at mri.jhu.edu Thu Oct 21 11:18:12 2010 From: xuli at mri.jhu.edu (Xu Li) Date: Thu, 21 Oct 2010 11:18:12 -0400 Subject: [Mristudio-users] problems with gradients In-Reply-To: References: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> <01150B9F5C05274F8013B909B04790E4D7CC9BC5B1@VEXCCR03.phsabc.ehcnet.ca> Message-ID: <44AE0C01-00AE-4E7D-A1E9-AF3CF65E6CB5@mri.jhu.edu> Dear Susumu, I have a quick question about the gradient table I got from the gradient_table_creator It gives me a table with the [0 0 0] and [100 100 100] at the bottom which seems to be different than those sample gradient table I have from DTI_studio. Should I just move the [0 0 0] to the top? Or the 3T Philips systems do the b0 scan at the end instead of at the beginning now? Thanks! Xu On Oct 20, 2010, at 10:19 PM, susumu mori wrote: > Hi Jill, > > I'm second to SC. When you are using Philips, even if you thought that you are using exactly the same parameters, you could end up in two different types of the gradient tables; overplus on and off. This is not recorded in the beginning of PAR file. > > So my suggestion is, try the "overplus on" option of the table calculator. > Also, if you find that you used "overplus on", you have to type in the oblique angle information in the calculator. The angle information is in the PAR file. > > The reason you didn't get the tractography right is most likely due to "+/-" signs of the gradient table you used. You can test "x/y/z flip" function of the tractography to test it. The best way is to use the gradient calculator, which should be able to sort out all the issues. > > Susumu > > On Tue, Oct 19, 2010 at 4:52 PM, Zwicker, Jill wrote: > Further to this message, the ROI values I get are consistent with the previous scans, so it is just the fiber tracking that I am suspicious of... > Thanks! > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Zwicker, Jill [JZwicker at cw.bc.ca] > Sent: October 19, 2010 1:26 PM > > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] problems with gradients > > Hi Susumu and SC, > You previously helped me with a tensor calc issue (see below). I have since used the gradient calculator and obtained more RAM, and have successfully analyzed two scans. However, the remaining scans are not processing properly (i.e., I do not get a proper colour map). In looking at the PAR files, the parameters are the same as the first two scans, with the exception of the rescale and scale slopes, window center and widths, and diffision parameters (nothing that changes what I enter to the online gradient table calculator). Since the gradient table I was using didn't work for successive scans, I took the gradients from the PAR file. This seemed to work, but the colours were reversed, so I switched coloumns around and got a seemingly accurate colour map. However, when I tried to fiber track, the CST seems too short and the values are not consistent with what I obtained in the previous 2 scans. > So...I am unsure why the previous gradient table didn't work and I don't think my trial and error method of getting a colour map is accurate. I would be happy to send you the PAR files (off the listserv) if that would help. > Thank you in advance for your guidance. > Jill > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] > Sent: September 1, 2010 6:25 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] problems with tensor calc > > I suspect memory problem. > Please use stricter threshold (like FA>0.3 and angle <30, for example) to see if it works. If it works, then it's memory problem (I mean, you need more memory). > > You can also save eigenvector0 and FA, close DtiStudio, and redo fiber tracking using the saved file. If you start from tensor calculation, you have all the raw data in your memory. > > 32-bit operating system can allocate only 1-1.5GB memory. 64bit is much better. > > susumu > > On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill wrote: > Thank you so much! After some trial and error, I figured out the correct gradient table. I can now get a beautiful colour map, but I have a new problem. The program crashes everytime I try to do fibre tracking. Any suggestions? > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] > Sent: Wednesday, September 01, 2010 10:56 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] problems with tensor calc > > Use the following link for the gradient table calculation. > You need to get some information required to fill in from Par file of your data. > If your data is not in ParRec format, get it first. > > http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html > > -SC. > > On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill wrote: > > Hi DTI Studio users, > > > > I am relatively new to DTI studio and have been using successfully to do > > tractography on infant brain data collected on a Seimens. I am now trying to > > analyze child brain data collected on a Philips. I can get a clear image, > > but as soon as I try a tensor calculation, the image quality degrades > > significantly (no matter what the background noise level I set it to). I > > made gradient tables from the PAR file (forwards and backwards) and also > > flipped the z as the tutorial suggests. Any suggestions on how I can solve > > this problem? > > > > Thanks for your help. > > > > > > > > Jill Zwicker, PhD, OT(C) > > > > Postdoctoral Fellow > > > > Child & Family Research Institute > > > > Developmental Neurosciences & Child Health > > > > L408 - 4480 Oak Street > > > > Vancouver, BC V6H 3V4 > > > > Phone: 604-875-2000 ext 6805 > > > > Fax: 604-875-3569 > > > > jzwicker at cw.bc.ca > > > > > > > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/ > > Unsubscribe, send a blank email to: > > mristudio-users-unsubscribe at mristudio.org > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101021/1ae6d0aa/attachment.html From susumu at mri.jhu.edu Thu Oct 21 11:39:52 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 21 Oct 2010 11:39:52 -0400 Subject: [Mristudio-users] problems with gradients In-Reply-To: <44AE0C01-00AE-4E7D-A1E9-AF3CF65E6CB5@mri.jhu.edu> References: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> <01150B9F5C05274F8013B909B04790E4D7CC9BC5B1@VEXCCR03.phsabc.ehcnet.ca> <44AE0C01-00AE-4E7D-A1E9-AF3CF65E6CB5@mri.jhu.edu> Message-ID: In Philips scanners, you can specify whether you want to save the b0 ([000]) image first or an the end. I believe the default is at the end. I suggest you to read your image using Mri3DView , figure out where is the b0 image (first or second from the last), and then grab the correct table. The last image is always a calculated isotoropic diffusion-weighted image, which is not used for DTI. [100, 100, 100] sends a message to DtiStudio to ignore this image. By the way, in old days, b0 was always in the beginning and you don't have the choice to change the order. It is only recently we start to see b0 at the end (ok, second from the last). Because most of the data I receive recently is in this way, I assume it is now the default way. On Thu, Oct 21, 2010 at 11:18 AM, Xu Li wrote: > Dear Susumu, > > I have a quick question about the gradient table I got from the > gradient_table_creator > > It gives me a table with the [0 0 0] and [100 100 100] at the bottom which > seems to be different than those sample gradient table I have from > DTI_studio. Should I just move the [0 0 0] to the top? Or the 3T Philips > systems do the b0 scan at the end instead of at the beginning now? > > Thanks! > > Xu > > > On Oct 20, 2010, at 10:19 PM, susumu mori wrote: > > Hi Jill, > > I'm second to SC. When you are using Philips, even if you thought that you > are using exactly the same parameters, you could end up in two different > types of the gradient tables; overplus on and off. This is not recorded in > the beginning of PAR file. > > So my suggestion is, try the "overplus on" option of the table calculator. > Also, if you find that you used "overplus on", you have to type in the > oblique angle information in the calculator. The angle information is in the > PAR file. > > The reason you didn't get the tractography right is most likely due to > "+/-" signs of the gradient table you used. You can test "x/y/z flip" > function of the tractography to test it. The best way is to use the gradient > calculator, which should be able to sort out all the issues. > > Susumu > > On Tue, Oct 19, 2010 at 4:52 PM, Zwicker, Jill wrote: > >> Further to this message, the ROI values I get are consistent with the >> previous scans, so it is just the fiber tracking that I am suspicious of... >> Thanks! >> ------------------------------ >> *From:* mristudio-users-bounces at mristudio.org [ >> mristudio-users-bounces at mristudio.org] On Behalf Of Zwicker, Jill [ >> JZwicker at cw.bc.ca] >> *Sent:* October 19, 2010 1:26 PM >> >> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support >> *Subject:* Re: [Mristudio-users] problems with gradients >> >> Hi Susumu and SC, >> You previously helped me with a tensor calc issue (see below). I have >> since used the gradient calculator and obtained more RAM, and have >> successfully analyzed two scans. However, the remaining scans are not >> processing properly (i.e., I do not get a proper colour map). In looking at >> the PAR files, the parameters are the same as the first two scans, with the >> exception of the rescale and scale slopes, window center and widths, and >> diffision parameters (nothing that changes what I enter to the online >> gradient table calculator). Since the gradient table I was using didn't work >> for successive scans, I took the gradients from the PAR file. This seemed to >> work, but the colours were reversed, so I switched coloumns around and got a >> seemingly accurate colour map. However, when I tried to fiber track, the CST >> seems too short and the values are not consistent with what I obtained in >> the previous 2 scans. >> So...I am unsure why the previous gradient table didn't work and I don't >> think my trial and error method of getting a colour map is accurate. I would >> be happy to send you the PAR files (off the listserv) if that would help. >> Thank you in advance for your guidance. >> Jill >> ------------------------------ >> *From:* mristudio-users-bounces at mristudio.org [ >> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [ >> susumu at mri.jhu.edu] >> *Sent:* September 1, 2010 6:25 PM >> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support >> *Subject:* Re: [Mristudio-users] problems with tensor calc >> >> I suspect memory problem. >> Please use stricter threshold (like FA>0.3 and angle <30, for example) to >> see if it works. If it works, then it's memory problem (I mean, you need >> more memory). >> >> You can also save eigenvector0 and FA, close DtiStudio, and redo fiber >> tracking using the saved file. If you start from tensor calculation, you >> have all the raw data in your memory. >> >> 32-bit operating system can allocate only 1-1.5GB memory. 64bit is much >> better. >> >> susumu >> >> On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill wrote: >> >>> Thank you so much! After some trial and error, I figured out the correct >>> gradient table. I can now get a beautiful colour map, but I have a new >>> problem. The program crashes everytime I try to do fibre tracking. Any >>> suggestions? >>> >>> -----Original Message----- >>> From: mristudio-users-bounces at mristudio.org [mailto: >>> mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] >>> Sent: Wednesday, September 01, 2010 10:56 AM >>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support >>> Subject: Re: [Mristudio-users] problems with tensor calc >>> >>> Use the following link for the gradient table calculation. >>> You need to get some information required to fill in from Par file of >>> your data. >>> If your data is not in ParRec format, get it first. >>> >>> http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html >>> >>> -SC. >>> >>> On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill wrote: >>> > Hi DTI Studio users, >>> > >>> > I am relatively new to DTI studio and have been using successfully to >>> do >>> > tractography on infant brain data collected on a Seimens. I am now >>> trying to >>> > analyze child brain data collected on a Philips. I can get a clear >>> image, >>> > but as soon as I try a tensor calculation, the image quality degrades >>> > significantly (no matter what the background noise level I set it to). >>> I >>> > made gradient tables from the PAR file (forwards and backwards) and >>> also >>> > flipped the z as the tutorial suggests. Any suggestions on how I can >>> solve >>> > this problem? >>> > >>> > Thanks for your help. >>> > >>> > >>> > >>> > Jill Zwicker, PhD, OT(C) >>> > >>> > Postdoctoral Fellow >>> > >>> > Child & Family Research Institute >>> > >>> > Developmental Neurosciences & Child Health >>> > >>> > L408 - 4480 Oak Street >>> > >>> > Vancouver, BC V6H 3V4 >>> > >>> > Phone: 604-875-2000 ext 6805 >>> > >>> > Fax: 604-875-3569 >>> > >>> > jzwicker at cw.bc.ca >>> > >>> > >>> > >>> > _______________________________________________ >>> > mristudio-users mailing list >>> > mristudio-users at mristudio.org >>> > http://lists.mristudio.org/mailman/listinfo/ >>> > Unsubscribe, send a blank email to: >>> > mristudio-users-unsubscribe at mristudio.org >>> > >>> > >>> >>> _______________________________________________ >>> mristudio-users mailing list >>> mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> mristudio-users-unsubscribe at mristudio.org >>> >>> _______________________________________________ >>> mristudio-users mailing list >>> mristudio-users at mristudio.org >>> http://lists.mristudio.org/mailman/listinfo/ >>> Unsubscribe, send a blank email to: >>> mristudio-users-unsubscribe at mristudio.org >>> >>> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101021/a1195dcc/attachment-0001.html From jcwu at uci.edu Fri Oct 22 13:15:07 2010 From: jcwu at uci.edu (Wu, Joseph) Date: Fri, 22 Oct 2010 10:15:07 -0700 Subject: [Mristudio-users] Need GE 3 tesla 25 direction DTI gradient table please, thanks In-Reply-To: <44AE0C01-00AE-4E7D-A1E9-AF3CF65E6CB5@mri.jhu.edu> References: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> <01150B9F5C05274F8013B909B04790E4D7CC9BC5B1@VEXCCR03.phsabc.ehcnet.ca> <44AE0C01-00AE-4E7D-A1E9-AF3CF65E6CB5@mri.jhu.edu> Message-ID: Hi Does somebody have GE 3 tesla 25 direction DTI gradient table that they can forward to : jcwu at uci.edu? That would be greatly appreciated. Thanks, Joe From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xu Li Sent: Thursday, October 21, 2010 8:18 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with gradients Dear Susumu, I have a quick question about the gradient table I got from the gradient_table_creator It gives me a table with the [0 0 0] and [100 100 100] at the bottom which seems to be different than those sample gradient table I have from DTI_studio. Should I just move the [0 0 0] to the top? Or the 3T Philips systems do the b0 scan at the end instead of at the beginning now? Thanks! Xu On Oct 20, 2010, at 10:19 PM, susumu mori wrote: Hi Jill, I'm second to SC. When you are using Philips, even if you thought that you are using exactly the same parameters, you could end up in two different types of the gradient tables; overplus on and off. This is not recorded in the beginning of PAR file. So my suggestion is, try the "overplus on" option of the table calculator. Also, if you find that you used "overplus on", you have to type in the oblique angle information in the calculator. The angle information is in the PAR file. The reason you didn't get the tractography right is most likely due to "+/-" signs of the gradient table you used. You can test "x/y/z flip" function of the tractography to test it. The best way is to use the gradient calculator, which should be able to sort out all the issues. Susumu On Tue, Oct 19, 2010 at 4:52 PM, Zwicker, Jill > wrote: Further to this message, the ROI values I get are consistent with the previous scans, so it is just the fiber tracking that I am suspicious of... Thanks! ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Zwicker, Jill [JZwicker at cw.bc.ca] Sent: October 19, 2010 1:26 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with gradients Hi Susumu and SC, You previously helped me with a tensor calc issue (see below). I have since used the gradient calculator and obtained more RAM, and have successfully analyzed two scans. However, the remaining scans are not processing properly (i.e., I do not get a proper colour map). In looking at the PAR files, the parameters are the same as the first two scans, with the exception of the rescale and scale slopes, window center and widths, and diffision parameters (nothing that changes what I enter to the online gradient table calculator). Since the gradient table I was using didn't work for successive scans, I took the gradients from the PAR file. This seemed to work, but the colours were reversed, so I switched coloumns around and got a seemingly accurate colour map. However, when I tried to fiber track, the CST seems too short and the values are not consistent with what I obtained in the previous 2 scans. So...I am unsure why the previous gradient table didn't work and I don't think my trial and error method of getting a colour map is accurate. I would be happy to send you the PAR files (off the listserv) if that would help. Thank you in advance for your guidance. Jill ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: September 1, 2010 6:25 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc I suspect memory problem. Please use stricter threshold (like FA>0.3 and angle <30, for example) to see if it works. If it works, then it's memory problem (I mean, you need more memory). You can also save eigenvector0 and FA, close DtiStudio, and redo fiber tracking using the saved file. If you start from tensor calculation, you have all the raw data in your memory. 32-bit operating system can allocate only 1-1.5GB memory. 64bit is much better. susumu On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill > wrote: Thank you so much! After some trial and error, I figured out the correct gradient table. I can now get a beautiful colour map, but I have a new problem. The program crashes everytime I try to do fibre tracking. Any suggestions? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, September 01, 2010 10:56 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc Use the following link for the gradient table calculation. You need to get some information required to fill in from Par file of your data. If your data is not in ParRec format, get it first. http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html -SC. On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill > wrote: > Hi DTI Studio users, > > I am relatively new to DTI studio and have been using successfully to do > tractography on infant brain data collected on a Seimens. I am now trying to > analyze child brain data collected on a Philips. I can get a clear image, > but as soon as I try a tensor calculation, the image quality degrades > significantly (no matter what the background noise level I set it to). I > made gradient tables from the PAR file (forwards and backwards) and also > flipped the z as the tutorial suggests. Any suggestions on how I can solve > this problem? > > Thanks for your help. > > > > Jill Zwicker, PhD, OT(C) > > Postdoctoral Fellow > > Child & Family Research Institute > > Developmental Neurosciences & Child Health > > L408 - 4480 Oak Street > > Vancouver, BC V6H 3V4 > > Phone: 604-875-2000 ext 6805 > > Fax: 604-875-3569 > > jzwicker at cw.bc.ca > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org ________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101022/1396b0f1/attachment.html From Roderick.McColl at utsouthwestern.edu Fri Oct 22 14:49:58 2010 From: Roderick.McColl at utsouthwestern.edu (Roderick McColl) Date: Fri, 22 Oct 2010 18:49:58 +0000 Subject: [Mristudio-users] Need GE 3 tesla 25 direction DTI gradient table please, thanks In-Reply-To: References: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> <01150B9F5C05274F8013B909B04790E4D7CC9BC5B1@VEXCCR03.phsabc.ehcnet.ca> <44AE0C01-00AE-4E7D-A1E9-AF3CF65E6CB5@mri.jhu.edu> Message-ID: Joe, unfortunately this is a variable. Depends on the release. The table has changed over the years. Do you know the release? The directions can also be obtained from the DICOM files if you have them. -roddy ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Wu, Joseph Sent: Friday, October 22, 2010 12:15 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: [Mristudio-users] Need GE 3 tesla 25 direction DTI gradient table please, thanks Hi Does somebody have GE 3 tesla 25 direction DTI gradient table that they can forward to : jcwu at uci.edu? That would be greatly appreciated. Thanks, Joe From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xu Li Sent: Thursday, October 21, 2010 8:18 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with gradients Dear Susumu, I have a quick question about the gradient table I got from the gradient_table_creator It gives me a table with the [0 0 0] and [100 100 100] at the bottom which seems to be different than those sample gradient table I have from DTI_studio. Should I just move the [0 0 0] to the top? Or the 3T Philips systems do the b0 scan at the end instead of at the beginning now? Thanks! Xu On Oct 20, 2010, at 10:19 PM, susumu mori wrote: Hi Jill, I'm second to SC. When you are using Philips, even if you thought that you are using exactly the same parameters, you could end up in two different types of the gradient tables; overplus on and off. This is not recorded in the beginning of PAR file. So my suggestion is, try the "overplus on" option of the table calculator. Also, if you find that you used "overplus on", you have to type in the oblique angle information in the calculator. The angle information is in the PAR file. The reason you didn't get the tractography right is most likely due to "+/-" signs of the gradient table you used. You can test "x/y/z flip" function of the tractography to test it. The best way is to use the gradient calculator, which should be able to sort out all the issues. Susumu On Tue, Oct 19, 2010 at 4:52 PM, Zwicker, Jill > wrote: Further to this message, the ROI values I get are consistent with the previous scans, so it is just the fiber tracking that I am suspicious of... Thanks! ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Zwicker, Jill [JZwicker at cw.bc.ca] Sent: October 19, 2010 1:26 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with gradients Hi Susumu and SC, You previously helped me with a tensor calc issue (see below). I have since used the gradient calculator and obtained more RAM, and have successfully analyzed two scans. However, the remaining scans are not processing properly (i.e., I do not get a proper colour map). In looking at the PAR files, the parameters are the same as the first two scans, with the exception of the rescale and scale slopes, window center and widths, and diffision parameters (nothing that changes what I enter to the online gradient table calculator). Since the gradient table I was using didn't work for successive scans, I took the gradients from the PAR file. This seemed to work, but the colours were reversed, so I switched coloumns around and got a seemingly accurate colour map. However, when I tried to fiber track, the CST seems too short and the values are not consistent with what I obtained in the previous 2 scans. So...I am unsure why the previous gradient table didn't work and I don't think my trial and error method of getting a colour map is accurate. I would be happy to send you the PAR files (off the listserv) if that would help. Thank you in advance for your guidance. Jill ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: September 1, 2010 6:25 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc I suspect memory problem. Please use stricter threshold (like FA>0.3 and angle <30, for example) to see if it works. If it works, then it's memory problem (I mean, you need more memory). You can also save eigenvector0 and FA, close DtiStudio, and redo fiber tracking using the saved file. If you start from tensor calculation, you have all the raw data in your memory. 32-bit operating system can allocate only 1-1.5GB memory. 64bit is much better. susumu On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill > wrote: Thank you so much! After some trial and error, I figured out the correct gradient table. I can now get a beautiful colour map, but I have a new problem. The program crashes everytime I try to do fibre tracking. Any suggestions? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, September 01, 2010 10:56 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc Use the following link for the gradient table calculation. You need to get some information required to fill in from Par file of your data. If your data is not in ParRec format, get it first. http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html -SC. On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill > wrote: > Hi DTI Studio users, > > I am relatively new to DTI studio and have been using successfully to do > tractography on infant brain data collected on a Seimens. I am now trying to > analyze child brain data collected on a Philips. I can get a clear image, > but as soon as I try a tensor calculation, the image quality degrades > significantly (no matter what the background noise level I set it to). I > made gradient tables from the PAR file (forwards and backwards) and also > flipped the z as the tutorial suggests. Any suggestions on how I can solve > this problem? > > Thanks for your help. > > > > Jill Zwicker, PhD, OT(C) > > Postdoctoral Fellow > > Child & Family Research Institute > > Developmental Neurosciences & Child Health > > L408 - 4480 Oak Street > > Vancouver, BC V6H 3V4 > > Phone: 604-875-2000 ext 6805 > > Fax: 604-875-3569 > > jzwicker at cw.bc.ca > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org ________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. ________________________________ UT Southwestern Medical Center The future of medicine, today. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101022/371bd0b3/attachment-0001.html From jcwu at uci.edu Fri Oct 22 20:28:48 2010 From: jcwu at uci.edu (Wu, Joseph) Date: Fri, 22 Oct 2010 17:28:48 -0700 Subject: [Mristudio-users] Need GE 3 tesla 25 direction DTI gradient table please, thanks In-Reply-To: References: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> <01150B9F5C05274F8013B909B04790E4D7CC9BC5B1@VEXCCR03.phsabc.ehcnet.ca> <44AE0C01-00AE-4E7D-A1E9-AF3CF65E6CB5@mri.jhu.edu> Message-ID: Hi Roddy, I got 2 dat files from Susumu (old and new) which I will try out. Thanks, Joe From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Roderick McColl Sent: Friday, October 22, 2010 11:50 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Need GE 3 tesla 25 direction DTI gradient table please, thanks Joe, unfortunately this is a variable. Depends on the release. The table has changed over the years. Do you know the release? The directions can also be obtained from the DICOM files if you have them. -roddy ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Wu, Joseph Sent: Friday, October 22, 2010 12:15 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: [Mristudio-users] Need GE 3 tesla 25 direction DTI gradient table please, thanks Hi Does somebody have GE 3 tesla 25 direction DTI gradient table that they can forward to : jcwu at uci.edu? That would be greatly appreciated. Thanks, Joe From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xu Li Sent: Thursday, October 21, 2010 8:18 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with gradients Dear Susumu, I have a quick question about the gradient table I got from the gradient_table_creator It gives me a table with the [0 0 0] and [100 100 100] at the bottom which seems to be different than those sample gradient table I have from DTI_studio. Should I just move the [0 0 0] to the top? Or the 3T Philips systems do the b0 scan at the end instead of at the beginning now? Thanks! Xu On Oct 20, 2010, at 10:19 PM, susumu mori wrote: Hi Jill, I'm second to SC. When you are using Philips, even if you thought that you are using exactly the same parameters, you could end up in two different types of the gradient tables; overplus on and off. This is not recorded in the beginning of PAR file. So my suggestion is, try the "overplus on" option of the table calculator. Also, if you find that you used "overplus on", you have to type in the oblique angle information in the calculator. The angle information is in the PAR file. The reason you didn't get the tractography right is most likely due to "+/-" signs of the gradient table you used. You can test "x/y/z flip" function of the tractography to test it. The best way is to use the gradient calculator, which should be able to sort out all the issues. Susumu On Tue, Oct 19, 2010 at 4:52 PM, Zwicker, Jill > wrote: Further to this message, the ROI values I get are consistent with the previous scans, so it is just the fiber tracking that I am suspicious of... Thanks! ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Zwicker, Jill [JZwicker at cw.bc.ca] Sent: October 19, 2010 1:26 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with gradients Hi Susumu and SC, You previously helped me with a tensor calc issue (see below). I have since used the gradient calculator and obtained more RAM, and have successfully analyzed two scans. However, the remaining scans are not processing properly (i.e., I do not get a proper colour map). In looking at the PAR files, the parameters are the same as the first two scans, with the exception of the rescale and scale slopes, window center and widths, and diffision parameters (nothing that changes what I enter to the online gradient table calculator). Since the gradient table I was using didn't work for successive scans, I took the gradients from the PAR file. This seemed to work, but the colours were reversed, so I switched coloumns around and got a seemingly accurate colour map. However, when I tried to fiber track, the CST seems too short and the values are not consistent with what I obtained in the previous 2 scans. So...I am unsure why the previous gradient table didn't work and I don't think my trial and error method of getting a colour map is accurate. I would be happy to send you the PAR files (off the listserv) if that would help. Thank you in advance for your guidance. Jill ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: September 1, 2010 6:25 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc I suspect memory problem. Please use stricter threshold (like FA>0.3 and angle <30, for example) to see if it works. If it works, then it's memory problem (I mean, you need more memory). You can also save eigenvector0 and FA, close DtiStudio, and redo fiber tracking using the saved file. If you start from tensor calculation, you have all the raw data in your memory. 32-bit operating system can allocate only 1-1.5GB memory. 64bit is much better. susumu On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill > wrote: Thank you so much! After some trial and error, I figured out the correct gradient table. I can now get a beautiful colour map, but I have a new problem. The program crashes everytime I try to do fibre tracking. Any suggestions? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, September 01, 2010 10:56 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc Use the following link for the gradient table calculation. You need to get some information required to fill in from Par file of your data. If your data is not in ParRec format, get it first. http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html -SC. On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill > wrote: > Hi DTI Studio users, > > I am relatively new to DTI studio and have been using successfully to do > tractography on infant brain data collected on a Seimens. I am now trying to > analyze child brain data collected on a Philips. I can get a clear image, > but as soon as I try a tensor calculation, the image quality degrades > significantly (no matter what the background noise level I set it to). I > made gradient tables from the PAR file (forwards and backwards) and also > flipped the z as the tutorial suggests. Any suggestions on how I can solve > this problem? > > Thanks for your help. > > > > Jill Zwicker, PhD, OT(C) > > Postdoctoral Fellow > > Child & Family Research Institute > > Developmental Neurosciences & Child Health > > L408 - 4480 Oak Street > > Vancouver, BC V6H 3V4 > > Phone: 604-875-2000 ext 6805 > > Fax: 604-875-3569 > > jzwicker at cw.bc.ca > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org ________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. ________________________________ UT Southwestern Medical Center The future of medicine, today. ________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101022/5f8f71d3/attachment-0001.html From erdalpanmd at gmail.com Sat Oct 23 03:52:27 2010 From: erdalpanmd at gmail.com (Erdal Pan) Date: Sat, 23 Oct 2010 10:52:27 +0300 Subject: [Mristudio-users] Dicom-siemens Message-ID: Hi all participants; I have trouble with dicom files while uploading to dtistudio -.dcm files does not appear , does somebody help me about this topic. thnx have a good day erdal -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101023/cdaea846/attachment.html From seigeweb at hotmail.com Sun Oct 24 23:26:40 2010 From: seigeweb at hotmail.com (chichesterchiche) Date: Mon, 25 Oct 2010 03:26:40 +0000 Subject: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? Message-ID: Dear DTIStudio Experts, We know we need to input the gradient table in DTIStudio. However, when doing tensor map calculation, which coordinate system is DTIStudio based on? Is DTIStudio based on DICOM patient coordinate system or image coordinate system? I acquired the DWI images by TOSHIBA MRI and the gradient vectors are based on patient coordiante. Can I input the patient-coordinate-based gradient vector to DTI Studio directly, or do I need to transform the patient-coordinate-based gradient vector to image coordinate system at first? Thank you. Qiqi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101025/ddec29ba/attachment.html From katja at bilkent.edu.tr Mon Oct 25 02:43:32 2010 From: katja at bilkent.edu.tr (Katja Doerschner) Date: Mon, 25 Oct 2010 09:43:32 +0300 Subject: [Mristudio-users] artifact Message-ID: Hi, (my initial post got stuck with the moderator because I attached an example image, sorry)-- I am inspecting my DTI data and find that for some gradient directions (almost 10 out of 30) a hole-like artifact (intensity drop out) near central sulcus (very superior) appears. I am attaching an example from a DTI studio screenshot and the b0 image as a reference. The images were acquired with a 3 Siemens Magnetom, 50 axial slices, slice thickness 3mm, TR 6400ms, TE 88 ms, 4 averages, FOV 128 x 128; Grappa, Accel. Fact 2, 30 gradient directions, Phase Enc Direction A->P, b value 800, the patient was anesthetized. I also think that there is quite a bit of b0 distortion (around inferior temporal lobes) despite parallel imaging. My questions are: 1) what causes these artifacts (I have seen them in other scans/patients at different locations, e.g. posterior tip of the occipital lobe) - could it be the effect of a large blood vessel or other kinds of motion)? 2) How can I avoid such artifacts? 3) Is there any way of 'saving' the data - other than throwing those images out 4) If I have to remove these images - how will that affect the tensor calculation/FA maps/fibertracking? Thank you very much. Katja -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101025/d98d1115/attachment.html From salvador.castaneda at med.uni-tuebingen.de Mon Oct 25 04:00:15 2010 From: salvador.castaneda at med.uni-tuebingen.de (Castaneda, Salvador) Date: Mon, 25 Oct 2010 10:00:15 +0200 Subject: [Mristudio-users] Need GE 3 tesla 25 direction DTI gradient tableplease, thanks In-Reply-To: References: <01150B9F5C05274F8013B909B04790E4D7CC9BC5AF@VEXCCR03.phsabc.ehcnet.ca> <01150B9F5C05274F8013B909B04790E4D7CC9BC5B1@VEXCCR03.phsabc.ehcnet.ca> <44AE0C01-00AE-4E7D-A1E9-AF3CF65E6CB5@mri.jhu.edu> Message-ID: <0AC64F4CB253074799B64FF8F0772D350126C635@azex2003.raddiag.med.uni-tuebingen.de> There in the header, i think ________________________________ Von: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] Im Auftrag von Wu, Joseph Gesendet: Freitag, 22. Oktober 2010 19:15 An: DTI Studio, ROI Editor, DiffeoMap Questions/Support Betreff: [Mristudio-users] Need GE 3 tesla 25 direction DTI gradient tableplease, thanks Hi Does somebody have GE 3 tesla 25 direction DTI gradient table that they can forward to : jcwu at uci.edu? That would be greatly appreciated. Thanks, Joe From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Xu Li Sent: Thursday, October 21, 2010 8:18 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with gradients Dear Susumu, I have a quick question about the gradient table I got from the gradient_table_creator It gives me a table with the [0 0 0] and [100 100 100] at the bottom which seems to be different than those sample gradient table I have from DTI_studio. Should I just move the [0 0 0] to the top? Or the 3T Philips systems do the b0 scan at the end instead of at the beginning now? Thanks! Xu On Oct 20, 2010, at 10:19 PM, susumu mori wrote: Hi Jill, I'm second to SC. When you are using Philips, even if you thought that you are using exactly the same parameters, you could end up in two different types of the gradient tables; overplus on and off. This is not recorded in the beginning of PAR file. So my suggestion is, try the "overplus on" option of the table calculator. Also, if you find that you used "overplus on", you have to type in the oblique angle information in the calculator. The angle information is in the PAR file. The reason you didn't get the tractography right is most likely due to "+/-" signs of the gradient table you used. You can test "x/y/z flip" function of the tractography to test it. The best way is to use the gradient calculator, which should be able to sort out all the issues. Susumu On Tue, Oct 19, 2010 at 4:52 PM, Zwicker, Jill wrote: Further to this message, the ROI values I get are consistent with the previous scans, so it is just the fiber tracking that I am suspicious of... Thanks! ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Zwicker, Jill [JZwicker at cw.bc.ca] Sent: October 19, 2010 1:26 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with gradients Hi Susumu and SC, You previously helped me with a tensor calc issue (see below). I have since used the gradient calculator and obtained more RAM, and have successfully analyzed two scans. However, the remaining scans are not processing properly (i.e., I do not get a proper colour map). In looking at the PAR files, the parameters are the same as the first two scans, with the exception of the rescale and scale slopes, window center and widths, and diffision parameters (nothing that changes what I enter to the online gradient table calculator). Since the gradient table I was using didn't work for successive scans, I took the gradients from the PAR file. This seemed to work, but the colours were reversed, so I switched coloumns around and got a seemingly accurate colour map. However, when I tried to fiber track, the CST seems too short and the values are not consistent with what I obtained in the previous 2 scans. So...I am unsure why the previous gradient table didn't work and I don't think my trial and error method of getting a colour map is accurate. I would be happy to send you the PAR files (off the listserv) if that would help. Thank you in advance for your guidance. Jill ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [susumu at mri.jhu.edu] Sent: September 1, 2010 6:25 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc I suspect memory problem. Please use stricter threshold (like FA>0.3 and angle <30, for example) to see if it works. If it works, then it's memory problem (I mean, you need more memory). You can also save eigenvector0 and FA, close DtiStudio, and redo fiber tracking using the saved file. If you start from tensor calculation, you have all the raw data in your memory. 32-bit operating system can allocate only 1-1.5GB memory. 64bit is much better. susumu On Wed, Sep 1, 2010 at 2:55 PM, Zwicker, Jill wrote: Thank you so much! After some trial and error, I figured out the correct gradient table. I can now get a beautiful colour map, but I have a new problem. The program crashes everytime I try to do fibre tracking. Any suggestions? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, September 01, 2010 10:56 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] problems with tensor calc Use the following link for the gradient table calculation. You need to get some information required to fill in from Par file of your data. If your data is not in ParRec format, get it first. http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html -SC. On Wed, Sep 1, 2010 at 1:46 PM, Zwicker, Jill wrote: > Hi DTI Studio users, > > I am relatively new to DTI studio and have been using successfully to do > tractography on infant brain data collected on a Seimens. I am now trying to > analyze child brain data collected on a Philips. I can get a clear image, > but as soon as I try a tensor calculation, the image quality degrades > significantly (no matter what the background noise level I set it to). I > made gradient tables from the PAR file (forwards and backwards) and also > flipped the z as the tutorial suggests. Any suggestions on how I can solve > this problem? > > Thanks for your help. > > > > Jill Zwicker, PhD, OT(C) > > Postdoctoral Fellow > > Child & Family Research Institute > > Developmental Neurosciences & Child Health > > L408 - 4480 Oak Street > > Vancouver, BC V6H 3V4 > > Phone: 604-875-2000 ext 6805 > > Fax: 604-875-3569 > > jzwicker at cw.bc.ca > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org ________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101025/be69327a/attachment-0001.html From susumu at mri.jhu.edu Mon Oct 25 07:43:03 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 25 Oct 2010 07:43:03 -0400 Subject: [Mristudio-users] artifact In-Reply-To: References: Message-ID: Hi Katja, It is difficult to say anything without looking at the images. Usually if you find a localized signal drop, that is due to motion. However, they appear typically around the 4th ventricle and rarely around the central sulcus. Also, 10 out of 30 seem too many. Siemens had some issues in the past with signal drop usually in the occipital lobe. I thought you can attach a small file with some screenshots? > My questions are: 1) what causes these artifacts (I have seen them in other > scans/patients at different locations, e.g. posterior tip of the occipital > lobe) - could it be the effect of a large blood vessel or other kinds of > motion)? > > I have to see the images. If you want, you can upload your data to our ftp site. 2) How can I avoid such artifacts? > > see above. > 3) Is there any way of 'saving' the data - other than throwing those images > out > > 10 out of 30 seem too many to save. Usually the artifacts are linked to a particular gradient axis; for example, whenever X axis is applied, the artifact appears. If so, you lose all X gradient orientations and the data can't be saved. > 4) If I have to remove these images - how will that affect the tensor > calculation/FA maps/fibertracking? > > see above > > Thank you very much. > Katja > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101025/efa83b96/attachment.html From katja at bilkent.edu.tr Mon Oct 25 07:58:47 2010 From: katja at bilkent.edu.tr (Katja Doerschner) Date: Mon, 25 Oct 2010 14:58:47 +0300 Subject: [Mristudio-users] artifact In-Reply-To: References: Message-ID: <0795AC1E-4EF7-4210-8149-E2F06DF6BBFF@bilkent.edu.tr> Thank you for your response, Susumu. I am attaching an example of the artifact. If Siemens had issues in the past it sounds as if they must have resolved this? Thank you very much. On Oct 25, 2010, at 2:43 PM, susumu mori wrote: > Hi Katja, > > It is difficult to say anything without looking at the images. Usually if you find a localized signal drop, that is due to motion. However, they appear typically around the 4th ventricle and rarely around the central sulcus. Also, 10 out of 30 seem too many. Siemens had some issues in the past with signal drop usually in the occipital lobe. > > I thought you can attach a small file with some screenshots? > > > My questions are: 1) what causes these artifacts (I have seen them in other scans/patients at different locations, e.g. posterior tip of the occipital lobe) - could it be the effect of a large blood vessel or other kinds of motion)? > > I have to see the images. If you want, you can upload your data to our ftp site. > > 2) How can I avoid such artifacts? > > see above. > 3) Is there any way of 'saving' the data - other than throwing those images out > > 10 out of 30 seem too many to save. Usually the artifacts are linked to a particular gradient axis; for example, whenever X axis is applied, the artifact appears. If so, you lose all X gradient orientations and the data can't be saved. > > 4) If I have to remove these images - how will that affect the tensor calculation/FA maps/fibertracking? > > see above > > Thank you very much. > Katja > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -- Katja Doerschner Assistant Professor Department of Psychology & National Center for Magnetic Resonance Research (UMRAM) Bilkent University Bilkent Cyberpark, C-Blok, 2. Kat http://www.bilkent.edu.tr/~katja/ office: +90 (312) 290 3004 cell: +90 (530) 640 31 33 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101025/638a18e9/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: artifact1.jpg Type: image/jpg Size: 14027 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101025/638a18e9/attachment-0001.jpg From hjiang at jhmi.edu Mon Oct 25 11:02:42 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Mon, 25 Oct 2010 11:02:42 -0400 Subject: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? In-Reply-To: References: Message-ID: <145933A2BE9E4F48AE079A201379BF2F244479C79C@RAD-EXCH1.win.ad.jhu.edu> hi, the gradients are defined on image coordinate system. (x,y,z) is corresponding to (column, row, slice) of the image volume. if the (x,y,z) system is consistent with the patient-coordinate (e.g. LPS, axial slicing), you may direcly apply the gradient vectors into the program. otherwise, you may need to adjust the given-vectors before the tensor calculation. regards, hangyi ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of chichesterchiche [seigeweb at hotmail.com] Sent: Sunday, October 24, 2010 11:26 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? Dear DTIStudio Experts, We know we need to input the gradient table in DTIStudio. However, when doing tensor map calculation, which coordinate system is DTIStudio based on? Is DTIStudio based on DICOM patient coordinate system or image coordinate system? I acquired the DWI images by TOSHIBA MRI and the gradient vectors are based on patient coordiante. Can I input the patient-coordinate-based gradient vector to DTI Studio directly, or do I need to transform the patient-coordinate-based gradient vector to image coordinate system at first? Thank you. Qiqi From susumu at mri.jhu.edu Mon Oct 25 12:19:14 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 25 Oct 2010 12:19:14 -0400 Subject: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? In-Reply-To: References: Message-ID: Hi Qiqi, I want to follow up Hangyi's comment. First of all, we have so many ways to define coordinates and the nomenclature could be also confusing. There are two very clear definition; 1) Image Coordinates: At the very end of data acquisition process, we get an image. The brain could seem upright or tilted. It doesn't matter. We have image X, Y, and Z. We do color-coded visualization (x: red, y: green, z: blue) and fiber tracking in this Image Coordinates. In the end, this is the most important coordinates. Likewise, the gradient table should be defined in this Image Coordinates. If a line of a table says, [1, 0, 0], this should be a gradient along the first axis of the image matrix (= image X). 2) Physical (gradient hardware) Coordinates: The very beginning of the coordinate system in the data acquisition process is the Physical Coordinates. This is there even before we put a subject. It's a physical entity. In this coordinate, gradient [1, 0, 0] means, "apply X gradient hardware". Usually, difference between Image and Physical Coordinates is only permutation. For example, X hardware gradient (Physical [1, 0, 0]) could be Image Y (Image [0, 1, 0]) depending on image prescription. However, things get complicated once you use oblique imaging as will be discussed later. In addition, there are two more ways; 3) Patient Coordinates: I believe that this is defined by the parameters we prescribe in the console. FH is foot-head, RL is right-left, and IS is inferior-superior. This tells overall orientation of the human body. By specifying these, we can link the Physical Coordinates and the patient position. For example, if we put a patient in head-first, face-up, and axial imaging, RL aligns to X gradient, FH to Z, and IS to Y gradient systems. Note that Patient Coordinates are not really anatomical coordinates. For example, even if we specify which is the RL orientation, the actual patient RL anatomy could be tilted. The exact anatomical RL axis is not considered here. Patient Coordinates just define the overall patient position. 4) Phase/Frequency/Slice orientation: This defines axial/coronal/sagittal image orientations. You don't have to worry all these unless you use oblique imaging. As soon as oblique angles are introduced, then these coordinate systems start to dissociate and things get very complicated. Please correct me if I'm wrong, but I believe Physical and Patient coordinates are always aligned within the relationship of permutation. Image Coordinates and Phase/Frequency/Slice are aligned within the relationship of permutation. Between these two groups, we need coordinate conversion calculation as soon as imaging plane is tilted (oblique imaging). Important questions are; 1) Which coordinate system DtiStudio uses? A: Always Image Coordinates. Gradient tables have to be in Image Coordinates. 2) Which coordinate system the vendor-provided gradient tables are? A: It depends. GE and Philips (gradient overplus = off) dynamically adjust the gradient table such that the gradient tables always follow the Image Coordinates. Namely, you can use the table as is no matter what the oblique angles are. A: For Siemens and Philips (gradient overplus = on), the gradient tables remain in Physical Coordinates. That means, you have to recalculate the gradient table based on oblique angles you used before fed into DtiStudio. For Siemens you can click "consider rotation if applicable" checkbox (if you are using Mosaic). For Philips, you can use a gradient table calculate at http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html. A: I believe Toshiba uses the GE way so that you don't need table recalculation based on oblique angles, but not 100% sure. 3) Which coordinate systems DICOM/Mosaic headers use? A: I am not 100% sure but so far our experience says, "Physical Coordinates". DtiStudio has a function to extract a gradient table from certain DICOM/Mosaic files. When they are extracted, they seem in Physical Coordinates. That means, you have to rotate them based on oblique angles ("consider rotation" needs to be checked). 4) How can I be sure if I'm doing it correctly? A: Please do the following test; a> Scan a subject in a regular way. Acquire one DTI dataset without any oblique angles. b> Tile the image plane severely, maybe 30-40 degree. Acquire one DTI dataset. c> Ask the subject to rotate the brain severely, maybe 30-40 degree. Acquire one DTI without oblique angles. d> Tile the image plane so that the brain looks upright. Acquire one DTI dataset. If everything is working correctly, in all these dataset images should look right; Image a and d: The brain looks upright. the corpus callosum is red at the mid-sagittal. All color should look symmetric. Image b and c: The brain looks tilted. The color of the corpus callosum do not look symmetric. All images: the fiber tracking should appear the same in 3D view. Simply put an ROI in the genu of the corpus callosum, and you can immediately tell if they look the same or something is not working Hope this helps. Susumu 2010/10/24 chichesterchiche > Dear DTIStudio Experts, > > We know we need to input the gradient table in DTIStudio. However, > when doing tensor map calculation, which coordinate system is DTIStudio > based on? Is DTIStudio based on DICOM patient coordinate system or image > coordinate system? I acquired the DWI images by TOSHIBA MRI and the gradient > vectors are based on patient coordiante. Can I input the > patient-coordinate-based gradient vector to DTI Studio directly, or do I > need to transform the patient-coordinate-based gradient vector to image > coordinate system at first? > > Thank you. > > Qiqi > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101025/db51127f/attachment.html From seigeweb at hotmail.com Mon Oct 25 23:20:49 2010 From: seigeweb at hotmail.com (chichesterchiche) Date: Tue, 26 Oct 2010 03:20:49 +0000 Subject: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F244479C79C@RAD-EXCH1.win.ad.jhu.edu> References: <145933A2BE9E4F48AE079A201379BF2F244479C79C@RAD-EXCH1.win.ad.jhu.edu> Message-ID: Hi Hangyi, Thank you for your timely reply. It is clear now. So, I need to transform patient-coordinate based gradient vector to image coordinate space, then input them to the DTI Studio. Qiqi > Date: Mon, 25 Oct 2010 11:02:42 -0400 > From: hjiang at jhmi.edu > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? > > hi, > > the gradients are defined on image coordinate system. (x,y,z) is corresponding to (column, row, slice) of the image volume. if the (x,y,z) system is consistent with the patient-coordinate (e.g. LPS, axial slicing), you may direcly apply the gradient vectors into the program. otherwise, you may need to adjust the given-vectors before the tensor calculation. > > regards, > > hangyi > > > > > > ________________________________ > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of chichesterchiche [seigeweb at hotmail.com] > Sent: Sunday, October 24, 2010 11:26 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? > > Dear DTIStudio Experts, > > We know we need to input the gradient table in DTIStudio. However, when doing tensor map calculation, which coordinate system is DTIStudio based on? Is DTIStudio based on DICOM patient coordinate system or image coordinate system? I acquired the DWI images by TOSHIBA MRI and the gradient vectors are based on patient coordiante. Can I input the patient-coordinate-based gradient vector to DTI Studio directly, or do I need to transform the patient-coordinate-based gradient vector to image coordinate system at first? > > Thank you. > > Qiqi > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101026/0cb8a224/attachment.html From seigeweb at hotmail.com Tue Oct 26 01:32:21 2010 From: seigeweb at hotmail.com (chichesterchiche) Date: Tue, 26 Oct 2010 05:32:21 +0000 Subject: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? In-Reply-To: References: Message-ID: Dear Mori-san, Thank you so much for your detailed comments. It really helps. Usually, I use DICOM patient coordiante and image coordinate spaces. Now, I need to process many oblique image volumes, such as coronal or saggital, or any oblique image volumes by DtiStudio. I confirmed with TOSHIBA MRI vendor. They said the gradient vector acquired by my current TOSHIBA MRI scanner is based on patient coordinate. By your reply, it is very clear that I need to transform the gradient vector from patient to image coordinates by the image orientation (DICOM TAG: 0020,0037), and then input them to DtiStudio. Let us suppose this transform matrix is MT. And I think that during tensor calcuation, this transform MT will affect eigen vector and its derived color map and fiber tracking results, however, this transform MT will not affect eigen value. So, there are two methods to apply this transform MT. 1> One is to apply MT to gradient vector and then input this new gradient table to DtiStudio to do tensor calculation. Then, we can get correct eigen value and eigen vector map images. 2> Another is to use the patient-coordinate-based gradient vector to call DtiStudio to do tensor calculation directly and then apply MT to the generated eigen vector and color map. I think that both of methods can get the same results. Is my understanding correct? > > That means, you have to rotate them based on oblique angles ("consider rotation" needs to be checked). > For DICOM images, I will try to check ON "consider rotation" in DtiStudio. Thank you for your information. Thank you for providing the method to verify the results. I will use your proposed method to verify whether it is correct or not. Sincerely, Qiqi Date: Mon, 25 Oct 2010 12:19:14 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org; xli16 at jhmi.edu Subject: Re: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? Hi Qiqi, I want to follow up Hangyi's comment. First of all, we have so many ways to define coordinates and the nomenclature could be also confusing. There are two very clear definition; 1) Image Coordinates: At the very end of data acquisition process, we get an image. The brain could seem upright or tilted. It doesn't matter. We have image X, Y, and Z. We do color-coded visualization (x: red, y: green, z: blue) and fiber tracking in this Image Coordinates. In the end, this is the most important coordinates. Likewise, the gradient table should be defined in this Image Coordinates. If a line of a table says, [1, 0, 0], this should be a gradient along the first axis of the image matrix (= image X). 2) Physical (gradient hardware) Coordinates: The very beginning of the coordinate system in the data acquisition process is the Physical Coordinates. This is there even before we put a subject. It's a physical entity. In this coordinate, gradient [1, 0, 0] means, "apply X gradient hardware". Usually, difference between Image and Physical Coordinates is only permutation. For example, X hardware gradient (Physical [1, 0, 0]) could be Image Y (Image [0, 1, 0]) depending on image prescription. However, things get complicated once you use oblique imaging as will be discussed later. In addition, there are two more ways; 3) Patient Coordinates: I believe that this is defined by the parameters we prescribe in the console. FH is foot-head, RL is right-left, and IS is inferior-superior. This tells overall orientation of the human body. By specifying these, we can link the Physical Coordinates and the patient position. For example, if we put a patient in head-first, face-up, and axial imaging, RL aligns to X gradient, FH to Z, and IS to Y gradient systems. Note that Patient Coordinates are not really anatomical coordinates. For example, even if we specify which is the RL orientation, the actual patient RL anatomy could be tilted. The exact anatomical RL axis is not considered here. Patient Coordinates just define the overall patient position. 4) Phase/Frequency/Slice orientation: This defines axial/coronal/sagittal image orientations. You don't have to worry all these unless you use oblique imaging. As soon as oblique angles are introduced, then these coordinate systems start to dissociate and things get very complicated. Please correct me if I'm wrong, but I believe Physical and Patient coordinates are always aligned within the relationship of permutation. Image Coordinates and Phase/Frequency/Slice are aligned within the relationship of permutation. Between these two groups, we need coordinate conversion calculation as soon as imaging plane is tilted (oblique imaging). Important questions are; 1) Which coordinate system DtiStudio uses? A: Always Image Coordinates. Gradient tables have to be in Image Coordinates. 2) Which coordinate system the vendor-provided gradient tables are? A: It depends. GE and Philips (gradient overplus = off) dynamically adjust the gradient table such that the gradient tables always follow the Image Coordinates. Namely, you can use the table as is no matter what the oblique angles are. A: For Siemens and Philips (gradient overplus = on), the gradient tables remain in Physical Coordinates. That means, you have to recalculate the gradient table based on oblique angles you used before fed into DtiStudio. For Siemens you can click "consider rotation if applicable" checkbox (if you are using Mosaic). For Philips, you can use a gradient table calculate at http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html. A: I believe Toshiba uses the GE way so that you don't need table recalculation based on oblique angles, but not 100% sure. 3) Which coordinate systems DICOM/Mosaic headers use? A: I am not 100% sure but so far our experience says, "Physical Coordinates". DtiStudio has a function to extract a gradient table from certain DICOM/Mosaic files. When they are extracted, they seem in Physical Coordinates. That means, you have to rotate them based on oblique angles ("consider rotation" needs to be checked). 4) How can I be sure if I'm doing it correctly? A: Please do the following test; a> Scan a subject in a regular way. Acquire one DTI dataset without any oblique angles. b> Tile the image plane severely, maybe 30-40 degree. Acquire one DTI dataset. c> Ask the subject to rotate the brain severely, maybe 30-40 degree. Acquire one DTI without oblique angles. d> Tile the image plane so that the brain looks upright. Acquire one DTI dataset. If everything is working correctly, in all these dataset images should look right; Image a and d: The brain looks upright. the corpus callosum is red at the mid-sagittal. All color should look symmetric. Image b and c: The brain looks tilted. The color of the corpus callosum do not look symmetric. All images: the fiber tracking should appear the same in 3D view. Simply put an ROI in the genu of the corpus callosum, and you can immediately tell if they look the same or something is not working Hope this helps. Susumu 2010/10/24 chichesterchiche Dear DTIStudio Experts, We know we need to input the gradient table in DTIStudio. However, when doing tensor map calculation, which coordinate system is DTIStudio based on? Is DTIStudio based on DICOM patient coordinate system or image coordinate system? I acquired the DWI images by TOSHIBA MRI and the gradient vectors are based on patient coordiante. Can I input the patient-coordinate-based gradient vector to DTI Studio directly, or do I need to transform the patient-coordinate-based gradient vector to image coordinate system at first? Thank you. Qiqi _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101026/a53b0857/attachment-0001.html From hjiang at jhmi.edu Tue Oct 26 09:40:39 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Tue, 26 Oct 2010 09:40:39 -0400 Subject: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? In-Reply-To: References: Message-ID: <145933A2BE9E4F48AE079A201379BF2F244479C79F@RAD-EXCH1.win.ad.jhu.edu> hi, Qiqi patient coordinate doesn't have same meaning as scanner's system all the time. please double check and make sure about it (following Dr. Mori's suggestion). if the gradients are given in scanner's system and there are patient orientation information in the DICOM header(some dicom files don't have such information), you can try to enable the "rotate the gradients" option in the open-dicom file dialog to see how does it work. if the gradients are wrong, it will affect the all the tensor calculation results, including tensor matrix, eigen vectors and eigen values. this is different with the gradient-sign flipping issue. you can using the original gradients for tensor calcualtion and then applying rotation transform to the results. however, please be careful, this transformation will be applied to tensor space, which is not that easy as the vector space. so, it is better to rotate the gradients before tensor calculation. regards, hangyi ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of chichesterchiche [seigeweb at hotmail.com] Sent: Tuesday, October 26, 2010 1:32 AM To: mristudio mristudio; Xin Li Subject: Re: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? Dear Mori-san, Thank you so much for your detailed comments. It really helps. Usually, I use DICOM patient coordiante and image coordinate spaces. Now, I need to process many oblique image volumes, such as coronal or saggital, or any oblique image volumes by DtiStudio. I confirmed with TOSHIBA MRI vendor. They said the gradient vector acquired by my current TOSHIBA MRI scanner is based on patient coordinate. By your reply, it is very clear that I need to transform the gradient vector from patient to image coordinates by the image orientation (DICOM TAG: 0020,0037), and then input them to DtiStudio. Let us suppose this transform matrix is MT. And I think that during tensor calcuation, this transform MT will affect eigen vector and its derived color map and fiber tracking results, however, this transform MT will not affect eigen value. So, there are two methods to apply this transform MT. 1> One is to apply MT to gradient vector and then input this new gradient table to DtiStudio to do tensor calculation. Then, we can get correct eigen value and eigen vector map images. 2> Another is to use the patient-coordinate-based gradient vector to call DtiStudio to do tensor calculation directly and then apply MT to the generated eigen vector and color map. I think that both of methods can get the same results. Is my understanding correct? > > That means, you have to rotate them based on oblique angles ("consider rotation" needs to be checked). > For DICOM images, I will try to check ON "consider rotation" in DtiStudio. Thank you for your information. Thank you for providing the method to verify the results. I will use your proposed method to verify whether it is correct or not. Sincerely, Qiqi ________________________________ Date: Mon, 25 Oct 2010 12:19:14 -0400 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org; xli16 at jhmi.edu Subject: Re: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? Hi Qiqi, I want to follow up Hangyi's comment. First of all, we have so many ways to define coordinates and the nomenclature could be also confusing. There are two very clear definition; 1) Image Coordinates: At the very end of data acquisition process, we get an image. The brain could seem upright or tilted. It doesn't matter. We have image X, Y, and Z. We do color-coded visualization (x: red, y: green, z: blue) and fiber tracking in this Image Coordinates. In the end, this is the most important coordinates. Likewise, the gradient table should be defined in this Image Coordinates. If a line of a table says, [1, 0, 0], this should be a gradient along the first axis of the image matrix (= image X). 2) Physical (gradient hardware) Coordinates: The very beginning of the coordinate system in the data acquisition process is the Physical Coordinates. This is there even before we put a subject. It's a physical entity. In this coordinate, gradient [1, 0, 0] means, "apply X gradient hardware". Usually, difference between Image and Physical Coordinates is only permutation. For example, X hardware gradient (Physical [1, 0, 0]) could be Image Y (Image [0, 1, 0]) depending on image prescription. However, things get complicated once you use oblique imaging as will be discussed later. In addition, there are two more ways; 3) Patient Coordinates: I believe that this is defined by the parameters we prescribe in the console. FH is foot-head, RL is right-left, and IS is inferior-superior. This tells overall orientation of the human body. By specifying these, we can link the Physical Coordinates and the patient position. For example, if we put a patient in head-first, face-up, and axial imaging, RL aligns to X gradient, FH to Z, and IS to Y gradient systems. Note that Patient Coordinates are not really anatomical coordinates. For example, even if we specify which is the RL orientation, the actual patient RL anatomy could be tilted. The exact anatomical RL axis is not considered here. Patient Coordinates just define the overall patient position. 4) Phase/Frequency/Slice orientation: This defines axial/coronal/sagittal image orientations. You don't have to worry all these unless you use oblique imaging. As soon as oblique angles are introduced, then these coordinate systems start to dissociate and things get very complicated. Please correct me if I'm wrong, but I believe Physical and Patient coordinates are always aligned within the relationship of permutation. Image Coordinates and Phase/Frequency/Slice are aligned within the relationship of permutation. Between these two groups, we need coordinate conversion calculation as soon as imaging plane is tilted (oblique imaging). Important questions are; 1) Which coordinate system DtiStudio uses? A: Always Image Coordinates. Gradient tables have to be in Image Coordinates. 2) Which coordinate system the vendor-provided gradient tables are? A: It depends. GE and Philips (gradient overplus = off) dynamically adjust the gradient table such that the gradient tables always follow the Image Coordinates. Namely, you can use the table as is no matter what the oblique angles are. A: For Siemens and Philips (gradient overplus = on), the gradient tables remain in Physical Coordinates. That means, you have to recalculate the gradient table based on oblique angles you used before fed into DtiStudio. For Siemens you can click "consider rotation if applicable" checkbox (if you are using Mosaic). For Philips, you can use a gradient table calculate at http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html. A: I believe Toshiba uses the GE way so that you don't need table recalculation based on oblique angles, but not 100% sure. 3) Which coordinate systems DICOM/Mosaic headers use? A: I am not 100% sure but so far our experience says, "Physical Coordinates". DtiStudio has a function to extract a gradient table from certain DICOM/Mosaic files. When they are extracted, they seem in Physical Coordinates. That means, you have to rotate them based on oblique angles ("consider rotation" needs to be checked). 4) How can I be sure if I'm doing it correctly? A: Please do the following test; a> Scan a subject in a regular way. Acquire one DTI dataset without any oblique angles. b> Tile the image plane severely, maybe 30-40 degree. Acquire one DTI dataset. c> Ask the subject to rotate the brain severely, maybe 30-40 degree. Acquire one DTI without oblique angles. d> Tile the image plane so that the brain looks upright. Acquire one DTI dataset. If everything is working correctly, in all these dataset images should look right; Image a and d: The brain looks upright. the corpus callosum is red at the mid-sagittal. All color should look symmetric. Image b and c: The brain looks tilted. The color of the corpus callosum do not look symmetric. All images: the fiber tracking should appear the same in 3D view. Simply put an ROI in the genu of the corpus callosum, and you can immediately tell if they look the same or something is not working Hope this helps. Susumu 2010/10/24 chichesterchiche > Dear DTIStudio Experts, We know we need to input the gradient table in DTIStudio. However, when doing tensor map calculation, which coordinate system is DTIStudio based on? Is DTIStudio based on DICOM patient coordinate system or image coordinate system? I acquired the DWI images by TOSHIBA MRI and the gradient vectors are based on patient coordiante. Can I input the patient-coordinate-based gradient vector to DTI Studio directly, or do I need to transform the patient-coordinate-based gradient vector to image coordinate system at first? Thank you. Qiqi _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From Madhura.Ingalhalikar at uphs.upenn.edu Tue Oct 26 12:01:32 2010 From: Madhura.Ingalhalikar at uphs.upenn.edu (Ingalhalikar, Madhura) Date: Tue, 26 Oct 2010 12:01:32 -0400 Subject: [Mristudio-users] 3D reconstruction/rendering of fibers Message-ID: <21B49EE396CA9D48883EF763F60B25510C4D7368@uphsmbx1.UPHS.PENNHEALTH.PRV> Is there any way to perform 3D reconstruction/rendering of the fiber tracts using DTI studio the way you can do it in Slicer. If not is there any plugin to convert fibers to vtk polyline format? Thanks, Madhura The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message. From susumu at mri.jhu.edu Tue Oct 26 12:09:37 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 26 Oct 2010 12:09:37 -0400 Subject: [Mristudio-users] 3D reconstruction/rendering of fibers In-Reply-To: <21B49EE396CA9D48883EF763F60B25510C4D7368@uphsmbx1.UPHS.PENNHEALTH.PRV> References: <21B49EE396CA9D48883EF763F60B25510C4D7368@uphsmbx1.UPHS.PENNHEALTH.PRV> Message-ID: I believe "DTI3DMRI" is a 3D visualization program that can read and display the fiber data stored as Amira format. You can download and try from www.mristudio.org. On Tue, Oct 26, 2010 at 12:01 PM, Ingalhalikar, Madhura < Madhura.Ingalhalikar at uphs.upenn.edu> wrote: > Is there any way to perform 3D reconstruction/rendering of the fiber tracts > using DTI studio the way you can do it in Slicer. If not is there any plugin > to convert fibers to vtk polyline format? > > Thanks, > > Madhura > > > The information contained in this e-mail message is intended only for the > personal and confidential use of the recipient(s) named above. If the reader > of this message is not the intended recipient or an agent responsible for > delivering it to the intended recipient, you are hereby notified that you > have received this document in error and that any review, dissemination, > distribution, or copying of this message is strictly prohibited. If you have > received this communication in error, please notify us immediately by > e-mail, and delete the original message. > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101026/0c2602e8/attachment.html From susumu at mri.jhu.edu Tue Oct 26 18:42:08 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 26 Oct 2010 18:42:08 -0400 Subject: [Mristudio-users] artifact In-Reply-To: <0795AC1E-4EF7-4210-8149-E2F06DF6BBFF@bilkent.edu.tr> References: <0795AC1E-4EF7-4210-8149-E2F06DF6BBFF@bilkent.edu.tr> Message-ID: Hmmmm, please check the following; List up the number of DWIs that are affected (e.g. 4th, 8th, 9th, etc) Look at the gradient table at the listed number. Try to find if the identified table lines always contain gradient values of X, Y, or Z. Also please show us the color map. For example, if this artifact shows up every time you apply X, the color map should become red for the area of the artifact. If you find this type of correlation between the applied gradient and artifacts, this is not a typical motion artifacts. You should contact to the manufacturer. On Mon, Oct 25, 2010 at 7:58 AM, Katja Doerschner wrote: > Thank you for your response, Susumu. > > I am attaching an example of the artifact. > If Siemens had issues in the past it sounds as if they must have resolved > this? > Thank you very much. > > > > On Oct 25, 2010, at 2:43 PM, susumu mori wrote: > > Hi Katja, > > It is difficult to say anything without looking at the images. Usually if > you find a localized signal drop, that is due to motion. However, they > appear typically around the 4th ventricle and rarely around the central > sulcus. Also, 10 out of 30 seem too many. Siemens had some issues in the > past with signal drop usually in the occipital lobe. > > I thought you can attach a small file with some screenshots? > > >> My questions are: 1) what causes these artifacts (I have seen them in >> other scans/patients at different locations, e.g. posterior tip of the >> occipital lobe) - could it be the effect of a large blood vessel or other >> kinds of motion)? >> > > I have to see the images. If you want, you can upload your data to our > ftp site. > > 2) How can I avoid such artifacts? >> > > see above. > >> 3) Is there any way of 'saving' the data - other than throwing those >> images out >> > > 10 out of 30 seem too many to save. Usually the artifacts are linked to a > particular gradient axis; for example, whenever X axis is applied, the > artifact appears. If so, you lose all X gradient orientations and the data > can't be saved. > > >> 4) If I have to remove these images - how will that affect the tensor >> calculation/FA maps/fibertracking? >> > > see above > >> >> Thank you very much. >> Katja >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > -- > > Katja Doerschner > Assistant Professor > Department of Psychology > & National Center for > Magnetic Resonance Research (UMRAM) > Bilkent University > Bilkent Cyberpark, C-Blok, 2. Kat > http://www.bilkent.edu.tr/~katja/ > office: +90 (312) 290 3004 > cell: +90 (530) 640 31 33 > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101026/ea112afa/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/jpg Size: 14027 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101026/ea112afa/attachment-0001.jpg From kongyouyong at gmail.com Tue Oct 26 20:27:29 2010 From: kongyouyong at gmail.com (=?GB2312?B?09PTwr/X?=) Date: Wed, 27 Oct 2010 08:27:29 +0800 Subject: [Mristudio-users] 3D reconstruction/rendering of fibers In-Reply-To: <21B49EE396CA9D48883EF763F60B25510C4D7368@uphsmbx1.UPHS.PENNHEALTH.PRV> References: <21B49EE396CA9D48883EF763F60B25510C4D7368@uphsmbx1.UPHS.PENNHEALTH.PRV> Message-ID: Dear Madhura, I think you can try the TrackVis software to display the fibers. Best regards, Youyong Kong 2010/10/27 Ingalhalikar, Madhura > Is there any way to perform 3D reconstruction/rendering of the fiber tracts > using DTI studio the way you can do it in Slicer. If not is there any plugin > to convert fibers to vtk polyline format? > > Thanks, > > Madhura > > > The information contained in this e-mail message is intended only for the > personal and confidential use of the recipient(s) named above. If the reader > of this message is not the intended recipient or an agent responsible for > delivering it to the intended recipient, you are hereby notified that you > have received this document in error and that any review, dissemination, > distribution, or copying of this message is strictly prohibited. If you have > received this communication in error, please notify us immediately by > e-mail, and delete the original message. > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101027/345dc52b/attachment.html From katja at bilkent.edu.tr Wed Oct 27 09:17:58 2010 From: katja at bilkent.edu.tr (Katja Doerschner) Date: Wed, 27 Oct 2010 16:17:58 +0300 Subject: [Mristudio-users] artifact In-Reply-To: References: <0795AC1E-4EF7-4210-8149-E2F06DF6BBFF@bilkent.edu.tr> Message-ID: <8904183A-94BE-4ABC-8494-E205FE59C1D1@bilkent.edu.tr> > > For example, if this artifact shows up every time you apply X, the color map should become red for the area of the artifact. > > If you find this type of correlation between the applied gradient and artifacts, this is not a typical motion artifacts. You should contact to the manufacturer. Yes, this is exactly what happens. Our Siemens technician is now looking into this. Thank you very much for helping me pinpoint the problem. Best, katja > > On Mon, Oct 25, 2010 at 7:58 AM, Katja Doerschner wrote: > Thank you for your response, Susumu. > > I am attaching an example of the artifact. > If Siemens had issues in the past it sounds as if they must have resolved this? > Thank you very much. > > > > > On Oct 25, 2010, at 2:43 PM, susumu mori wrote: > >> Hi Katja, >> >> It is difficult to say anything without looking at the images. Usually if you find a localized signal drop, that is due to motion. However, they appear typically around the 4th ventricle and rarely around the central sulcus. Also, 10 out of 30 seem too many. Siemens had some issues in the past with signal drop usually in the occipital lobe. >> >> I thought you can attach a small file with some screenshots? >> >> >> My questions are: 1) what causes these artifacts (I have seen them in other scans/patients at different locations, e.g. posterior tip of the occipital lobe) - could it be the effect of a large blood vessel or other kinds of motion)? >> > I have to see the images. If you want, you can upload your data to our ftp site. >> >> 2) How can I avoid such artifacts? >> > see above. >> 3) Is there any way of 'saving' the data - other than throwing those images out >> > 10 out of 30 seem too many to save. Usually the artifacts are linked to a particular gradient axis; for example, whenever X axis is applied, the artifact appears. If so, you lose all X gradient orientations and the data can't be saved. >> >> 4) If I have to remove these images - how will that affect the tensor calculation/FA maps/fibertracking? >> > see above >> >> Thank you very much. >> Katja >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > -- > > Katja Doerschner > Assistant Professor > Department of Psychology > & National Center for > Magnetic Resonance Research (UMRAM) > Bilkent University > Bilkent Cyberpark, C-Blok, 2. Kat > http://www.bilkent.edu.tr/~katja/ > office: +90 (312) 290 3004 > cell: +90 (530) 640 31 33 > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -- Katja Doerschner Assistant Professor Department of Psychology & National Center for Magnetic Resonance Research (UMRAM) Bilkent University Bilkent Cyberpark, C-Blok, 2. Kat http://www.bilkent.edu.tr/~katja/ office: +90 (312) 290 3004 cell: +90 (530) 640 31 33 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101027/eb4488ba/attachment.html From xuli at mri.jhu.edu Wed Oct 27 10:44:02 2010 From: xuli at mri.jhu.edu (Xu Li) Date: Wed, 27 Oct 2010 10:44:02 -0400 Subject: [Mristudio-users] Questions about frames In-Reply-To: References: Message-ID: Dear Susumu and Hangyi, I have one quick questions about the eigenvectors we can get from DTI-Studio. Are they defined in the image frame or the lab frame? I understand that the gradient is applied according to the image frame but the correct gradient table should be defined in lab frame (i.e. if we acquire 0 angulation data, the very first gradient vector would be [0 0 1] or some thing like that). But after we do the tensor fitting and eigenvalue decomposition, are they still in lab frame? I guess it is, but just want to confirm. Thanks! Xu From hjiang at jhmi.edu Wed Oct 27 10:58:12 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Wed, 27 Oct 2010 10:58:12 -0400 Subject: [Mristudio-users] Questions about frames In-Reply-To: References: Message-ID: <145933A2BE9E4F48AE079A201379BF2F244584A123@RAD-EXCH1.win.ad.jhu.edu> the results are based on image frame. in the end, we are doing image analyze, which is based the images in our hand. :) hangyi ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Xu Li [xuli at mri.jhu.edu] Sent: Wednesday, October 27, 2010 10:44 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: [Mristudio-users] Questions about frames Dear Susumu and Hangyi, I have one quick questions about the eigenvectors we can get from DTI-Studio. Are they defined in the image frame or the lab frame? I understand that the gradient is applied according to the image frame but the correct gradient table should be defined in lab frame (i.e. if we acquire 0 angulation data, the very first gradient vector would be [0 0 1] or some thing like that). But after we do the tensor fitting and eigenvalue decomposition, are they still in lab frame? I guess it is, but just want to confirm. Thanks! Xu _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From susumu at mri.jhu.edu Wed Oct 27 11:02:03 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 27 Oct 2010 11:02:03 -0400 Subject: [Mristudio-users] Questions about frames In-Reply-To: References: Message-ID: Lab frame may be used in data acquisition, but in the image analysis world, everything has to be in the image frame. If you don't use oblique imaging, these two frames are the same (aligned). So, you don't have to worry about it. The only freedom left is permutation. For example, [0 0 1] in lab frame (Z gradient), could be image X, Y, or Z, depending on your slice orientations (coronal -> Y, sagittal -> Y, axial -> Z). If you use oblique imaging, lab frame [0 0 1] could be image frame [0, 0.25, 0.97] if the image is 15 degree rotated. In image analysis, you want to use [0, 0.25, 0.97] and usually forget about [0 0 1] because you don't retain the information "15 degree" in image analysis. As long as you throw away (we usually throw away) this "15 degree" information, the image frame you are working on is dissociated from the lab frame. In the end, what you are interested in is brain anatomy, not the absolute orientation of the lab frame, which we don't care. On Wed, Oct 27, 2010 at 10:44 AM, Xu Li wrote: > Dear Susumu and Hangyi, > > I have one quick questions about the eigenvectors we can get from > DTI-Studio. Are they defined in the image frame or the lab frame? I > understand that the gradient is applied according to the image frame but the > correct gradient table should be defined in lab frame (i.e. if we acquire 0 > angulation data, the very first gradient vector would be [0 0 1] or some > thing like that). But after we do the tensor fitting and eigenvalue > decomposition, are they still in lab frame? I guess it is, but just want to > confirm. > > Thanks! > > Xu > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101027/3f8159b4/attachment.html From xuli at mri.jhu.edu Wed Oct 27 11:41:10 2010 From: xuli at mri.jhu.edu (Xu Li) Date: Wed, 27 Oct 2010 11:41:10 -0400 Subject: [Mristudio-users] Questions about frames In-Reply-To: References: Message-ID: <3CB2FCED-44E4-46A2-A089-E8BFD105EA3F@mri.jhu.edu> Thanks a lot for clarifying. One follow up question is how can we transfer them back to the lab frame, which we are interested in for our project. Is there a way we can get the transfer matrix? Or when we transfer from lab frame to the image frame, does the DTI_studio use the rotation order like T = T_RL*T_AP*T_FH? Supposing the T_FH is the rotation matrix defined by the FH angulation in the scanner and etc. Thanks! Xu On Oct 27, 2010, at 11:02 AM, susumu mori wrote: > Lab frame may be used in data acquisition, but in the image analysis world, everything has to be in the image frame. If you don't use oblique imaging, these two frames are the same (aligned). So, you don't have to worry about it. The only freedom left is permutation. For example, [0 0 1] in lab frame (Z gradient), could be image X, Y, or Z, depending on your slice orientations (coronal -> Y, sagittal -> Y, axial -> Z). > > If you use oblique imaging, lab frame [0 0 1] could be image frame [0, 0.25, 0.97] if the image is 15 degree rotated. In image analysis, you want to use [0, 0.25, 0.97] and usually forget about [0 0 1] because you don't retain the information "15 degree" in image analysis. As long as you throw away (we usually throw away) this "15 degree" information, the image frame you are working on is dissociated from the lab frame. In the end, what you are interested in is brain anatomy, not the absolute orientation of the lab frame, which we don't care. > > On Wed, Oct 27, 2010 at 10:44 AM, Xu Li wrote: > Dear Susumu and Hangyi, > > I have one quick questions about the eigenvectors we can get from DTI-Studio. Are they defined in the image frame or the lab frame? I understand that the gradient is applied according to the image frame but the correct gradient table should be defined in lab frame (i.e. if we acquire 0 angulation data, the very first gradient vector would be [0 0 1] or some thing like that). But after we do the tensor fitting and eigenvalue decomposition, are they still in lab frame? I guess it is, but just want to confirm. > > Thanks! > > Xu > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101027/f8421496/attachment.html From ICHORD at email.chop.edu Wed Oct 27 16:17:58 2010 From: ICHORD at email.chop.edu (Ichord, Rebecca) Date: Wed, 27 Oct 2010 16:17:58 -0400 Subject: [Mristudio-users] Questions about frames In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F244584A123@RAD-EXCH1.win.ad.jhu.edu> References: <145933A2BE9E4F48AE079A201379BF2F244584A123@RAD-EXCH1.win.ad.jhu.edu> Message-ID: <3247206BF1134F449D545E5FCA7978B638B00D9AC2@EX7CCRPW04V1.chop.edu> Dear Sirs, I seem to inadvertently have registered to receive your email alerts. Please kindly can you remove my name from your mail list. thx, Rebecca Ichord MD Associate Professor, Neurology University of Pennsylvania School of Medicine Director, Pediatric Stroke Program Dept. Neurology, CTRB 10th Floor Children's Hospital of Philadelphia 3501 Civic Ctr Blvd Philadelphia, PA 19104 Ph. 215-590-4142 Fax 215-590-5120 email: ichord at emailchop.edu ATTN: This email may contain confidential, personal and/or health information (information which may be suject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distributioni by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this email in error, please contact the sender and delete all copies. ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Hangyi Jiang [hjiang at jhmi.edu] Sent: Wednesday, October 27, 2010 10:58 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Questions about frames the results are based on image frame. in the end, we are doing image analyze, which is based the images in our hand. :) hangyi ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Xu Li [xuli at mri.jhu.edu] Sent: Wednesday, October 27, 2010 10:44 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: [Mristudio-users] Questions about frames Dear Susumu and Hangyi, I have one quick questions about the eigenvectors we can get from DTI-Studio. Are they defined in the image frame or the lab frame? I understand that the gradient is applied according to the image frame but the correct gradient table should be defined in lab frame (i.e. if we acquire 0 angulation data, the very first gradient vector would be [0 0 1] or some thing like that). But after we do the tensor fitting and eigenvalue decomposition, are they still in lab frame? I guess it is, but just want to confirm. Thanks! Xu _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From mksarma at gmail.com Wed Oct 27 20:03:32 2010 From: mksarma at gmail.com (manoj sarma) Date: Wed, 27 Oct 2010 17:03:32 -0700 Subject: [Mristudio-users] LDDMM processing Message-ID: Hi, I am new to Diffeomap. Can anyone please tell me how to do LDDMM processing? Thanks, Manoj -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101027/b6e63bda/attachment.html From susumu at mri.jhu.edu Wed Oct 27 20:45:23 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 27 Oct 2010 20:45:23 -0400 Subject: [Mristudio-users] LDDMM processing In-Reply-To: References: Message-ID: There are two great sources of education (well, maybe not that great but good place to start); 1) Video Tutorial at https://www.mristudio.org/wiki/user_manual 2) Getting started at https://www.mristudio.org/wiki/user_manual/diffeomap Then we offer once a month 2-day tutorial. Please be alert for announcement in this mailing list. The information can also be found at https://www.mristudio.org/wiki/Tutorial. All announced tutorial is already full. If you want to reserve a slot in a future tutorial, please send an email to Xin Li (xli16 at jhmi.edu). We'll put you in the waiting list. On Wed, Oct 27, 2010 at 8:03 PM, manoj sarma wrote: > Hi, > > I am new to Diffeomap. Can anyone please tell me how to do LDDMM > processing? > > Thanks, > Manoj > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101027/8dac7e93/attachment.html From fventrice at fleni.org.ar Thu Oct 28 12:07:31 2010 From: fventrice at fleni.org.ar (Fernando Ventrice) Date: Thu, 28 Oct 2010 13:07:31 -0300 Subject: [Mristudio-users] DTI Data question Message-ID: Hi I would like to know why there are several DTIs (31, 41, 51,...) for each individual of the DTI DATA that is on the website. Are they corrected images with different angulation? I measured FA values from different regions and have slight different FA values for the same region. Thank you very much, Fernando Ventrice El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales est? dirigido, pudiendo contener informaci?n legalmente protegida. Queda prohibida la revisi?n, divulgaci?n, publicaci?n, modificaci?n, copia, distribuci?n o acci?n en relaci?n con esta informaci?n, por personas o entidades distintas al destinatario. Si usted, por alguna raz?n, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opini?n de FLENI. http://www.fleni.org.ar From seigeweb at hotmail.com Fri Oct 29 01:06:31 2010 From: seigeweb at hotmail.com (chichesterchiche) Date: Fri, 29 Oct 2010 05:06:31 +0000 Subject: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F244479C79F@RAD-EXCH1.win.ad.jhu.edu> References: <145933A2BE9E4F48AE079A201379BF2F244479C79F@RAD-EXCH1.win.ad.jhu.edu> Message-ID: Dear Hangyi, > so, it is better to rotate the gradients before tensor calculation. > OK. I will follow your suggestion to transform the gradients before tensor calcualtion. Thank you. Sincerely, Qiqi > Date: Tue, 26 Oct 2010 09:40:39 -0400 > From: hjiang at jhmi.edu > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? > > hi, Qiqi > patient coordinate doesn't have same meaning as scanner's system all the time. please double check and make sure about it (following Dr. Mori's suggestion). > > if the gradients are given in scanner's system and there are patient orientation information in the DICOM header(some dicom files don't have such information), you can try to enable the "rotate the gradients" option in the open-dicom file dialog to see how does it work. > > if the gradients are wrong, it will affect the all the tensor calculation results, including tensor matrix, eigen vectors and eigen values. this is different with the gradient-sign flipping issue. > > you can using the original gradients for tensor calcualtion and then applying rotation transform to the results. however, please be careful, this transformation will be applied to tensor space, which is not that easy as the vector space. so, it is better to rotate the gradients before tensor calculation. > > regards, > > hangyi > > > > > > ________________________________ > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of chichesterchiche [seigeweb at hotmail.com] > Sent: Tuesday, October 26, 2010 1:32 AM > To: mristudio mristudio; Xin Li > Subject: Re: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? > > Dear Mori-san, > > Thank you so much for your detailed comments. It really helps. > > Usually, I use DICOM patient coordiante and image coordinate spaces. Now, I need to process many oblique image volumes, such as coronal or saggital, or any oblique image volumes by DtiStudio. > > I confirmed with TOSHIBA MRI vendor. They said the gradient vector acquired by my current TOSHIBA MRI scanner is based on patient coordinate. By your reply, it is very clear that I need to transform the gradient vector from patient to image coordinates by the image orientation (DICOM TAG: 0020,0037), and then input them to DtiStudio. Let us suppose this transform matrix is MT. > > And I think that during tensor calcuation, this transform MT will affect eigen vector and its derived color map and fiber tracking results, however, this transform MT will not affect eigen value. So, there are two methods to apply this transform MT. > > 1> One is to apply MT to gradient vector and then input this new gradient table to DtiStudio to do tensor calculation. Then, we can get correct eigen value and eigen vector map images. > > 2> Another is to use the patient-coordinate-based gradient vector to call DtiStudio to do tensor calculation directly and then apply MT to the generated eigen vector and color map. > > I think that both of methods can get the same results. Is my understanding correct? > > > > > That means, you have to rotate them based on oblique angles ("consider rotation" needs to be checked). > > > For DICOM images, I will try to check ON "consider rotation" in DtiStudio. Thank you for your information. > > Thank you for providing the method to verify the results. I will use your proposed method to verify whether it is correct or not. > > Sincerely, > > Qiqi > > ________________________________ > Date: Mon, 25 Oct 2010 12:19:14 -0400 > From: susumu at mri.jhu.edu > To: mristudio-users at mristudio.org; xli16 at jhmi.edu > Subject: Re: [Mristudio-users] Is DTIStudio based on DICOM patient coordinate system or image coordinate system? > > Hi Qiqi, > > I want to follow up Hangyi's comment. > > First of all, we have so many ways to define coordinates and the nomenclature could be also confusing. There are two very clear definition; > > 1) Image Coordinates: At the very end of data acquisition process, we get an image. The brain could seem upright or tilted. It doesn't matter. We have image X, Y, and Z. We do color-coded visualization (x: red, y: green, z: blue) and fiber tracking in this Image Coordinates. In the end, this is the most important coordinates. Likewise, the gradient table should be defined in this Image Coordinates. If a line of a table says, [1, 0, 0], this should be a gradient along the first axis of the image matrix (= image X). > > 2) Physical (gradient hardware) Coordinates: The very beginning of the coordinate system in the data acquisition process is the Physical Coordinates. This is there even before we put a subject. It's a physical entity. In this coordinate, gradient [1, 0, 0] means, "apply X gradient hardware". > > Usually, difference between Image and Physical Coordinates is only permutation. For example, X hardware gradient (Physical [1, 0, 0]) could be Image Y (Image [0, 1, 0]) depending on image prescription. However, things get complicated once you use oblique imaging as will be discussed later. > > In addition, there are two more ways; > 3) Patient Coordinates: I believe that this is defined by the parameters we prescribe in the console. FH is foot-head, RL is right-left, and IS is inferior-superior. This tells overall orientation of the human body. By specifying these, we can link the Physical Coordinates and the patient position. For example, if we put a patient in head-first, face-up, and axial imaging, RL aligns to X gradient, FH to Z, and IS to Y gradient systems. Note that Patient Coordinates are not really anatomical coordinates. For example, even if we specify which is the RL orientation, the actual patient RL anatomy could be tilted. The exact anatomical RL axis is not considered here. Patient Coordinates just define the overall patient position. > > 4) Phase/Frequency/Slice orientation: This defines axial/coronal/sagittal image orientations. > > You don't have to worry all these unless you use oblique imaging. As soon as oblique angles are introduced, then these coordinate systems start to dissociate and things get very complicated. Please correct me if I'm wrong, but I believe Physical and Patient coordinates are always aligned within the relationship of permutation. Image Coordinates and Phase/Frequency/Slice are aligned within the relationship of permutation. Between these two groups, we need coordinate conversion calculation as soon as imaging plane is tilted (oblique imaging). > > Important questions are; > > 1) Which coordinate system DtiStudio uses? > A: Always Image Coordinates. Gradient tables have to be in Image Coordinates. > 2) Which coordinate system the vendor-provided gradient tables are? > A: It depends. GE and Philips (gradient overplus = off) dynamically adjust the gradient table such that the gradient tables always follow the Image Coordinates. Namely, you can use the table as is no matter what the oblique angles are. > A: For Siemens and Philips (gradient overplus = on), the gradient tables remain in Physical Coordinates. That means, you have to recalculate the gradient table based on oblique angles you used before fed into DtiStudio. For Siemens you can click "consider rotation if applicable" checkbox (if you are using Mosaic). For Philips, you can use a gradient table calculate at http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html. > A: I believe Toshiba uses the GE way so that you don't need table recalculation based on oblique angles, but not 100% sure. > 3) Which coordinate systems DICOM/Mosaic headers use? > A: I am not 100% sure but so far our experience says, "Physical Coordinates". DtiStudio has a function to extract a gradient table from certain DICOM/Mosaic files. When they are extracted, they seem in Physical Coordinates. That means, you have to rotate them based on oblique angles ("consider rotation" needs to be checked). > 4) How can I be sure if I'm doing it correctly? > A: Please do the following test; > a> Scan a subject in a regular way. Acquire one DTI dataset without any oblique angles. > b> Tile the image plane severely, maybe 30-40 degree. Acquire one DTI dataset. > c> Ask the subject to rotate the brain severely, maybe 30-40 degree. Acquire one DTI without oblique angles. > d> Tile the image plane so that the brain looks upright. Acquire one DTI dataset. > > If everything is working correctly, in all these dataset images should look right; > Image a and d: The brain looks upright. the corpus callosum is red at the mid-sagittal. All color should look symmetric. > Image b and c: The brain looks tilted. The color of the corpus callosum do not look symmetric. > All images: the fiber tracking should appear the same in 3D view. Simply put an ROI in the genu of the corpus callosum, and you can immediately tell if they look the same or something is not working > > Hope this helps. > > Susumu > > 2010/10/24 chichesterchiche > > Dear DTIStudio Experts, > > We know we need to input the gradient table in DTIStudio. However, when doing tensor map calculation, which coordinate system is DTIStudio based on? Is DTIStudio based on DICOM patient coordinate system or image coordinate system? I acquired the DWI images by TOSHIBA MRI and the gradient vectors are based on patient coordiante. Can I input the patient-coordinate-based gradient vector to DTI Studio directly, or do I need to transform the patient-coordinate-based gradient vector to image coordinate system at first? > > Thank you. > > Qiqi > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101029/9f5dfc83/attachment.html From susumu at mri.jhu.edu Fri Oct 29 06:43:47 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 29 Oct 2010 06:43:47 -0400 Subject: [Mristudio-users] DTI Data question In-Reply-To: References: Message-ID: There are three repeated scans. By using all three, you can improve the SNR. You can consider it as regular scan average (NEX). If you use 3 scan average, you get one complete DTI set. If the subject moved during the scan, you get scans before motion and after motion averaged by the scanner. If you submit 3 scans independently and saved independently, you can co-register them to reduce the effect of motion. That is why we usually submit 3 independent scans rather than using 3 signal averaging. If you are using Siemens with a new operating system, you can use 3 signal averaging instead of submitting 3 repeated scans because Siemens scanners do not average the scans and save them separately in Mosaic files. 2010/10/28 Fernando Ventrice : > Hi I would like to know why there are several DTIs (31, 41, 51,...) ?for each individual of the DTI DATA that is on the website. Are they corrected images with different angulation? I measured FA values from different regions and have slight different FA values for the same region. > Thank you very much, > Fernando Ventrice > > El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales est? dirigido, pudiendo contener informaci?n legalmente protegida. Queda prohibida la revisi?n, divulgaci?n, publicaci?n, modificaci?n, copia, distribuci?n o acci?n en relaci?n con esta informaci?n, por personas o entidades distintas al destinatario. Si usted, por alguna raz?n, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opini?n de FLENI. > http://www.fleni.org.ar > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > From mksarma at gmail.com Fri Oct 29 16:01:23 2010 From: mksarma at gmail.com (manoj sarma) Date: Fri, 29 Oct 2010 13:01:23 -0700 Subject: [Mristudio-users] makeaheader.exe for DiffeoMap Message-ID: Dear all, I would like to use DiffeoMap. I have a problem: I do not manage to compile makeaheader.exe, alignlinear.exe, align_warp.exe and invert_air.exe for windows from AIR. Can anyone send me these files ? thanks, Manoj -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101029/6371537c/attachment-0001.html From susumu at mri.jhu.edu Sat Oct 30 19:01:00 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sat, 30 Oct 2010 19:01:00 -0400 Subject: [Mristudio-users] question regarding the diagonal components In-Reply-To: References: Message-ID: Hi Amir, This is an interesting question and allow me to share with other users in the mailing list. The 3 gradient systems of MRI usually do not have exactly the same gradient strengths (it's almost impossible to make X, Y, and Z gradients with exactly the same strengths). Therefore, it is one of the important setup procedures to calibrate the gradient strengths. Suppose X, Y, and Z gradients have 20, 20, and 10G/cm strength (I exaggerated). Once calibrated and if you want to deliver 10G/cm gradient in all three directions, even if you instruct [10, 10, 10 G/cm], the actual instruction to hardware goes [50, 50, 100%]. In this way, gradients systems are calibrated. If the gradient systems are not calibrated, a sphere object would have oval appearance in imaging. To ensure the anatomical fidelity, all gradient axes must be calibrated. Therefore, it is usually unthinkable that diffusion gradients (b vector) have calibration error; if so, your brain images would also have a wrong aspect ratio. You also mentioned about "orientation of tensor component". This is a different question from gradient strength. Please refer to my recent answers to one of the questions asking about physical and image coordinates. It is your b-table that defines what coordinate you are using. Unless you use oblique imaging, image and physical coordinates are aligned and there is not much to worry about. When you use oblique imaging, there are two ways to define the b-table; Physical and Image coordinates. If you use a gradient table in physical coordinates (gradient axes), the resultant fiber angles are defined by the physical coordinates; if the fiber orientation is [1, 0, 0], that is along the magnet X gradient. If you process the same data using a table defined in the image coordinates, then the fiber angle are defined in X, Y, Z coordinates of the image matrix; If the fiber orientation is [1, 0, 0], then the fiber is along Image X axis. Obviously, you want the image coordinates, I believe. Hope this clarify your questions. On Sat, Oct 30, 2010 at 3:19 PM, Amir Zolal wrote: > Dear dr. Susumu Mori, > I have a simple question, are the components of the diffusion tensor matrix > oriented along the physical scanner gradients or does the position of the > scan play a role? I conducted an experiment where I expected the > longitudinal (z) component to react differently than the x and y, because of > the unequal strength of the gradients. This did not happen (ie. i could not > see any significant difference between the changes in Dxx, Dyy and Dzz > components) and I am looking for an explanation .. > Thank you in advance for the answer, > Amir Zolal From dc02hana at m6.gyao.ne.jp Sun Oct 31 04:10:10 2010 From: dc02hana at m6.gyao.ne.jp (hanaie) Date: Sun, 31 Oct 2010 17:10:10 +0900 Subject: [Mristudio-users] Theory Image Tool Message-ID: <000001cb78d3$09d44550$1d7ccff0$@gyao.ne.jp> Hi, To evaluate the quality of DTI data, I used ?theory Image Tool?. Because I have only 1 data set. After using ?theory Image Tool? , I checked images. But these image looks like strange. Issue is third row. In these images, first row is scan#1 and second row is theory image ,third row is ?(theory,scan#1). In my image , third row looks like almost black with a little bit white point. I read the paper titled ?How should we evaluate the quality of our DTI data?? In that paper, third row looks like grey. Why does my image looks like almost black? Is wrong gradient table responsibility for it? ??1.5.jpg Thanks, Ryuzo -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101031/bb41c1dc/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/jpeg Size: 10107 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101031/bb41c1dc/attachment.jpe From susumu at mri.jhu.edu Sun Oct 31 07:40:01 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sun, 31 Oct 2010 07:40:01 -0400 Subject: [Mristudio-users] Theory Image Tool In-Reply-To: <000001cb78d3$09d44550$1d7ccff0$@gyao.ne.jp> References: <000001cb78d3$09d44550$1d7ccff0$@gyao.ne.jp> Message-ID: It depends on how you use this tool. For example, after you start tensor calculation, you get an initial "DTI Map Option" window, in which you can find two checkboxes at the lower left corner saying "create ,,,,,". If you proceed to "standard linear fitting", then you should get one row of theory image and another row of error (subtracted) images. In this window, if you choose to use "pixel rejection", instead of "standard linear fitting", you get 3 options in "Verify the results" section. Here we recommend to use "binary mask" instead of "error map". If you choose "binary mask", the bottom row is not error maps, but showing which pixels were rejected due to large errors. If you case, I suspect your images did not contain obvious outliers and therefore the bottom row images are mostly blank. 2010/10/31 hanaie > Hi, > > > > To evaluate the quality of DTI data, I used ?theory Image Tool?. > > Because I have only 1 data set. > > After using ?theory Image Tool? , I checked images. But these image looks > like strange. > > Issue is third row. > > > > In these images, first row is scan#1 and second row is theory image ,third > row is ?(theory,scan#1). > > In my image , third row looks like almost black with a little bit white > point. > > > > I read the paper titled ?How should we evaluate the quality of our DTI > data?? > > In that paper, third row looks like grey. > > > > Why does my image looks like almost black? > > Is wrong gradient table responsibility for it? > > > > > > [image: ??1.5.jpg] > > > > > > Thanks, > > > > Ryuzo > > > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101031/ff693351/attachment-0001.html From dc02hana at m6.gyao.ne.jp Sun Oct 31 11:23:39 2010 From: dc02hana at m6.gyao.ne.jp (hanaie) Date: Mon, 01 Nov 2010 00:23:39 +0900 Subject: [Mristudio-users] Theory Image Tool In-Reply-To: References: <000001cb78d3$09d44550$1d7ccff0$@gyao.ne.jp> Message-ID: <002201cb790f$985d9010$c918b030$@gyao.ne.jp> Dear Dr Mori, Thank you for your kindness, detailed explanation. I did in a way you`ve shown. I checked ?standard linear fitting? and the two checkboxes. But I got row of error image with mostly blank(the bottom row image). Not after ?outliner pixel rejection?. Is this something wrong and could you tell me why this occur ? Sorry, I am fairly a beginner and poor in English. Thanks . Ryuzo From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Sunday, October 31, 2010 8:40 PM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] Theory Image Tool It depends on how you use this tool. For example, after you start tensor calculation, you get an initial "DTI Map Option" window, in which you can find two checkboxes at the lower left corner saying "create ,,,,,". If you proceed to "standard linear fitting", then you should get one row of theory image and another row of error (subtracted) images. In this window, if you choose to use "pixel rejection", instead of "standard linear fitting", you get 3 options in "Verify the results" section. Here we recommend to use "binary mask" instead of "error map". If you choose "binary mask", the bottom row is not error maps, but showing which pixels were rejected due to large errors. If you case, I suspect your images did not contain obvious outliers and therefore the bottom row images are mostly blank. 2010/10/31 hanaie Hi, To evaluate the quality of DTI data, I used ?theory Image Tool?. Because I have only 1 data set. After using ?theory Image Tool? , I checked images. But these image looks like strange. Issue is third row. In these images, first row is scan#1 and second row is theory image ,third row is ?(theory,scan#1). In my image , third row looks like almost black with a little bit white point. I read the paper titled ?How should we evaluate the quality of our DTI data?? In that paper, third row looks like grey. Why does my image looks like almost black? Is wrong gradient table responsibility for it? ???! ???????????????? Thanks, Ryuzo _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101101/47ea5a6b/attachment.html From susumu at mri.jhu.edu Sun Oct 31 11:44:27 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Sun, 31 Oct 2010 11:44:27 -0400 Subject: [Mristudio-users] Theory Image Tool In-Reply-To: <002201cb790f$985d9010$c918b030$@gyao.ne.jp> References: <000001cb78d3$09d44550$1d7ccff0$@gyao.ne.jp> <002201cb790f$985d9010$c918b030$@gyao.ne.jp> Message-ID: Oh, that's strange. We have to investigate it. Could you upload your data and the DtiStudio executable to our ftp site? Zhipeng will contact you for the ftp site. On Sun, Oct 31, 2010 at 11:23 AM, hanaie wrote: > Dear Dr Mori, > > > > Thank you for your kindness, detailed explanation. > > > > I did in a way you`ve shown. > > I checked ?standard linear fitting? and the two checkboxes. > > But I got row of error image with mostly blank(the bottom row image). > > Not after ?outliner pixel rejection?. > > > > Is this something wrong and could you tell me why this occur ? > > > > > > Sorry, I am fairly a beginner and poor in English. > > > > Thanks . > > > > Ryuzo > > > > > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori > Sent: Sunday, October 31, 2010 8:40 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] Theory Image Tool > > > > It depends on how you use this tool. For example, after you start tensor > calculation, you get an initial "DTI Map Option" window, in which you can > find two checkboxes at the lower left corner saying "create ,,,,,". If you > proceed to "standard linear fitting", then you should get one row of theory > image and another row of error (subtracted) images. > > > > In this window, if you choose to use "pixel rejection", instead of "standard > linear fitting", you get 3 options in "Verify the results" section. Here we > recommend to use "binary mask" instead of "error map". If you choose "binary > mask", the bottom row is not error maps, but showing which pixels were > rejected due to large errors. > > > > If you case, I suspect your images did not contain obvious outliers and > therefore the bottom row images are mostly blank. > > 2010/10/31 hanaie > > Hi, > > > > To evaluate the quality of DTI data, I used ?theory Image Tool?. > > Because I have only 1 data set. > > After using ?theory Image Tool? , I checked images. But these image looks > like strange. > > Issue is third row. > > > > In these images, first row is scan#1 and second row is theory image ,third > row is ?(theory,scan#1). > > In my image , third row looks like almost black with a little bit white > point. > > > > I read the paper titled ?How should we evaluate the quality of our DTI > data?? > > In that paper, third row looks like grey. > > > > Why does my image looks like almost black? > > Is wrong gradient table responsibility for it? > > > > > > ???! ???????????????? > > > > > > Thanks, > > > > Ryuzo > > > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > From dc02hana at m6.gyao.ne.jp Mon Nov 1 09:03:15 2010 From: dc02hana at m6.gyao.ne.jp (hanaie) Date: Mon, 01 Nov 2010 22:03:15 +0900 Subject: [Mristudio-users] Theory Image Tool In-Reply-To: References: <000001cb78d3$09d44550$1d7ccff0$@gyao.ne.jp> <002201cb790f$985d9010$c918b030$@gyao.ne.jp> Message-ID: <000c01cb79c5$25e5da90$71b18fb0$@gyao.ne.jp> Dear Dr Mori, I deeply appreciate your help. I look forward to contacting from Zhipeng. Ryuzo -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori Sent: Monday, November 01, 2010 12:44 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; Zhipeng Hou Subject: Re: [Mristudio-users] Theory Image Tool Oh, that's strange. We have to investigate it. Could you upload your data and the DtiStudio executable to our ftp site? Zhipeng will contact you for the ftp site. On Sun, Oct 31, 2010 at 11:23 AM, hanaie wrote: > Dear Dr Mori, > > > > Thank you for your kindness, detailed explanation. > > > > I did in a way you`ve shown. > > I checked ?standard linear fitting? and the two checkboxes. > > But I got row of error image with mostly blank(the bottom row image). > > Not after ?outliner pixel rejection?. > > > > Is this something wrong and could you tell me why this occur ? > > > > > > Sorry, I am fairly a beginner and poor in English. > > > > Thanks . > > > > Ryuzo > > > > > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori > Sent: Sunday, October 31, 2010 8:40 PM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] Theory Image Tool > > > > It depends on how you use this tool. For example, after you start tensor > calculation, you get an initial "DTI Map Option" window, in which you can > find two checkboxes at the lower left corner saying "create ,,,,,". If you > proceed to "standard linear fitting", then you should get one row of theory > image and another row of error (subtracted) images. > > > > In this window, if you choose to use "pixel rejection", instead of "standard > linear fitting", you get 3 options in "Verify the results" section. Here we > recommend to use "binary mask" instead of "error map". If you choose "binary > mask", the bottom row is not error maps, but showing which pixels were > rejected due to large errors. > > > > If you case, I suspect your images did not contain obvious outliers and > therefore the bottom row images are mostly blank. > > 2010/10/31 hanaie > > Hi, > > > > To evaluate the quality of DTI data, I used ?theory Image Tool?. > > Because I have only 1 data set. > > After using ?theory Image Tool? , I checked images. But these image looks > like strange. > > Issue is third row. > > > > In these images, first row is scan#1 and second row is theory image ,third > row is ?(theory,scan#1). > > In my image , third row looks like almost black with a little bit white > point. > > > > I read the paper titled ?How should we evaluate the quality of our DTI > data?? > > In that paper, third row looks like grey. > > > > Why does my image looks like almost black? > > Is wrong gradient table responsibility for it? > > > > > > ???! ???????????????? > > > > > > Thanks, > > > > Ryuzo > > > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From CSIDIRO1 at hfhs.org Sat Nov 6 22:06:06 2010 From: CSIDIRO1 at hfhs.org (Sidiropoulos, Christos (Neurology)) Date: Sat, 06 Nov 2010 22:06:06 -0400 Subject: [Mristudio-users] Troubleshooting Message-ID: Hi all, this is the first time I am writing to you as I am very new to DTI studio. I downloaded the PNO1 raw pediatric data file form your website and tried to run it on DTI studio. My PC has 2 GB RAM. Whenever I am on the DWI parameters window, using any of the gradient combinations I come upon an error message that the file size is either smaller or bigger than the DWI size. Also after DTI calculations when I click on the DTI map, original ADC-Mean-STD I come upon an error message an invalid argument was encountered. I would be grateful for your advise. Christos Sidiropoulos Henry Ford Hospital Dept of Neurology ============================================================================== CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. 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If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us. ============================================================================== From buchmann2 at wisc.edu Sun Nov 7 10:42:13 2010 From: buchmann2 at wisc.edu (Andreas Buchmann) Date: Sun, 07 Nov 2010 09:42:13 -0600 Subject: [Mristudio-users] Image data display Message-ID: <0LBI00EE8UACE550@smtpauth3.wiscmail.wisc.edu> Dear DTI Studio Experts, I'm trying to assess image data with right-click and "image data display". This works fine for the raw images and the FA images, but not for the diffusivities (where all numbers equal 0.00). Any solutions? Thanks a lot Andreas -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101107/a5395a1b/attachment.html From buchmann2 at wisc.edu Mon Nov 8 09:43:18 2010 From: buchmann2 at wisc.edu (Andreas Buchmann) Date: Mon, 08 Nov 2010 08:43:18 -0600 Subject: [Mristudio-users] FW: Image data display Message-ID: <0LBK001RZM83YA30@smtpauth3.wiscmail.wisc.edu> _____ From: Andreas Buchmann [mailto:buchmann2 at wisc.edu] Sent: Sonntag, 7. November 2010 09:42 To: 'mristudio-users at mristudio.org' Subject: Image data display Dear DTI Studio Experts, I'm trying to assess image data with right-click and "image data display". This works fine for the raw images and the FA images, but not for the diffusivities (where all numbers equal 0.00). Any solutions? Thanks a lot Andreas -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101108/36b18b1a/attachment.html From luca.binotto at unipd.it Tue Nov 9 15:09:17 2010 From: luca.binotto at unipd.it (luca.binotto at unipd.it) Date: Tue, 09 Nov 2010 21:09:17 +0100 Subject: [Mristudio-users] Siemens Allegra gradient table Message-ID: Dear All, I am looking for gradient table for Siemens Allegra 3 tesla MR System with 30 directions. Can I use the one posted in this mailinglist for Siemens Avanto? Many thanks in advance, Luca Binotto From susumu at mri.jhu.edu Tue Nov 9 15:16:49 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 09 Nov 2010 15:16:49 -0500 Subject: [Mristudio-users] Siemens Allegra gradient table In-Reply-To: References: Message-ID: I hope this will do. If not, please let me know. You have to change the format to the MriStudio format. On Tue, Nov 9, 2010 at 3:09 PM, wrote: > Dear All, > > I am looking for gradient table for Siemens Allegra 3 tesla MR System > with 30 directions. > Can I use the one posted in this mailinglist for Siemens Avanto? > > Many thanks in advance, > > Luca Binotto > > > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101109/e5ca96ae/attachment-0001.html -------------- next part -------------- case 1: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = PRS ; switch (cFlag) { case 'P': setVector (0, 1.0, 0, 0) ; break ; case 'R': setVector (0, 0, 1.0, 0) ; break ; case 'S': setVector (0, 0, 0, 1.0) ; break ; default: if ( ! isContextPrepForBinarySearch || (m_lDebugLevel & DEBUG_RETURN) ) TRACE_PUT2 (TC_INFO, TF_SEQ, "%s ERROR: Invalid control flag '%c' in sequence code.", ptModule, cFlag) ; return false ; } break ; case 3: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; switch (cFlag) { case 'O': m_eCoordinateSystem = PRS ; setVector (0, 1.0, 0, 0) ; setVector (1, 0, 1.0, 0) ; setVector (2, 0, 0, 1.0) ; break ; case 'T': m_eCoordinateSystem = XYZ ; setVector (0, 1.0, 1.0, -0.5) ; setVector (1, 1.0, -0.5, 1.0) ; setVector (2, -0.5, 1.0, 1.0) ; break ; default: if ( ! isContextPrepForBinarySearch || (m_lDebugLevel & DEBUG_RETURN) ) TRACE_PUT2 (TC_INFO, TF_SEQ, "%s ERROR: Invalid control flag '%c' in sequence code.", ptModule, cFlag) ; return false ; } break ; case 6: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // (Note: do not modify the following comments - doxygen greps for them) // vector set for 6 directions (normalised to maximum) setVector (0, 1.0, 0.0, 1.0) ; setVector (1, -1.0, 0.0, 1.0) ; setVector (2, 0.0, 1.0, 1.0) ; setVector (3, 0.0, 1.0, -1.0) ; setVector (4, 1.0, 1.0, 0.0) ; setVector (5, -1.0, 1.0, 0.0) ; break ; case 10: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 10 directions (normalised to maximum) setVector (0, 0.000000, 0.809017, 0.618034 ) ; setVector (1, 0.000000, 0.190983, 1.000000 ) ; setVector (2, -0.587785, 0.809017, 0.190983 ) ; setVector (3, -0.951057, 0.190983, 0.309017 ) ; setVector (4, -0.363271, 0.809017, -0.500000 ) ; setVector (5, -0.587785, 0.190983, -0.809017 ) ; setVector (6, 0.363271, 0.809017, -0.500000 ) ; setVector (7, 0.587785, 0.190983, -0.809017 ) ; setVector (8, 0.587785, 0.809017, 0.190983 ) ; setVector (9, 0.951057, 0.190983, 0.309017 ) ; break ; case 12: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 12 directions (normalised to maximum) setVector (0, 1.000000, 0.414250, -0.414250 ); setVector (1, 1.000000, -0.414250, -0.414250 ); setVector (2, 1.000000, -0.414250, 0.414250 ); setVector (3, 1.000000, 0.414250, 0.414250 ); setVector (4, 0.414250, 0.414250, 1.000000 ); setVector (5, 0.414250, 1.000000, 0.414250 ); setVector (6, 0.414250, 1.000000, -0.414250 ); setVector (7, 0.414250, 0.414250, -1.000000 ); setVector (8, 0.414250, -0.414250, -1.000000 ); setVector (9, 0.414250, -1.000000, -0.414250 ); setVector (10, 0.414250, -1.000000, 0.414250 ); setVector (11, 0.414250, -0.414250, 1.000000 ); break ; case 20: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 20 directions (normalised to maximum) setVector (0, 1.000000, 0.000000, 0.000000) ; setVector (1, 0.000000, 1.000000, 0.000000) ; setVector (2, -0.031984, 0.799591, 0.599693) ; setVector (3, 0.856706, 0.493831, -0.148949) ; setVector (4, 0.834429, 0.309159, 0.456234) ; setVector (5, 0.834429, -0.309159, 0.456234) ; setVector (6, 0.856706, -0.493831, -0.148949) ; setVector (7, 0.822228, 0.000000, -0.569158) ; setVector (8, 0.550834, 0.425872, -0.717784) ; setVector (9, 0.468173, 0.834308, -0.291108) ; setVector (10, 0.515933, 0.808894, 0.281963) ; setVector (11, 0.391890, 0.515855, 0.761785) ; setVector (12, 0.478151, 0.000000, 0.878278) ; setVector (13, 0.391890, -0.515855, 0.761785) ; setVector (14, 0.515933, -0.808894, 0.281963) ; setVector (15, 0.468173, -0.834308, -0.291108) ; setVector (16, 0.550834, -0.425872, -0.717784) ; setVector (17, 0.111012, -0.264029, -0.958105) ; setVector (18, 0.111012, 0.264029, -0.958105) ; setVector (19, 0.031984, 0.799591, -0.599693) ; break ; 0: 0, 0, 0 1: 1.000000, 0.000000, 0.000000; 2: 0.000000, 1.000000, 0.000000; 3: -0.031984, 0.799591, 0.599693; 4: 0.856706, 0.493831, -0.148949; 5: 0.834429, 0.309159, 0.456234; 6: 0.834429, -0.309159, 0.456234; 7: 0.856706, -0.493831, -0.148949; 8: 0.822228, 0.000000, -0.569158; 9: 0.550834, 0.425872, -0.717784 ; 10: 0.468173, 0.834308, -0.291108 ; 11: 0.515933, 0.808894, 0.281963 ; 12: 0.391890, 0.515855, 0.761785 ; 13: 0.478151, 0.000000, 0.878278 ; 14: 0.391890, -0.515855, 0.761785 ; 15: 0.515933, -0.808894, 0.281963 ; 16: 0.468173, -0.834308, -0.291108 ; 17: 0.550834, -0.425872, -0.717784 ; 18: 0.111012, -0.264029, -0.958105 ; 19: 0.111012, 0.264029, -0.958105 ; 20: 0.031984, 0.799591, -0.599693 ; case 30: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 30 directions (normalised to maximum) setVector (0, -0.208098, 0.525514, 0.850005 ) ; setVector (1, 0.202387, 0.526131, 0.851002 ) ; setVector (2, 0.409956, 0.175267, 0.918257 ) ; setVector (3, -0.412630, 0.742620, 0.565889 ) ; setVector (4, -0.207127, 0.959492, 0.280092 ) ; setVector (5, -0.872713, 0.525505, 0.064764 ) ; setVector (6, -0.746815, 0.526129, 0.455449 ) ; setVector (7, -0.415238, 0.175473, 0.915841 ) ; setVector (8, -0.746636, 0.175268, 0.673642 ) ; setVector (9, -0.665701, 0.742619, -0.217574 ) ; setVector (10, -0.330391, 0.959489, -0.110458 ) ; setVector (11, -0.331275, 0.525513, -0.809983 ) ; setVector (12, -0.663936, 0.526130, -0.569521 ) ; setVector (13, -0.999332, 0.175474, -0.111904 ) ; setVector (14, -0.871398, 0.175267, -0.501922 ) ; setVector (15, 0.001214, 0.742616, -0.700356 ) ; setVector (16, 0.002949, 0.959483, -0.348370 ) ; setVector (17, 0.667975, 0.525509, -0.565356 ) ; setVector (18, 0.336490, 0.526126, -0.807431 ) ; setVector (19, 0.202383, -0.175470, 0.985002 ) ; setVector (20, 0.208094, 0.175265, -0.983848 ) ; setVector (21, 0.666452, 0.742619, -0.215262 ) ; setVector (22, 0.332212, 0.959489, -0.104850 ) ; setVector (23, 0.205064, 0.958364, 0.285421 ) ; setVector (24, 0.412630, 0.742620, 0.565889 ) ; setVector (25, 0.746093, 0.175315, 0.674232 ) ; setVector (26, 0.744110, 0.525505, 0.460568 ) ; setVector (27, 0.871894, 0.526125, 0.070507 ) ; setVector (28, 0.874264, 0.175471, -0.496841 ) ; setVector (29, 1.000000, 0.175267, -0.106112 ) ; break ; case 64: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 64 directions (normalised to maximum) setVector (0, 1.000000, 0.000000, 0.000000); setVector (1, 0.000000, 1.000000, 0.000000); setVector (2, -0.026007, 0.649170, 0.760199); setVector (3, 0.591136, -0.766176, 0.252058); setVector (4, -0.236071, -0.524158, 0.818247); setVector (5, -0.893021, -0.259006, 0.368008); setVector (6, 0.796184, 0.129030, 0.591137); setVector (7, 0.233964, 0.929855, 0.283956); setVector (8, 0.935686, 0.139953, 0.323891); setVector (9, 0.505827, -0.844710, -0.174940); setVector (10, 0.346220, -0.847539, -0.402256); setVector (11, 0.456968, -0.630956, -0.626956); setVector (12, -0.486997, -0.388997, 0.781995); setVector (13, -0.617845, 0.672831, 0.406898); setVector (14, -0.576984, -0.104997, -0.809978); setVector (15, -0.826695, -0.520808, 0.212921); setVector (16, 0.893712, -0.039987, -0.446856); setVector (17, 0.290101, -0.541189, -0.789276); setVector (18, 0.115951, -0.962591, -0.244896); setVector (19, -0.800182, 0.403092, -0.444101); setVector (20, 0.513981, 0.839970, 0.173994); setVector (21, -0.788548, 0.152912, -0.595659); setVector (22, 0.949280, -0.233069, 0.211062); setVector (23, 0.232964, 0.782880, 0.576911); setVector (24, -0.020999, -0.187990, -0.981946); setVector (25, 0.216932, -0.955701, 0.198938); setVector (26, 0.774003, -0.604002, 0.190001); setVector (27, -0.160928, 0.355840, 0.920587); setVector (28, -0.147035, 0.731173, -0.666158); setVector (29, 0.888141, 0.417066, 0.193031); setVector (30, -0.561971, 0.231988, -0.793959); setVector (31, -0.380809, 0.142928, 0.913541); setVector (32, -0.306000, -0.199000, -0.931001); setVector (33, -0.332086, -0.130034, 0.934243); setVector (34, -0.963226, -0.265062, 0.044010); setVector (35, -0.959501, 0.205107, 0.193101); setVector (36, 0.452965, -0.888932, 0.067995); setVector (37, -0.773133, 0.628108, 0.088015); setVector (38, 0.709082, 0.408047, 0.575066); setVector (39, -0.692769, 0.023992, 0.720760); setVector (40, 0.681659, 0.528735, -0.505747); setVector (41, -0.141995, -0.724976, 0.673978); setVector (42, -0.740168, 0.388088, 0.549125); setVector (43, -0.103006, 0.822044, 0.560030); setVector (44, 0.584037, -0.596038, 0.551035); setVector (45, -0.088008, -0.335031, 0.938088); setVector (46, -0.552263, -0.792377, 0.259123); setVector (47, 0.838158, -0.458086, -0.296056); setVector (48, 0.362995, -0.560993, 0.743990); setVector (49, -0.184062, 0.392133, -0.901306); setVector (50, -0.720938, -0.692941, 0.008999); setVector (51, 0.433101, 0.682159, -0.589137); setVector (52, 0.502114, 0.690157, 0.521119); setVector (53, -0.170944, -0.508833, -0.843722); setVector (54, 0.462968, 0.422971, 0.778946); setVector (55, 0.385030, -0.809064, 0.444035); setVector (56, -0.713102, -0.247035, 0.656094); setVector (57, 0.259923, 0.884737, -0.386885); setVector (58, 0.001000, 0.077002, -0.997030); setVector (59, 0.037002, -0.902057, 0.430027); setVector (60, 0.570320, -0.303170, -0.763428); setVector (61, -0.282105, 0.145054, -0.948354); setVector (62, 0.721098, 0.608082, 0.332045); setVector (63, 0.266985, 0.959945, -0.084995); break ; case 256: m_lDirections = lDirections ; delete [] m_sVector ; m_sVector = new VectorStruct [m_lDirections] ; m_eCoordinateSystem = XYZ ; // vector set for 256 directions (normalised to maximum) setVector (0, 0.059010, -0.013002, 0.998173); setVector (1, 0.070008, 0.157018, 0.985111); setVector (2, -0.078038, 0.083041, 0.993486); setVector (3, -0.092987, -0.086988, 0.991860); setVector (4, 0.046987, -0.178952, 0.982735); setVector (5, 0.199944, -0.108970, 0.973729); setVector (6, 0.211021, 0.052005, 0.976097); setVector (7, 0.210999, 0.212999, 0.953997); setVector (8, -0.050982, 0.250913, 0.966666); setVector (9, -0.208056, 0.186050, 0.960259); setVector (10, -0.355044, 0.120015, 0.927114); setVector (11, -0.225050, 0.016004, 0.974216); setVector (12, -0.239998, -0.156999, 0.957994); setVector (13, -0.107055, -0.253129, 0.961491); setVector (14, 0.031988, -0.337873, 0.940648); setVector (15, 0.191053, -0.268075, 0.944264); setVector (16, 0.333011, -0.202007, 0.921030); setVector (17, 0.350043, -0.034004, 0.936116); setVector (18, 0.353962, 0.131986, 0.925900); setVector (19, 0.321087, 0.303082, 0.897243); setVector (20, 0.124035, 0.337095, 0.933264); setVector (21, -0.028007, 0.395092, 0.918214); setVector (22, -0.189921, 0.343856, 0.919616); setVector (23, -0.340929, 0.281942, 0.896814); setVector (24, -0.483028, 0.214012, 0.849048); setVector (25, -0.492017, 0.052002, 0.869031); setVector (26, -0.364886, -0.049984, 0.929710); setVector (27, -0.376988, -0.226993, 0.897972); setVector (28, -0.251019, -0.327024, 0.911068); setVector (29, -0.116041, -0.415148, 0.902323); setVector (30, 0.027007, -0.490130, 0.871231); setVector (31, 0.176089, -0.413208, 0.893450); setVector (32, 0.323985, -0.380982, 0.865960); setVector (33, 0.451026, -0.272016, 0.850049); setVector (34, 0.477203, -0.106045, 0.872371); setVector (35, 0.487906, 0.059988, 0.870832); setVector (36, 0.468001, 0.231001, 0.853003); setVector (37, 0.426147, 0.394136, 0.814282); setVector (38, 0.266963, 0.442939, 0.855883); setVector (39, 0.120952, 0.485807, 0.865657); setVector (40, -0.024989, 0.534766, 0.844631); setVector (41, -0.176029, 0.491082, 0.853142); setVector (42, -0.323126, 0.437171, 0.839328); setVector (43, -0.463978, 0.371982, 0.803961); setVector (44, -0.613900, 0.139977, 0.776874); setVector (45, -0.617975, -0.018999, 0.785968); 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setVector (196, 0.218003, 0.934014, 0.283004); setVector (197, 0.147000, 0.978001, 0.148000); setVector (198, 0.050005, 0.955101, 0.292031); setVector (199, -0.120044, 0.950347, 0.287105); setVector (200, -0.287133, 0.918424, 0.272126); setVector (201, -0.444757, 0.861529, 0.244866); setVector (202, -0.582982, 0.786976, 0.201994); setVector (203, -0.707118, 0.690116, 0.154026); setVector (204, -0.823874, 0.547916, 0.144978); setVector (205, -0.895869, 0.373945, 0.239965); setVector (206, -0.956936, 0.266982, 0.113992); setVector (207, -0.984969, 0.108997, 0.133996); setVector (208, -0.987109, -0.053006, 0.151017); setVector (209, -0.962464, -0.213103, 0.168081); setVector (210, -0.907966, -0.372986, 0.190993); setVector (211, -0.822992, -0.528995, 0.206998); setVector (212, -0.712235, -0.666220, 0.221073); setVector (213, -0.584746, -0.777662, 0.230900); setVector (214, -0.445210, -0.866409, 0.226107); setVector (215, -0.302832, -0.932484, 0.196891); setVector (216, -0.155030, -0.975188, 0.158031); 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setVector (238, -0.026001, 0.988038, 0.152006); setVector (239, -0.200088, 0.969424, 0.142062); setVector (240, -0.365992, 0.922979, 0.118997); setVector (241, -0.510695, 0.856488, 0.074955); setVector (242, -0.640958, 0.766950, 0.030998); setVector (243, -0.764977, 0.643980, 0.010000); setVector (244, 0.857996, -0.512998, 0.026000); setVector (245, -0.901024, 0.423011, 0.096003); setVector (246, 0.938499, -0.343182, 0.038020); setVector (247, 0.983769, -0.177958, 0.022995); setVector (248, 0.999898, -0.012999, 0.005999); setVector (249, -0.988633, -0.149944, 0.010996); setVector (250, -0.949788, -0.310931, 0.034992); setVector (251, -0.883406, -0.464213, 0.064029); setVector (252, -0.783923, -0.615940, 0.077992); setVector (253, -0.660104, -0.746118, 0.087014); setVector (254, -0.521822, -0.848711, 0.085971); setVector (255, -0.380935, -0.922844, 0.056990); break ; From naamab at stanford.edu Wed Nov 10 15:18:24 2010 From: naamab at stanford.edu (Naama Barnea-Goraly) Date: Wed, 10 Nov 2010 12:18:24 -0800 Subject: [Mristudio-users] Can this scan be saved? Message-ID: We have a scan with 2 reps from a child. First repetition is fine, however it seems that the kid moved between repetitions (not within repetition). I tried using AIR in dtistudio and diffeomap to register the images however the result is not better. Is there anything else we can do? Thanks, Naama Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you. From susumu at mri.jhu.edu Wed Nov 10 16:24:53 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 10 Nov 2010 16:24:53 -0500 Subject: [Mristudio-users] Can this scan be saved? In-Reply-To: References: Message-ID: Hi Naama, Please take a look at the documented in https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2. There is a nice description about available intra-DTI data registration. DiffeoMap is for cross-subject registration, not for intra-dataset. Please let me know how different registration tools perform. I would appreciate it if you share your experience and results of the registraiton. Susumu On Wed, Nov 10, 2010 at 3:18 PM, Naama Barnea-Goraly wrote: > > We have a scan with 2 reps from a child. First repetition is fine, > however it seems that the kid moved between repetitions (not within > repetition). I tried using AIR in dtistudio and diffeomap to register > the images however the result is not better. Is there anything else we > can do? > > Thanks, > > Naama > > > > > Naama Barnea-Goraly M.D. > Instructor > Center for Interdisciplinary Brain Sciences Research > Stanford University Division of Child and Adolescent Psychiatry > 401 Quarry Rd. MC 5795 > Stanford University School of Medicine > Stanford, CA 94305-5795 > Phone: (650) 736-1874, fax: (650) 724-4794 > > > CONFIDENTIALITY NOTICE: This e-mail communication and any attachments > may contain confidential information for the use of the designated > recipients named above. If you are not the intended recipient, you > are hereby notified that you have received this communication in error > and that any review, disclosure, dissemination, distribution or > copying of it or its contents is prohibited. If you have received > this communication in error, please notify Stanford Medical Center > immediately by telephone at (650) 725-5722 and destroy all copies of > this communication and any attachments. Thank you. > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101110/ac0e2d6b/attachment.html From binwang87828 at gmail.com Sat Nov 13 04:58:10 2010 From: binwang87828 at gmail.com (bin wang) Date: Sat, 13 Nov 2010 17:58:10 +0800 Subject: [Mristudio-users] import analyze format binary AAL into dtistudio Message-ID: Dear All, *Is there an easy way to import analyze format binary AAL into dtistudio? Thanks In Advance* *Bin* -- ++++++++++++++++++++++++++++++ Bin Wang major?apply psychology South China Normal University Zhongshan Avenue West 55, Tianhe District Guangzhou 510631 P. R. China Tel: 13416157706 ++++++++++++++++++++++++++++++ ?? ?????? ?????? * ??? *??? ??? ??? ???? ?55? ???510631 ??? 13416157706 (??, ??) +++++++++++++++++++++++++ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101113/bcfb7bcc/attachment.html From akolasny at jhu.edu Sat Nov 13 08:51:50 2010 From: akolasny at jhu.edu (akolasny at jhu.edu) Date: Sat, 13 Nov 2010 08:51:50 -0500 (EST) Subject: [Mristudio-users] MRI STUDIO OFFLINE: Nov. 13 @ 10PM - Nov. 14 @ 8AM Message-ID: <39298.68.50.209.72.1289656310.squirrel@webmail.cis.jhu.edu> Greetings: Mristudio website, mailing list and remote processing will be offline Nov. 13 @ 10PM - Nov. 14 @ 8AM. There is a power outage to the building. All systems will be off line during the power outage. Remote processing will be queued and restarted when the systems come back online. -Anthony ------------------------------------------------------------------- Anthony Kolasny email:akolasny at jhu.edu Center for Imaging Science phone:410.516.4278 Johns Hopkins University FAX:410.516.4594 301 Clark Hall 3400 N. Charles Street Baltimore, Maryland 21218 From kevinspitler at ucla.edu Sun Nov 14 12:05:35 2010 From: kevinspitler at ucla.edu (Kevin Spitler) Date: Sun, 14 Nov 2010 09:05:35 -0800 Subject: [Mristudio-users] problem calculating Tensor, ADC Map Message-ID: Hi, I am able to load my data into DTI Studio and can (on the DtiMap tab) run Original ADC Mean STD Mean (DWIs, B0s) My problem is that when I try either Calculation >> Tensor , Color Map, etc or Calculation >> ADC Map I get completely black views for axial, sagital, and coronal (and the 3d view in the upper left). I do not get an error message. What could be causing this? I get the same results regardless of choosing "create a mask image based on the background noise level 10" or choosing to "Select a mask image b0" I am using DTI Studio 3.0.3 (Sept 2010) on Windows 7 OS. My old data files load and I can do tractography on my old data. I am using Siemens Gradient: 0: 0, 0, 0 1: 1.000000, 0.414250, -0.414250 2: 1.000000, -0.414250, -0.414250 3: 1.000000, -0.414250, 0.414250 4: 1.000000, 0.414250, 0.414250 5: 0.414250, 0.414250, 1.000000 6: 0.414250, 1.000000, 0.414250 7: 0.414250, 1.000000, -0.414250 8: 0.414250, 0.414250, -1.000000 9: 0.414250, -0.414250, -1.000000 10: 0.414250, -1.000000, -0.414250 11: 0.414250, -1.000000, 0.414250 12: 0.414250, -0.414250, 1.000000 Thanks for your help Kevin From miguel.burgaleta at uam.es Sun Nov 14 19:25:56 2010 From: miguel.burgaleta at uam.es (Miguel Burgaleta) Date: Mon, 15 Nov 2010 01:25:56 +0100 Subject: [Mristudio-users] saving fibers - flipping? Message-ID: <47E10083-C46F-48D3-9787-169573914483@uam.es> Hi DTIStudio experts, I am saving my fibers in Analyze format and trying to export them into FSL to do some stats in batch mode, but the resulting binary files seem to experience an unexpected anterior-posterior flipping. I was wondering if this is a known issue. Any advice to safely export fibers will be highly appreciated. Best, Miguel From susumu at mri.jhu.edu Mon Nov 15 21:43:28 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 15 Nov 2010 21:43:28 -0500 Subject: [Mristudio-users] saving fibers - flipping? In-Reply-To: <47E10083-C46F-48D3-9787-169573914483@uam.es> References: <47E10083-C46F-48D3-9787-169573914483@uam.es> Message-ID: Do you think FAQ15 in https://www.mristudio.org/wiki/faq answers the question? On Sun, Nov 14, 2010 at 7:25 PM, Miguel Burgaleta wrote: > > Hi DTIStudio experts, > > I am saving my fibers in Analyze format and trying to export them into > FSL to do some stats in batch mode, but the resulting binary files > seem to experience an unexpected anterior-posterior flipping. I was > wondering if this is a known issue. Any advice to safely export fibers > will be highly appreciated. > > Best, > Miguel > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101115/a1fa165f/attachment.html From susumu at mri.jhu.edu Mon Nov 15 21:46:08 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 15 Nov 2010 21:46:08 -0500 Subject: [Mristudio-users] problem calculating Tensor, ADC Map In-Reply-To: References: Message-ID: Please make sure that you didn't put 0 or a negative value at "b-value" section. On Sun, Nov 14, 2010 at 12:05 PM, Kevin Spitler wrote: > Hi, > > I am able to load my data into DTI Studio and can (on the DtiMap tab) run > Original ADC Mean STD > Mean (DWIs, B0s) > > My problem is that when I try either Calculation >> Tensor , Color Map, etc > or Calculation >> ADC Map > > I get completely black views for axial, sagital, and coronal (and the > 3d view in the upper left). I do not get an error message. What > could be causing this? > > I get the same results regardless of choosing "create a mask image > based on the background noise level 10" or choosing to "Select a mask > image b0" > > I am using DTI Studio 3.0.3 (Sept 2010) on Windows 7 OS. > > My old data files load and I can do tractography on my old data. > > I am using Siemens Gradient: > 0: 0, 0, 0 > 1: 1.000000, 0.414250, -0.414250 > 2: 1.000000, -0.414250, -0.414250 > 3: 1.000000, -0.414250, 0.414250 > 4: 1.000000, 0.414250, 0.414250 > 5: 0.414250, 0.414250, 1.000000 > 6: 0.414250, 1.000000, 0.414250 > 7: 0.414250, 1.000000, -0.414250 > 8: 0.414250, 0.414250, -1.000000 > 9: 0.414250, -0.414250, -1.000000 > 10: 0.414250, -1.000000, -0.414250 > 11: 0.414250, -1.000000, 0.414250 > 12: 0.414250, -0.414250, 1.000000 > > Thanks for your help > Kevin > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101115/ddcd53a5/attachment-0001.html From kevinspitler at gmail.com Tue Nov 16 09:56:01 2010 From: kevinspitler at gmail.com (Kevin Spitler) Date: Tue, 16 Nov 2010 06:56:01 -0800 Subject: [Mristudio-users] problem calculating Tensor, ADC Map In-Reply-To: References: Message-ID: I have tried b-values of 0,600,1200 with the same results. I also tried setting the b-value to 1 with the same results. Interestingly, when clicking on calculate the ADC map in the DtiMap tab, I can uncheck the "Consider B-Value" box in the ADC-Map Options pop up window and I still get the same results. Does this mean that there is another problem, not the b-value? Thanks, Kevin On Mon, Nov 15, 2010 at 6:46 PM, susumu mori wrote: > Please make sure that you didn't put 0 or a negative value at "b-value" > section. > > On Sun, Nov 14, 2010 at 12:05 PM, Kevin Spitler > wrote: >> >> Hi, >> >> I am able to load my data into DTI Studio and can (on the DtiMap tab) run >> Original ADC Mean STD >> Mean (DWIs, B0s) >> >> My problem is that when I try either Calculation >> Tensor , Color Map, >> etc >> or Calculation >> ADC Map >> >> I get completely black views for axial, sagital, and coronal (and the >> 3d view in the upper left). ?I do not get an error message. ?What >> could be causing this? >> >> I get the same results regardless of choosing "create a mask image >> based on the background noise level 10" or choosing to "Select a mask >> image b0" >> >> I am using DTI Studio 3.0.3 (Sept 2010) on Windows 7 OS. >> >> My old data files load and I can do tractography on my old data. >> >> I am using Siemens Gradient: >> 0: 0, 0, 0 >> 1: ?1.000000, 0.414250, -0.414250 >> 2: ?1.000000, -0.414250, -0.414250 >> 3: ?1.000000, -0.414250, 0.414250 >> 4: ?1.000000, 0.414250, 0.414250 >> 5: ?0.414250, 0.414250, 1.000000 >> 6: ?0.414250, 1.000000, 0.414250 >> 7: ?0.414250, 1.000000, -0.414250 >> 8: ?0.414250, 0.414250, -1.000000 >> 9: ?0.414250, -0.414250, -1.000000 >> 10: ?0.414250, -1.000000, -0.414250 >> 11: ?0.414250, -1.000000, 0.414250 >> 12: ?0.414250, -0.414250, 1.000000 >> >> Thanks for your help >> Kevin >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > From basketballmouse at 163.com Tue Nov 16 12:03:37 2010 From: basketballmouse at 163.com (=?GBK?B?u8a6o8fl?=) Date: Wed, 17 Nov 2010 01:03:37 +0800 (CST) Subject: [Mristudio-users] Fiber Tracking with two ROI files In-Reply-To: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> References: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> Message-ID: <1dda817b.19.12c55a443ae.Coremail.basketballmouse@163.com> Hi, I have got two ROI files ( A.dat and B.dat ) and finished the fiber tracking step on my DTI data. In DTIStudio, I can acquire each single ROI's fiber tracking results. I want to get the fibers that cross both the two ROIs, but it seems that the "and" operation doesn't work for ROI files. Could you give me any suggestion? Thank you! Bests, Haiqing -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101117/726e242e/attachment.html From susumu at mri.jhu.edu Tue Nov 16 14:05:50 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 16 Nov 2010 14:05:50 -0500 Subject: [Mristudio-users] Fiber Tracking with two ROI files In-Reply-To: <1dda817b.19.12c55a443ae.Coremail.basketballmouse@163.com> References: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> <1dda817b.19.12c55a443ae.Coremail.basketballmouse@163.com> Message-ID: I assume that you have ROI files exported from another program? If so, FAQ16 in https://www.mristudio.org/wiki/faq may help. 2010/11/16 ??? > Hi, > > I have got two ROI files ( A.dat and B.dat ) and finished the fiber > tracking step on my DTI data. In DTIStudio, I can acquire each single ROI's > fiber tracking results. I want to get the fibers that cross both the two > ROIs, but it seems that the "and" operation doesn't work for ROI files. > Could you give me any suggestion? Thank you! > > Bests, > > Haiqing > > > ------------------------------ > ??163/126???????iphone ipad???? > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101116/63b28c66/attachment.html From fijoy at jhu.edu Wed Nov 3 15:22:09 2010 From: fijoy at jhu.edu (Fijoy Vadakkumpadan) Date: Wed, 03 Nov 2010 19:22:09 -0000 Subject: [Mristudio-users] Affine transformation Message-ID: Hi all, Would anyone know how to interpret the .dat file format used to save affine transformations in Landmarker? This file seems to contain a 4x4 matrix, but I cannot figure out what the numbers mean. I would like to use the affine transformation generated by Landmarker and use it in a Matlab code. I am using Landmarker 1.4. Thanks for any hints. Fijoy From miguel.burgaleta at uam.es Fri Nov 19 05:16:04 2010 From: miguel.burgaleta at uam.es (Miguel Burgaleta) Date: Fri, 19 Nov 2010 11:16:04 +0100 Subject: [Mristudio-users] saving fibers - flipping? In-Reply-To: References: <47E10083-C46F-48D3-9787-169573914483@uam.es> Message-ID: Hi Susumu, Not sure if that solves my problem... Also, Hangyi's answer was: > please beware that the Analyze file is in Format 7.5. it is left- > handed system. > if you loaded it as Nifti-Analyze, the program may loaded as Nifti > format, which is right-hand system. Let me give you more info. I processed my DWI in FSL for motion and eddy currents correction. Saved the images as 4D with .img extension, and opened them in DTIStudio as REC (the only option that worked out... when trying to open as Analyze, it complained about the header. None of the other format options worked). Did the fiber tracking and saved the fiber as Analyze. Please see attached a capture of a small bundle (but strategically located in the brain to track potential rotations) as it was reproduced in DTIStudio, and then opened with fslview. First, in DTIStudio, right seems to be right. Second, it looks like, when importing into FSL, the fiber is flipped along the AP and SI axes, and perhaps LR as well... This looks like a real mess...Any suggestions? Perhaps start from the scratch?? ;) Thanks, Miguel On Nov 16, 2010, at 3:43 AM, susumu mori wrote: > Do you think FAQ15 in https://www.mristudio.org/wiki/faq answers the > question? > > On Sun, Nov 14, 2010 at 7:25 PM, Miguel Burgaleta > wrote: > > Hi DTIStudio experts, > > I am saving my fibers in Analyze format and trying to export them into > FSL to do some stats in batch mode, but the resulting binary files > seem to experience an unexpected anterior-posterior flipping. I was > wondering if this is a known issue. Any advice to safely export fibers > will be highly appreciated. > > Best, > Miguel > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101119/519b3928/attachment-0002.html -------------- next part -------------- A non-text attachment was scrubbed... Name: pics.zip Type: application/zip Size: 167663 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101119/519b3928/attachment-0001.zip -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101119/519b3928/attachment-0003.html From gmak at poczta.onet.pl Wed Oct 13 02:49:53 2010 From: gmak at poczta.onet.pl (gmak at poczta.onet.pl) Date: Wed, 13 Oct 2010 06:49:53 -0000 Subject: [Mristudio-users] not valid VTK data File Message-ID: <57DC34D55E854BE583AB144CE703A8A6@zxzPC> Hi. I have a problem when I try to combine matrices. I have information " The file you want to load is not a valid VTK data file" what may cause this problem? I created two times Kimap and Hmap and there was the same message each time. I correctly combine metrices in 25subjects and this trouble have in 2 subjects. How to solve this problem? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101013/4780c91f/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: blad.JPG Type: image/jpeg Size: 41185 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101013/4780c91f/attachment.jpe -------------- next part -------------- A non-text attachment was scrubbed... Name: b?ad.JPG Type: image/jpeg Size: 124468 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101013/4780c91f/attachment-0001.jpe From jchu at hmc.psu.edu Tue Oct 19 17:33:03 2010 From: jchu at hmc.psu.edu (Jonathan Chu) Date: Tue, 19 Oct 2010 21:33:03 -0000 Subject: [Mristudio-users] Loading DICOM Message-ID: <4CBDD635.B5BF.0099.1@hmc.psu.edu> Hello, I am having some trouble loading my DICOM images in DTI studio. When I tried to the load the series via the Philips DICOM option, the result is stretched out in the inferior-superior direction; it doesn't seem to be reading the slice thickness correctly. When I tried to load the series via the Siemens and Toshiba DICOM options, the program crashed both times. Also, when I have DTI image loaded, it will not allow me to make a mean ADC map. How do I accomplish this? Thanks, I really appreciate your help. Jon Jonathan S. Chu Medical Student, Year III Penn State College of Medicine Milton S. Hershey Medical Center jchu at hmc.psu.edu 717-781-5990 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101019/45a1663e/attachment-0001.html From katja at bilkent.edu.tr Fri Oct 22 03:15:57 2010 From: katja at bilkent.edu.tr (Katja Doerschner) Date: Fri, 22 Oct 2010 07:15:57 -0000 Subject: [Mristudio-users] artifact Message-ID: <27E0629A-AF9C-4314-AA61-789F3F094B2F@bilkent.edu.tr> Hi, I am inspecting my DTI data and find that for some gradient directions (almost 10 out of 30) this hole-like artifact near central sulcus (very superior) appears. I am attaching an example from a DTI studio screenshot and the b0 image as a reference. The images were acquired with a 3 Siemens Magnetom, 50 axial slices, slice thickness 3mm, TR 6400ms, TE 88 ms, 4 averages, FOV 128 x 128; Grappa, Accel. Fact 2, 30 gradient directions, Phase Enc Direction A->P, b value 800, the patient was anesthetized. I also think that there is quite a bit of b0 distortion despite parallel imaging. My questions are: 1) what causes these artifacts (I have seen them in other scans/patients at different locations - could it be the effect of a large blood vessel or other kinds of motion)? 2) How can I avoid such artifacts? 3) Is there any way of 'saving' the data - other than throwing those images out 4) If I have to remove these images - how will that affect the tensor calculation/FA maps/fibertracking? Thank you very much. Katja -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101022/29cd1fbf/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: artifact.jpg Type: image/jpg Size: 173906 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101022/29cd1fbf/attachment-0002.jpg -------------- next part -------------- A non-text attachment was scrubbed... Name: b0.jpg Type: image/jpg Size: 134255 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101022/29cd1fbf/attachment-0003.jpg From kevinspitler at ucla.edu Sat Nov 13 21:08:14 2010 From: kevinspitler at ucla.edu (Kevin Spitler) Date: Sat, 13 Nov 2010 18:08:14 -0800 Subject: [Mristudio-users] problem calculating Tensor and ADC Map Message-ID: Hi, I am able to load my data into DTI Studio and can (on the DtiMap tab) run Original ADC Mean STD Mean (DWIs, B0s) My problem is that when I try either Calculation >> Tensor , Color Map, etc or Calculation >> ADC Map I get completely black views for axial, sagital, and coronal (and the 3d view in the upper left). I do not get an error message. What could be causing this? I get the same results regardless of choosing "create a mask image based on the background noise level 10" or choosing to "Select a mask image b0" I am using DTI Studio 3.0.3 (Sept 2010) on Windows 7 OS. I attached screen shots of the problem. My old data files load and I can do tractography on my old data. I am using Siemens Gradient: 0: 0, 0, 0 1:? 1.000000, 0.414250, -0.414250 2:? 1.000000, -0.414250, -0.414250 3:? 1.000000, -0.414250, 0.414250 4:? 1.000000, 0.414250, 0.414250 5:? 0.414250, 0.414250, 1.000000 6:? 0.414250, 1.000000, 0.414250 7:? 0.414250, 1.000000, -0.414250 8:? 0.414250, 0.414250, -1.000000 9:? 0.414250, -0.414250, -1.000000 10:? 0.414250, -1.000000, -0.414250 11:? 0.414250, -1.000000, 0.414250 12:? 0.414250, -0.414250, 1.000000 Thanks for your help Kevin -------------- next part -------------- A non-text attachment was scrubbed... Name: load but cannot do tractography.doc Type: application/msword Size: 855040 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101113/8d5098a8/attachment-0001.doc From hjiang at jhmi.edu Fri Nov 19 09:03:39 2010 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Fri, 19 Nov 2010 09:03:39 -0500 Subject: [Mristudio-users] saving fibers - flipping? In-Reply-To: References: <47E10083-C46F-48D3-9787-169573914483@uam.es> Message-ID: <145933A2BE9E4F48AE079A201379BF2F244584A188@RAD-EXCH1.win.ad.jhu.edu> hi, Miguel, if your file is in Analyze, you should open/load it as Analyze, not Philips REC (athough the .img looks like .rec file) . their coordinate system are different. Analyze uses left-hand system, REC is right-handed. in DtiStudio -> DTI Mapping, it does't accept Analzye file because it only takes the original DW-Image, not pre-processed images (which may contain scaling factors, and affact the tenosr calculation results). you may try: Dtistudio->MriView3D-> load Analyze files -> resave all images as on "RAW" file and then Dtistudio->DtiMapping-> load "RAW" file as Philips REC format..... OK basically, when you loaded the Analyze file, the program will adjust its coordinate system accordingly, and re-construct the images correctly. then, resaved "RAW" file is in same format as that of Philips REC. in this way, you can processing the "RAW" file as REC format. regards, hangyi ________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Miguel Burgaleta [miguel.burgaleta at uam.es] Sent: Friday, November 19, 2010 5:16 AM To: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: Re: [Mristudio-users] saving fibers - flipping? Hi Susumu, Not sure if that solves my problem... Also, Hangyi's answer was: please beware that the Analyze file is in Format 7.5. it is left-handed system. if you loaded it as Nifti-Analyze, the program may loaded as Nifti format, which is right-hand system. Let me give you more info. I processed my DWI in FSL for motion and eddy currents correction. Saved the images as 4D with .img extension, and opened them in DTIStudio as REC (the only option that worked out... when trying to open as Analyze, it complained about the header. None of the other format options worked). Did the fiber tracking and saved the fiber as Analyze. Please see attached a capture of a small bundle (but strategically located in the brain to track potential rotations) as it was reproduced in DTIStudio, and then opened with fslview. First, in DTIStudio, right seems to be right. Second, it looks like, when importing into FSL, the fiber is flipped along the AP and SI axes, and perhaps LR as well... This looks like a real mess...Any suggestions? Perhaps start from the scratch?? ;) Thanks, Miguel From susumu at mri.jhu.edu Fri Nov 19 09:30:41 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Fri, 19 Nov 2010 09:30:41 -0500 Subject: [Mristudio-users] Affine transformation In-Reply-To: References: Message-ID: Fijoy, Xin Li can help you about the exact format of the transformation matrix shortly. I just want to point out that Landmarker 1.4 is an obsolete version and you may want to try the latest DiffeoMap (Landmarker is terminated and changed to DiffeoMap). Susumu On Wed, Nov 3, 2010 at 3:22 PM, Fijoy Vadakkumpadan wrote: > Hi all, > > Would anyone know how to interpret the .dat file format used to save > affine transformations in Landmarker? This file seems to contain a 4x4 > matrix, but I cannot figure out what the numbers mean. I would like to > use the affine transformation generated by Landmarker and use it in a > Matlab code. I am using Landmarker 1.4. > > Thanks for any hints. > > Fijoy > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101119/1e3319da/attachment.html From xli16 at jhmi.edu Fri Nov 19 09:48:59 2010 From: xli16 at jhmi.edu (Xin Li) Date: Fri, 19 Nov 2010 09:48:59 -0500 Subject: [Mristudio-users] not valid VTK data File In-Reply-To: <57DC34D55E854BE583AB144CE703A8A6@zxzPC> References: <57DC34D55E854BE583AB144CE703A8A6@zxzPC> Message-ID: <71f0f450649d.4ce6480b@johnshopkins.edu> Hello, As I remember, you already asked this question before. I have already tested your lddmm map files on my machine. They work fine. I can combine them using DiffeoMap. Xin ----- Original Message ----- From: gmak at poczta.onet.pl Date: Friday, November 19, 2010 8:02 am Subject: [Mristudio-users] not valid VTK data File To: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" > Hi. > I have a problem when I try to combine matrices. > I have information " The file you want to load is not a valid VTK > data file" > what may cause this problem? > I created two times Kimap and Hmap and there was the same message > each time. > I correctly combine metrices in 25subjects and this trouble have in 2 > subjects. > How to solve this problem? > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Fri Nov 19 09:51:36 2010 From: xli16 at jhmi.edu (Xin Li) Date: Fri, 19 Nov 2010 09:51:36 -0500 Subject: [Mristudio-users] Affine transformation In-Reply-To: References: Message-ID: <7150f0f41036.4ce648a8@johnshopkins.edu> Hello, Did you get this matrix file by running landmark-based affine? Xin ----- Original Message ----- From: Fijoy Vadakkumpadan Date: Friday, November 19, 2010 8:00 am Subject: [Mristudio-users] Affine transformation To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Hi all, > > Would anyone know how to interpret the .dat file format used to save > affine transformations in Landmarker? This file seems to contain a 4x4 > matrix, but I cannot figure out what the numbers mean. I would like to > use the affine transformation generated by Landmarker and use it in a > Matlab code. I am using Landmarker 1.4. > > Thanks for any hints. > > Fijoy > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Fri Nov 19 09:59:55 2010 From: xli16 at jhmi.edu (Xin Li) Date: Fri, 19 Nov 2010 09:59:55 -0500 Subject: [Mristudio-users] not valid VTK data File In-Reply-To: <57DC34D55E854BE583AB144CE703A8A6@zxzPC> References: <57DC34D55E854BE583AB144CE703A8A6@zxzPC> Message-ID: <722093bb38ad.4ce64a9b@johnshopkins.edu> This is the thread about the same question you asked before. http://lists.mristudio.org/pipermail/mristudio-users/2010/001705.html After I received the map files you sent to me last time, I tested them on my machine. They work fine. I have also sent you an email to tell you about this. I don't know why they didn't work on your machine. How about resending these two lddmm jobs? Xin ----- Original Message ----- From: gmak at poczta.onet.pl Date: Friday, November 19, 2010 8:02 am Subject: [Mristudio-users] not valid VTK data File To: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" > Hi. > I have a problem when I try to combine matrices. > I have information " The file you want to load is not a valid VTK > data file" > what may cause this problem? > I created two times Kimap and Hmap and there was the same message > each time. > I correctly combine metrices in 25subjects and this trouble have in 2 > subjects. > How to solve this problem? > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From gmakowicz at gmail.com Fri Nov 19 13:19:45 2010 From: gmakowicz at gmail.com (gmakowicz at gmail.com) Date: Fri, 19 Nov 2010 19:19:45 +0100 Subject: [Mristudio-users] not valid VTK data File In-Reply-To: <71f0f450649d.4ce6480b@johnshopkins.edu> References: <57DC34D55E854BE583AB144CE703A8A6@zxzPC> <71f0f450649d.4ce6480b@johnshopkins.edu> Message-ID: HI This is the same question... I did not ask it again... I resended these two LDDMM like you suggested and only one worked correctly. I resended the second LDDMM four times and there was still the same message. ----- Original Message ----- From: "Xin Li" To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" Sent: Friday, November 19, 2010 3:48 PM Subject: Re: [Mristudio-users] not valid VTK data File > Hello, > > As I remember, you already asked this question before. I have already > tested your lddmm map files on my machine. They work fine. I can combine > them using DiffeoMap. > > Xin > > ----- Original Message ----- > From: gmak at poczta.onet.pl > Date: Friday, November 19, 2010 8:02 am > Subject: [Mristudio-users] not valid VTK data File > To: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" > > > >> Hi. >> I have a problem when I try to combine matrices. >> I have information " The file you want to load is not a valid VTK >> data file" >> what may cause this problem? >> I created two times Kimap and Hmap and there was the same message >> each time. >> I correctly combine metrices in 25subjects and this trouble have in 2 >> subjects. >> How to solve this problem? >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org From xli16 at jhmi.edu Fri Nov 19 14:44:18 2010 From: xli16 at jhmi.edu (Xin Li) Date: Fri, 19 Nov 2010 14:44:18 -0500 Subject: [Mristudio-users] not valid VTK data File In-Reply-To: References: <57DC34D55E854BE583AB144CE703A8A6@zxzPC> <71f0f450649d.4ce6480b@johnshopkins.edu> Message-ID: <72b098ae7991.4ce68d42@johnshopkins.edu> Sorry, I didn't notice about the sent time of the email. Yes, the email is the same one you sent before. Somehow it was sent out by the server again. It may be because that the server was rebooted. Xin ----- Original Message ----- From: gmakowicz at gmail.com Date: Friday, November 19, 2010 1:20 pm Subject: Re: [Mristudio-users] not valid VTK data File To: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" > HI > This is the same question... I did not ask it again... > > I resended these two LDDMM like you suggested and only one worked correctly. > I resended the second LDDMM four times and there was still the same > > message. > > > > ----- Original Message ----- > From: "Xin Li" > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > > Sent: Friday, November 19, 2010 3:48 PM > Subject: Re: [Mristudio-users] not valid VTK data File > > > > Hello, > > > > As I remember, you already asked this question before. I have > already > > tested your lddmm map files on my machine. They work fine. I can > combine > > them using DiffeoMap. > > > > Xin > > > > ----- Original Message ----- > > From: gmak at poczta.onet.pl > > Date: Friday, November 19, 2010 8:02 am > > Subject: [Mristudio-users] not valid VTK data File > > To: "DTI Studio, ROI Editor,DiffeoMap Questions/Support" > > > > > > > >> Hi. > >> I have a problem when I try to combine matrices. > >> I have information " The file you want to load is not a valid VTK > >> data file" > >> what may cause this problem? > >> I created two times Kimap and Hmap and there was the same message > >> each time. > >> I correctly combine metrices in 25subjects and this trouble have > in 2 > >> subjects. > >> How to solve this problem? > >> _______________________________________________ > >> mristudio-users mailing list > >> mristudio-users at mristudio.org > >> > >> Unsubscribe, send a blank email to: > >> mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > > mristudio-users mailing list > > mristudio-users at mristudio.org > > > > Unsubscribe, send a blank email to: > > mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From luca.binotto at unipd.it Sat Nov 20 08:14:46 2010 From: luca.binotto at unipd.it (luca.binotto at unipd.it) Date: Sat, 20 Nov 2010 14:14:46 +0100 Subject: [Mristudio-users] Siemens Allegra gradient table In-Reply-To: References: Message-ID: Hello, thanks for your previous help! Unfortunately the Siemens Avanto gradient table doesn't work for Siemens Allegra. I entered the table in the followiong format: 0: 0, 0, 0 1: 0, 0, 0 2: 0, 0, 0 3: -0.208098, 0.525514, 0.850005 4: 0.202387, 0.526131, 0.851002 5: 0.409956, 0.175267, 0.918257 6: -0.412630, 0.742620, 0.565889 7: -0.207127, 0.959492, 0.280092 8: -0.872713, 0.525505, 0.064764 9: -0.746815, 0.526129, 0.455449 etcetera Can you sand me an other kind of table to try. ? many thanks in any case. Luca > I hope this will do. > If not, please let me know. > You have to change the format to the MriStudio format. > > On Tue, Nov 9, 2010 at 3:09 PM, wrote: > >> Dear All, >> >> I am looking for gradient table for Siemens Allegra 3 tesla MR System >> with 30 directions. >> Can I use the one posted in this mailinglist for Siemens Avanto? >> >> Many thanks in advance, >> >> Luca Binotto >> >> >> >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > From luca.binotto at unipd.it Sat Nov 20 14:05:37 2010 From: luca.binotto at unipd.it (luca.binotto at unipd.it) Date: Sat, 20 Nov 2010 20:05:37 +0100 Subject: [Mristudio-users] Siemens Allegra gradient table In-Reply-To: References: Message-ID: Hello Dr. Susumu, as I said, I need a gradient table with 30 directions for Siemens Allegra 3 tesla. I tried to enter in DtiStudio the previous table you kindly sent to me (GRADIENT TABLE SIEMENS a list of VB13 gradient table), in the following format, ( dti data is composed of 3 b=0 volumes and 30 diffusion volumes): 0: 0, 0, 0 1: 0, 0, 0 2: 0, 0, 0 3: -0.208098, 0.525514, 0.850005 4: 0.202387, 0.526131, 0.851002 5: 0.409956, 0.175267, 0.918257 6: -0.412630, 0.742620, 0.565889 7: -0.207127, 0.959492, 0.280092 8: -0.872713, 0.525505, 0.064764 9: -0.746815, 0.526129, 0.455449 10: -0.415238, 0.175473, 0.915841 11: -0.746636, 0.175268, 0.673642 12: -0.665701, 0.742619, -0.217574 13: -0.330391, 0.959489, -0.110458 14: -0.331275, 0.525513, -0.809983 15: -0.663936, 0.526130, -0.569521 16: -0.999332, 0.175474, -0.111904 17: -0.871398, 0.175267, -0.501922 18: 0.001214, 0.742616, -0.700356 19: 0.002949, 0.959483, -0.348370 20: 0.667975, 0.525509, -0.565356 21: 0.336490, 0.526126, -0.807431 22: 0.202383, -0.175470, 0.985002 23: 0.208094, 0.175265, -0.983848 24: 0.666452, 0.742619, -0.215262 25: 0.332212, 0.959489, -0.104850 26: 0.205064, 0.958364, 0.285421 27: 0.412630, 0.742620, 0.565889 28: 0.746093, 0.175315, 0.674232 29: 0.744110, 0.525505, 0.460568 30: 0.871894, 0.526125, 0.070507 31: 0.874264, 0.175471, -0.496841 32: 1.000000, 0.175267, -0.106112 but I got very bad results, meaning that I used the wrong table. In 2000, Siemens launched Allegra 3T MR scanner, while TRIO was launched an year later. In mristudio mailing list it was posted a 12 directions gradient table for TRIO scanner. I would try to use a TRIO 30 directions table if you could find it. The only info I found in the dicom dti scan header was : Syngo MR 2004A 4VA25A software version. Many thanks again, Luca > I hope this will do. > If not, please let me know. > You have to change the format to the MriStudio format. > > On Tue, Nov 9, 2010 at 3:09 PM, wrote: > >> Dear All, >> >> I am looking for gradient table for Siemens Allegra 3 tesla MR System >> with 30 directions. >> Can I use the one posted in this mailinglist for Siemens Avanto? >> >> Many thanks in advance, >> >> Luca Binotto >> >> >> >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > From ycai_0901 at hotmail.com Mon Nov 22 00:22:43 2010 From: ycai_0901 at hotmail.com (yu cai) Date: Mon, 22 Nov 2010 13:22:43 +0800 Subject: [Mristudio-users] Fiber Tracking with two ROI files In-Reply-To: References: <213b1e.11ebe.12b10c645ce.Coremail.basketballmouse@163.com> <1dda817b.19.12c55a443ae.Coremail.basketballmouse@163.com> Message-ID: COuld help me unscribe from this list. Thanks Yu Date: Tue, 16 Nov 2010 14:05:50 -0500 From: susumu at mri.jhu.edu To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Fiber Tracking with two ROI files I assume that you have ROI files exported from another program? If so, FAQ16 in https://www.mristudio.org/wiki/faq may help. 2010/11/16 ??? Hi, I have got two ROI files ( A.dat and B.dat ) and finished the fiber tracking step on my DTI data. In DTIStudio, I can acquire each single ROI's fiber tracking results. I want to get the fibers that cross both the two ROIs, but it seems that the "and" operation doesn't work for ROI files. Could you give me any suggestion? Thank you! Bests, Haiqing ??163/126???????iphone ipad???? _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101122/d6808690/attachment.html From czhou4 at gmail.com Tue Nov 23 11:15:15 2010 From: czhou4 at gmail.com (Chunxiao Zhou) Date: Tue, 23 Nov 2010 11:15:15 -0500 Subject: [Mristudio-users] FOV of sample data Message-ID: Hello, In the tutorial video, you set the FOV as 212 for the sample data ik20070731dti2.2_5_1.rec. But I got the FOV (ap,fh,rl) [mm] : 211.00 143.00 211.00 from the ik20070731dti2.2_5_1.par file. Why should we set the FOV as 212 instead of 211? Thank you. Chunxiao(Andrew) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101123/7bae0ed3/attachment.html From susumu at mri.jhu.edu Tue Nov 23 11:52:25 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 23 Nov 2010 11:52:25 -0500 Subject: [Mristudio-users] FOV of sample data In-Reply-To: References: Message-ID: If PAR says 211, it must be 211. Maybe I was confused. On Tue, Nov 23, 2010 at 11:15 AM, Chunxiao Zhou wrote: > Hello, > > In the tutorial video, you set the FOV as 212 for the sample data > ik20070731dti2.2_5_1.rec. But I got the FOV (ap,fh,rl) [mm] : 211.00 > 143.00 211.00 from the ik20070731dti2.2_5_1.par file. Why should we set the > FOV as 212 instead of 211? Thank you. > > Chunxiao(Andrew) > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101123/1767e6a6/attachment.html From czhou4 at gmail.com Tue Nov 23 11:59:52 2010 From: czhou4 at gmail.com (Chunxiao Zhou) Date: Tue, 23 Nov 2010 11:59:52 -0500 Subject: [Mristudio-users] FOV of sample data In-Reply-To: References: Message-ID: Thank you! Chunxiao(Andrew) On Tue, Nov 23, 2010 at 11:52 AM, susumu mori wrote: > If PAR says 211, it must be 211. Maybe I was confused. > > On Tue, Nov 23, 2010 at 11:15 AM, Chunxiao Zhou wrote: > >> Hello, >> >> In the tutorial video, you set the FOV as 212 for the sample data >> ik20070731dti2.2_5_1.rec. But I got the FOV (ap,fh,rl) [mm] : 211.00 >> 143.00 211.00 from the ik20070731dti2.2_5_1.par file. Why should we set the >> FOV as 212 instead of 211? Thank you. >> >> Chunxiao(Andrew) >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101123/46d396cd/attachment-0001.html From czhou4 at gmail.com Tue Nov 23 17:07:19 2010 From: czhou4 at gmail.com (Chunxiao Zhou) Date: Tue, 23 Nov 2010 17:07:19 -0500 Subject: [Mristudio-users] Gradient Table for Philips Message-ID: Hello, When I do tensor calculation for my own data , there is a warning message "File size is bigger than DW-image size, continue anyway?". I get all image size parameters from my .par file ( I use Philip .REC .PAR data). I guess the reason is that I use the default ParRec gradient table from your GradientTable file. How could I get my gradient table from my file? Thank you. Chunxiao(Andrew) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101123/a09b719f/attachment.html From alex.dresner at philips.com Tue Nov 23 17:21:27 2010 From: alex.dresner at philips.com (Dresner, Alex) Date: Tue, 23 Nov 2010 23:21:27 +0100 Subject: [Mristudio-users] Gradient Table for Philips In-Reply-To: References: Message-ID: Dear Chunxiao, Your gradient table is also in the .PAR file. You should be able to read the .PAR file with any text reader such as WordPad, NotePad or Word; lower in the file is a table of parameters per-image. On the right-hand-side of that table are the diffusion directions in three columns. Regards, Alex ____________________ M. Alex Dresner, Ph.D. MR Clinical Scientist alex.dresner at philips.com ____________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Chunxiao Zhou Sent: Tuesday, November 23, 2010 5:07 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Gradient Table for Philips Hello, When I do tensor calculation for my own data , there is a warning message "File size is bigger than DW-image size, continue anyway?". I get all image size parameters from my .par file ( I use Philip .REC .PAR data). I guess the reason is that I use the default ParRec gradient table from your GradientTable file. How could I get my gradient table from my file? Thank you. Chunxiao(Andrew) ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101123/02ef4c5f/attachment.html From susumu at mri.jhu.edu Wed Nov 24 06:26:36 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Wed, 24 Nov 2010 06:26:36 -0500 Subject: [Mristudio-users] Gradient Table for Philips In-Reply-To: References: Message-ID: 1) Please read your REC file using Mri3DView. Use the image dimensions you get from the PAR file. 2) After the images are read, please go through the images using the pull-down menu in the right column of the viewing window. Check if all the images (b0 and DWIs) look fine. 3) Find out how many 3D images are loaded. If you used Philips "High" gradient orientation, you should have 34 images loaded; one b0, 32 DWIs, and one calculated DWIs (I think this is the sum of all DWIs). 4) Make sure where is b0. It could be the first or the second from the last. The calculated DWI is always at the end. 5) Close the window and start DtiMapping. 6) Cut&Paste your gradient table to the appropriate section. You have to make sure several things here; a: The position of b0; First or the second from the last b: The number of rows; It has to be 34. Sometimes you find a table with only 33 lines ignoring the last calculated image. In this case, you get the error message, complaining that the file size doesn't match. Because the last image is not used anyway, you can ignore the message and proceed. The last image is thrown away. Or, you can increase the number of row to 34 by adding 33: 100, 100, 100, in which [100, 100, 100] send the message to DtiStudio to remove this image. c: Please make sure if you used "gradient overplus ON" or "OFF", because you have to use different tables. 7) If you still get the file size error message, something is wrong. On Tue, Nov 23, 2010 at 5:21 PM, Dresner, Alex wrote: > Dear Chunxiao, > > Your gradient table is also in the .PAR file. You should be able to read > the .PAR file with any text reader such as WordPad, NotePad or Word; lower > in the file is a table of parameters per-image. On the right-hand-side of > that table are the diffusion directions in three columns. > > > > Regards, > > Alex > > > > ____________________ > > M. Alex Dresner, Ph.D. > > MR Clinical Scientist > > alex.dresner at philips.com > > ____________________ > > > > > > > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Chunxiao Zhou > *Sent:* Tuesday, November 23, 2010 5:07 PM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] Gradient Table for Philips > > > > Hello, > > > > When I do tensor calculation for my own data , there is a warning message > "File size is bigger than DW-image size, continue anyway?". I get all image > size parameters from my .par file ( I use Philip .REC .PAR data). I guess > the reason is that I use the default ParRec gradient table from your > GradientTable file. How could I get my gradient table from my file? > > > > Thank you. > > > > Chunxiao(Andrew) > > ------------------------------ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101124/c5157f3b/attachment.html From miguel.burgaleta at uam.es Wed Nov 24 10:05:57 2010 From: miguel.burgaleta at uam.es (Miguel Burgaleta) Date: Wed, 24 Nov 2010 16:05:57 +0100 Subject: [Mristudio-users] saving fibers - flipping? In-Reply-To: <145933A2BE9E4F48AE079A201379BF2F244584A188@RAD-EXCH1.win.ad.jhu.edu> References: <47E10083-C46F-48D3-9787-169573914483@uam.es> <145933A2BE9E4F48AE079A201379BF2F244584A188@RAD-EXCH1.win.ad.jhu.edu> Message-ID: <3B2FF3EB-918C-433E-AE85-12C6BB16D5C7@uam.es> Hi Hangyi, Thanks for your email. I'm afraid I'm not able to load my Analyze files with MriView3D either. The message is: CMriView3DDoc()::CreateImgWithAnalyzeFile() Unrecognized Analyze Header File: And then the path and filename of the header. Any suggestions? Thanks again, Miguel On Nov 19, 2010, at 3:03 PM, Hangyi Jiang wrote: > hi, Miguel, > > if your file is in Analyze, you should open/load it as Analyze, not > Philips REC (athough the .img looks like .rec file) . their > coordinate system are different. Analyze uses left-hand system, REC > is right-handed. > > in DtiStudio -> DTI Mapping, it does't accept Analzye file because > it only takes the original DW-Image, not pre-processed images (which > may contain scaling factors, and affact the tenosr calculation > results). > > you may try: Dtistudio->MriView3D-> load Analyze files -> resave > all images as on "RAW" file and then > Dtistudio->DtiMapping-> load "RAW" file as > Philips REC format..... OK > > > basically, when you loaded the Analyze file, the program will adjust > its coordinate system accordingly, and re-construct the images > correctly. then, resaved "RAW" file is in same format as that of > Philips REC. in this way, you can processing the "RAW" file as REC > format. > > regards, > > hangyi > > > > > > > > > > ________________________________ > From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org > ] On Behalf Of Miguel Burgaleta [miguel.burgaleta at uam.es] > Sent: Friday, November 19, 2010 5:16 AM > To: DTI Studio, ROI Editor, DiffeoMap Questions/Support > Subject: Re: [Mristudio-users] saving fibers - flipping? > > > Hi Susumu, > > Not sure if that solves my problem... Also, Hangyi's answer was: > > please beware that the Analyze file is in Format 7.5. it is left- > handed system. > if you loaded it as Nifti-Analyze, the program may loaded as Nifti > format, which is right-hand system. > > Let me give you more info. > > I processed my DWI in FSL for motion and eddy currents correction. > Saved the images as 4D with .img extension, and opened them in > DTIStudio as REC (the only option that worked out... when trying to > open as Analyze, it complained about the header. None of the other > format options worked). Did the fiber tracking and saved the fiber > as Analyze. > > Please see attached a capture of a small bundle (but strategically > located in the brain to track potential rotations) as it was > reproduced in DTIStudio, and then opened with fslview. First, in > DTIStudio, right seems to be right. Second, it looks like, when > importing into FSL, the fiber is flipped along the AP and SI axes, > and perhaps LR as well... > > This looks like a real mess...Any suggestions? Perhaps start from > the scratch?? ;) > Thanks, > Miguel > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From czhou4 at gmail.com Wed Nov 24 10:38:51 2010 From: czhou4 at gmail.com (Chunxiao Zhou) Date: Wed, 24 Nov 2010 10:38:51 -0500 Subject: [Mristudio-users] Gradient Table for Philips In-Reply-To: References: Message-ID: Prof. Susumu, Thank you very much for your very detailed information and help! Have a nice holiday! Chunxiao(Andrew) On Wed, Nov 24, 2010 at 6:26 AM, susumu mori wrote: > 1) Please read your REC file using Mri3DView. Use the image dimensions you > get from the PAR file. > 2) After the images are read, please go through the images using the > pull-down menu in the right column of the viewing window. Check if all the > images (b0 and DWIs) look fine. > 3) Find out how many 3D images are loaded. If you used Philips "High" > gradient orientation, you should have 34 images loaded; one b0, 32 DWIs, and > one calculated DWIs (I think this is the sum of all DWIs). > 4) Make sure where is b0. It could be the first or the second from the > last. The calculated DWI is always at the end. > 5) Close the window and start DtiMapping. > 6) Cut&Paste your gradient table to the appropriate section. You have to > make sure several things here; > a: The position of b0; First or the second from the last > b: The number of rows; It has to be 34. Sometimes you find a table with > only 33 lines ignoring the last calculated image. In this case, you get the > error message, complaining that the file size doesn't match. Because the > last image is not used anyway, you can ignore the message and proceed. The > last image is thrown away. Or, you can increase the number of row to 34 by > adding 33: 100, 100, 100, in which [100, 100, 100] send the message to > DtiStudio to remove this image. > c: Please make sure if you used "gradient overplus ON" or "OFF", because > you have to use different tables. > 7) If you still get the file size error message, something is wrong. > > On Tue, Nov 23, 2010 at 5:21 PM, Dresner, Alex wrote: > >> Dear Chunxiao, >> >> Your gradient table is also in the .PAR file. You should be able to read >> the .PAR file with any text reader such as WordPad, NotePad or Word; lower >> in the file is a table of parameters per-image. On the right-hand-side of >> that table are the diffusion directions in three columns. >> >> >> >> Regards, >> >> Alex >> >> >> >> ____________________ >> >> M. Alex Dresner, Ph.D. >> >> MR Clinical Scientist >> >> alex.dresner at philips.com >> >> ____________________ >> >> >> >> >> >> >> >> *From:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *On Behalf Of *Chunxiao Zhou >> *Sent:* Tuesday, November 23, 2010 5:07 PM >> *To:* mristudio-users at mristudio.org >> *Subject:* [Mristudio-users] Gradient Table for Philips >> >> >> >> Hello, >> >> >> >> When I do tensor calculation for my own data , there is a warning message >> "File size is bigger than DW-image size, continue anyway?". I get all image >> size parameters from my .par file ( I use Philip .REC .PAR data). I guess >> the reason is that I use the default ParRec gradient table from your >> GradientTable file. How could I get my gradient table from my file? >> >> >> >> Thank you. >> >> >> >> Chunxiao(Andrew) >> >> ------------------------------ >> The information contained in this message may be confidential and legally >> protected under applicable law. The message is intended solely for the >> addressee(s). If you are not the intended recipient, you are hereby notified >> that any use, forwarding, dissemination, or reproduction of this message is >> strictly prohibited and may be unlawful. If you are not the intended >> recipient, please contact the sender by return e-mail and destroy all copies >> of the original message. >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101124/aeb45930/attachment.html From gonzalo.rojas.costa at gmail.com Wed Nov 24 14:30:33 2010 From: gonzalo.rojas.costa at gmail.com (Gonzalo Rojas) Date: Wed, 24 Nov 2010 16:30:33 -0300 Subject: [Mristudio-users] gradient directions table... In-Reply-To: References: Message-ID: Hi: ?I need the gradient directions table (6 directions) in a Siemens Avanto MRI equipment release Syngo MR B13... Could you please send me?... ?Sincerely, Gonzalo Roajs Costa Department of Radiology Clinica Las Condes Santiago Chile From gonzalo.rojas.costa at gmail.com Wed Nov 24 15:25:31 2010 From: gonzalo.rojas.costa at gmail.com (Gonzalo Rojas) Date: Wed, 24 Nov 2010 17:25:31 -0300 Subject: [Mristudio-users] gradient directions table... Message-ID: Hi: I need the gradient directions table (6 directions) in a Siemens Avanto MRI equipment release Syngo MR B13... Could you please send me ?... Sincerely, Gonzalo Roajs Costa Department of Radiology Clinica Las Condes Santiago Chile From ftam-lists at rotman-baycrest.on.ca Wed Nov 24 22:16:35 2010 From: ftam-lists at rotman-baycrest.on.ca (Fred Tam) Date: Thu, 25 Nov 2010 03:16:35 +0000 Subject: [Mristudio-users] artifact In-Reply-To: <27E0629A-AF9C-4314-AA61-789F3F094B2F@bilkent.edu.tr> References: <27E0629A-AF9C-4314-AA61-789F3F094B2F@bilkent.edu.tr> Message-ID: <1290654996.7037.68.camel@fissure.rotman-baycrest.on.ca> Hello, Katja. Your artifact looks somewhat like the one examined (and corrected/avoided) here: Gallichan D, Scholz J, Bartsch A, Behrens TE, Robson MD, Miller KL (2010): Addressing a Systematic Vibration Artifact in diffusion-Weighted MRI. Hum Brain Mapp 31:193-202. Fred On Fri, 2010-10-22 at 10:15 +0300, Katja Doerschner wrote: > Hi, > > > I am inspecting my DTI data and find that for some gradient directions > (almost 10 out of 30) this hole-like artifact near central sulcus > (very superior) appears. I am attaching an example from a DTI studio > screenshot and the b0 image as a reference. > The images were acquired with a 3 Siemens Magnetom, 50 axial slices, > slice thickness 3mm, TR 6400ms, TE 88 ms, 4 averages, FOV 128 x 128; > Grappa, Accel. Fact 2, 30 gradient directions, Phase Enc Direction > A->P, b value 800, the patient was anesthetized. > > > I also think that there is quite a bit of b0 distortion despite > parallel imaging. > > > My questions are: 1) what causes these artifacts (I have seen them in > other scans/patients at different locations - could it be the effect > of a large blood vessel or other kinds of motion)? > 2) How can I avoid such artifacts? > 3) Is there any way of 'saving' the data - other than throwing those > images out > 4) If I have to remove these images - how will that affect the tensor > calculation/FA maps/fibertracking? > > > Thank you very much. > Katja > > > > From katja at bilkent.edu.tr Wed Nov 24 23:29:36 2010 From: katja at bilkent.edu.tr (Katja Doerschner) Date: Thu, 25 Nov 2010 06:29:36 +0200 Subject: [Mristudio-users] artifact In-Reply-To: <1290654996.7037.68.camel@fissure.rotman-baycrest.on.ca> References: <27E0629A-AF9C-4314-AA61-789F3F094B2F@bilkent.edu.tr> <1290654996.7037.68.camel@fissure.rotman-baycrest.on.ca> Message-ID: <42758FF6-69CB-466A-886D-BFF734B13052@bilkent.edu.tr> Yes! It does, and it is also highly gradient direction dependent (in my data it is also the x gradient direction). Thank you very much for this source. Best, katja On Nov 25, 2010, at 5:16 AM, Fred Tam wrote: > Hello, Katja. Your artifact looks somewhat like the one examined (and > corrected/avoided) here: > > Gallichan D, Scholz J, Bartsch A, Behrens TE, Robson MD, Miller KL > (2010): Addressing a Systematic Vibration Artifact in diffusion-Weighted > MRI. Hum Brain Mapp 31:193-202. > > Fred > > > On Fri, 2010-10-22 at 10:15 +0300, Katja Doerschner wrote: >> Hi, >> >> >> I am inspecting my DTI data and find that for some gradient directions >> (almost 10 out of 30) this hole-like artifact near central sulcus >> (very superior) appears. I am attaching an example from a DTI studio >> screenshot and the b0 image as a reference. >> The images were acquired with a 3 Siemens Magnetom, 50 axial slices, >> slice thickness 3mm, TR 6400ms, TE 88 ms, 4 averages, FOV 128 x 128; >> Grappa, Accel. Fact 2, 30 gradient directions, Phase Enc Direction >> A->P, b value 800, the patient was anesthetized. >> >> >> I also think that there is quite a bit of b0 distortion despite >> parallel imaging. >> >> >> My questions are: 1) what causes these artifacts (I have seen them in >> other scans/patients at different locations - could it be the effect >> of a large blood vessel or other kinds of motion)? >> 2) How can I avoid such artifacts? >> 3) Is there any way of 'saving' the data - other than throwing those >> images out >> 4) If I have to remove these images - how will that affect the tensor >> calculation/FA maps/fibertracking? >> >> >> Thank you very much. >> Katja >> >> >> >> > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From miguel.burgaleta at uam.es Thu Nov 25 11:35:22 2010 From: miguel.burgaleta at uam.es (Miguel Burgaleta) Date: Thu, 25 Nov 2010 17:35:22 +0100 Subject: [Mristudio-users] 32 vs 64 bits Message-ID: Hi DTIStudio experts, We are about to start a new project and several "raters" will reproduce the same tracts. We are assuming that there will be no bias if some of them use DTIStudio 32 bits and others the 64 bits version, as long as they work with the latest release of the program. Is this correct? Thanks, Miguel From susumu at mri.jhu.edu Thu Nov 25 11:58:52 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 25 Nov 2010 11:58:52 -0500 Subject: [Mristudio-users] 32 vs 64 bits In-Reply-To: References: Message-ID: yes. there is no difference between 32 and 64 bit versions. On Thu, Nov 25, 2010 at 11:35 AM, Miguel Burgaleta wrote: > > Hi DTIStudio experts, > > We are about to start a new project and several "raters" will > reproduce the same tracts. We are assuming that there will be no bias > if some of them use DTIStudio 32 bits and others the 64 bits version, > as long as they work with the latest release of the program. Is this > correct? > > Thanks, > Miguel > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101125/58fbae0f/attachment.html From ssaksena21 at gmail.com Thu Nov 25 12:06:44 2010 From: ssaksena21 at gmail.com (Saurabh) Date: Thu, 25 Nov 2010 12:06:44 -0500 Subject: [Mristudio-users] 32 vs 64 bits In-Reply-To: References: Message-ID: <54DBB8AF-8694-4AC1-B229-4FA547F9C49B@gmail.com> Dear Sir, I would sincerely request you to please remove me from the mailing list. I have sent repeated reminders and have also sent email to unsubscribe without any luck. Please do that at your earliest convenience. Best regards Saurabh Sent from my iPhone On Nov 25, 2010, at 11:58 AM, susumu mori wrote: > yes. there is no difference between 32 and 64 bit versions. > > On Thu, Nov 25, 2010 at 11:35 AM, Miguel Burgaleta > wrote: > > Hi DTIStudio experts, > > We are about to start a new project and several "raters" will > reproduce the same tracts. We are assuming that there will be no bias > if some of them use DTIStudio 32 bits and others the 64 bits version, > as long as they work with the latest release of the program. Is this > correct? > > Thanks, > Miguel > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101125/dfc6c60d/attachment.html From gonzalo.rojas.costa at gmail.com Thu Nov 25 14:07:40 2010 From: gonzalo.rojas.costa at gmail.com (Gonzalo Rojas) Date: Thu, 25 Nov 2010 16:07:40 -0300 Subject: [Mristudio-users] SIEMENS Avanto Gradient Directions (6) Message-ID: Hi: I got the following gradient directions table from the DICOM TAG (19, 100E): 1: 0.70817843 0.00571112 -0.70389509 2: 0.70889196 -0.00570537 0.70318659 3: 0.03170213 0.0 -0.03170213 4: 0.03168621 0.0 -0.03168621 5: 0.70427267 -0.70853239 0.00567962 6: 0.7039208 0.70959758 0.00425759 Why the directions 3 and 4 are equal ?... Sincerely, Gonzalo Rojas Costa > ?I need the gradient directions table (6 directions) in a Siemens > Avanto MRI equipment release Syngo MR B13... Could you please send me?... > > ?Sincerely, > > > Gonzalo Roajs Costa > Department of Radiology > Clinica Las Condes > Santiago > Chile From susumu at mri.jhu.edu Thu Nov 25 14:27:19 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Thu, 25 Nov 2010 14:27:19 -0500 Subject: [Mristudio-users] SIEMENS Avanto Gradient Directions (6) In-Reply-To: References: Message-ID: I believe this is Siemens 6 0: 0, 0, 0 1: 1, 0, 1 2: -1, 0, 1 3: 0, 1, 1 4: 0, 1, -1 5: 1, 1, 0 6: -1, 1, 0 You can see this table is almost identical to yours (yours is unit-vector normalized). The small deviation is, I believe, the table in DICOM file includes the small contributions from imaging gradients. #3 and #4 of your table indeed look strange. I heard that the DICOM gradient information in the latest operating system is correct. I'm not sure if that implies the information in the old operating system is not right... On Thu, Nov 25, 2010 at 2:07 PM, Gonzalo Rojas < gonzalo.rojas.costa at gmail.com> wrote: > Hi: > > I got the following gradient directions table from the DICOM TAG (19, > 100E): > > 1: 0.70817843 0.00571112 -0.70389509 > > 2: 0.70889196 -0.00570537 0.70318659 > > 3: 0.03170213 0.0 -0.03170213 > > 4: 0.03168621 0.0 -0.03168621 > > 5: 0.70427267 -0.70853239 0.00567962 > > 6: 0.7039208 0.70959758 0.00425759 > > > Why the directions 3 and 4 are equal ?... > > Sincerely, > > > Gonzalo Rojas Costa > > > > ?I need the gradient directions table (6 directions) in a Siemens > > Avanto MRI equipment release Syngo MR B13... Could you please send me?... > > > > ?Sincerely, > > > > > > Gonzalo Roajs Costa > > Department of Radiology > > Clinica Las Condes > > Santiago > > Chile > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101125/bf46fae2/attachment.html From petya_dti at yahoo.com Fri Nov 26 17:19:23 2010 From: petya_dti at yahoo.com (Petya R) Date: Fri, 26 Nov 2010 14:19:23 -0800 (PST) Subject: [Mristudio-users] LDDMM Message-ID: <671334.11035.qm@web121702.mail.ne1.yahoo.com> Hello, We are trying to use LDDMM, but it seems that we are not able to submit files via the DiffeoMap program. I've followed the steps outlined in: https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_StepTwo_NonlinearNormalization_FAb0 However, I'm not receiving a confirmation message at the end (as listed towards the end of the website above) that "The image data have been sent to the server successfully...". I've tried this step several times (over the last 3 days)-- but the program still doesn't show the confirmation message, and I have not received email(s) with "Md5 String" number(s). Also, I've turned off my firewall, and followed the instructions to connect to the ftp.mristudio.org server (included below from an older message)-- but these still didn't seem to help. Please let me know if you might have any suggestions, and/or if there is anything else I can do. Thank you very much for your help and consideration! Petya **************************************************************************************** [Mristudio-users] Landmarker LDDMM error Xin Li xli16 at jhmi.edu Tue May 12 10:41:27 EDT 2009 * Previous message: [Mristudio-users] Landmarker LDDMM error * Next message: [Mristudio-users] Landmarker LDDMM error * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Fijoy, Please test if your computer can access our ftp server. In Command Prompt Window, please try the ftp program. It should look like: C:\Documents and Setting\Administrator>ftp ftp.mristudio.org Connected to ftp.mristudio.org. 220 Welcome to MRI STudio FTP service. -- Turn off Passive Mode. User (ftp.mristudio.org:(none)): anonymous 331 Please specify the password. Password: 230 Login successful. ftp> dir Please let me the test result. Xin ----- Original Message ----- From: Fijoy Vadakkumpadan Date: Monday, May 11, 2009 7:50 pm Subject: [Mristudio-users] Landmarker LDDMM error To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >Hi all, > >I am trying to run single channel remote volume LDDMM using the >Landmarker 1.4. The Landmarker is installed on a 64-bit Windows Vista >virtual machine (VMware Player). In addition to the intensity >information, I am using landmarks also for the LDDMM registration. >However, I am receiving the following pop-up error message: > >"Cannot upload this file: d39d65436099132a2a82efb0dfc8810a.zip" > >Could anyone please help me with resolving this problem? > >Thank you, >Fijoy >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org > * Previous message: [Mristudio-users] Landmarker LDDMM error * Next message: [Mristudio-users] Landmarker LDDMM error * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the Mristudio-users mailing list -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101126/09ea2af7/attachment-0001.html From akolasny at jhu.edu Fri Nov 26 18:00:27 2010 From: akolasny at jhu.edu (akolasny at jhu.edu) Date: Fri, 26 Nov 2010 18:00:27 -0500 (EST) Subject: [Mristudio-users] LDDMM In-Reply-To: <671334.11035.qm@web121702.mail.ne1.yahoo.com> References: <671334.11035.qm@web121702.mail.ne1.yahoo.com> Message-ID: <51156.68.50.209.72.1290812427.squirrel@webmail.cis.jhu.edu> Petya, There were 8 entries that had 0 bytes. It appears the data never completely transfered to the servers for processing. Be sure that passive mode is turned off. Thanks, Anthony > Hello, > > We are trying to use LDDMM, but it seems that we are not able to submit > files > via the DiffeoMap program. > > I've followed the steps outlined in: > https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_StepTwo_NonlinearNormalization_FAb0 > > However, I'm not receiving a confirmation message at the end (as listed > towards > the end of the website above) that "The image data have been sent to the > server > successfully...". I've tried this step several times (over the last 3 > days)-- > but the program still doesn't show the confirmation message, and I have > not > received email(s) with "Md5 String" number(s). Also, I've turned off my > firewall, and followed the instructions to connect to the > ftp.mristudio.org > server (included below from an older message)-- but these still didn't > seem to > help. Please let me know if you might have any suggestions, and/or if > there is > anything else I can do. > > Thank you very much for your help and consideration! > Petya > > > **************************************************************************************** > > > [Mristudio-users] Landmarker LDDMM error > Xin Li xli16 at jhmi.edu > Tue May 12 10:41:27 EDT 2009 > * Previous message: [Mristudio-users] Landmarker LDDMM error > * Next message: [Mristudio-users] Landmarker LDDMM error > * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > Fijoy, > > Please test if your computer can access our ftp server. > > In Command Prompt Window, please try the ftp program. It should look like: > > C:\Documents and Setting\Administrator>ftp ftp.mristudio.org > Connected to ftp.mristudio.org. > 220 Welcome to MRI STudio FTP service. -- Turn off Passive Mode. > User (ftp.mristudio.org:(none)): anonymous > 331 Please specify the password. > Password: > 230 Login successful. > ftp> dir > > Please let me the test result. > > Xin > > > > ----- Original Message ----- > From: Fijoy Vadakkumpadan > Date: Monday, May 11, 2009 7:50 pm > Subject: [Mristudio-users] Landmarker LDDMM error > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > mristudio.org> > > >>Hi all, >> >>I am trying to run single channel remote volume LDDMM using the >>Landmarker 1.4. The Landmarker is installed on a 64-bit Windows Vista >>virtual machine (VMware Player). In addition to the intensity >>information, I am using landmarks also for the LDDMM registration. >>However, I am receiving the following pop-up error message: >> >>"Cannot upload this file: d39d65436099132a2a82efb0dfc8810a.zip" >> >>Could anyone please help me with resolving this problem? >> >>Thank you, >>Fijoy >>_______________________________________________ >>Mristudio-users mailing list >>Mristudio-users at mristudio.org >> > * Previous message: [Mristudio-users] Landmarker LDDMM error > * Next message: [Mristudio-users] Landmarker LDDMM error > * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > More information about the Mristudio-users mailing list > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > From petya_dti at yahoo.com Sat Nov 27 17:25:40 2010 From: petya_dti at yahoo.com (Petya R) Date: Sat, 27 Nov 2010 14:25:40 -0800 (PST) Subject: [Mristudio-users] LDDMM In-Reply-To: <51156.68.50.209.72.1290812427.squirrel@webmail.cis.jhu.edu> References: <671334.11035.qm@web121702.mail.ne1.yahoo.com> <51156.68.50.209.72.1290812427.squirrel@webmail.cis.jhu.edu> Message-ID: <848423.57299.qm@web121701.mail.ne1.yahoo.com> Dear Anthony, Thank you very much for your email! How could I make sure that the passive mode is turned off? I tried going to the Control Panel--> Internet Options--> Advanced tab, and made sure that the "Use passive ftp (for firewall and DSL model compatibiligy)" option does not have a check mark-- though I don't know if this is sufficient... I'm still not receiving a confirmation message when I try to submit data for LDDMM. Please let me know if you might have any other suggestions. Thank you very much for your help! Petya ________________________________ From: "akolasny at jhu.edu" To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" Sent: Fri, November 26, 2010 6:00:27 PM Subject: Re: [Mristudio-users] LDDMM Petya, There were 8 entries that had 0 bytes. It appears the data never completely transfered to the servers for processing. Be sure that passive mode is turned off. Thanks, Anthony > Hello, > > We are trying to use LDDMM, but it seems that we are not able to submit > files > via the DiffeoMap program. > > I've followed the steps outlined in: >https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_StepTwo_NonlinearNormalization_FAb0 >0 > > However, I'm not receiving a confirmation message at the end (as listed > towards > the end of the website above) that "The image data have been sent to the > server > successfully...". I've tried this step several times (over the last 3 > days)-- > but the program still doesn't show the confirmation message, and I have > not > received email(s) with "Md5 String" number(s). Also, I've turned off my > firewall, and followed the instructions to connect to the > ftp.mristudio.org > server (included below from an older message)-- but these still didn't > seem to > help. Please let me know if you might have any suggestions, and/or if > there is > anything else I can do. > > Thank you very much for your help and consideration! > Petya > > >**************************************************************************************** >* > > > [Mristudio-users] Landmarker LDDMM error > Xin Li xli16 at jhmi.edu > Tue May 12 10:41:27 EDT 2009 > * Previous message: [Mristudio-users] Landmarker LDDMM error > * Next message: [Mristudio-users] Landmarker LDDMM error > * Messages sorted by: [ date ] [ thread ] [ subject ] [ >author ] > Fijoy, > > Please test if your computer can access our ftp server. > > In Command Prompt Window, please try the ftp program. It should look like: > > C:\Documents and Setting\Administrator>ftp ftp.mristudio.org > Connected to ftp.mristudio.org. > 220 Welcome to MRI STudio FTP service. -- Turn off Passive Mode. > User (ftp.mristudio.org:(none)): anonymous > 331 Please specify the password. > Password: > 230 Login successful. > ftp> dir > > Please let me the test result. > > Xin > > > > ----- Original Message ----- > From: Fijoy Vadakkumpadan > Date: Monday, May 11, 2009 7:50 pm > Subject: [Mristudio-users] Landmarker LDDMM error > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > mristudio.org> > > >>Hi all, >> >>I am trying to run single channel remote volume LDDMM using the >>Landmarker 1.4. The Landmarker is installed on a 64-bit Windows Vista >>virtual machine (VMware Player). In addition to the intensity >>information, I am using landmarks also for the LDDMM registration. >>However, I am receiving the following pop-up error message: >> >>"Cannot upload this file: d39d65436099132a2a82efb0dfc8810a.zip" >> >>Could anyone please help me with resolving this problem? >> >>Thank you, >>Fijoy >>_______________________________________________ >>Mristudio-users mailing list >>Mristudio-users at mristudio.org >> > * Previous message: [Mristudio-users] Landmarker LDDMM error > * Next message: [Mristudio-users] Landmarker LDDMM error > * Messages sorted by: [ date ] [ thread ] [ subject ] [ >author ] > More information about the Mristudio-users mailing list > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101127/67b096b7/attachment.html From akolasny at jhu.edu Sat Nov 27 17:39:25 2010 From: akolasny at jhu.edu (akolasny at jhu.edu) Date: Sat, 27 Nov 2010 17:39:25 -0500 (EST) Subject: [Mristudio-users] LDDMM In-Reply-To: <848423.57299.qm@web121701.mail.ne1.yahoo.com> References: <671334.11035.qm@web121702.mail.ne1.yahoo.com> <51156.68.50.209.72.1290812427.squirrel@webmail.cis.jhu.edu> <848423.57299.qm@web121701.mail.ne1.yahoo.com> Message-ID: <56340.68.50.209.72.1290897565.squirrel@webmail.cis.jhu.edu> Dear Petya, DiffeoMap should transfer the data correctly. If you are manually sending data to the ftp server, the 'status' option will provide the information. The server is running several jobs from other people. There is no data in the queue at this time. Things seem to be working correctly. -Anthony > Dear Anthony, > Thank you very much for your email! How could I make sure that the > passive mode > is turned off? I tried going to the Control Panel--> Internet Options--> > Advanced tab, and made sure that the "Use passive ftp (for firewall and > DSL > model compatibiligy)" option does not have a check mark-- though I don't > know if > this is sufficient... I'm still not receiving a confirmation message when > I try > to submit data for LDDMM. Please let me know if you might have any other > suggestions. > Thank you very much for your help! > Petya > > > > > > ________________________________ > From: "akolasny at jhu.edu" > To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" > > Sent: Fri, November 26, 2010 6:00:27 PM > Subject: Re: [Mristudio-users] LDDMM > > Petya, > > There were 8 entries that had 0 bytes. It appears the data never > completely transfered to the servers for processing. > > Be sure that passive mode is turned off. > > Thanks, > Anthony > >> Hello, >> >> We are trying to use LDDMM, but it seems that we are not able to submit >> files >> via the DiffeoMap program. >> >> I've followed the steps outlined in: >>https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_StepTwo_NonlinearNormalization_FAb0 >>0 >> >> However, I'm not receiving a confirmation message at the end (as listed >> towards >> the end of the website above) that "The image data have been sent to the >> server >> successfully...". I've tried this step several times (over the last 3 >> days)-- >> but the program still doesn't show the confirmation message, and I have >> not >> received email(s) with "Md5 String" number(s). Also, I've turned off my >> firewall, and followed the instructions to connect to the >> ftp.mristudio.org >> server (included below from an older message)-- but these still didn't >> seem to >> help. Please let me know if you might have any suggestions, and/or if >> there is >> anything else I can do. >> >> Thank you very much for your help and consideration! >> Petya >> >> >>**************************************************************************************** >>* >> >> >> [Mristudio-users] Landmarker LDDMM error >> Xin Li xli16 at jhmi.edu >> Tue May 12 10:41:27 EDT 2009 >> * Previous message: [Mristudio-users] Landmarker LDDMM error >> * Next message: [Mristudio-users] Landmarker LDDMM error >> * Messages sorted by: [ date ] [ thread ] [ subject ] [ >>author ] >> Fijoy, >> >> Please test if your computer can access our ftp server. >> >> In Command Prompt Window, please try the ftp program. It should look >> like: >> >> C:\Documents and Setting\Administrator>ftp ftp.mristudio.org >> Connected to ftp.mristudio.org. >> 220 Welcome to MRI STudio FTP service. -- Turn off Passive Mode. >> User (ftp.mristudio.org:(none)): anonymous >> 331 Please specify the password. >> Password: >> 230 Login successful. >> ftp> dir >> >> Please let me the test result. >> >> Xin >> >> >> >> ----- Original Message ----- >> From: Fijoy Vadakkumpadan >> Date: Monday, May 11, 2009 7:50 pm >> Subject: [Mristudio-users] Landmarker LDDMM error >> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >> > mristudio.org> >> >> >>>Hi all, >>> >>>I am trying to run single channel remote volume LDDMM using the >>>Landmarker 1.4. The Landmarker is installed on a 64-bit Windows Vista >>>virtual machine (VMware Player). In addition to the intensity >>>information, I am using landmarks also for the LDDMM registration. >>>However, I am receiving the following pop-up error message: >>> >>>"Cannot upload this file: d39d65436099132a2a82efb0dfc8810a.zip" >>> >>>Could anyone please help me with resolving this problem? >>> >>>Thank you, >>>Fijoy >>>_______________________________________________ >>>Mristudio-users mailing list >>>Mristudio-users at mristudio.org >>> >> * Previous message: [Mristudio-users] Landmarker LDDMM error >> * Next message: [Mristudio-users] Landmarker LDDMM error >> * Messages sorted by: [ date ] [ thread ] [ subject ] [ >>author ] >> More information about the Mristudio-users mailing list >> >> >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: >> mristudio-users-unsubscribe at mristudio.org >> > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > From czhou4 at gmail.com Mon Nov 29 10:42:48 2010 From: czhou4 at gmail.com (Chunxiao Zhou) Date: Mon, 29 Nov 2010 10:42:48 -0500 Subject: [Mristudio-users] Background noise level Message-ID: Dear DTIstudio experts, When I move my cursor over the DWIs, I found the intensity values of most brain region are large. And background intensities range from 0-30. But a few pixels have intensity range from 3-10. I am wondering if I still can set the background noise level to 10, or even higher? Does the background noise level should guarantee to keep whole brain or allow exclusion of a few pixels within brain? Thank you! Chunxiao(Andrew) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101129/bc08d480/attachment-0001.html From susumu at mri.jhu.edu Mon Nov 29 11:02:34 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 29 Nov 2010 11:02:34 -0500 Subject: [Mristudio-users] Background noise level In-Reply-To: References: Message-ID: The brain masking by a simple threshold does not guarantee suppression of all extra-cranial signals. It is very common that a threshold level that doesn't mask any brain tissues leave some pixels outside the brain. If you want a very clean brain extraction, you can try region growing or skull-strip tools in RoiEditor or other software. On Mon, Nov 29, 2010 at 10:42 AM, Chunxiao Zhou wrote: > Dear DTIstudio experts, > > When I move my cursor over the DWIs, I found the intensity values of most > brain region are large. And background intensities range from 0-30. But a > few pixels have intensity range from 3-10. I am wondering if I still can set > the background noise level to 10, or even higher? Does the background noise > level should guarantee to keep whole brain or allow exclusion of a few > pixels within brain? > > Thank you! > > Chunxiao(Andrew) > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101129/0a635606/attachment.html From mer.reid at gmail.com Mon Nov 29 12:46:41 2010 From: mer.reid at gmail.com (Meredith Reid) Date: Mon, 29 Nov 2010 11:46:41 -0600 Subject: [Mristudio-users] multiple repetitions or multiple b-values? Message-ID: DTI experts, I have been considering the options of multiple repetitions versus multiple b-values. In light of Correia et al.'s simulations ( http://www.ncbi.nlm.nih.gov/pubmed/18687552), it seems to me that 30 directions at 2 different b-values may be advantageous (versus 2 repetitions of one b-value at 30 directions) since I am interested in both scalar measures and tractography. Any thoughts on this? Has anyone compared these scenarios in acquired data? Thanks, Meredith Reid -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20101129/b41ddc98/attachment.html From susumu at mri.jhu.edu Mon Nov 29 20:55:42 2010 From: susumu at mri.jhu.edu (susumu mori) Date: Mon, 29 Nov 2010 20:55:42 -0500 Subject: [Mristudio-users] multiple repetitions or multiple b-values? In-Reply-To: References: