From amira at med.asu.edu.eg Sun Jun 2 10:02:39 2019 From: amira at med.asu.edu.eg (amira adel ahmed ibrahim) Date: Sun, 2 Jun 2019 14:02:39 +0000 Subject: [MRIStudio-users] technical problem while using DTI studio programe Message-ID: Good afternoon, I?m using DTI studio in postprocessing of cases of focal epilepsy using FACT and tractography The values of Radial Diffusivity, Axial Diffusivity & Mean Diffusivity are as follow: eg.Values of Forceps major: RD Max. of ImgVal: 1.5199 Min. of ImgVal: 0.000e+000 Mean of ImgVal: 0.3990 Std. of ImgVal: 0.1994 EigenVal_0.dat Max. of ImgVal: 2.5828 Min. of ImgVal: 0.3662 Mean of ImgVal: 1.2132 Std. of ImgVal: 0.2615 Trace.dat Max. of ImgVal: 5.3796 Min. of ImgVal: 0.5247 Mean of ImgVal: 2.0112 Std. of ImgVal: 0.5677 With pronounced difference when compared to normal controls, although the tract volume and density and shape seems normal I postprocessed the controls using the same steps the values of controls came as follow : Forceps major values in age matched control: RD.dat Max. of ImgVal: 2.469e-003 Min. of ImgVal: 0.000e+000 Mean of ImgVal: 4.852e-004 Std. of ImgVal: 2.465e-004 EigenVal_0.dat Max. of ImgVal: 3.602e-003 Min. of ImgVal: 5.082e-004 Mean of ImgVal: 1.482e-003 Std. of ImgVal: 2.832e-004 Trace.dat Max. of ImgVal: 8.331e-003 Min. of ImgVal: 6.321e-004 Mean of ImgVal: 2.452e-003 Std. of ImgVal: 6.028e-004 So I think I have a problem in registration steps may be so I?m asking is this normal or am i missing certain step Thanks in advance I?m a fellow in radiodiagnosis in Ain Shams University, Cairo, Egypt -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoriw at gmail.com Tue Jun 4 10:34:21 2019 From: smoriw at gmail.com (Susumu Mori) Date: Tue, 4 Jun 2019 10:34:21 -0400 Subject: [MRIStudio-users] [Mristudio-users] MRI - Head Motion issue In-Reply-To: References: <1490619413906.25060@jhmi.edu> Message-ID: Hi all, I want to add few more things. Motion artifacts are indeed clear issues for all kind of MRI studies, especially for those based on multiple images such as DTI, fMRI, ASL, etc. For DTI, there were active research studies on motion artifacts and many tools were developed in late '90s and early '00s. DtiStudio and MriCloud perform usual image registration and eddy current corrections and provide reports about the amount of motions, eddy currents, and the number of rejected voxels during the corrections. However, motion correction is an ill-posed scheme. No matter which tool you use, it can correct only a portion of problems. Suppose you register a 3D image A and B and the registration tool says, "there was x translation and y rotation", this statement is accurate only if the registration is accurate. Then, how do we know if the registration is accurate? The software judges the accuracy based on a cost function it monitors; the minimum (or maximum) of the cost function is the best registration. The problem is, there is no guarantee that the minimum cost function is indeed the metric of accurate registration. Unfortunately, we don't have a magic cost function that is truly accurate. Also, there are types of motion we can't correct. For example, DTI is based on multiple 2D slices, usually axial slices. Often, the odd-number slices are acquired first followed by even-number slices. If motion happens between the first odd-number scan and second even-number scan, you can't correct them by usual 3D registration scheme (the motion problems reside within the 3D image). Imagine how things get complicated if sagittal rotation happens during multi-slice axial 2D scans. In addition, motion often causes signal changes. Even if voxel locations are corrected accurately, we don't have means to correct the intensity. So, as Barbara pointed out, at some point, we need to take some level of motion artifacts as noise in our data. We only hope there are similar amounts of motion artifacts across groups. If there is a possibility that patient groups have more motion artifacts, this causes typical co-variate issues. It is always a good practice to monitor the registration reports (assuming the numbers in the reports reflect the truth about the extent of motion) and check the absence of significant differences among groups. I must admit that I haven't fully utilized the reports, though... On Mon, Jun 3, 2019 at 11:04 AM Barbara Kreilkamp wrote: > Dear Dr Mohammad, > > This paper you are referring to (Yendiki et al. 2013 neuroimage) reports > on the methods used to correct for motion and the spurious group > differences present even when accounting for motion with special > correction tools. > > If there are differences in motion between groups that you are > comparing, then yes, motion can be have confounding effects on your > results even if they have been 'corrected'. This is because motion > always also means loss of information (e.g. slice dropout etc.) which > cannot be easily mitigated. > > FSL and Freesurfer (Tracula) offer tools to extract motion parameters > for individual subjects so you can compare gross motion across groups > and account for it in your analysis. It's always a great idea to > visually check your unprocessed DTI data as well for any signal loss etc. > > Best wishes, > > Barbara > > > > On 27/03/2017 14:56, Michael McLane wrote: > > FYI - ? > > ________________________________________ > > From: mristudio-users on behalf > of Shaimaa Abdelsattar > > Sent: Sunday, March 26, 2017 2:05 PM > > To: MRI Studio > > Subject: [Mristudio-users] Head Motion issue > > > > Hello, > > There are papers in the literature discussing the effect of head motion > on DTI analysis as it can induce spurious differences among groups. I would > like to ask if this motion is still a concern even after eddy current > correction and registration into b0 image using AIR tool in DTI studio for > tractography. > > Thank you in advance > > Dr.Shaimaa Mohammad, MD > > > > Sent from my 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 > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From chanhyuk at gmail.com Mon Jul 15 21:53:42 2019 From: chanhyuk at gmail.com (Chan Hyuk Park) Date: Tue, 16 Jul 2019 10:53:42 +0900 Subject: [MRIStudio-users] Some question about DTI studio Message-ID: Dear I am doctor on rehabilitaiton medicine I used DTI studio However, when processing fiber tracking, "out of memory" was shown My PC had 12GB ram. when showing "out of memory", possible momery was 7G. For DTI studio, 7GB ram was not enough? if memroy was insufficinet , Please let me know enough memory. Thanks and regrad -- Thanks and Best Regards CH Park(TEL: 010-8860-7994) -------------- next part -------------- An HTML attachment was scrubbed... URL: From 827125753 at qq.com Tue Jul 16 06:40:30 2019 From: 827125753 at qq.com (=?gb18030?B?1ty3vA==?=) Date: Tue, 16 Jul 2019 18:40:30 +0800 Subject: [MRIStudio-users] =?gb18030?b?u9i4tKO6IFNvbWUgcXVlc3Rpb24gYWJv?= =?gb18030?q?ut_DTI_studio?= In-Reply-To: References: Message-ID: sorry,I didn't use DTI studio processing fiber tracking I'm so sorry I can't help you Good luck to you ------------------ ???? ------------------ ???: "Chan Hyuk Park"; ????: 2019?7?16?(???) ??9:53 ???: "mristudio-users"; ??: [MRIStudio-users] Some question about DTI studio Dear I am doctor on rehabilitaiton medicine I used DTI studio However, when processing fiber tracking, "out of memory" was shown My PC had 12GB ram. when showing "out of memory", possible momery was 7G. For DTI studio, 7GB ram was not enough? if memroy was insufficinet , Please let me know enough memory. Thanks and regrad -- Thanks and Best Regards CH Park(TEL: 010-8860-7994) -------------- next part -------------- An HTML attachment was scrubbed... URL: From Makki.Malek at chu-amiens.fr Tue Jul 16 07:21:56 2019 From: Makki.Malek at chu-amiens.fr (Makki Malek) Date: Tue, 16 Jul 2019 11:21:56 +0000 Subject: [MRIStudio-users] =?utf-8?b?5Zue5aSN77yaIFNvbWUgcXVlc3Rpb24gYWJv?= =?utf-8?q?ut_DTI_studio?= In-Reply-To: References: Message-ID: <497dcb726135445d8c45bee0753eafe4@Graves.chu-amiens.local> Hello How many slices you prescribed? How many directions and what is the spatial resolution? The problem might come from the original amount of data Regards ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Malek I. MAKKI, HDR, PhD, MBA MRI Physicist Director MRI Research CHU Amiens-Picardie Amiens Cedex 1 France Tel : +33(0)3 22 08 74 86 makki.malek at chu-amiens.fr ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ De : mristudio-users [mailto:mristudio-users-bounces at mristudio.org] De la part de ?? Envoy? : mardi 16 juillet 2019 12:41 ? : DTI Studio, ROI Editor,DiffeoMap Questions/Support Objet : [MRIStudio-users] ??? Some question about DTI studio sorry,I didn't use DTI studio processing fiber tracking I'm so sorry I can't help you Good luck to you ------------------ ???? ------------------ ???: "Chan Hyuk Park"; ????: 2019?7?16?(???) ??9:53 ???: "mristudio-users"; ??: [MRIStudio-users] Some question about DTI studio Dear I am doctor on rehabilitaiton medicine I used DTI studio However, when processing fiber tracking, "out of memory" was shown My PC had 12GB ram. when showing "out of memory", possible momery was 7G. For DTI studio, 7GB ram was not enough? if memroy was insufficinet , Please let me know enough memory. Thanks and regrad -- Thanks and Best Regards CH Park(TEL: 010-8860-7994) -------------- next part -------------- An HTML attachment was scrubbed... URL: From NoReply at aon.nl Tue Jul 16 07:23:43 2019 From: NoReply at aon.nl (NoReply Aon) Date: Tue, 16 Jul 2019 11:23:43 +0000 Subject: [MRIStudio-users] =?big5?b?pl7OYKFHIFNvbWUgcXVlc3Rpb24gYWJvdXQg?= =?big5?b?RFRJIHN0dWRpbw==?= Message-ID: Geachte klant, Bedankt voor uw mail, deze is goed aangekomen. Helaas duurt een inhoudelijke reactie momenteel langer dan u van ons mag verwachten. Heeft uw vraag spoed? Neem dan telefonisch contact met ons op. U bereikt ons op maandag tot en met vrijdag van 8.30 tot 18.00 uur op (040) 261 18 88. Onze excuses voor het ongemak. We doen er alles aan om u zo snel en goed mogelijk te helpen. Dank voor uw geduld. Met vriendelijke groet, Aon Nederland Van: Makki Malek [Makki.Malek at chu-amiens.fr] Verzonden: dinsdag 16 juli 2019 13:21 Aan: DTI Studio, ROI Editor, DiffeoMap Questions/Support Onderwerp: Re: [MRIStudio-users] ??? Some question about DTI studio Hello How many slices you prescribed? How many directions and what is the spatial resolution? The problem might come from the original amount of data Regards ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Malek I. MAKKI, HDR, PhD, MBA MRI Physicist Director MRI Research CHU Amiens-Picardie Amiens Cedex 1 France Tel : +33(0)3 22 08 74 86 makki.malek at chu-amiens.fr ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ De : mristudio-users [mailto:mristudio-users-bounces at mristudio.org] De la part de ?? Envoye : mardi 16 juillet 2019 12:41 A : DTI Studio, ROI Editor,DiffeoMap Questions/Support Objet : [MRIStudio-users] ??? Some question about DTI studio sorry,I didn't use DTI studio processing fiber tracking I'm so sorry I can't help you Good luck to you ------------------ ???? ------------------ ???: "Chan Hyuk Park"; ????: 2019?7?16?(???) ??9:53 ???: "mristudio-users"; ??: [MRIStudio-users] Some question about DTI studio Dear I am doctor on rehabilitaiton medicine I used DTI studio However, when processing fiber tracking, "out of memory" was shown My PC had 12GB ram. when showing "out of memory", possible momery was 7G. For DTI studio, 7GB ram was not enough? if memroy was insufficinet , Please let me know enough memory. Thanks and regrad -- Thanks and Best Regards CH Park(TEL: 010-8860-7994) ________________________________ KVK Rotterdam 24061634 This e-mail message and its attachments are subject to the disclaimer published at the following website of Aon: http://www.aon.nl/disclaimer -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ATT00001.txt URL: From chanhyuk at gmail.com Fri Oct 11 03:05:23 2019 From: chanhyuk at gmail.com (Chan Hyuk Park) Date: Fri, 11 Oct 2019 16:05:23 +0900 Subject: [MRIStudio-users] Some question about DTI studio In-Reply-To: References: Message-ID: dear sir I have one question I have used DTI studio 64 bit I would like to aquire Mean diffusionity How do I do for obtain this data? Perhaps, mean fibers/voxels is the same MD? thanks and regard 2019? 7? 16? (?) ?? 10:53, Chan Hyuk Park ?? ??: > Dear > > I am doctor on rehabilitaiton medicine > > I used DTI studio > > However, when processing fiber tracking, "out of memory" was shown > > My PC had 12GB ram. when showing "out of memory", possible momery was 7G. > > For DTI studio, 7GB ram was not enough? if memroy was insufficinet , > Please let me know enough memory. > > Thanks and regrad > > -- > Thanks and Best Regards > CH Park(TEL: 010-8860-7994) > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Donna.Zehner at bcm.edu Mon Dec 9 15:19:16 2019 From: Donna.Zehner at bcm.edu (Zehner, Donna Renee) Date: Mon, 9 Dec 2019 20:19:16 +0000 Subject: [MRIStudio-users] Problem Opening Program Message-ID: Hi, I am currently trying to install DiffeoMAP 64bit on a Windows 10 computer. I am currently running in to the issue where I get an error when I try to open DiffeoMap. The error says: "The application has failed to start because its side-byside configuration is incorrect. Please see the application event log or use the command-line sxstrace.exe tool for more detail." I am not sure what this means or what to do. Thanks, Donna Zehner -------------- next part -------------- An HTML attachment was scrubbed... URL: From insu5812 at korea.ac.kr Fri Oct 11 07:47:21 2019 From: insu5812 at korea.ac.kr (Sekwang Lee) Date: Fri, 11 Oct 2019 11:47:21 -0000 Subject: [MRIStudio-users] [SUSPECTED SPAM]Re: Some question about DTI studio In-Reply-To: References: Message-ID: ??? ???. ?? ????? ????? ???? ??? ?????? ???. ? ????? ????? ????? ??? ??? ?? ? ?? ? ???. 010-5322-3226?? ?????. ??? ??. 2019? 10? 11? (?) ?? 7:59, Chan Hyuk Park ?? ??: > dear sir > I have one question > > I have used DTI studio 64 bit > > I would like to aquire Mean diffusionity > > How do I do for obtain this data? > > Perhaps, mean fibers/voxels is the same MD? > > thanks and regard > > 2019? 7? 16? (?) ?? 10:53, Chan Hyuk Park ?? ??: > >> Dear >> >> I am doctor on rehabilitaiton medicine >> >> I used DTI studio >> >> However, when processing fiber tracking, "out of memory" was shown >> >> My PC had 12GB ram. when showing "out of memory", possible momery was 7G. >> >> For DTI studio, 7GB ram was not enough? if memroy was insufficinet , >> Please let me know enough memory. >> >> Thanks and regrad >> >> -- >> Thanks and Best Regards >> CH Park(TEL: 010-8860-7994) >> > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: > mristudio-users-unsubscribe at mristudio.org > -- Sekwang Lee, MD Technical Research Personnel Department of Neuroscience Korea University College of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From xli16 at jhmi.edu Mon Dec 9 15:36:52 2019 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 9 Dec 2019 20:36:52 +0000 Subject: [MRIStudio-users] Problem Opening Program In-Reply-To: References: Message-ID: The Microsoft Visual Studio Redistribution package needs to be installed on your machine before you run the MRIStudio applications. Please download vcredist_x64.exe from https://www.mristudio.org/wiki/installation and then double click vcredist_x64.exe. Xin ________________________________ From: mristudio-users on behalf of Zehner, Donna Renee Sent: Monday, December 9, 2019 3:19 PM To: mristudio-users at mristudio.org Subject: [MRIStudio-users] Problem Opening Program Hi, I am currently trying to install DiffeoMAP 64bit on a Windows 10 computer. I am currently running in to the issue where I get an error when I try to open DiffeoMap. The error says: "The application has failed to start because its side-byside configuration is incorrect. Please see the application event log or use the command-line sxstrace.exe tool for more detail." I am not sure what this means or what to do. Thanks, Donna Zehner -------------- next part -------------- An HTML attachment was scrubbed... URL: From Donna.Zehner at bcm.edu Thu Dec 19 10:40:48 2019 From: Donna.Zehner at bcm.edu (Zehner, Donna Renee) Date: Thu, 19 Dec 2019 15:40:48 +0000 Subject: [MRIStudio-users] DiffeoMap Help Message-ID: Hello, I am currently working on a Windows 10 computer using DiffeoMap. I use DiffeoMAP to resample my images, perform an air alignment, convert the images into Byte files, and perform histogram matching; all before finalizing the subject and template files and sending them to the John Hopkins LDDMM server. I am running into the error where I send the files but DiffeoMap remains unresponsive for days. To solve this problem I tried inputting other registered MRI studio email addresses from people who were able to send the data from their computers. I also tried using various types of internet (thinking it could be my wifi); however, people also working on the same project as myself were able to send using the wifi I was on. We believe the reason I am not able to send my images is because I am on a Windows 10 computer and they are on a Windows 7 computer. Do you have any suggestions as to what could be happening or if it is because I am on a windows 10 computer how I can fix this problem? Thanks, Donna Zehner -------------- next part -------------- An HTML attachment was scrubbed... URL: From xli16 at jhmi.edu Thu Dec 19 10:55:37 2019 From: xli16 at jhmi.edu (Xin Li) Date: Thu, 19 Dec 2019 15:55:37 +0000 Subject: [MRIStudio-users] DiffeoMap Help In-Reply-To: References: Message-ID: Hi Donna, Windows 10 should not be the reason. DiffeoMap works in Windows 10. After you sent the data, did you receive the message from DiffeMap that the images uploaded successfully? Xin ________________________________ From: mristudio-users on behalf of Zehner, Donna Renee Sent: Thursday, December 19, 2019 10:40 AM To: mristudio-users at mristudio.org Subject: [MRIStudio-users] DiffeoMap Help Hello, I am currently working on a Windows 10 computer using DiffeoMap. I use DiffeoMAP to resample my images, perform an air alignment, convert the images into Byte files, and perform histogram matching; all before finalizing the subject and template files and sending them to the John Hopkins LDDMM server. I am running into the error where I send the files but DiffeoMap remains unresponsive for days. To solve this problem I tried inputting other registered MRI studio email addresses from people who were able to send the data from their computers. I also tried using various types of internet (thinking it could be my wifi); however, people also working on the same project as myself were able to send using the wifi I was on. We believe the reason I am not able to send my images is because I am on a Windows 10 computer and they are on a Windows 7 computer. Do you have any suggestions as to what could be happening or if it is because I am on a windows 10 computer how I can fix this problem? Thanks, Donna Zehner -------------- next part -------------- An HTML attachment was scrubbed... URL: