From support at mristudio.org Wed Jan 2 13:12:55 2008 From: support at mristudio.org (support at mristudio.org) Date: Wed, 2 Jan 2008 13:12:55 -0500 (EST) Subject: [Mristudio-users] Welcome - Supporting 'DTI Studio', 'Landmarker' and 'ROI Editor' In-Reply-To: References: Message-ID: <44790.128.220.140.158.1199297575.squirrel@webmail.mristudio.org> Greetings: The purpose of this mailing list is to provide community support for 'DTI Studio', 'Landmarker' and 'ROI Editor'. All messages sent to this group will also be sent to 'support at mristudio.org'. We will do our best to promply respond to questions. Happy New Year! MRI Studio Support Group From support at mristudio.org Wed Jan 23 11:06:10 2008 From: support at mristudio.org (support at mristudio.org) Date: Wed, 23 Jan 2008 11:06:10 -0500 (EST) Subject: [Mristudio-users] [Fwd: short course] Message-ID: <3283.162.129.28.88.1201104370.squirrel@webmail.mristudio.org> Dear DtiStudio users, AS you may already know, we established a new website, www.mristudio.org last year. In this site, there are two ways to communicate with us and get support. 1) mristudio-users at mristudio.org: This is an email list and the message is delivered to everybody in the list. The activity is also archived as threads, which can be seen anytime. This is a great way to ask questions to the community including us. You can also see the archives ("Community" -> "Mailing List") for past Q & A activities. We are currently modifying the archive so that questions can also be directly posted in the archive instead of sending emails to everybody. Please use this method when you have questions, comments, and suggestions. 2) Support at mristudio.org: This email will be read by us and responded individually. Many of you tend to choose this method when there is a question. This is a great way to get support from us, but one issue is the Q & A activities cannot be seen by other users. For the common questions, we move them to "FAQ" sections. If we feel that the questions could be of interest for many users, we anonymize the questions and forward them to "mristudio-users at mristudio.org" so that they can be read by many users and also archived in the website. So here is the first one I want to share with you. Sincerely, Susumu Mori QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ Hi, Are there any training courses available for learning DTIStudio, especially with the addition of the ROIEditor and Landmarker modules. Pretty difficult to learn from the limited online manuals for a novice like me. Thank you for your response, AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA Yes, we realized that RoiEditor and Landmarker, while they are very powerful, are difficult to learn with so many functions. We are trying to make our manual (www.mristudio.org -> "Documentation" -> "User Manual") more complete, but they are still lagging behind. We are currently preparing for tutorial courses in following times and locations. 1) Johns Hopkins Medical Campus in Feb. This is for a testing of the tutorial course, open to only local users (I don't want users to spend $$$ to come, only to find it doesn't work). 2) Kyoto University, Japan, 3/2. 3) ISMRM, Toronto, 5/3 or 5/4. Is there any user who is working in Toronto and willing to provide a large conference room? This is how it works; 1) Users are required to download DtiStudio, RoiEditor, and Landmarker to their own laptops and bring them to the tutorial 2) Users are required to download sample data from our website (currently in "Download" section of the website). 3) Users are required to follow web-based tutorials which will be posted soon. These #1-#3 steps will make sure that you have working versions of our programs and sample data. In this way, all we have to do is to book a room and prepare a lot of electric outlets. The tutorial will be free unless the room costs us a lot. The tutorial will be very unformal without a strict schedule, but it will have 1-hour PPT presentation about DTI and the software, followed by actual step-by-step instructions. I'm thinking about 20 people / session. At this point, we just want to have some idea about how many users are interested in the tutorial. So any comments, suggestions, and information would be welcome. Thanks, Susumu Mori From carly at ualberta.ca Mon Feb 4 13:55:47 2008 From: carly at ualberta.ca (carly at ualberta.ca) Date: Mon, 04 Feb 2008 11:55:47 -0700 Subject: [Mristudio-users] saving a ROI Message-ID: <20080204115547.1aqkz8ihugwsokw4@webmail.ualberta.ca> Hi, I'm trying to save an ROI after attaining a tract on an image. I'm using the save button above the statistics button under the fiber tab to save, and the load button beside the same save button to bring up the image with the tract. My problem is that some of these save properly - bring up the tract and the regions on each slice circled - but others do not save anything. What am I doing wrong? Thanks, carly From susumu at mri.jhu.edu Mon Feb 4 15:41:37 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 04 Feb 2008 15:41:37 -0500 Subject: [Mristudio-users] Save ROIs Message-ID: <6i7avk$frfm2@ipex2.johnshopkins.edu> Dear MriStudio_users; Here is a question from a user which may interest you. ---------------------------------------------------------------------------- I recently started using DTIStudio to draw ROIs and examine the diffusion in certain white matter regions. Is there a way to save ROIs in DTIStudio as Analyze files instead of '.dat' files? Thank you for your time. ---------------------------------------------------------------------------- ROI functions of DtiStudio are not very strong. This is partly because we developed a new program called RoiEditor. This software can communicate with DtiStudio through saved files and images. RoiEditor has much stronger ROI functions, including ROI-based quantification and ROI generation for fiber tracking. I recommend you to look into RoiEditor, which can save and load raw (.dat) as well as Analyze format. It also has a format called "binary map", which is specifically designed for fiber tracking. Thanks, Susumu From lei at wustl.edu Mon Feb 18 15:42:14 2008 From: lei at wustl.edu (Lei Wang) Date: Mon, 18 Feb 2008 14:42:14 -0600 Subject: [Mristudio-users] Tutorial question Message-ID: <002201c8726e$bf47c560$3dd75020$@edu> Hi, The DTIstudio tutorial states: Loading Rec data into DTI Studio 1. Start DTI Studio by double clicking on the program icon. 2. Click on File -> DTI Mapping... 3. A File Selection window pops up. Select the Philips Rec radial button and click Continue >> 4. An Image Parameter window opens. Cut and paste the gradient table into the space below the Gradient Table heading. I wanted to load the sample data, is there a sample gradient table to use here? Thanks, --Lei -- Lei Wang, Ph.D. ---------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134???? Renard Hospital, Room 6604???????????? Tel. office: 314-362-2417 660 South Euclid?????????????????????? Tel. lab:??? 314-362-5239 St. Louis, MO 63110??????????????????? Fax. lab:??? 314-747-2182 http://conte.wustl.edu/??????????????? Email:????? lei at wustl.edu ---------------------------------------------------------------- From lei at wustl.edu Mon Feb 18 15:49:31 2008 From: lei at wustl.edu (Lei Wang) Date: Mon, 18 Feb 2008 14:49:31 -0600 Subject: [Mristudio-users] Tutorial question In-Reply-To: <002201c8726e$bf47c560$3dd75020$@edu> References: <002201c8726e$bf47c560$3dd75020$@edu> Message-ID: <002501c8726f$c3c20d70$4b462850$@edu> Never mind, I just saw the link to download the gradient tables. --Lei -- Lei Wang, Ph.D. ---------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134???? Renard Hospital, Room 6604???????????? Tel. office: 314-362-2417 660 South Euclid?????????????????????? Tel. lab:??? 314-362-5239 St. Louis, MO 63110??????????????????? Fax. lab:??? 314-747-2182 http://conte.wustl.edu/??????????????? Email:????? lei at wustl.edu ---------------------------------------------------------------- > -----Original Message----- > From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users- > bounces at mristudio.org] On Behalf Of Lei Wang > Sent: Monday, February 18, 2008 2:42 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] Tutorial question > > Hi, > > The DTIstudio tutorial states: > > Loading Rec data into DTI Studio > 1. Start DTI Studio by double clicking on the program icon. > 2. Click on File -> DTI Mapping... > 3. A File Selection window pops up. Select the Philips Rec radial > button > and click Continue >> > 4. An Image Parameter window opens. Cut and paste the gradient table > into the space below the Gradient Table heading. > > I wanted to load the sample data, is there a sample gradient table to use > here? > > Thanks, > > --Lei > > -- > Lei Wang, Ph.D. > ---------------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > Renard Hospital, Room 6604???????????? Tel. office: 314-362-2417 > 660 South Euclid?????????????????????? Tel. lab:??? 314-362-5239 > St. Louis, MO 63110??????????????????? Fax. lab:??? 314-747-2182 > http://conte.wustl.edu/??????????????? Email:????? lei at wustl.edu > ---------------------------------------------------------------- > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users From rchu at nbresearch.com Fri Feb 1 19:15:44 2008 From: rchu at nbresearch.com (Russell Chu) Date: Sat, 02 Feb 2008 00:15:44 -0000 Subject: [Mristudio-users] saving DtiStudio ROIs as Analyze files Message-ID: Hi Everyone, I recently started using DTIStudio to draw ROIs and examine the diffusion in certain white matter regions. Is there a way to save ROIs in DTIStudio as Analyze files instead of '.dat' files? Thank you for your time. Best regards, Russell From Srinivasan at kennedykrieger.org Thu Feb 14 12:08:48 2008 From: Srinivasan at kennedykrieger.org (Priti Srinivasan) Date: Thu, 14 Feb 2008 12:08:48 -0500 Subject: [Mristudio-users] Tutorial on ROI editor Message-ID: <47B42E96.E224.0081.0@kennedykrieger.org> I am currently working on white matter segmentation and was looking at atlas based automated parcellation method that is supposedly implemented in the Roi editor module. I would like to know how to go about doing it. Is there any online tutorial for using the application. Every time I try loading a previously saved data file, I get a message " Please enter an integer between 1 and 4096. I tried changing all the parameters but nothing worked. Any help in this regard would be really appreciated. Thanks, Priti Srinivasan. 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/20080214/31ec515b/attachment-0001.html From susumu at mri.jhu.edu Mon Feb 18 16:04:59 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 18 Feb 2008 16:04:59 -0500 Subject: [Mristudio-users] JHU Tutorial on 2/25 Message-ID: <6i7avk$nj4ae@ipex2.johnshopkins.edu> Dear MriStudio_User subscribers, The tutorial in JHU will take place in Darner Conference Room / Ross Building basement on 2/25, 1-5 pm. I attached a map in which the Ross Building is indicated by a red asterisk (720 Rutland Ave., Baltimore, MD). One of the visitor parking lots is shown by a blue arrow. All users expressed their interest are welcome (currently we count 24 attendees). The tutorial is free. Please make sure that you follow the instruction in "Workshop" section of www.mristudio.org to pre-condition your laptop. We are trying to post the latest Landmarker this week that includes a new single-subject atlas that is required for non-linear image registration. If we can make it in time, I'll send you another email. The second (3/2) and third tutorial (5/4) are still scheduled as notified in the second announcement. Thanks, Susumu -------------- next part -------------- A non-text attachment was scrubbed... Name: JHUTutorial.ppt Type: application/vnd.ms-powerpoint Size: 961536 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080218/bcf81710/attachment-0001.ppt From susumu at mri.jhu.edu Fri Feb 22 08:55:39 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 22 Feb 2008 08:55:39 -0500 Subject: [Mristudio-users] Tutorial on ROI editor Message-ID: <10BF0895FDAF4E4DB989CAF254DF21BA@LTBWYMORI> Hi Priti, That's correct. Landmarker and RoiEditor is desigend to perform the atlas-based quantification. When you download them, they come with several versions of white matter altases we developed recently. The best way to learn them is to come to one of our tutorials, but please don't hesitate to ask questions here in this forum. Susumu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080222/e89dd53e/attachment.html From zackowski at kennedykrieger.org Fri Feb 22 13:50:43 2008 From: zackowski at kennedykrieger.org (Kathy Zackowski) Date: Fri, 22 Feb 2008 13:50:43 -0500 Subject: [Mristudio-users] question about workshop Message-ID: <47BED273.D104.0003.0@kennedykrieger.org> Hi, Can you clarify what I need to do to prepare my laptop for Monday's training session? I could not find the "workshop" section that Susumu had mentioned in a previous note. Thanks, Kathy Kathy Zackowski, PhD, OTR Motion Analysis Laboratory Kennedy Krieger Institute Assistant Professor Depts PM&R, Neurology Johns Hopkins University School of Medicine 707 North Broadway Baltimore, MD 21224 443-923-2717 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/20080222/444afc5c/attachment.html From lei at wustl.edu Fri Feb 22 14:03:24 2008 From: lei at wustl.edu (Lei Wang) Date: Fri, 22 Feb 2008 13:03:24 -0600 Subject: [Mristudio-users] question about workshop In-Reply-To: <47BED273.D104.0003.0@kennedykrieger.org> References: <47BED273.D104.0003.0@kennedykrieger.org> Message-ID: <007601c87585$9b89d220$d29d7660$@edu> Please follow this link. https://www.mristudio.org/wiki/Tutorial -- Lei Wang, Ph.D. ---------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel. office: 314-362-2417 660 South Euclid Tel. lab: 314-362-5239 St. Louis, MO 63110 Fax. lab: 314-747-2182 http://conte.wustl.edu/ Email: lei at wustl.edu ---------------------------------------------------------------- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Kathy Zackowski Sent: Friday, February 22, 2008 12:51 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] question about workshop Hi, Can you clarify what I need to do to prepare my laptop for Monday's training session? I could not find the "workshop" section that Susumu had mentioned in a previous note. Thanks, Kathy Kathy Zackowski, PhD, OTR Motion Analysis Laboratory Kennedy Krieger Institute Assistant Professor Depts PM&R, Neurology Johns Hopkins University School of Medicine 707 North Broadway Baltimore, MD 21224 443-923-2717 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/20080222/2e679013/attachment.html From susumu at mri.jhu.edu Thu Feb 28 11:51:50 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 28 Feb 2008 11:51:50 -0500 Subject: [Mristudio-users] Tutorial on 3/2 Message-ID: <6i7avk$sl2ga@ipex2.johnshopkins.edu> Dear MriStudio Users, The tutorial on 3/2 in Kyoto will be held at Kyoto University, Department of Radiology. The detailed information about the location can be found at http://www.kuhp.kyoto-u.ac.jp/~diag_rad/ and the map at http://www.kuhp.kyoto-u.ac.jp/~diag_rad/info/map-rin1.gif. It will start at 1:00 pm. All users expressed the interest are welcome. The registration is free. Please make sure to pre-condition your laptop as described in www.mristudio.org -> Workshop. Sincerely, MriStudio Support From darshanp20 at yahoo.com Thu Feb 28 13:05:21 2008 From: darshanp20 at yahoo.com (darshan pai) Date: Thu, 28 Feb 2008 10:05:21 -0800 (PST) Subject: [Mristudio-users] Landmarker Message-ID: <470386.31802.qm@web32201.mail.mud.yahoo.com> I have been using landmarker for 2 weeks now. still trying to figure out . Have some problems that I need to discuss. 1) firstly . is there any way I can load the fibers that I tracked from DTIStudio so that they are transformed too. 2) What is the purpose of load landmarks in the template and the subject. I actually saved these landmarks, but when i loaded them again and ran LDDMM , it gives me a message "Landmark mapping failed. 3) Do the landmarks have to be in sequence . I mean if i choose a land mark in axial , then sagittal and then back to axial, does it create a problem? because i still get "Landmark mapping failed" Regards ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From susumu at mri.jhu.edu Thu Feb 28 13:54:53 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 28 Feb 2008 13:54:53 -0500 Subject: [Mristudio-users] Landmarker Message-ID: <6i7avk$sngif@ipex2.johnshopkins.edu> Hi Darshan, 1) You need to save the tracking results as the "binary" image, which save the data as 1/0 map with the dimensions same as the original data. The pixels that contain the tract becomes 1 and everything else is 0. You can transform this 3D map in the same way you transform images. Of course, you can not directly normalize this 1/0 map, because it doesn't look like a brain. So, you need to use an anatomical image, like b0, for the transformation, and apply the transformation to this 1/0 map. 2) it is difficult to know exactly which problem you had, but in general, here are the things you need to know. > Both the atlas and your data must have the same number of landmarks placed on the corresponding structures. > You need a certain number of landmarks distributed in 3D space to run 3D normalization. For example, if you place only 3 landmarks in one 2D plane and try to run 3D normalization, you get an error 3) No there is no meaning in the order of landmarks. However, each landmark in the template and your data have to be placed in the corresponding locations and order. For example, if you place landmarks at the cerebral peduncle (#1), internal capsule (#2), and cingulum (#3) in the template and place them in the order of the cerebral peduncle - cingulum - internal capsule in the subject brain, it won't do the correct transformation. Hope this will help. Susumu From lyric_jorgenson at yahoo.com Mon Mar 3 14:36:55 2008 From: lyric_jorgenson at yahoo.com (Lyric Jorgenson) Date: Mon, 03 Mar 2008 11:36:55 -0800 (PST) Subject: [Mristudio-users] seed region Message-ID: <796849.41995.qm@web90603.mail.mud.yahoo.com> Hello- I am trying to use the grow seed region function. How does this function work? I am trying to define a 3D ROI. Is there a simpler way of doing this than drawing a 2D ROI on each individual slice along one axis? Thanks, Lyric Jorgenson Lyric A Jorgenson Cognitive Development Neuroimaging Laboratory Institute of Child Development University of Minnesota Minneapolis, MN 55455 Office Address: Room #154 Office Phone: 612-624-3870 ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping From xli16 at jhmi.edu Mon Mar 3 15:28:42 2008 From: xli16 at jhmi.edu (XIN LI) Date: Mon, 03 Mar 2008 15:28:42 -0500 Subject: [Mristudio-users] seed region In-Reply-To: <796849.41995.qm@web90603.mail.mud.yahoo.com> References: <796849.41995.qm@web90603.mail.mud.yahoo.com> Message-ID: Lyric, The tools "threshold" and "seeded region growing" can let you create 3D ROIs. When you click the button "seeded region growing", you will see a pop up window. If you click "3D" in that window, you can get the largest connected 3D region. By clicking with the left mouse button on a pixel lets you select a seed. "Absolute" lets you get a region where the absolute intensities of all the pixels are within this range while "Percentage" can define the range of the intensities relative to the intensity of the seed. Xin ----- Original Message ----- From: Lyric Jorgenson Date: Monday, March 3, 2008 2:37 pm Subject: [Mristudio-users] seed region To: mristudio-users at mristudio.org > Hello- > I am trying to use the grow seed region function. How > does this function work? I am trying to define a 3D > ROI. Is there a simpler way of doing this than drawing > a 2D ROI on each individual slice along one axis? > > Thanks, > Lyric Jorgenson > > Lyric A Jorgenson > Cognitive Development Neuroimaging Laboratory > Institute of Child Development > University of Minnesota > Minneapolis, MN 55455 > Office Address: Room #154 > Office Phone: 612-624-3870 > > > ____________________________________________________________________________________ > Looking for last minute shopping deals? > Find them fast with Yahoo! Search. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From lei at wustl.edu Wed Mar 5 15:16:54 2008 From: lei at wustl.edu (Lei Wang) Date: Wed, 05 Mar 2008 14:16:54 -0600 Subject: [Mristudio-users] view panel char length Message-ID: <00ce01c87efd$dbde6530$939b2f90$@edu> In DTI-Studio -> DTI_Mapping primary viewing panel, the drop down menu for which direction to show (right panel) sometimes cannot show the entire name - see snapshot below. At least after you select one, the particular direction shows up in the title bar. Other than changing file names, is there a way around this? -- Lei Wang, Ph.D. ---------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel. office: 314-362-2417 660 South Euclid Tel. lab: 314-362-5239 St. Louis, MO 63110 Fax. lab: 314-747-2182 http://conte.wustl.edu/ Email: lei at wustl.edu ---------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080305/28c4f176/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/jpeg Size: 30535 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080305/28c4f176/attachment-0001.jpe From GHana at lifespan.org Wed Mar 5 16:53:21 2008 From: GHana at lifespan.org (Hana, George) Date: Wed, 05 Mar 2008 16:53:21 -0500 Subject: [Mristudio-users] Siemens Mosaic Message-ID: <6367968C266D3045B8CC5A015CF35DBB0396D1@LSCOEXCH1.lsmaster.lifespan.org> Hello, I'm having trouble Fiber-tracking using Siemens Mosaic data. I can load my 74 dicoms in MRI View3d. Then in DTI Mapping, I change the "Slices to be Processed" to All Slices. I then choose " Add Folder" and look at all files as my files don't have .dcm extension. It loads well. I've included a JPEG (DTI_1) at this stage. Here is my problem...if I go to the DtiMap tab, and press Tensor, Color Map, etc. calculation then it will iterate 14 times, for about 5 seconds, giving me an odd result, as shown in the second JPEG (DTI_2). Looking at the FA, and the first 2 eigenvectors, it seems that I haven't gotten many images, and they are very blurry(DTI_3). Lastly, when I press on the Fiber Tracking button, it will open a new tab immediately...and I will be unable to visualize any fibers. I hope that you can provide some guidance. Thank you immensely for any help. Please take care. George Hana -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080305/fdd7716f/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: DTI_1.JPG Type: image/pjpeg Size: 109733 bytes Desc: DTI_1.JPG Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080305/fdd7716f/attachment-0003.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: DTI_2.JPG Type: image/pjpeg Size: 121681 bytes Desc: DTI_2.JPG Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080305/fdd7716f/attachment-0004.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: DTI_3.JPG Type: image/pjpeg Size: 224834 bytes Desc: DTI_3.JPG Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080305/fdd7716f/attachment-0005.bin From support at mristudio.org Thu Mar 6 10:56:19 2008 From: support at mristudio.org (support at mristudio.org) Date: Thu, 6 Mar 2008 10:56:19 -0500 (EST) Subject: [Mristudio-users] Siemens Mosaic In-Reply-To: <6367968C266D3045B8CC5A015CF35DBB0396D1@LSCOEXCH1.lsmaster.lifespan.or g> References: <6367968C266D3045B8CC5A015CF35DBB0396D1@LSCOEXCH1.lsmaster.lifespan.org> Message-ID: <2993.162.129.28.138.1204818979.squirrel@webmail.mristudio.org> hi, please make sure all image volumes were re-constructed correctly before you do tensor calcualtion and fiber tracking. I noticed that the DTI_2 has only 1 or 2 slices, but DTI_1 has more (you can verify this from 2D image in coronal view). after the images loaded in, please check the all image volumes (using image list of the "image" tab; or clicking the first button of the "DtiMap" button); also, please check the gradient table; the number of gradients shoule match with the number of images. regards, hangyi > Hello, > I'm having trouble Fiber-tracking using Siemens Mosaic data. I can load my 74 > dicoms in MRI View3d. Then in DTI Mapping, I change the "Slices to be > Processed" to All Slices. I then choose " Add Folder" and look at all files as > my files don't have .dcm extension. It loads well. I've included a JPEG > (DTI_1) at this stage. > > Here is my problem...if I go to the DtiMap tab, and press Tensor, Color Map, > etc. calculation then it will iterate 14 times, for about 5 seconds, giving me > an odd result, as shown in the second JPEG (DTI_2). Looking at the FA, and the > first 2 eigenvectors, it seems that I haven't gotten many images, and they are > very blurry(DTI_3). > > Lastly, when I press on the Fiber Tracking button, it will open a new tab > immediately...and I will be unable to visualize any fibers. I hope that you can > provide some guidance. Thank you immensely for any help. Please take care. > > George Hana > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From klimenat at yahoo.ca Sat Mar 15 14:56:00 2008 From: klimenat at yahoo.ca (Alexi Klimenko) Date: Sat, 15 Mar 2008 14:56:00 -0400 (EDT) Subject: [Mristudio-users] DTI Studio Message-ID: <186917.78582.qm@web38801.mail.mud.yahoo.com> Hi Everyone, I have a question about Dtistudio and image registration. In the attached file you can find two standard deviations images, one of them is processed with AIR. I am leaning towards choosing the first series (stdA top row) as the second one show consistent ring-type intensities. Which one is suitable for further processing? To my suprise, however, stdB bottow row, is the one processed with AIR. Thank you. Alexi --------------------------------- Instant message from any web browser! Try the new Yahoo! Canada Messenger for the Web BETA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080315/2ef544b3/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: dtistudio.jpg Type: image/jpeg Size: 24516 bytes Desc: 1878715898-dtistudio.jpg Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080315/2ef544b3/attachment-0001.jpg From susumu at mri.jhu.edu Sat Mar 15 15:22:36 2008 From: susumu at mri.jhu.edu (susumu) Date: Sat, 15 Mar 2008 15:22:36 -0400 Subject: [Mristudio-users] DTI Studio In-Reply-To: <186917.78582.qm@web38801.mail.mud.yahoo.com> Message-ID: <6i7avk$15s830@ipex2.johnshopkins.edu> Hi Alexi, Thank you for the posting. You are right. It seems that AIR made the registration worse. This is how the STD images and image inspection window should be used; to check the registration quality as well as image quality. If you have multiple repetition data, you can calculate the STD image (actually subtracted image if you have only two repetitions). Misregistration would show up as a ring around the brain as you found. If you don't have repetition, you can also calculate discrepancies between fitted (back-calculated from tensor fitting results) and raw DWIs. These images can be obtained by choosing "Outlier Rejection = yes" when you do tensor calculation and activate "create images of DWI-fitting from the estimated tensor" and "create images of the difference between DWI-fitting and original" boxes. The outlier rejection algorithm itself is still not working perfectly (better version is coming out soon), but the "discrepancy" images (raw minus fitted images) are handy to detect misregistration, eddy current, and image corruption. Now, your question is, why AIR made registration worse. I don't have a definite answer, but the most probable reason is the wrong threshold value. Unfortunately AIR is very sensitive to the threshold value (the default is 50). The threshold is used to erase the noise floor and avoid AIR to try to match noises. In my experience AIR tends to work better with higher thresholds. The value 50 usually works for Philips scanner, but Siemens tends to have much higher values. So, 150-250 seem to work better (I don't know which scanner you are using). If you get poor results with AIR, the first thing I recommend is to try higher threshold values. Once you get a right value, usually you don't have to change it unless you have a major upgrade or switch the scanner manufacture. Please try it and let us know the results. Thanks, Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Alexi Klimenko Sent: Saturday, March 15, 2008 2:56 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] DTI Studio Hi Everyone, I have a question about Dtistudio and image registration. In the attached file you can find two standard deviations images, one of them is processed with AIR. I am leaning towards choosing the first series (stdA top row) as the second one show consistent ring-type intensities. Which one is suitable for further processing? To my suprise, however, stdB bottow row, is the one processed with AIR. Thank you. Alexi _____ Instant message from any web browser! Try the new Yahoo! Canada Messenger for the Web BETA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080315/e3d65db7/attachment.html From mayuresh.korgaonkar at gmail.com Tue Mar 25 13:21:37 2008 From: mayuresh.korgaonkar at gmail.com (Mayuresh Korgaonkar) Date: Tue, 25 Mar 2008 13:21:37 -0400 Subject: [Mristudio-users] Saving Eigen Vectors Message-ID: <66bddc1c0803251021x47f4ec8am728dbcd219176f1f@mail.gmail.com> Hello all, I have a question with regards to saving the eigen vector images using DTIstudio. My goal is to read these images in MATLAB. Is there a way to read the "DTIstudio raw data format"? Saving these images in Analyze format doesnt seem to work. Thankyou for your time, Regards, -- ~Mayuresh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080325/7e42c1c1/attachment.html From darshanp20 at yahoo.com Tue Mar 25 14:31:15 2008 From: darshanp20 at yahoo.com (darshan pai) Date: Tue, 25 Mar 2008 11:31:15 -0700 (PDT) Subject: [Mristudio-users] Saving Eigen Vectors Message-ID: <870296.24750.qm@web32208.mail.mud.yahoo.com> Mayuresh, ev0 files are vector files so you wont be able to open ev0 files in analyze using regular softwares like for example MRIcro. The attributes at each voxel is a 3-d vector. so at each voxel_index u read the components of x y z in that order. The same would work with RAW files. Please keep in mind though that Raw follows right-hand coordinate system whereas analyze is left-handed HTH Darshan ----- Original Message ---- From: Mayuresh Korgaonkar To: mristudio-users at mristudio.org Sent: Tuesday, March 25, 2008 1:21:37 PM Subject: [Mristudio-users] Saving Eigen Vectors Hello all, I have a question with regards to saving the eigen vector images using DTIstudio. My goal is to read these images in MATLAB. Is there a way to read the "DTIstudio raw data format"? Saving these images in Analyze format doesnt seem to work. Thankyou for your time, Regards, -- ~Mayuresh -----Inline Attachment Follows----- _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080325/d43101e3/attachment.html From jmcentee at jhmi.edu Thu Mar 27 16:40:21 2008 From: jmcentee at jhmi.edu (JULIE E MCENTEE) Date: Thu, 27 Mar 2008 16:40:21 -0400 Subject: [Mristudio-users] problem opening .d file in Landmarker Message-ID: I have processed 2 DTI scans using DtiStudio, saving all output files accordingly. I am now attempting to normalize the iso-image (mean of DWI's) to the ICBM-MNI-DWI template using Landmarker. I am able to open the iso-image and load the FA, b0, eigenvalues, and trace files (are they supposed to look like anything, because mine just look like white lines across a black background?). Anyway, when I try to open the tensor (.d) file, I get an error message: File size is smaller than expected value. Does anyone know what I am doing wrong? Thanks in advance- 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 xli16 at jhmi.edu Thu Mar 27 17:22:07 2008 From: xli16 at jhmi.edu (XIN LI) Date: Thu, 27 Mar 2008 17:22:07 -0400 Subject: [Mristudio-users] problem opening .d file in Landmarker In-Reply-To: References: Message-ID: Julie, It means that the tensor image file you want to load does not have the same dimensions as the other loaded images. If you don't mind, you can send me the FA image and the tensor data. I will take a look at them. Xin ----- Original Message ----- From: JULIE E MCENTEE Date: Thursday, March 27, 2008 4:40 pm Subject: [Mristudio-users] problem opening .d file in Landmarker To: mristudio-users at mristudio.org > I have processed 2 DTI scans using DtiStudio, saving all output files > accordingly. I am now attempting to normalize the iso-image (mean of > DWI's) to the ICBM-MNI-DWI template using Landmarker. I am able to > open the iso-image and load the FA, b0, eigenvalues, and trace files > (are they supposed to look like anything, because mine just look like > white lines across a black background?). Anyway, when I try to open > the tensor (.d) file, I get an error message: > > File size is smaller than expected value. > > Does anyone know what I am doing wrong? > > Thanks in advance- > > 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 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From susumu at mri.jhu.edu Thu Mar 27 17:25:57 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 27 Mar 2008 17:25:57 -0400 Subject: [Mristudio-users] problem opening .d file in Landmarker In-Reply-To: Message-ID: <6i7avk$1c1abg@ipex2.johnshopkins.edu> Hi julie, The tensor file has to be opened using a dedicated button saying "open .d". You can't open them from the regular "open" icon. This is because Landmarker needs to know when a tensor file is loaded so that it can do proper reorientation calculation for the tensor. The tensor file should be 6xdimension 1xdimension 2xdimension 3, if you save them correctly by DtiStudio, meaning dxx, dyy, dzz, dxy, dxz, dyz are stored in one file. The trace image should look like a brain. You see white lines across a background when the matrix size is not properly set. You could email me the trace file if you want me to check. Please let me know if you have further question. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of JULIE E MCENTEE Sent: Thursday, March 27, 2008 4:40 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] problem opening .d file in Landmarker I have processed 2 DTI scans using DtiStudio, saving all output files accordingly. I am now attempting to normalize the iso-image (mean of DWI's) to the ICBM-MNI-DWI template using Landmarker. I am able to open the iso-image and load the FA, b0, eigenvalues, and trace files (are they supposed to look like anything, because mine just look like white lines across a black background?). Anyway, when I try to open the tensor (.d) file, I get an error message: File size is smaller than expected value. Does anyone know what I am doing wrong? Thanks in advance- 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 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From budha at nbrc.res.in Thu Apr 3 01:42:51 2008 From: budha at nbrc.res.in (budha) Date: Thu, 03 Apr 2008 11:12:51 +0530 Subject: [Mristudio-users] Error while processing DTI Mapping Message-ID: <000f01c8954d$8ea02720$3600a8c0@nbrc.ac.in> Dear All, I am Graduate Student working in the field of DTI. I have been trying to use DTI Studio for my research. I was able to find the eigenvalues, eigenvectors of DTI images. The problem is somehow now while running DTIStudio, it is able to process images, I can see the DTI Map display window, but the moment I try to run ADC map, Tensor Eigenvalues etc., I get an a error message which I have attached. Can anyone tell me where the problem is ? Thanking you, Budha NBRC, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080403/1845da48/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: Error Message.doc Type: application/msword Size: 145408 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080403/1845da48/attachment-0001.doc From susumu at mri.jhu.edu Thu Apr 3 09:41:14 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 03 Apr 2008 09:41:14 -0400 Subject: [Mristudio-users] Error while processing DTI Mapping In-Reply-To: <000f01c8954d$8ea02720$3600a8c0@nbrc.ac.in> Message-ID: <6i7avk$1fjpvs@ipex2.johnshopkins.edu> Hi Budha, It is most likely memory shortage. To check if it is really a memory problem, please try "partial" processing. After you choose "DtiMapping" and a data format, you get an window to input image dimensions, b-table, and data file names. In this window, you can find "Slices to be processed". For example, if you have 50-slice images, you can process slice # 0 - 24, for the first batch and slice # 25-49 for the second batch. In this way, you can reduce the data size. If this approach works, it is a memory problem. If you get a memory problem, you can do one of following things; 1) Of course, increase RAM. You can see improvement up to 2 GB of RAM, usually. 2) 64-bit Windows XP is really the solution because 32-bit Windows can allocate only up to 1-1.5GB of RAM to a single task. 3) Use the slice-divided tensor calculation and save calculated images such as FA, ADC, tensor. For example, you can get FA0-24 and FA25-49. Then you can load them into one window and save together to get FA0-49. Please let me know if it is really a memory issue. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of budha Sent: Thursday, April 03, 2008 1:43 AM To: mristudio-users at mristudio.org Cc: budhakh at gmail.com Subject: [Mristudio-users] Error while processing DTI Mapping Dear All, ? I am Graduate Student working? in the field of DTI. I have been trying to use DTI Studio for my research. I was able to find the eigenvalues, eigenvectors of DTI images. The problem is somehow now while running DTIStudio,?it is able to process images,?I can?see the DTI Map display window, but the moment I try to run ADC map, Tensor Eigenvalues etc., I get an a error message?which I have attached.?? Can anyone tell me where the problem is ? ? Thanking you, ? Budha NBRC, India ? ? From jmcentee at jhmi.edu Thu Apr 3 17:05:54 2008 From: jmcentee at jhmi.edu (JULIE E MCENTEE) Date: Thu, 03 Apr 2008 17:05:54 -0400 Subject: [Mristudio-users] fiber tracking after updating in Landmarker Message-ID: I normalised my Air.fa image to the ICBM-MNI-FA template using Landmarker. I am now trying to do fiber tracking (whole brain) using the Updated_Air.fa image in DtiStudio. The only way I was able to get DtiStudio to do the fiber tracking was to normalise the eigenvectors (0, 1, 2) to the ICBM-MNI-FA template in Landmarker, but then I am only able to load one 'updated' eigenvector as the Principle Vector in DtiStudio. The result is some white lines against black background. What should I be doing here? Thank you for your help! 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 susumu at mri.jhu.edu Thu Apr 3 18:00:11 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 03 Apr 2008 18:00:11 -0400 Subject: [Mristudio-users] fiber tracking after updating in Landmarker In-Reply-To: Message-ID: <6i7avk$1frv8d@ipex2.johnshopkins.edu> Hi Julie, When you got "white lines against black background", it's most likely a wrong image matrix. Please make sure that you load the data as a "vector" file. Also, after the normalization to ICBM-MNI, all image should be 181x217x181. So, if you got the vector file transformed correctly, you should get this matrix size after you select "vector" as the file format. There is one important issue, though. We don't recommend any transformation of vector files. This is because vector transformation is very unstable. If you want to do tracking after DTI image transformation, I strongly suggest to use "tensor transformation", not FA and vector transformation. This is simple. You need to open a tensor file using the "open .d" button. Then you can apply the AIR transformation matrix. Once your tensor is normalized to ICBM, your can read the transformed tensor file to DtiStudio and recalculate all the FA, ADC, vector things. Please let me know if you have further question. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of JULIE E MCENTEE Sent: Thursday, April 03, 2008 5:06 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] fiber tracking after updating in Landmarker I normalised my Air.fa image to the ICBM-MNI-FA template using Landmarker. I am now trying to do fiber tracking (whole brain) using the Updated_Air.fa image in DtiStudio. The only way I was able to get DtiStudio to do the fiber tracking was to normalise the eigenvectors (0, 1, 2) to the ICBM-MNI-FA template in Landmarker, but then I am only able to load one 'updated' eigenvector as the Principle Vector in DtiStudio. The result is some white lines against black background. What should I be doing here? Thank you for your help! 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 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From pkroy at nbrc.ac.in Thu Apr 3 23:52:07 2008 From: pkroy at nbrc.ac.in (pkroy at nbrc.ac.in) Date: Fri, 04 Apr 2008 09:22:07 +0530 (IST) Subject: [Mristudio-users] Error while processing DTI Mapping In-Reply-To: <6i7avk$1fjpvs@ipex2.johnshopkins.edu> References: <6i7avk$1fjpvs@ipex2.johnshopkins.edu> Message-ID: <23430.192.168.0.7.1207281127.squirrel@webmail.nbrc.ac.in> Dear Susumu, A million thanks for helping me and my PhD student Budha! Kindest regards, Prasun National Neuro-Imaging Facility National Brain Research Centre Delhi, India ==================== > Hi Budha, > > It is most likely memory shortage. To check if it is really a memory > problem, please try "partial" processing. After you choose "DtiMapping" > and > a data format, you get an window to input image dimensions, b-table, and > data file names. In this window, you can find "Slices to be processed". > For > example, if you have 50-slice images, you can process slice # 0 - 24, for > the first batch and slice # 25-49 for the second batch. In this way, you > can > reduce the data size. If this approach works, it is a memory problem. > > If you get a memory problem, you can do one of following things; > > 1) Of course, increase RAM. You can see improvement up to 2 GB of RAM, > usually. > 2) 64-bit Windows XP is really the solution because 32-bit Windows can > allocate only up to 1-1.5GB of RAM to a single task. > 3) Use the slice-divided tensor calculation and save calculated images > such > as FA, ADC, tensor. For example, you can get FA0-24 and FA25-49. Then you > can load them into one window and save together to get FA0-49. > > Please let me know if it is really a memory issue. > > Susumu > > ________________________________________ > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of budha > Sent: Thursday, April 03, 2008 1:43 AM > To: mristudio-users at mristudio.org > Cc: budhakh at gmail.com > Subject: [Mristudio-users] Error while processing DTI Mapping > > Dear All, > ? > I am Graduate Student working? in the field of DTI. I have been trying to > use DTI Studio for my research. I was able to find the eigenvalues, > eigenvectors of DTI images. The problem is somehow now while running > DTIStudio,?it is able to process images,?I can?see the DTI Map display > window, but the moment I try to run ADC map, Tensor Eigenvalues etc., I > get > an a error message?which I have attached.?? Can anyone tell me where the > problem is ? > ? > Thanking you, > ? > Budha > NBRC, India > ? > ? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > From pkroy at nbrc.ac.in Thu Apr 3 23:52:07 2008 From: pkroy at nbrc.ac.in (pkroy at nbrc.ac.in) Date: Fri, 04 Apr 2008 09:22:07 +0530 (IST) Subject: [Mristudio-users] Error while processing DTI Mapping In-Reply-To: <6i7avk$1fjpvs@ipex2.johnshopkins.edu> References: <6i7avk$1fjpvs@ipex2.johnshopkins.edu> Message-ID: <23431.192.168.0.7.1207281127.squirrel@webmail.nbrc.ac.in> Dear Susumu, A million thanks for helping me and my PhD student Budha! Kindest regards, Prasun National Neuro-Imaging Facility National Brain Research Centre Delhi, India ==================== > Hi Budha, > > It is most likely memory shortage. To check if it is really a memory > problem, please try "partial" processing. After you choose "DtiMapping" > and > a data format, you get an window to input image dimensions, b-table, and > data file names. In this window, you can find "Slices to be processed". > For > example, if you have 50-slice images, you can process slice # 0 - 24, for > the first batch and slice # 25-49 for the second batch. In this way, you > can > reduce the data size. If this approach works, it is a memory problem. > > If you get a memory problem, you can do one of following things; > > 1) Of course, increase RAM. You can see improvement up to 2 GB of RAM, > usually. > 2) 64-bit Windows XP is really the solution because 32-bit Windows can > allocate only up to 1-1.5GB of RAM to a single task. > 3) Use the slice-divided tensor calculation and save calculated images > such > as FA, ADC, tensor. For example, you can get FA0-24 and FA25-49. Then you > can load them into one window and save together to get FA0-49. > > Please let me know if it is really a memory issue. > > Susumu > > ________________________________________ > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of budha > Sent: Thursday, April 03, 2008 1:43 AM > To: mristudio-users at mristudio.org > Cc: budhakh at gmail.com > Subject: [Mristudio-users] Error while processing DTI Mapping > > Dear All, > ? > I am Graduate Student working? in the field of DTI. I have been trying to > use DTI Studio for my research. I was able to find the eigenvalues, > eigenvectors of DTI images. The problem is somehow now while running > DTIStudio,?it is able to process images,?I can?see the DTI Map display > window, but the moment I try to run ADC map, Tensor Eigenvalues etc., I > get > an a error message?which I have attached.?? Can anyone tell me where the > problem is ? > ? > Thanking you, > ? > Budha > NBRC, India > ? > ? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > From gustav at andreisek.de Fri Apr 4 00:08:57 2008 From: gustav at andreisek.de (Gustav Andreisek) Date: Fri, 04 Apr 2008 00:08:57 -0400 Subject: [Mristudio-users] ADC values decrease with increasing b-values Message-ID: <000601c89609$9b688710$d2399530$@de> Dear All, We imaged a cohort of volunteers at different b-values and determined the ADC values. We found decreasing ADC with increasing b-values. This would be in accordance to the literature, as long as we can assume that DTIstudio does not automatically uses a correction factor for varying SNR at different diffusion weightings (Dietrich O, Heiland S, Sartor K. Noise correction for the exact determination of apparent diffusion coefficients at low SNR. Magn Reson Med 2001; 45:448-453.). Is that true? Best regards and greetings from Canada, Gustav Gustav Andreisek, M.D. Postdoctoral Research Fellow Department of Medical Imaging, 5th Floor Mount Sinai Hospital and the University Health Network University of Toronto 600 University Ave Toronto, ON, M5G 1X5 Canada Tel: +1 416 586 4800 ext 2935 Fax: +1 416 586 8695 E-mail: gustav at andreisek.de -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080404/e3a4a039/attachment.html From susumu at mri.jhu.edu Fri Apr 4 10:43:23 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 04 Apr 2008 10:43:23 -0400 Subject: [Mristudio-users] fiber tracking after updating in Landmarker In-Reply-To: Message-ID: <6i7avk$1g68bk@ipex2.johnshopkins.edu> Good question. It is a bit complicated because you can't open a tensor file directly by DtiStudio. 1) First you need to open a scalar image file such as FA, ADC, DWI, b0 with the same image dimension. Usually one of those images of the same subject. 2) Once you get the image opened in a viewing window, you can find the "Open.d" button at the right column. Click this button. 3) A new dialog window shows up. Make sure that all the dimensions and voxel sizes are correct and specify the "DtiStudio" format. 4) Don't forget to click a check box saying "Get eigen-value/vectors,,,,". Specify the file name. 5) Click "ok". This will load your tensor file and recalculate all the scalar images and vector images. Please let me know if you have any question. -----Original Message----- From: JULIE E MCENTEE [mailto:jmcentee at jhmi.edu] Sent: Friday, April 04, 2008 10:21 AM To: susumu at mri.jhu.edu Subject: Re: [Mristudio-users] fiber tracking after updating in Landmarker How do I read the (updated?) tensor file into DtiStudio? Thanks- 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: susumu Date: Thursday, April 3, 2008 6:00 pm Subject: Re: [Mristudio-users] fiber tracking after updating in Landmarker To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > Hi Julie, > > When you got "white lines against black background", it's most likely > a > wrong image matrix. Please make sure that you load the data as a "vector" > file. Also, after the normalization to ICBM-MNI, all image should be > 181x217x181. So, if you got the vector file transformed correctly, you > should get this matrix size after you select "vector" as the file format. > > There is one important issue, though. We don't recommend any transformation > of vector files. This is because vector transformation is very > unstable. If > you want to do tracking after DTI image transformation, I strongly suggest > to use "tensor transformation", not FA and vector transformation. > > This is simple. You need to open a tensor file using the "open .d" button. > Then you can apply the AIR transformation matrix. > > Once your tensor is normalized to ICBM, your can read the transformed > tensor > file to DtiStudio and recalculate all the FA, ADC, vector things. > > Please let me know if you have further question. > > Susumu > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [ On Behalf Of JULIE E MCENTEE > Sent: Thursday, April 03, 2008 5:06 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] fiber tracking after updating in Landmarker > > I normalised my Air.fa image to the ICBM-MNI-FA template using > Landmarker. I > am now trying to do fiber tracking (whole brain) using the Updated_Air.fa > image in DtiStudio. The only way I was able to get DtiStudio to do > the fiber > tracking was to normalise the eigenvectors (0, 1, 2) to the ICBM-MNI-FA > template in Landmarker, but then I am only able to load one 'updated' > eigenvector as the Principle Vector in DtiStudio. The result is some > white > lines against black background. > > What should I be doing here? > > Thank you for your help! > > 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 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From susumu at mri.jhu.edu Fri Apr 4 12:45:36 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 04 Apr 2008 12:45:36 -0400 Subject: [Mristudio-users] ADC values decrease with increasing b-values In-Reply-To: <000601c89609$9b688710$d2399530$@de> Message-ID: <6i7avk$1g85vo@ipex2.johnshopkins.edu> Hi Gustav, Your observation is correct. When we determine ADC, we perform mono-exponential fitting, but the signal decay is hardly mono-exponential. When the intensity as a function of b-value is plotted in a log scale, it should be a straight line if it is mono-exponential, but reality is, it curves. That means, if we do 2-point measurements like 0 and 500, 0 and 1000, or 0 and 1,500, the determined slope gets less and less steep. I attached our internal data acquired by Ming-Chung Chou. You can see very strong dependency of ADC on b. This could be due to hitting a noise floor but even with high SNR, the non mon-exponential behavior can be observed. As a matter of fact, if we do simulation with different SNR, ADC values are more stable than FA. This is somewhat the opposite of FA (second slide). Again this is Ming-Chung's data. As you can see from the graph, FA is rather stable in 750-1500 range, but as we know, FA values is sensitive to SNR when SNR is low. Hope this will help. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Gustav Andreisek Sent: Friday, April 04, 2008 12:09 AM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] ADC values decrease with increasing b-values Dear All, We imaged a cohort of volunteers at different b-values and determined the ADC values. We found decreasing ADC with increasing b-values. This would be in accordance to the literature, as long as we can assume that DTIstudio does not automatically uses a correction factor for varying SNR at different diffusion weightings (Dietrich O, Heiland S, Sartor K. Noise correction for the exact determination of apparent diffusion coefficients at low SNR. Magn Reson Med 2001; 45:448-453.). Is that true? Best regards and greetings from Canada, Gustav Gustav Andreisek, M.D. Postdoctoral Research Fellow Department of Medical Imaging, 5th Floor Mount Sinai Hospital and the University Health Network University of Toronto 600 University Ave Toronto, ON, M5G 1X5 Canada? Tel:???? +1 416 586 4800 ext 2935 Fax: ?? +1 416 586 8695 E-mail: gustav at andreisek.de -------------- next part -------------- A non-text attachment was scrubbed... Name: TraceADC.ppt Type: application/vnd.ms-powerpoint Size: 163840 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080404/2bbe4e2c/attachment-0001.ppt From Srinivasan at kennedykrieger.org Fri Apr 4 13:54:31 2008 From: Srinivasan at kennedykrieger.org (Priti Srinivasan) Date: Fri, 04 Apr 2008 13:54:31 -0400 Subject: [Mristudio-users] Loading a subject onto Landmarker Message-ID: <47F63318.E224.0081.0@kennedykrieger.org> Hi All, I have a very basic question. I am having problems loading a subject onto landmarker. I loaded the ICBM_MNI_DWI of the landmarker. The subject that i am supposed to load into the landmarker for registration/normalization should have the dimensions 181x217x181. I am able to set the first two dimensions, but the third dimension (Image slice is always greyed out.). That value is by default 108 in this case and I am not able to change it. If I do not change it I can only see white lines and grey lines and not the brain (which I assume is because the image matrix is not correct). Any suggestions on how the Image slices parameter can be changed? Thanks in advance, Priti 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. From xli16 at jhmi.edu Fri Apr 4 14:23:32 2008 From: xli16 at jhmi.edu (XIN LI) Date: Fri, 04 Apr 2008 14:23:32 -0400 Subject: [Mristudio-users] Loading a subject onto Landmarker In-Reply-To: <47F63318.E224.0081.0@kennedykrieger.org> References: <47F63318.E224.0081.0@kennedykrieger.org> Message-ID: Priti, The value of image slices are automatically calculated out based on the size of the image file, the image width, the image height and the image data format. That's why it is always grayed out. Please check if the image data format is set to be the right one. Xin ----- Original Message ----- From: Priti Srinivasan Date: Friday, April 4, 2008 1:56 pm Subject: [Mristudio-users] Loading a subject onto Landmarker To: mristudio-users at mristudio.org > Hi All, > > I have a very basic question. I am having problems loading a subject > onto landmarker. I loaded the ICBM_MNI_DWI of the landmarker. The > subject that i am supposed to load into the landmarker for > registration/normalization should have the dimensions 181x217x181. I > am able to set the first two dimensions, but the third dimension > (Image slice is always greyed out.). That value is by default 108 in > this case and I am not able to change it. If I do not change it I can > only see white lines and grey lines and not the brain (which I assume > is because the image matrix is not correct). Any suggestions on how > the Image slices parameter can be changed? > > Thanks in advance, > > Priti > > > > > 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 > From susumu at mri.jhu.edu Fri Apr 4 21:40:38 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 04 Apr 2008 21:40:38 -0400 Subject: [Mristudio-users] Loading a subject onto Landmarker In-Reply-To: <47F63318.E224.0081.0@kennedykrieger.org> Message-ID: <6i7avk$1gf0en@ipex2.johnshopkins.edu> As Xin said, the slice number is calculated from the file size. Your data doesn't have to be the same as the template you choose (in this case, ICBM). The ICBM is 181x217x181. After linear normalization, no matter the matrix size of your original data, it is changed to that of template. If you want to use AIR-based nonlinear or LDDMM, the matrix sizes of the template and your data must be the same. So, you should first do AIR-linear (rigid or affine). Please let me know if you still have a problem. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Priti Srinivasan Sent: Friday, April 04, 2008 1:55 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Loading a subject onto Landmarker Hi All, I have a very basic question. I am having problems loading a subject onto landmarker. I loaded the ICBM_MNI_DWI of the landmarker. The subject that i am supposed to load into the landmarker for registration/normalization should have the dimensions 181x217x181. I am able to set the first two dimensions, but the third dimension (Image slice is always greyed out.). That value is by default 108 in this case and I am not able to change it. If I do not change it I can only see white lines and grey lines and not the brain (which I assume is because the image matrix is not correct). Any suggestions on how the Image slices parameter can be changed? Thanks in advance, Priti 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 http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Sun Apr 6 08:10:03 2008 From: susumu at mri.jhu.edu (susumu) Date: Sun, 06 Apr 2008 08:10:03 -0400 Subject: [Mristudio-users] Saving Eigen Vectors In-Reply-To: <66bddc1c0803251021x47f4ec8am728dbcd219176f1f@mail.gmail.com> Message-ID: <6i7avk$1h5v97@ipex2.johnshopkins.edu> Hi Mayuresh, Currently DtiStudio support "Raw" and "Analyze" formats for data output. In both cases, the images are saved as a simple raw matrix without headers. For example, FA map is a floating point, d1 x d2 x d3 matrix, where d1, 2, 3 are matrix dimensions. As Darshan already pointed out, for the vector files, they are saved as floating point, 3 x d1 x d2 x d3. It should be possible to write a Matlab code to read this matrix. Please let us know if you have any problems in reading the data. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Mayuresh Korgaonkar Sent: Tuesday, March 25, 2008 1:22 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Saving Eigen Vectors Hello all, I have a question with regards to saving the eigen vector images using DTIstudio. My goal is to read these images in MATLAB. Is there a way to read the "DTIstudio raw data format"? Saving these images in Analyze format doesnt seem to work. Thankyou for your time, Regards, -- ~Mayuresh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080406/fae906ea/attachment.html From Srinivasan at kennedykrieger.org Wed Apr 9 16:40:19 2008 From: Srinivasan at kennedykrieger.org (Priti Srinivasan) Date: Wed, 09 Apr 2008 16:40:19 -0400 Subject: [Mristudio-users] Hi, Message-ID: <47FCF172.E224.0081.0@kennedykrieger.org> Hi, My images were in the Analyze format and I was trying to import it as raw file, thats why it was turning out to be weird. As per Susumu's advice I warped my images to the MNI template using linear registration. I had another question here. I warped my mdw, b0 and fa images in ANALYZE format to the MNI space. I would like to do fiber tracking for the subjects in the MNI space, but I am not sure as to how to warp the vector images to the MNI template. I usually use the .fa and .vec file that CATNAP spits out to create the color FA maps and then do the fiber tracking on that. Since these are vectors/tensor images I am not sure how the impact of warping will be on the image. What is the best way to convert these vector images to the standard space? Thanks for you time and patience. Sincerely, Priti, The value of image slices are automatically calculated out based on the size of the image file, the image width, the image height and the image data format. That's why it is always grayed out. Please check if the image data format is set to be the right one. Xin ----- Original Message ----- From: Priti Srinivasan Date: Friday, April 4, 2008 1:56 pm Subject: [Mristudio-users] Loading a subject onto Landmarker To: mristudio-users at mristudio.org > Hi All, > > I have a very basic question. I am having problems loading a subject > onto landmarker. I loaded the ICBM_MNI_DWI of the landmarker. The > subject that i am supposed to load into the landmarker for > registration/normalization should have the dimensions 181x217x181. I > am able to set the first two dimensions, but the third dimension > (Image slice is always greyed out.). That value is by default 108 in > this case and I am not able to change it. If I do not change it I can > only see white lines and grey lines and not the brain (which I assume > is because the image matrix is not correct). Any suggestions on how > the Image slices parameter can be changed? > > Thanks in advance, > > Priti > > > > > 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 > From susumu at mri.jhu.edu Thu Apr 10 13:37:47 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 10 Apr 2008 13:37:47 -0400 Subject: [Mristudio-users] Hi, In-Reply-To: <47FCF172.E224.0081.0@kennedykrieger.org> Message-ID: <6i7deu$1ns84p@ipex1.johnshopkins.edu> Hi Priti, There is a related thread called, "fiber tracking after updating in Landmarker". Please refer it first. I don't recommend to transform vector images, because vector transformation has inherent instability. If you want to have fiber orientations to be transformed (unlike other scalar image transformation), you have to transform a tensor map which consists of 6xd1xd2xd3, where d1-3 are matrix dimensions. To load a tensor map to Landmarker, you have to use dedicated button, "open .d" so that Landmarker knows that it has to perform special transformation. My another thread explains how to load the transformed tensor map and recalculate a vector map. Please let me know if you have any question. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Priti Srinivasan Sent: Wednesday, April 09, 2008 4:40 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Hi, Hi, My images were in the Analyze format and I was trying to import it as raw file, thats why it was turning out to be weird. As per Susumu's advice I warped my images to the MNI template using linear registration. I had another question here. I warped my mdw, b0 and fa images in ANALYZE format to the MNI space. I would like to do fiber tracking for the subjects in the MNI space, but I am not sure as to how to warp the vector images to the MNI template. I usually use the .fa and .vec file that CATNAP spits out to create the color FA maps and then do the fiber tracking on that. Since these are vectors/tensor images I am not sure how the impact of warping will be on the image. What is the best way to convert these vector images to the standard space? Thanks for you time and patience. Sincerely, Priti, The value of image slices are automatically calculated out based on the size of the image file, the image width, the image height and the image data format. That's why it is always grayed out. Please check if the image data format is set to be the right one. Xin ----- Original Message ----- From: Priti Srinivasan Date: Friday, April 4, 2008 1:56 pm Subject: [Mristudio-users] Loading a subject onto Landmarker To: mristudio-users at mristudio.org > Hi All, > > I have a very basic question. I am having problems loading a subject > onto landmarker. I loaded the ICBM_MNI_DWI of the landmarker. The > subject that i am supposed to load into the landmarker for > registration/normalization should have the dimensions 181x217x181. I > am able to set the first two dimensions, but the third dimension > (Image slice is always greyed out.). That value is by default 108 in > this case and I am not able to change it. If I do not change it I can > only see white lines and grey lines and not the brain (which I assume > is because the image matrix is not correct). Any suggestions on how > the Image slices parameter can be changed? > > Thanks in advance, > > Priti > > > > > 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 > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Thu Apr 10 15:33:46 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 10 Apr 2008 15:33:46 -0400 Subject: [Mristudio-users] Tutorial in Toronto Message-ID: <6i7deu$1nv7bm@ipex1.johnshopkins.edu> Dear MriStudio Users, Thank you for your interest in our tutorial in Toronto on 5/4. This tutorial was made possible by the kind support from Dr. Karen Davis' group in Division of Brain, Imaging and Behaviour-Systems Neuroscience in University of Toronto. I also thank to Keri for arranging the site. Here is the map of the site: http://maps.google.com/maps?f=d &hl=en&geocode=&saddr=399+bathurst+street,+toronto,+on&daddr=255+Front+St+W, +Toronto,+Toronto,+Ontario+M5V,+Canada&mra=pe&mrcr=0&sll=43.649033,-79.38522 2&sspn=0.022513,0.057335&ie=UTF8&ll=43.648746,-79.405489&spn=0.022513,0.0573 35&z=15&om=0 I attached an attendant list. If you don't find your name, please let us know. The tutorial is free. It'll start at 1:00 and end at 5:00, although it may take longer depending on how many questions we get. It is very important for you to "pre-condition" your laptops. Please visit www.mristudio.org -> Workshop and download proper software and data. This will make sure that your laptop has a working version of DtiStudio/Landmarker/RoiEditor. We will provide only power outlets. So, you need to bring your own laptops. Please let us know if you have any questions. Sincerely, Susumu Mori -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080410/01fced6d/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: tutorial_Toronto_list.xls Type: application/vnd.ms-excel Size: 18944 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080410/01fced6d/attachment-0001.xls From johnlsherman at hotmail.com Thu Apr 10 22:47:53 2008 From: johnlsherman at hotmail.com (John Sherman) Date: Thu, 10 Apr 2008 20:47:53 -0600 Subject: [Mristudio-users] Tutorial in Toronto In-Reply-To: References: Message-ID: Hello, I am a radiologist in private practice in Colorado working with a two different 3.0 T systems (G.E and Phillips) in three states. I desperately need a standalone workstation/laptop to work with this data. Will the Toronto tutorial enable me to get DTI Studio up and running so that I can use this data in clinical practice? I am waiting to hear from you before I make my air reservation. Can you suggest a nearby hotel? Thanks John Sherman, M.D. From: SEWILSON at aol.comDate: Thu, 10 Apr 2008 15:49:14 -0400Subject: Fwd: [Mristudio-users] Tutorial in TorontoTo: johnlsherman at hotmail.com From: susumu at mri.jhu.eduReply-to: mristudio-users at mristudio.orgTo: mristudio-users at mristudio.orgCC: ktaylor at uhnres.utoronto.caSent: 4/10/2008 12:34:35 P.M. Pacific Daylight TimeSubj: [Mristudio-users] Tutorial in Toronto Dear MriStudio Users, Thank you for your interest in our tutorial in Toronto on 5/4. This tutorial was made possible by the kind support from Dr. Karen Davis' group in Division of Brain, Imaging and Behaviour-Systems Neuroscience in University of Toronto. I also thank to Keri for arranging the site. Here is the map of the site: http://maps.google.com/maps?f=d&hl=en&geocode=&saddr=399+bathurst+street,+toronto,+on&daddr=255+Front+St+W,+Toronto,+Toronto,+Ontario+M5V,+Canada&mra=pe&mrcr=0&sll=43.649033,-79.385222&sspn=0.022513,0.057335&ie=UTF8&ll=43.648746,-79.405489&spn=0.022513,0.057335&z=15&om=0 I attached an attendant list. If you don't find your name, please let us know. The tutorial is free. It'll start at 1:00 and end at 5:00, although it may take longer depending on how many questions we get. It is very important for you to "pre-condition" your laptops. Please visit www.mristudio.org -> Workshop and download proper software and data. This will make sure that your laptop has a working version of DtiStudio/Landmarker/RoiEditor. We will provide only power outlets. So, you need to bring your own laptops. Please let us know if you have any questions. Sincerely, Susumu Mori_______________________________________________Mristudio-users mailing listMristudio-users at mristudio.orghttp://lists.mristudio.org/mailman/listinfo/mristudio-users Planning your summer road trip? Check out AOL Travel Guides. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080410/76ea5dd9/attachment.html From susumu at mri.jhu.edu Fri Apr 11 11:06:27 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 11 Apr 2008 11:06:27 -0400 Subject: [Mristudio-users] Tutorial in Toronto In-Reply-To: Message-ID: <6i7deu$1ol2ng@ipex1.johnshopkins.edu> Hi John, You need to download all software and data into your laptop BEFORE you come to the Toronto meeting. We will not provide software, data, and laptops in Toronto to maximize the time-efficiency (we have only 4 hours). All attendants need to bring their laptops with all software and data pre-installed. The website (www.mristudio.org -> Workshop) also includes a small pre-tutorial course you need to follow to make sure that the programs are functional in your laptop. The tutorial starts with a Powerpoint presentation about the overview of our DTI processing software (DtiStudio) and atlas-based image analysis software (Landmarker and RoiEditor), followed by actual step-by-step software operations. The tutorial will be mostly about practical aspects of the software rather than DTI itself. One important note: our software is for research only and can not be used for clinical purposes. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of John Sherman Sent: Thursday, April 10, 2008 10:48 PM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Tutorial in Toronto Hello, I am a radiologist in private practice in Colorado working with a two different 3.0 T systems (G.E and Phillips) in three states. I desperately need a standalone workstation/laptop to work with this data. Will the Toronto tutorial enable me to get DTI Studio up and running so that I can use this data in clinical practice? I am waiting to hear from you before I make my air reservation. Can you suggest a nearby hotel? Thanks John Sherman, M.D. _____ From: SEWILSON at aol.com Date: Thu, 10 Apr 2008 15:49:14 -0400 Subject: Fwd: [Mristudio-users] Tutorial in Toronto To: johnlsherman at hotmail.com _____ From: susumu at mri.jhu.edu Reply-to: mristudio-users at mristudio.org To: mristudio-users at mristudio.org CC: ktaylor at uhnres.utoronto.ca Sent: 4/10/2008 12:34:35 P.M. Pacific Daylight Time Subj: [Mristudio-users] Tutorial in Toronto Dear MriStudio Users, Thank you for your interest in our tutorial in Toronto on 5/4. This tutorial was made possible by the kind support from Dr. Karen Davis' group in Division of Brain, Imaging and Behaviour-Systems Neuroscience in University of Toronto. I also thank to Keri for arranging the site. Here is the map of the site: http://maps.google.com/maps?f=d &hl=en&geocode=&saddr=399+bathurst+street,+toronto,+on&daddr=255+Front+St+W, +Toronto,+Toronto,+Ontario+M5V,+Canada&mra=pe&mrcr=0&sll=43.649033,-79.38522 2&sspn=0.022513,0.057335&ie=UTF8&ll=43.648746,-79.405489&spn=0.022513,0.0573 35&z=15&om=0 I attached an attendant list. If you don't find your name, please let us know. The tutorial is free. It'll start at 1:00 and end at 5:00, although it may take longer depending on how many questions we get. It is very important for you to "pre-condition" your laptops. Please visit www.mristudio.org -> Workshop and download proper software and data. This will make sure that your laptop has a working version of DtiStudio/Landmarker/RoiEditor. We will provide only power outlets. So, you need to bring your own laptops. Please let us know if you have any questions. Sincerely, Susumu Mori _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _____ Planning your summer road trip? Check out AOL Travel Guides. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080411/144ebe69/attachment-0001.html From shereeda at email.uc.edu Fri Apr 11 12:58:46 2008 From: shereeda at email.uc.edu (Duke Shereen) Date: Fri, 11 Apr 2008 12:58:46 -0400 (EDT) Subject: [Mristudio-users] Toronto tutorial Message-ID: <20080411125846.CAA38593@mirapoint.uc.edu> Hi all, Thank you Dr. Mori and colleagues for hosting this tutorial at the ISMRM conference in Toronto. As a graduate student working in DTI, it is nice to see I'm not the only one struggling with a few of the nuances in DTI data processing. My question is: will the tutorial be recorded? I think it would be useful to have a videotape of the tutorial made public, especially for those who would have liked to join but couldn't...as well as for those of us who go but don't remember everything. Duke From llanyon at eyecarecentre.org Fri Apr 11 13:09:10 2008 From: llanyon at eyecarecentre.org (llanyon at eyecarecentre.org) Date: Fri, 11 Apr 2008 17:09:10 +0000 (GMT) Subject: [Mristudio-users] Toronto tutorial Message-ID: <1193319890.214731207933750747.JavaMail.mail@webmail01> An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080411/82181aed/attachment.html From vinod.bioinfo at gmail.com Fri Apr 11 13:34:49 2008 From: vinod.bioinfo at gmail.com (sri krishna) Date: Fri, 11 Apr 2008 19:34:49 +0200 Subject: [Mristudio-users] Toronto tutorial In-Reply-To: <1193319890.214731207933750747.JavaMail.mail@webmail01> References: <1193319890.214731207933750747.JavaMail.mail@webmail01> Message-ID: Hey duke, it's good idea. it will be good to have a video from this Tutorial session. I request too for making a video and put on google video or youtube or ftp. regards vinod On Fri, Apr 11, 2008 at 7:09 PM, wrote: > As someone who is very interested but can't make the tutorial, I agree > this would be a very nice feature indeed! I hope it can be arranged. > > > > Thanks! > > Linda Lanyon > > > > On Apr 11, 2008, *shereeda at email.uc.edu* wrote: > > Hi all, > Thank you Dr. Mori and colleagues for hosting this tutorial at the ISMRM > conference in Toronto. As a graduate student working in DTI, it is nice to > see I'm not the only one struggling with a few of the nuances in DTI data > processing. > > My question is: will the tutorial be recorded? I think it would be > useful to have a videotape of the tutorial made public, especially for those > who would have liked to join but couldn't...as well as for those of us who > go but don't remember everything. > > Duke > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080411/b4b22e6e/attachment.html From j.haenggi at psychologie.uzh.ch Tue Apr 15 13:19:30 2008 From: j.haenggi at psychologie.uzh.ch (Juergen Haenggi, Psychological Institute) Date: Tue, 15 Apr 2008 19:19:30 +0200 Subject: [Mristudio-users] Forget gradient of B0-image? error message Message-ID: Dear MRI Studio users I tried to run DTI Mapping. Although I specified three B0-images (the first three acqusitions), the following error occurred: Forget gradient of B0-image? From the examples on the MRI Studio website I recognized that there is always the last image which is not diffusion-weighted. Does the last image have to be a B0-image? What happens? Any help is appreciated. Best regards Juergen Haenggi ------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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) ------------------------------------------------- From alinajurcoane at hotmail.com Tue Apr 15 13:36:05 2008 From: alinajurcoane at hotmail.com (Alina Jurcoane) Date: Tue, 15 Apr 2008 19:36:05 +0200 Subject: [Mristudio-users] Forget gradient of B0-image? error message References: Message-ID: Hi Juergen, I always had the B0 images at the beginning and it always worked, so it should work for you too. Are you sure you defined well the gradient table? For your case, it should look like this for a hypotethical example of 3B0+12Grads: first 3 lines zero in all directions and the following 12 lines with the gradient values. Something like this: 0: 0.0000, 0.0000, 0.0000 1: 0.0000, 0.0000, 0.0000 2: 0.0000, 0.0000, 0.0000 3: 1.0000, 0.0000, 0.5000 4: 0.0000, 0.5000, 1.0000 5: 0.5000, 1.0000, 0.0000 6: 1.0000, 0.5000, 0.0000 7: 0.0000, 1.0000, 0.5000 8: 0.5000, 0.0000, 1.0000 9: 1.0000, 0.0000, -0.5000 10: 0.0000, -0.5000, 1.0000 11: -0.5000, 1.0000, 0.0000 12: 1.0000, -0.5000, 0.0000 13: 0.0000, 1.0000, -0.5000 14: -0.5000, 0.0000, 1.0000 Hope it helps. Regards, Alina ______________________________________ Alina Jurcoane Klinikum der JWGoethe Universit?t Institut f?r Neuroradiologie Schleusenweg 2-16 (Haus 95) 60528 Frankfurt/M, DE Tel +49 (0)69 6301-6617 ----- Original Message ----- From: "Juergen Haenggi, Psychological Institute" To: Sent: Tuesday, April 15, 2008 7:19 PM Subject: [Mristudio-users] Forget gradient of B0-image? error message > Dear MRI Studio users > > I tried to run DTI Mapping. Although I specified three B0-images (the > first > three acqusitions), the following error occurred: > > Forget gradient of B0-image? > > From the examples on the MRI Studio website I recognized that there is > always the last image which is not diffusion-weighted. > > Does the last image have to be a B0-image? > > What happens? Any help is appreciated. > > Best regards > Juergen Haenggi > > ------------------------------------------------- > Juergen Haenggi > Ph.D. (Dr. des.) > Division of 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) > ------------------------------------------------- > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From support at mristudio.org Tue Apr 15 13:57:14 2008 From: support at mristudio.org (support at mristudio.org) Date: Tue, 15 Apr 2008 13:57:14 -0400 (EDT) Subject: [Mristudio-users] Load ROI's drawn in fMRI images on DTI image In-Reply-To: <48048BD5020000B500016F6E@n6mcgw16.cchmc.org> References: <48048BD5020000B500016F6E@n6mcgw16.cchmc.org> Message-ID: <3980.71.245.167.142.1208282234.squirrel@webmail.mristudio.org> Hi Akila, This is a good question. I want to answer your question in a more generic way, "how can we load ROI files defined by other software programs?". It could be a fMRI activation map or manually drawn ROIs. The ROI-drawing capability of DtiStudio is not very strong. It is also a viable option to use RoiEditor to define multiple 3D ROIs and then load them to DtiStudio for fiber tracking. Either way, they can be best done by using "Binary Mapping" format you can find in DtiStudio and RoiEditor. To understand this format, First please perform fiber tracking by DtiStudio. It can be anything. Please just use two ROIs; one for "OR" and the second for "AND". After the tracking, click the "Save" icon in the "ROI Operation" section. Then you can find "Binary Mapping" as one of the options. Please choose this format and save it. If you open the directory where you saved the file, you should find three new files. Two files with *.dat extension are 3D binary files. If your image has 192x192x60 dimension, they should have the same dimension with pixels with "1" indicate the location of the ROI. The third file has *.map extension. This is an ASCII file. So, you can open it by a texteditor. It should be straightfoward to understand this file. It also has an explanation section at the bottom. Once you understand this file, you can modify them to read and combine any 3D binary 1/0 ROI files for fiber tracking. If you are using RoiEditor, you can create multiple 3D files, save them by "Binary Mapping", modify them to specify how you want to combine multiple ROIs ("OR", "AND", "NOT", "CUT" operations), read the file to DtiStudio, and fiber tracking is automatic. If you are using another software program, please make sure to save each ROI as 1/0 raw binary data. Then, you can simply specify the file path in the *.map file and read them into DtiStudio. Please let me know if you have any questions. Susumu > Hi, > > I am trying to draw a ROI in functional image in a different software and > then save it in a format that DTI Studio can read inorder to load the ROI on > DTI image. > > Can I please get the source code for ROI Editor inorder to understand the > formatting of ROI better in DTI Studio? > > Thanks, > Akhila. > > From j.haenggi at psychologie.uzh.ch Tue Apr 15 14:15:02 2008 From: j.haenggi at psychologie.uzh.ch (Juergen Haenggi) Date: Tue, 15 Apr 2008 20:15:02 +0200 Subject: [Mristudio-users] Forget gradient of B0-image? error message In-Reply-To: Message-ID: Hi Alina Thanks for confirming that it works with B0 images in the first place. It was a formatting problem with the bvecs files originated from Mac. Now it works. Regards Juergen On 15.4.2008 19:36 Uhr, "Alina Jurcoane" wrote: > Hi Juergen, > > I always had the B0 images at the beginning and it always worked, so it > should work for you too. Are you sure you defined well the gradient table? > For your case, it should look like this for a hypotethical example of > 3B0+12Grads: first 3 lines zero in all directions and the following 12 lines > with the gradient values. Something like this: > > 0: 0.0000, 0.0000, 0.0000 > 1: 0.0000, 0.0000, 0.0000 > 2: 0.0000, 0.0000, 0.0000 > 3: 1.0000, 0.0000, 0.5000 > 4: 0.0000, 0.5000, 1.0000 > 5: 0.5000, 1.0000, 0.0000 > 6: 1.0000, 0.5000, 0.0000 > 7: 0.0000, 1.0000, 0.5000 > 8: 0.5000, 0.0000, 1.0000 > 9: 1.0000, 0.0000, -0.5000 > 10: 0.0000, -0.5000, 1.0000 > 11: -0.5000, 1.0000, 0.0000 > 12: 1.0000, -0.5000, 0.0000 > 13: 0.0000, 1.0000, -0.5000 > 14: -0.5000, 0.0000, 1.0000 > > Hope it helps. > > Regards, > Alina > ______________________________________ > Alina Jurcoane > Klinikum der JWGoethe Universit?t > Institut f?r Neuroradiologie > Schleusenweg 2-16 (Haus 95) > 60528 Frankfurt/M, DE > Tel +49 (0)69 6301-6617 > > ----- Original Message ----- > From: "Juergen Haenggi, Psychological Institute" > > To: > Sent: Tuesday, April 15, 2008 7:19 PM > Subject: [Mristudio-users] Forget gradient of B0-image? error message > > >> Dear MRI Studio users >> >> I tried to run DTI Mapping. Although I specified three B0-images (the >> first >> three acqusitions), the following error occurred: >> >> Forget gradient of B0-image? >> >> From the examples on the MRI Studio website I recognized that there is >> always the last image which is not diffusion-weighted. >> >> Does the last image have to be a B0-image? >> >> What happens? Any help is appreciated. >> >> Best regards >> Juergen Haenggi >> >> ------------------------------------------------- >> Juergen Haenggi >> Ph.D. (Dr. des.) >> Division of 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) >> ------------------------------------------------- >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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) ----------------------------------------------------------- From graeme.schwindt at gmail.com Fri Apr 18 12:28:19 2008 From: graeme.schwindt at gmail.com (Graeme Schwindt) Date: Fri, 18 Apr 2008 12:28:19 -0400 Subject: [Mristudio-users] Analyze ROIs Message-ID: <8640b26c0804180928y2327ecd4r25f2fac0b2301704@mail.gmail.com> Hello, I am a new DTIStudio user, and am experiencing some confusion regarding ROI data formats. I have two issues: 1) I would like to import ROIs drawn in MRICro (analyze format) into ROIEditor for statistics calculation, However, it appears that ROIEditor will not read the analyze files, and gives an roi header file open error. It also refers to a .roihdr file in the error, rather than a .hdr file. Is there anyway to solve this issue? 2) I would also like to import ROIs into DTIStudio fiber tracking, in order to delinate seed and target ROIs for tracking of fibers. I noticed an earlier mailing list post about using ROIEditor to make these ROIs, and then save them as binary map files for the fiber tracking ROI module in dtistudio. I did this, and the file was saved as a .dat file by ROIEditor. However, then when I went to load the roi in dtistudio's fiber tracking tab in binary map format, it was asking for a .map file. I forced it to open the binary map file I had saved in ROIEditor (ending in _map.dat), and while it appeared to load, it did not appear on the image, nor did any fibers appear when the 'selected' radio button was highlighted. I feel I must be making some simple mistake here. Thanks for any help or advice and for supporting this mailing list! Graeme -- Graeme C. Schwindt, HBSc MD/PhD Student University of Toronto graeme.schwindt at gmail.com 416.546.5453 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080418/f45b7ced/attachment.html From graeme.schwindt at gmail.com Fri Apr 18 13:21:21 2008 From: graeme.schwindt at gmail.com (Graeme Schwindt) Date: Fri, 18 Apr 2008 13:21:21 -0400 Subject: [Mristudio-users] Analyze ROIs Message-ID: <8640b26c0804181021w54c132f0i7eeb8693b1a60510@mail.gmail.com> Hello, I am a new DTIStudio user, and am experiencing some confusion regarding ROI data formats. I have two issues: 1) I would like to import ROIs drawn in MRICro (analyze format) into ROIEditor for statistics calculation, However, it appears that ROIEditor will not read the analyze files, and gives an roi header file open error. It also refers to a .roihdr file in the error, rather than a .hdr file. Is there anyway to solve this issue? 2) I would also like to import ROIs into DTIStudio fiber tracking, in order to delinate seed and target ROIs for tracking of fibers. I noticed an earlier mailing list post about using ROIEditor to make these ROIs, and then save them as binary map files for the fiber tracking ROI module in dtistudio. I did this, and the file was saved as a .dat file by ROIEditor. However, then when I went to load the roi in dtistudio's fiber tracking tab in binary map format, it was asking for a .map file. I forced it to open the binary map file I had saved in ROIEditor (ending in _map.dat), and while it appeared to load, it did not appear on the image, nor did any fibers appear when the 'selected' radio button was highlighted. I feel I must be making some simple mistake here. Thanks for any help or advice and for supporting this mailing list! Graeme -- Graeme C. Schwindt, HBSc MD/PhD Student University of Toronto graeme.schwindt at gmail.com 416.546.5453 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080418/b7573a2b/attachment.html From xli16 at jhmi.edu Fri Apr 18 15:00:59 2008 From: xli16 at jhmi.edu (XIN LI) Date: Fri, 18 Apr 2008 15:00:59 -0400 Subject: [Mristudio-users] Analyze ROIs In-Reply-To: <8640b26c0804181021w54c132f0i7eeb8693b1a60510@mail.gmail.com> References: <8640b26c0804181021w54c132f0i7eeb8693b1a60510@mail.gmail.com> Message-ID: Graeme, 1) If the analyze image file you created in MRICro is a byte data file, it can be loaded into ROIEditor as "Raw Data (Byte)". You can find this selection in the "Load ROI File" window. 2) If you want to load the ROI binary map files created by ROIEditor into DtiStudio, you need to modify the *_map.dat file to specify how you want to combine multiple ROIs ("OR", "AND", "NOT", "CUT" operations). The script you need to add is like this: "Operation: 0". I have attached two *_map.dat files to this email. One is created by ROIEditor and the other is by DtiStudio. You can easily find the difference between them. Please refer to this post http://lists.mristudio.org/pipermail/mristudio-users/2008/000050.html Please let us know if you still have any problems. Xin ----- Original Message ----- From: Graeme Schwindt Date: Friday, April 18, 2008 1:21 pm Subject: [Mristudio-users] Analyze ROIs To: mristudio-users at mristudio.org > Hello, > > I am a new DTIStudio user, and am experiencing some confusion > regarding ROI > data formats. I have two issues: > > 1) I would like to import ROIs drawn in MRICro (analyze format) into > ROIEditor for statistics calculation, However, it appears that ROIEditor > will not read the analyze files, and gives an roi header file open > error. It > also refers to a .roihdr file in the error, rather than a .hdr file. > Is > there anyway to solve this issue? > > 2) I would also like to import ROIs into DTIStudio fiber tracking, in > order > to delinate seed and target ROIs for tracking of fibers. I noticed an > earlier mailing list post about using ROIEditor to make these ROIs, > and then > save them as binary map files for the fiber tracking ROI module in > dtistudio. I did this, and the file was saved as a .dat file by ROIEditor. > However, then when I went to load the roi in dtistudio's fiber > tracking tab > in binary map format, it was asking for a .map file. I forced it to > open > the binary map file I had saved in ROIEditor (ending in _map.dat), > and while > it appeared to load, it did not appear on the image, nor did any fibers > appear when the 'selected' radio button was highlighted. I feel I > must be > making some simple mistake here. > > Thanks for any help or advice and for supporting this mailing list! > > Graeme > > -- > Graeme C. Schwindt, HBSc > MD/PhD Student > University of Toronto > graeme.schwindt at gmail.com > 416.546.5453 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > -------------- next part -------------- A non-text attachment was scrubbed... Name: RoiMap_mapbyDtiStudio.dat Type: application/octet-stream Size: 491 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080418/be85d8b1/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: ROIMap_mapbyROIEditor.dat Type: application/octet-stream Size: 392 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080418/be85d8b1/attachment-0001.obj From Srinivasan at kennedykrieger.org Fri Apr 18 16:57:11 2008 From: Srinivasan at kennedykrieger.org (Priti Srinivasan) Date: Fri, 18 Apr 2008 16:57:11 -0400 Subject: [Mristudio-users] Fiber tracking after updating in landmarker Message-ID: <4808D2ED.E224.0081.0@kennedykrieger.org> Hi All, My goal is to do fiber tracking after registering my target to the MNI template and as per your advice I did the following. 1. Created and the tensor.d file from the Dtimap tab in DTI studio. 2. Registered the tensor image to the MNI space in Landmarker. 3. Saved the updated tensor image. 4. Re-opened DTI studio and opened a DWI image (not warped to the MNI template) and used the open.d option and opened the tensor image to recalculate all the vectors, ADC and FA images Result: White lines against a black background. 5. Re-opened DTI studio and opened a DWI image (that was warped to MNI template using) landmarker and used the open.d option (as I assumed it must have been a problem with the dimensions) to recalculate my images Results: Weird images not like the one before but it looked more like a distorted image matrix. All the recalculated images looked like this. Any suggestion on where I am going wrong? Thanks, Priti Good question. It is a bit complicated because you can't open a tensor file directly by DtiStudio. 1) First you need to open a scalar image file such as FA, ADC, DWI, b0 with the same image dimension. Usually one of those images of the same subject. 2) Once you get the image opened in a viewing window, you can find the "Open.d" button at the right column. Click this button. 3) A new dialog window shows up. Make sure that all the dimensions and voxel sizes are correct and specify the "DtiStudio" format. 4) Don't forget to click a check box saying "Get eigen-value/vectors,,,,". Specify the file name. 5) Click "ok". This will load your tensor file and recalculate all the scalar images and vector images. Please let me know if you have any question. -----Original Message----- From: JULIE E MCENTEE [mailto:jmcentee at jhmi.edu] Sent: Friday, April 04, 2008 10:21 AM To: susumu at mri.jhu.edu Subject: Re: [Mristudio-users] fiber tracking after updating in Landmarker How do I read the (updated?) tensor file into DtiStudio? Thanks- 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: susumu Date: Thursday, April 3, 2008 6:00 pm Subject: Re: [Mristudio-users] fiber tracking after updating in Landmarker To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > Hi Julie, > > When you got "white lines against black background", it's most likely > a > wrong image matrix. Please make sure that you load the data as a "vector" > file. Also, after the normalization to ICBM-MNI, all image should be > 181x217x181. So, if you got the vector file transformed correctly, you > should get this matrix size after you select "vector" as the file format. > > There is one important issue, though. We don't recommend any transformation > of vector files. This is because vector transformation is very > unstable. If > you want to do tracking after DTI image transformation, I strongly suggest > to use "tensor transformation", not FA and vector transformation. > > This is simple. You need to open a tensor file using the "open .d" button. > Then you can apply the AIR transformation matrix. > > Once your tensor is normalized to ICBM, your can read the transformed > tensor > file to DtiStudio and recalculate all the FA, ADC, vector things. > > Please let me know if you have further question. > > Susumu > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [ On Behalf Of JULIE E MCENTEE > Sent: Thursday, April 03, 2008 5:06 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] fiber tracking after updating in Landmarker > > I normalised my Air.fa image to the ICBM-MNI-FA template using > Landmarker. I > am now trying to do fiber tracking (whole brain) using the Updated_Air.fa > image in DtiStudio. The only way I was able to get DtiStudio to do > the fiber > tracking was to normalise the eigenvectors (0, 1, 2) to the ICBM-MNI-FA > template in Landmarker, but then I am only able to load one 'updated' > eigenvector as the Principle Vector in DtiStudio. The result is some > white > lines against black background. > > What should I be doing here? > > Thank you for your help! > > 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 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users 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. From Srinivasan at kennedykrieger.org Fri Apr 18 17:07:36 2008 From: Srinivasan at kennedykrieger.org (Priti Srinivasan) Date: Fri, 18 Apr 2008 17:07:36 -0400 Subject: [Mristudio-users] Compatibility issue with opening CATNAP tensor images in DTI studio Message-ID: <4808D560.E224.0081.0@kennedykrieger.org> I also have a couple of other questions. 1. If this problem is solved and I get the updated set of images in DTIstudio, then which files should I specifically save for fiber tracking. (I know that we need .fa and .vec file for fiber tracking). I am assuming that I should save the FA image and the Eigen vector image (0 or 1 or 2 or all the three togather). Are my assumptions correct? 2. If I do the motion correction and preprocessing using CATNAP (As I am not comfortable with detecting the motion manually), the output gives me all the images that I get in DTIstudio in the native space. I imported all the images from CATNAP to DTI studio and created a tensor.d file using all the tensor image matrices. Then I reopened a DWI image in landmarker and opened this tensor matrix created using CATNAP images (using the open.d option). These tensor images are blank screens (black, white, different grayscales for each tensor image..no image was present). But when I open a tensor.d file for the same subject created using DTI studio from scratch it gives me all the images perfectly. Is this a compatibility issue between the softwares. If so is there any means to solve this issue? Thanks for all the help, Priti 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. From xli16 at jhmi.edu Fri Apr 18 17:31:10 2008 From: xli16 at jhmi.edu (XIN LI) Date: Fri, 18 Apr 2008 17:31:10 -0400 Subject: [Mristudio-users] Compatibility issue with opening CATNAP tensor images in DTI studio In-Reply-To: <4808D560.E224.0081.0@kennedykrieger.org> References: <4808D560.E224.0081.0@kennedykrieger.org> Message-ID: Priti, There are two selections "DTI-Studio" and "DTI-Map" for "File Format" in the "Open Tensor Image File" window. Please try the alternative selection if the tensor file you try to load into DtiStudio or Landmarker is displayed as black and white lines. That may solve your second problem. Xin ----- Original Message ----- From: Priti Srinivasan Date: Friday, April 18, 2008 5:08 pm Subject: [Mristudio-users] Compatibility issue with opening CATNAP tensor images in DTI studio To: mristudio-users at mristudio.org Cc: bennett at bme.jhu.edu > I also have a couple of other questions. > > 1. If this problem is solved and I get the updated set of images in > DTIstudio, then which files should I specifically save for fiber > tracking. (I know that we need .fa and .vec file for fiber tracking). > I am assuming that I should save the FA image and the Eigen vector > image (0 or 1 or 2 or all the three togather). Are my assumptions correct? > > 2. If I do the motion correction and preprocessing using CATNAP (As > I am not comfortable with detecting the motion manually), the output > gives me all the images that I get in DTIstudio in the native space. I > imported all the images from CATNAP to DTI studio and created a > tensor.d file using all the tensor image matrices. Then I reopened a > DWI image in landmarker and opened this tensor matrix created using > CATNAP images (using the open.d option). These tensor images are blank > screens (black, white, different grayscales for each tensor image..no > image was present). But when I open a tensor.d file for the same > subject created using DTI studio from scratch it gives me all the > images perfectly. Is this a compatibility issue between the softwares. > If so is there any means to solve this issue? > > Thanks for all the help, > > Priti > > > > > 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 > From bjweiland at gmail.com Sat Apr 19 12:01:32 2008 From: bjweiland at gmail.com (Barbara Weiland) Date: Sat, 19 Apr 2008 12:01:32 -0400 Subject: [Mristudio-users] functional overlays Message-ID: <523a72ef0804190901t7df6a7a2y68a61d4b5968f91f@mail.gmail.com> Hi, This is not a specific DTIStudio question but here it is: I want to overlay functional results (MEG) onto an anatomical scan and then add fibers as well. I have found that I can add 2 functional overlays in MRIcro but cannot see a way to combine the volumes and save them. Even if I could save the anatomical with one overlay I could then build the fibers on that in DTIStudio? I have also tried Mindseer which has a command under the Advanced tab to combine volumes - but it never finishes processing. Any hints or suggested software (preferrably PC based) would be appreciated. Barbara Weiland, PhD Post Doc Fellow/MEG Physicist Neuromagnetism Laboratory Neurology Research Henry Ford Health System 2799 W. Grand Blvd., CFP 79 Detroit, MI 48202-2689 313-916-1075 bjweiland at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080419/87d9eae0/attachment.html From susumu at mri.jhu.edu Sat Apr 19 14:51:26 2008 From: susumu at mri.jhu.edu (susumu) Date: Sat, 19 Apr 2008 14:51:26 -0400 Subject: [Mristudio-users] functional overlays References: <523a72ef0804190901t7df6a7a2y68a61d4b5968f91f@mail.gmail.com> Message-ID: <9DF4514DA00F4141B0A4FAA0350EE676@LTBWYMORI> Hi Barbara, Is your question purely for visualization or related to fiber tracking based on ROIs transferred from another software programs (e.g. functional results)? If the former is the case, I must admit that DtiStudio has only a limited capability in visualization. It can show superimpose of fiber coordinates on 2D or triplane images, but I don't think it can show three objects (2 images and 1 fiber objects) simultaneously. Susumu ----- Original Message ----- From: Barbara Weiland To: Mristudio-users at mristudio.org Sent: Saturday, April 19, 2008 12:01 PM Subject: [Mristudio-users] functional overlays Hi, This is not a specific DTIStudio question but here it is: I want to overlay functional results (MEG) onto an anatomical scan and then add fibers as well. I have found that I can add 2 functional overlays in MRIcro but cannot see a way to combine the volumes and save them. Even if I could save the anatomical with one overlay I could then build the fibers on that in DTIStudio? I have also tried Mindseer which has a command under the Advanced tab to combine volumes - but it never finishes processing. Any hints or suggested software (preferrably PC based) would be appreciated. Barbara Weiland, PhD Post Doc Fellow/MEG Physicist Neuromagnetism Laboratory Neurology Research Henry Ford Health System 2799 W. Grand Blvd., CFP 79 Detroit, MI 48202-2689 313-916-1075 bjweiland at gmail.com ------------------------------------------------------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080419/8ab71353/attachment.html From susumu at mri.jhu.edu Sat Apr 19 15:10:52 2008 From: susumu at mri.jhu.edu (susumu) Date: Sat, 19 Apr 2008 15:10:52 -0400 Subject: [Mristudio-users] Analyze ROIs References: <8640b26c0804180928y2327ecd4r25f2fac0b2301704@mail.gmail.com> Message-ID: <750BCC292F0345F8892FE967B82A1B39@LTBWYMORI> Hi Graeme, I want to follow up Xin's comments. First, please don't be confused by "binary" and "binary map" formats. The "binary" format simply saves the ROI as 0/1 maps (default extension is *.dat). The "binary map" format saves not only the binary ROI files (*.dat files) but also an additional text file, (*.map file) which you can open and see. To load all files saved as the "binary map" format to DtiStudio, you have to load it as, of course, "binary map" format in DtiStudio. Then DtiStudio looks for the ".map" text file, not the actual 1/0 binary ROI files (*.dat files). There is one catch, though. When you saved the ROI files by RoiEditor, you can't specify which ROI is for "AND" and which ROI is for "OR". There are "AND", "OR", "NOT", and "CUT" operations you can choose to combine multiple ROIs. Without this information in the *.map text file, DtiStudio doesn't know what to do. The best way to learn the syntax of the "*.map" file is to create this file using DtiStudio and study the inside. You can do usual fiber tracking by DtiStudio manually. Please make sure that you draw more than 1 ROI and combine them "AND" or "NOT", as you want. Then try "save"->"Binary Map" in the ROI operation section. Once you saved your ROIs using DtiStudio, look for the saved ROI files. You should be able to find a "*.map" file you just saved. Open the "*.map" file by a texteditor. The file contains not only information about your ROI data, but also some explanation about the syntax at the bottom. Please let me know, if you have any more questions. Susumu ----- Original Message ----- From: Graeme Schwindt To: mristudio-users at mristudio.org Sent: Friday, April 18, 2008 12:28 PM Subject: [Mristudio-users] Analyze ROIs Hello, I am a new DTIStudio user, and am experiencing some confusion regarding ROI data formats. I have two issues: 1) I would like to import ROIs drawn in MRICro (analyze format) into ROIEditor for statistics calculation, However, it appears that ROIEditor will not read the analyze files, and gives an roi header file open error. It also refers to a .roihdr file in the error, rather than a .hdr file. Is there anyway to solve this issue? 2) I would also like to import ROIs into DTIStudio fiber tracking, in order to delinate seed and target ROIs for tracking of fibers. I noticed an earlier mailing list post about using ROIEditor to make these ROIs, and then save them as binary map files for the fiber tracking ROI module in dtistudio. I did this, and the file was saved as a .dat file by ROIEditor. However, then when I went to load the roi in dtistudio's fiber tracking tab in binary map format, it was asking for a .map file. I forced it to open the binary map file I had saved in ROIEditor (ending in _map.dat), and while it appeared to load, it did not appear on the image, nor did any fibers appear when the 'selected' radio button was highlighted. I feel I must be making some simple mistake here. Thanks for any help or advice and for supporting this mailing list! Graeme -- Graeme C. Schwindt, HBSc MD/PhD Student University of Toronto graeme.schwindt at gmail.com 416.546.5453 ------------------------------------------------------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080419/c8964ab8/attachment.html From bjweiland at gmail.com Sat Apr 19 16:19:57 2008 From: bjweiland at gmail.com (Barbara Weiland) Date: Sat, 19 Apr 2008 16:19:57 -0400 Subject: [Mristudio-users] functional overlays In-Reply-To: <9DF4514DA00F4141B0A4FAA0350EE676@LTBWYMORI> References: <523a72ef0804190901t7df6a7a2y68a61d4b5968f91f@mail.gmail.com> <9DF4514DA00F4141B0A4FAA0350EE676@LTBWYMORI> Message-ID: <523a72ef0804191319i549b7843yd4440e691c3a0068@mail.gmail.com> The answer is a bit of both - I have corregistered by MEG data to the 3d volumetric MRI which was corregistered to the B0 set of DTI scan. So I can move ROIs between these sets but I would like to be able to see them all together. Thanks, Barbara On Sat, Apr 19, 2008 at 2:51 PM, susumu wrote: > Hi Barbara, > > Is your question purely for visualization or related to fiber tracking > based on ROIs transferred from another software programs (e.g. functional > results)? > If the former is the case, I must admit that DtiStudio has only a limited > capability in visualization. It can show superimpose of fiber coordinates on > 2D or triplane images, but I don't think it can show three objects (2 images > and 1 fiber objects) simultaneously. > > Susumu > > ----- Original Message ----- > *From:* Barbara Weiland > *To:* Mristudio-users at mristudio.org > *Sent:* Saturday, April 19, 2008 12:01 PM > *Subject:* [Mristudio-users] functional overlays > > Hi, This is not a specific DTIStudio question but here it is: I want to > overlay functional results (MEG) onto an anatomical scan and then add fibers > as well. I have found that I can add 2 functional overlays in MRIcro but > cannot see a way to combine the volumes and save them. Even if I could save > the anatomical with one overlay I could then build the fibers on that in > DTIStudio? I have also tried Mindseer which has a command under the > Advanced tab to combine volumes - but it never finishes processing. Any > hints or suggested software (preferrably PC based) would be appreciated. > > Barbara Weiland, PhD > Post Doc Fellow/MEG Physicist > Neuromagnetism Laboratory > Neurology Research > Henry Ford Health System > 2799 W. Grand Blvd., CFP 79 > Detroit, MI 48202-2689 > 313-916-1075 > bjweiland at gmail.com > > ------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080419/392862a5/attachment-0001.html From rileyj at uci.edu Mon Apr 21 18:27:16 2008 From: rileyj at uci.edu (Riley, Jeffrey) Date: Mon, 21 Apr 2008 15:27:16 -0700 Subject: [Mristudio-users] DtiStudio and multiple acquisitions Message-ID: Hi - I have a question regarding multiple dti acquisitions in DtiStudio; namely, how does the program incorporate both acquisitions into the tensor calculations (i.e. are the two runs averaged, and then the tensor calculation is done?) and at what part of the processing pipeline does this occur? Thanks for your help, Jeff -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080421/8c49af53/attachment.html From susumu at mri.jhu.edu Mon Apr 21 19:22:06 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 21 Apr 2008 19:22:06 -0400 Subject: [Mristudio-users] DtiStudio and multiple acquisitions References: Message-ID: <0B3A737C85284D5E9C4409EE0E7C94D9@LTBWYMORI> DtiStudio and multiple acquisitionsHi Jeff, Let me try to answer your question in a generic way. As you know, we need at least 1 b0 and 6 DWIs for DTI. If you have these 7 images, obtaining the tensor elements requires to "solve" the tensor equation. If you have more than 6 DWIs, then you have to do "fitting" to obtain the elements. This is very similar to the simple linear fitting. If you have two points, you solve the equation to get the slope. If you have 3 points, you do fitting for the best fit. When you have more than 6 DWIs, you have two choices; more orientations or more repetitions. In the analogy of the linear fitting, if you have 4 points, you can spread the 4 points along the x axis, or you can sample twice at two locations along the x axis. Statistically, there is not much difference between these two approaches. I guess my point is, the two datapoints at a fixed x value (or two DWIs with the same b-orientation) doesn't have to be averaged or need any special calculation. These are just dataponts to be fitted. For the tensor fitting, we can use the same math regardless of multiple points spread over different gradient orientations or repeated with the same orientation set. Hope this answers your question. Susumu ----- Original Message ----- From: Riley, Jeffrey To: mristudio-users at mristudio.org Sent: Monday, April 21, 2008 6:27 PM Subject: [Mristudio-users] DtiStudio and multiple acquisitions Hi - I have a question regarding multiple dti acquisitions in DtiStudio; namely, how does the program incorporate both acquisitions into the tensor calculations (i.e. are the two runs averaged, and then the tensor calculation is done?) and at what part of the processing pipeline does this occur? Thanks for your help, Jeff ------------------------------------------------------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080421/b1b6dcc8/attachment.html From susumu at mri.jhu.edu Tue Apr 22 11:54:26 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 22 Apr 2008 11:54:26 -0400 Subject: [Mristudio-users] functional overlays In-Reply-To: <523a72ef0804191319i549b7843yd4440e691c3a0068@mail.gmail.com> Message-ID: <6i7deu$22seic@ipex1.johnshopkins.edu> Hi Barbara, I see. Unfortunately, DtiStudio doesn't have very strong support for the image superimposition.... _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Barbara Weiland Sent: Saturday, April 19, 2008 4:20 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] functional overlays The answer is a bit of both - I have corregistered by MEG data to the 3d volumetric MRI which was corregistered to the B0 set of DTI scan. So I can move ROIs between these sets but I would like to be able to see them all together. Thanks, Barbara On Sat, Apr 19, 2008 at 2:51 PM, susumu wrote: Hi Barbara, Is your question purely for visualization or related to fiber tracking based on ROIs transferred from another software programs (e.g. functional results)? If the former is the case, I must admit that DtiStudio has only a limited capability in visualization. It can show superimpose of fiber coordinates on 2D or triplane images, but I don't think it can show three objects (2 images and 1 fiber objects) simultaneously. Susumu ----- Original Message ----- From: Barbara Weiland To: Mristudio-users at mristudio.org Sent: Saturday, April 19, 2008 12:01 PM Subject: [Mristudio-users] functional overlays Hi, This is not a specific DTIStudio question but here it is: I want to overlay functional results (MEG) onto an anatomical scan and then add fibers as well. I have found that I can add 2 functional overlays in MRIcro but cannot see a way to combine the volumes and save them. Even if I could save the anatomical with one overlay I could then build the fibers on that in DTIStudio? I have also tried Mindseer which has a command under the Advanced tab to combine volumes - but it never finishes processing. Any hints or suggested software (preferrably PC based) would be appreciated. Barbara Weiland, PhD Post Doc Fellow/MEG Physicist Neuromagnetism Laboratory Neurology Research Henry Ford Health System 2799 W. Grand Blvd., CFP 79 Detroit, MI 48202-2689 313-916-1075 bjweiland at gmail.com _____ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080422/fff91634/attachment.html From korolevi at msu.edu Sun Apr 27 22:57:26 2008 From: korolevi at msu.edu (Igor Korolev) Date: Sun, 27 Apr 2008 22:57:26 -0400 Subject: [Mristudio-users] Axial / radial Message-ID: Dear All, Is there a way to obtain the radial and axial diffusivity values from a 3D image in DTIStudio in the same way that FA values can be obtained? Also, are there any solid review articles you would recommend on the biological significance of radial and axial diffusivity as measured with DTI? Thank you, Igor -- ------------------------------------------------------------------ Igor O. Korolev Physician-Scientist Training Program (D.O./Ph.D.) College of Osteopathic Medicine Neuroscience Program Michigan State University Email: Igor.Korolev at radiology.msu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080427/019013e5/attachment-0001.html From korolevi at msu.edu Sun Apr 27 22:59:30 2008 From: korolevi at msu.edu (Igor Korolev) Date: Sun, 27 Apr 2008 22:59:30 -0400 Subject: [Mristudio-users] Axial / radial diffusivity Message-ID: Dear All, Is there a way to obtain the radial and axial diffusivity values from a 3D image in DTIStudio in the same way that FA values can be obtained? Also, are there any solid review articles you would recommend on the biological significance of radial and axial diffusivity as measured with DTI? Thank you, Igor -- ------------------------------------------------------------------ Igor O. Korolev Physician-Scientist Training Program (D.O./Ph.D.) College of Osteopathic Medicine Neuroscience Program Michigan State University Email: Igor.Korolev at radiology.msu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080427/25f7f936/attachment.html From kdavis at uhnres.utoronto.ca Mon Apr 28 15:17:35 2008 From: kdavis at uhnres.utoronto.ca (kdavis) Date: Mon, 28 Apr 2008 15:17:35 -0400 Subject: [Mristudio-users] Tutorial in Toronto References: <6i7deu$1nv7bm@ipex1.johnshopkins.edu> Message-ID: <481622CF.BD0F1094@uhnres.utoronto.ca> Hi Susumu, Just to clarify, the room number is TWH FP6-103. That is the Toronto Western Hospital, Fell Pavilion, 6th floor, room 103 (399 Bathurst Street Toronto, Ontario, Canada M5T 2S8 ) Karen susumu wrote: > Dear MriStudio Users, > > Thank you for your interest in our tutorial in Toronto on 5/4. > > This tutorial was made possible by the kind support from Dr. Karen Davis' > group in Division of Brain, Imaging and Behaviour-Systems Neuroscience > in University of Toronto. I also thank to Keri for arranging the site. > > Here is the map of the site: > > > ttp://maps.google.com/maps?f=d&hl=en&geocode=&saddr=399+bathurst+street,+toronto,+on&daddr=255+Front+St+W,+Toronto,+Toronto,+Ontario+M5V,+Canada&mra=pe&mrcr=0&sll=43.649033,-79.385222&sspn=0.022513,0.057335&ie=UTF8&ll=43.648746,-79.405489&spn=0.022513,0.057335&z=15&om=0 > > I attached an attendant list. If you don't find your name, please let us know. > The tutorial is free. It'll start at 1:00 and end at 5:00, although it may > take longer depending on how many questions we get. > > It is very important for you to "pre-condition" your laptops. Please visit > www.mristudio.org -> Workshop and download proper software and data. This will > make sure that your laptop has a working version of > DtiStudio/Landmarker/RoiEditor. We will provide only power outlets. So, you > need to bring your own laptops. > > Please let us know if you have any questions. > > Sincerely, > > Susumu Mori > -- Karen D. Davis, Ph.D. Professor, Department of Surgery, Graduate Coordinator, Institute of Medical Science, and Canada Research Chair in Brain and Behaviour, University of Toronto Head, Division of Brain, Imaging and Behaviour-Systems Neuroscience Toronto Western Research Institute Toronto Western Hospital Room: MP14-306 399 Bathurst Street Toronto, Ontario Canada M5T 2S8 (416) 603-5662 (phone) (416) 603-5745 (fax) kdavis at uhnres.utoronto.ca -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080428/939de6bd/attachment.html From susumu at mri.jhu.edu Tue Apr 29 11:28:33 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 29 Apr 2008 11:28:33 -0400 Subject: [Mristudio-users] Axial / radial In-Reply-To: Message-ID: <6i7deu$2973sj@ipex1.johnshopkins.edu> Hi Igor, Axial diffusivity is the same as Eigenvalue0 in DtiStudio. Radial diffusivity is (Eigenvalue1 + Eigenvalue2)/2. DtiStudio doesn't provide this number. I think we should add this for the next version. You can create (Eigenvalue1 + Eigenvalue2) image using the calculation function of RoiEditor, once you saved Eigenvalues. The advantage of using the axial / radial diffusivity is this; When you observe "lower FA", there are two possible mechanisms; 1) It's low because the longest axis (Eigenvalue0 or axial diffusivity) decreased 2) It's low because the second and third (Eigenvalue1 and Eigenvalue2 or radial diffusivity) increased. These two possible mechanisms can't be differentiated by FA (information degeneration), which may carry important biological information. In many cases, #1 and #2 occur simultaneously, though. You may want to read the SK (Victor) Song's series of papers on this subject. I'm not aware of review papers about it. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor Korolev Sent: Sunday, April 27, 2008 10:57 PM To: mristudio-users at mristudio.org Cc: Andrea Bozoki Subject: [Mristudio-users] Axial / radial Dear All, Is there a way to obtain the radial and axial diffusivity values from a 3D image in DTIStudio in the same way that FA values can be obtained? Also, are there any solid review articles you would recommend on the biological significance of radial and axial diffusivity as measured with DTI? Thank you, Igor -- ------------------------------------------------------------------ Igor O. Korolev Physician-Scientist Training Program (D.O./Ph.D.) College of Osteopathic Medicine Neuroscience Program Michigan State University Email: Igor.Korolev at radiology.msu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080429/592e3656/attachment.html From susumu at mri.jhu.edu Tue Apr 29 11:41:40 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 29 Apr 2008 11:41:40 -0400 Subject: [Mristudio-users] Tutorial in Toronto, 5/2 Message-ID: <6i7deu$297h0u@ipex1.johnshopkins.edu> Dear MriStudio Users who are planning to attend the tutorial in Toronto, Thank you for your attendance to the tutorial that will be held in Toronto this Sunday. I also want to send special thanks to Dr. Karen Davis who will host this session. This will be a free and casual session. To maximize the efficiency of the tutorial, please read the following instructions very carefully. 1) We will not provide any computers. Please bring your own laptops. 2) Please go to www.mristudio.org -> Workshop and follow the instructions. This will precondition your laptop. 3) Please download all the software (DtiStudio, Landmarker, RoiEditor) and sample data in the "Workshop". A new sample data ("ProcessedData) were added recently. Even if you have already download them, please make sure to visit there once more and make sure you already have all the posted data, especially "ProcessedData". Please let us know if you have any questions. Sincerely, Susumu Mori -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080429/045e07e4/attachment-0001.html From susumu at mri.jhu.edu Tue Apr 29 15:10:17 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 29 Apr 2008 15:10:17 -0400 Subject: [Mristudio-users] correction Message-ID: <6i7deu$29d40c@ipex1.johnshopkins.edu> Hi all, I'm sorry that I wrote 5/2 for the tutorial date. It is 5/4. Also, while Dr. Davis' lab will provide power outlets, please make sure to fully charge the batteries of your laptops before the tutorial to avoid overloading the supply. It is a good idea to turn off wireless, which drains your battery. There is no wireless anyway. Please let me know if you have any questions. Sincerely, Susumu Mori -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080429/13651195/attachment.html From lyric_jorgenson at yahoo.com Thu May 1 13:26:14 2008 From: lyric_jorgenson at yahoo.com (Lyric Jorgenson) Date: Thu, 01 May 2008 10:26:14 -0700 (PDT) Subject: [Mristudio-users] importing ROIs into DTI Studio Message-ID: <618252.34493.qm@web90607.mail.mud.yahoo.com> Hello- I have been trying to import seed regions created in ROI editor into DTI studio. I read the previous posting to member "Akila" and tried Xin's advice (Perform fiber tracking by DTIStudio... use two ROIs, click "Save... choose "Binary Maps"). After studying this file i tried to reload the original saved ROIs into DTI studio and received the following error "File Open error". Thus, i cannot open the original ROI created in DTIStudio or the edited ROI editor file in DTIStudio. What am i doing wrong? Please advise. Sincerely, Lyric Jorgenson Lyric A Jorgenson Cognitive Development Neuroimaging Laboratory Institute of Child Development University of Minnesota Minneapolis, MN 55455 Office Address: Room #154 Office Phone: 612-624-3870 ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From kennedkr at yahoo.com Thu May 1 13:35:42 2008 From: kennedkr at yahoo.com (Kristen Kennedy) Date: Thu, 01 May 2008 10:35:42 -0700 (PDT) Subject: [Mristudio-users] pre-compiled AIR exe files? In-Reply-To: Message-ID: <398062.3480.qm@web82103.mail.mud.yahoo.com> Hi, I am trying to get the AIR software installed in preparation for the tutorial workshop this weekend, but am having trouble figuring out how to do it on my Vista machine. Is there a way that I can get the precompiled .exe files (makeaheader.exe, alignlinear.exe and align_warp.exe) from someone who has already done it and then just copy them to my own Landmarker directory? Thanks for the help! Kristen mristudio-users-request at mristudio.org wrote: Send Mristudio-users mailing list submissions to mristudio-users at mristudio.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.mristudio.org/mailman/listinfo/mristudio-users or, via email, send a message with subject or body 'help' to mristudio-users-request at mristudio.org You can reach the person managing the list at mristudio-users-owner at mristudio.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Mristudio-users digest..." Today's Topics: 1. Axial / radial diffusivity (Igor Korolev) 2. Re: Tutorial in Toronto (kdavis) 3. Re: Axial / radial (susumu) 4. Tutorial in Toronto, 5/2 (susumu) ---------------------------------------------------------------------- Message: 1 Date: Sun, 27 Apr 2008 22:59:30 -0400 From: Igor Korolev Subject: [Mristudio-users] Axial / radial diffusivity To: mristudio-users , Andrea Bozoki Message-ID: Content-Type: text/plain; charset="iso-8859-1" Dear All, Is there a way to obtain the radial and axial diffusivity values from a 3D image in DTIStudio in the same way that FA values can be obtained? Also, are there any solid review articles you would recommend on the biological significance of radial and axial diffusivity as measured with DTI? Thank you, Igor -- ------------------------------------------------------------------ Igor O. Korolev Physician-Scientist Training Program (D.O./Ph.D.) College of Osteopathic Medicine Neuroscience Program Michigan State University Email: Igor.Korolev at radiology.msu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080427/25f7f936/attachment-0001.html ------------------------------ Message: 2 Date: Mon, 28 Apr 2008 15:17:35 -0400 From: kdavis Subject: Re: [Mristudio-users] Tutorial in Toronto To: susumu Cc: mristudio-users at mristudio.org, 'Keri Taylor' Message-ID: <481622CF.BD0F1094 at uhnres.utoronto.ca> Content-Type: text/plain; charset="us-ascii" Hi Susumu, Just to clarify, the room number is TWH FP6-103. That is the Toronto Western Hospital, Fell Pavilion, 6th floor, room 103 (399 Bathurst Street Toronto, Ontario, Canada M5T 2S8 ) Karen susumu wrote: > Dear MriStudio Users, > > Thank you for your interest in our tutorial in Toronto on 5/4. > > This tutorial was made possible by the kind support from Dr. Karen Davis' > group in Division of Brain, Imaging and Behaviour-Systems Neuroscience > in University of Toronto. I also thank to Keri for arranging the site. > > Here is the map of the site: > > > ttp://maps.google.com/maps?f=d&hl=en&geocode=&saddr=399+bathurst+street,+toronto,+on&daddr=255+Front+St+W,+Toronto,+Toronto,+Ontario+M5V,+Canada&mra=pe&mrcr=0&sll=43.649033,-79.385222&sspn=0.022513,0.057335&ie=UTF8&ll=43.648746,-79.405489&spn=0.022513,0.057335&z=15&om=0 > > I attached an attendant list. If you don't find your name, please let us know. > The tutorial is free. It'll start at 1:00 and end at 5:00, although it may > take longer depending on how many questions we get. > > It is very important for you to "pre-condition" your laptops. Please visit > www.mristudio.org -> Workshop and download proper software and data. This will > make sure that your laptop has a working version of > DtiStudio/Landmarker/RoiEditor. We will provide only power outlets. So, you > need to bring your own laptops. > > Please let us know if you have any questions. > > Sincerely, > > Susumu Mori > -- Karen D. Davis, Ph.D. Professor, Department of Surgery, Graduate Coordinator, Institute of Medical Science, and Canada Research Chair in Brain and Behaviour, University of Toronto Head, Division of Brain, Imaging and Behaviour-Systems Neuroscience Toronto Western Research Institute Toronto Western Hospital Room: MP14-306 399 Bathurst Street Toronto, Ontario Canada M5T 2S8 (416) 603-5662 (phone) (416) 603-5745 (fax) kdavis at uhnres.utoronto.ca -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080428/939de6bd/attachment-0001.html ------------------------------ Message: 3 Date: Tue, 29 Apr 2008 11:28:33 -0400 From: susumu Subject: Re: [Mristudio-users] Axial / radial To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" Message-ID: <6i7deu$2973sj at ipex1.johnshopkins.edu> Content-Type: text/plain; charset="us-ascii" Hi Igor, Axial diffusivity is the same as Eigenvalue0 in DtiStudio. Radial diffusivity is (Eigenvalue1 + Eigenvalue2)/2. DtiStudio doesn't provide this number. I think we should add this for the next version. You can create (Eigenvalue1 + Eigenvalue2) image using the calculation function of RoiEditor, once you saved Eigenvalues. The advantage of using the axial / radial diffusivity is this; When you observe "lower FA", there are two possible mechanisms; 1) It's low because the longest axis (Eigenvalue0 or axial diffusivity) decreased 2) It's low because the second and third (Eigenvalue1 and Eigenvalue2 or radial diffusivity) increased. These two possible mechanisms can't be differentiated by FA (information degeneration), which may carry important biological information. In many cases, #1 and #2 occur simultaneously, though. You may want to read the SK (Victor) Song's series of papers on this subject. I'm not aware of review papers about it. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Igor Korolev Sent: Sunday, April 27, 2008 10:57 PM To: mristudio-users at mristudio.org Cc: Andrea Bozoki Subject: [Mristudio-users] Axial / radial Dear All, Is there a way to obtain the radial and axial diffusivity values from a 3D image in DTIStudio in the same way that FA values can be obtained? Also, are there any solid review articles you would recommend on the biological significance of radial and axial diffusivity as measured with DTI? Thank you, Igor -- ------------------------------------------------------------------ Igor O. Korolev Physician-Scientist Training Program (D.O./Ph.D.) College of Osteopathic Medicine Neuroscience Program Michigan State University Email: Igor.Korolev at radiology.msu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080429/592e3656/attachment-0001.html ------------------------------ Message: 4 Date: Tue, 29 Apr 2008 11:41:40 -0400 From: susumu Subject: [Mristudio-users] Tutorial in Toronto, 5/2 To: mristudio-users at mristudio.org Message-ID: <6i7deu$297h0u at ipex1.johnshopkins.edu> Content-Type: text/plain; charset="us-ascii" Dear MriStudio Users who are planning to attend the tutorial in Toronto, Thank you for your attendance to the tutorial that will be held in Toronto this Sunday. I also want to send special thanks to Dr. Karen Davis who will host this session. This will be a free and casual session. To maximize the efficiency of the tutorial, please read the following instructions very carefully. 1) We will not provide any computers. Please bring your own laptops. 2) Please go to www.mristudio.org -> Workshop and follow the instructions. This will precondition your laptop. 3) Please download all the software (DtiStudio, Landmarker, RoiEditor) and sample data in the "Workshop". A new sample data ("ProcessedData) were added recently. Even if you have already download them, please make sure to visit there once more and make sure you already have all the posted data, especially "ProcessedData". Please let us know if you have any questions. Sincerely, Susumu Mori -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080429/045e07e4/attachment.html ------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users End of Mristudio-users Digest, Vol 3, Issue 11 ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080501/6ba12f91/attachment-0001.html From susumu at mri.jhu.edu Thu May 1 16:21:47 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 01 May 2008 16:21:47 -0400 Subject: [Mristudio-users] importing ROIs into DTI Studio In-Reply-To: <618252.34493.qm@web90607.mail.mud.yahoo.com> Message-ID: <6i7deu$2agp8g@ipex1.johnshopkins.edu> Hi Lyric, Please make sure the following things; 1) You saved the ROI file as the "Binary Map" format. 1) You are trying to load the ROI file into DtiStudio as the "Binary Map" format. 2) You are trying to load the ROI file into DtiStudio after you finished fiber tracking. This means, you loaded a vector and a FA map through "Fiber-Tracking" and fiber tracking of the whole brain is already completed. 3) You are loading the ROI file using the "load" icon in "Fiber" tab, "ROI-Operation" section. Please confirm these. Also, as I explained in the previous posts, you have to modify "*.map" file to indicate operators (AND, OR, NOT) for each ROI. Let me know if you have further questions. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Lyric Jorgenson Sent: Thursday, May 01, 2008 1:26 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] importing ROIs into DTI Studio Hello- I have been trying to import seed regions created in ROI editor into DTI studio. I read the previous posting to member "Akila" and tried Xin's advice (Perform fiber tracking by DTIStudio... use two ROIs, click "Save... choose "Binary Maps"). After studying this file i tried to reload the original saved ROIs into DTI studio and received the following error "File Open error". Thus, i cannot open the original ROI created in DTIStudio or the edited ROI editor file in DTIStudio. What am i doing wrong? Please advise. Sincerely, Lyric Jorgenson Lyric A Jorgenson Cognitive Development Neuroimaging Laboratory Institute of Child Development University of Minnesota Minneapolis, MN 55455 Office Address: Room #154 Office Phone: 612-624-3870 ____________________________________________________________________________ ________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From benjamin.dhont at gmail.com Tue May 6 10:13:37 2008 From: benjamin.dhont at gmail.com (Benjamin D'hont) Date: Tue, 06 May 2008 10:13:37 -0400 Subject: [Mristudio-users] [MRIstudio-users] script for map extraction Message-ID: Hello, I would like to extract FA maps at MINC format from 110 DTI datasets. Is there any possibility to get it done with a script or must I do it by hand? Sincerely, Benjamin D'hont McGill University / Montr?al Neurological Institute -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080506/99d5084e/attachment.html From susumu at mri.jhu.edu Wed May 7 11:32:59 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 07 May 2008 11:32:59 -0400 Subject: [Mristudio-users] [MRIstudio-users] script for map extraction In-Reply-To: Message-ID: <6i7deu$2db3v5@ipex1.johnshopkins.edu> Hi Benjamin, We are working with Pedro in MNI for the MINC format. Pedro and Hangyi, do we have a version with MINC? Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Benjamin D'hont Sent: Tuesday, May 06, 2008 10:14 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [MRIstudio-users] script for map extraction Hello, I would like to extract FA maps at MINC format from 110 DTI datasets. Is there any possibility to get it done with a script or must I do it by hand? Sincerely, Benjamin D'hont McGill University / Montr?al Neurological Institute From nany at bnu.edu.cn Wed May 7 20:06:40 2008 From: nany at bnu.edu.cn (=?gb2312?B?xM/Uxg==?=) Date: Thu, 08 May 2008 08:06:40 +0800 Subject: [Mristudio-users] [MRIstudio-users] ROIEditor-latest-x86.rar download Message-ID: <410205200.03855@bnu.edu.cn> Hello, After registration, I have successfully downloaded all the required software offered by your website except ROIEditor-latest-x86.rar. For ROIEditor-latest-x86.rar, I couldn't get the saving prompt after entered my username and password, but a whole page of scrambled letters instead. And worst of all, each time my firefox has to be restarted to regain normal function. I've tried not only in my desktop but also my laptop, with both firefox and ie browser. Could you give me a hint on what I did was wrong? I am really eager to learn more about DTI and keen on getting all the preparing work done ASAP. Thanks very much for your help! Best, Yun ????????????????????: >From: susumu >Reply-To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" >Subject: Re: [Mristudio-users] [MRIstudio-users] script for map extraction >Date:Wed, 07 May 2008 11:32:59 -0400 > >Hi Benjamin, > >We are working with Pedro in MNI for the MINC format. Pedro and Hangyi, do >we have a version with MINC? > >Susumu > >________________________________________ >From: mristudio-users-bounces at mristudio.org >[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Benjamin D'hont >Sent: Tuesday, May 06, 2008 10:14 AM >To: mristudio-users at mristudio.org >Subject: [Mristudio-users] [MRIstudio-users] script for map extraction > >Hello, > >I would like to extract FA maps at MINC format from 110 DTI datasets. >Is there any possibility to get it done with a script or must I do it by >hand? > >Sincerely, > >Benjamin D'hont >McGill University / Montr?al Neurological Institute > > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users From tangjinsonghn at yahoo.com.cn Fri May 9 10:52:35 2008 From: tangjinsonghn at yahoo.com.cn (jinsong tang) Date: Fri, 09 May 2008 22:52:35 +0800 (CST) Subject: [Mristudio-users] comine the high resolution 3D image with the DTI image Message-ID: <689441.21052.qm@web15607.mail.cnb.yahoo.com> Hello, I want to use DTIstudio to do fiber tracking. I have 2 kinds of dada: DTI and 3D. So, how to comine the high resolution 3D image with the DTI image? jinsong --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080509/dd6bf654/attachment.html From darshanp20 at yahoo.com Fri May 9 12:16:44 2008 From: darshanp20 at yahoo.com (darshan pai) Date: Fri, 09 May 2008 09:16:44 -0700 (PDT) Subject: [Mristudio-users] comine the high resolution 3D image with the DTI image In-Reply-To: <689441.21052.qm@web15607.mail.cnb.yahoo.com> Message-ID: <484741.98701.qm@web32205.mail.mud.yahoo.com> What do you mean by 3D image ? There are actually various ways depending on what format you have. DICOM format will require you to key in the gradient values in the text area provided. dpf files is convenient which can be used for Analyze as well as RAW image. I am not sure abt 3D, but if you are referring to registration then DTIStudio dont do it . Not that i know of .. --- jinsong tang wrote: > Hello, > > I want to use DTIstudio to do fiber tracking. I > have 2 kinds of dada: DTI and 3D. So, how to comine > the high resolution 3D image with the DTI image? > > jinsong > > > --------------------------------- > ???????????????????????? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From steinja at ucla.edu Wed May 14 19:37:12 2008 From: steinja at ucla.edu (Jason Stein) Date: Wed, 14 May 2008 16:37:12 -0700 Subject: [Mristudio-users] Loading an Image and Changing Pixel Dimensions Message-ID: <1bb422f90805141637u411fdde3u474185b830675f5c@mail.gmail.com> Hello, I am new to DTIstudio so I apologize if this question is too basic. I am trying to load an Analyze image into DTIstudio. When I click on any image to open it, the image parameters screen comes up in the DTI studio window. There, I make sure that Analyze radio button is selected. The pixel dimensions are set to Pixel size - Width: -0.9375 and Height: 0.9000. When I click OK, I get the error that "Please enter a number between 0 and 4096". I think this might be because the pixel dimension is set to be a negative number? However, I am unable to change the values in the boxes. Also, if I try opening up an image with different voxel sizes, the same pixel size and width are shown in the box. These are incorrect, and I'm not sure why they do not change when I open a new image. Also, why can I not change it manually? Any image I load brings the same pixel width and height. Thanks in advance for any help, Jason -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080514/ba15ad40/attachment.html From steinja at ucla.edu Thu May 15 12:54:59 2008 From: steinja at ucla.edu (Jason Stein) Date: Thu, 15 May 2008 09:54:59 -0700 Subject: [Mristudio-users] Loading an Image and Changing Pixel Dimensions In-Reply-To: <482C138E020000630001219B@cis27.hosts.jhmi.edu> References: <482C138E020000630001219B@cis27.hosts.jhmi.edu> Message-ID: <1bb422f90805150954x749a42e9s7075746716413611@mail.gmail.com> Hi Hangyi, Thanks very much. Unfortunately, when I downloaded this new file and changed the extension, I still get the same problem. I attached a screenshot if that helps. I think the problem may be that the program is storing information from the previously opened files somewhere on my hard drive and then using those values each time. I think this because when I downloaded your new program and went to the file menu, there were some previously opened files there. It did this even when I deleted the program and re-downloaded it. Do you think this could be fooling the program into thinking that the voxel dimensions were the same as the previous image? Where would this be stored so I could delete it and try again? Thanks again very much for your help, Jason On Thu, May 15, 2008 at 7:42 AM, Hangyi Jiang wrote: > hi, jason, > > seems that your version has a bug. :)) > > you can got the latest version in our website. for your convenience, I > attached the program as a ".data" file. please rename it back to > "DtiStudio.exe" before you can play with it in you PC. > > let me know if you have more questions. > > regards, > > hangyi > > > > > >>> Jason Stein 05/14/08 7:37 PM >>> > Hello, > > I am new to DTIstudio so I apologize if this question is too basic. > > I am trying to load an Analyze image into DTIstudio. When I click on any > image to open it, the image parameters screen comes up in the DTI studio > window. There, I make sure that Analyze radio button is selected. The > pixel dimensions are set to Pixel size - Width: -0.9375 and Height: 0.9000. > When I click OK, I get the error that "Please enter a number between 0 and > 4096". I think this might be because the pixel dimension is set to be a > negative number? However, I am unable to change the values in the boxes. > > Also, if I try opening up an image with different voxel sizes, the same > pixel size and width are shown in the box. These are incorrect, and I'm > not > sure why they do not change when I open a new image. Also, why can I not > change it manually? Any image I load brings the same pixel width and > height. > > Thanks in advance for any help, > Jason > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080515/3e7f0eae/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: DTIstudioscreenshot.jpg Type: image/jpeg Size: 89802 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080515/3e7f0eae/attachment-0001.jpg From darshanp20 at yahoo.com Thu May 15 15:50:24 2008 From: darshanp20 at yahoo.com (darshan pai) Date: Thu, 15 May 2008 12:50:24 -0700 (PDT) Subject: [Mristudio-users] Loading an Image and Changing Pixel Dimensions In-Reply-To: <1bb422f90805150954x749a42e9s7075746716413611@mail.gmail.com> Message-ID: <849543.60976.qm@web32208.mail.mud.yahoo.com> I am still wondering why your width parameter says -0.9375 . I never seen a negative slice thickness. Does this Analyze file open in MRIcro? I think maybe u need to check ur Analyze header and change it to 0.9375 and check what happens --- Jason Stein wrote: > Hi Hangyi, > > Thanks very much. Unfortunately, when I downloaded > this new file and > changed the extension, I still get the same problem. > I attached a > screenshot if that helps. I think the problem may > be that the program is > storing information from the previously opened files > somewhere on my hard > drive and then using those values each time. I > think this because when I > downloaded your new program and went to the file > menu, there were some > previously opened files there. It did this even > when I deleted the program > and re-downloaded it. Do you think this could be > fooling the program into > thinking that the voxel dimensions were the same as > the previous image? > Where would this be stored so I could delete it and > try again? > > Thanks again very much for your help, > Jason > > On Thu, May 15, 2008 at 7:42 AM, Hangyi Jiang > wrote: > > > hi, jason, > > > > seems that your version has a bug. :)) > > > > you can got the latest version in our website. for > your convenience, I > > attached the program as a ".data" file. please > rename it back to > > "DtiStudio.exe" before you can play with it in you > PC. > > > > let me know if you have more questions. > > > > regards, > > > > hangyi > > > > > > > > > > >>> Jason Stein 05/14/08 7:37 > PM >>> > > Hello, > > > > I am new to DTIstudio so I apologize if this > question is too basic. > > > > I am trying to load an Analyze image into > DTIstudio. When I click on any > > image to open it, the image parameters screen > comes up in the DTI studio > > window. There, I make sure that Analyze radio > button is selected. The > > pixel dimensions are set to Pixel size - Width: > -0.9375 and Height: 0.9000. > > When I click OK, I get the error that "Please > enter a number between 0 and > > 4096". I think this might be because the pixel > dimension is set to be a > > negative number? However, I am unable to change > the values in the boxes. > > > > Also, if I try opening up an image with different > voxel sizes, the same > > pixel size and width are shown in the box. These > are incorrect, and I'm > > not > > sure why they do not change when I open a new > image. Also, why can I not > > change it manually? Any image I load brings the > same pixel width and > > height. > > > > Thanks in advance for any help, > > Jason > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From susumu at mri.jhu.edu Thu May 15 18:01:38 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 15 May 2008 18:01:38 -0400 Subject: [Mristudio-users] Loading an Image and Changing Pixel Dimensions In-Reply-To: <1bb422f90805150954x749a42e9s7075746716413611@mail.gmail.com> Message-ID: <6i7deu$2ibdif@ipex1.johnshopkins.edu> Hi Jason, If you are reading Analyze data, I believe all the info about data dimensions is read from the hdr file. The boxes for image dimensions and pixel sizes are deactivated. It may show some numbers but they are not meaningful and you can't change them. Only after you choose the "analyze" format and data are read, correct dimension info is loaded from the hdr file. Now, it is possible that the data input window still remembers old invalid numbers, which interferes with the data loading. Please try following; 1) First choose the "raw" format and activate image dimensions and fov windows. 2) Type in some meaningful numbers. This will erase prohibited numbers such as minus values remain in the windows. 3) Then switch to the "analyze" format. All "voxel size" windows should be deactivated 4) Click OK. I hope it will work. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jason Stein Sent: Thursday, May 15, 2008 12:55 PM To: Hangyi Jiang Cc: mristudio-users at mristudio.org; Ilya Eckstein Subject: Re: [Mristudio-users] Loading an Image and Changing Pixel Dimensions Hi Hangyi, Thanks very much. Unfortunately, when I downloaded this new file and changed the extension, I still get the same problem. I attached a screenshot if that helps. I think the problem may be that the program is storing information from the previously opened files somewhere on my hard drive and then using those values each time. I think this because when I downloaded your new program and went to the file menu, there were some previously opened files there. It did this even when I deleted the program and re-downloaded it. Do you think this could be fooling the program into thinking that the voxel dimensions were the same as the previous image? Where would this be stored so I could delete it and try again? Thanks again very much for your help, Jason On Thu, May 15, 2008 at 7:42 AM, Hangyi Jiang wrote: hi, jason, seems that your version has a bug. :)) you can got the latest version in our website. for your convenience, I attached the program as a ".data" file. please rename it back to "DtiStudio.exe" before you can play with it in you PC. let me know if you have more questions. regards, hangyi >>> Jason Stein 05/14/08 7:37 PM >>> Hello, I am new to DTIstudio so I apologize if this question is too basic. I am trying to load an Analyze image into DTIstudio. When I click on any image to open it, the image parameters screen comes up in the DTI studio window. There, I make sure that Analyze radio button is selected. The pixel dimensions are set to Pixel size - Width: -0.9375 and Height: 0.9000. When I click OK, I get the error that "Please enter a number between 0 and 4096". I think this might be because the pixel dimension is set to be a negative number? However, I am unable to change the values in the boxes. Also, if I try opening up an image with different voxel sizes, the same pixel size and width are shown in the box. These are incorrect, and I'm not sure why they do not change when I open a new image. Also, why can I not change it manually? Any image I load brings the same pixel width and height. Thanks in advance for any help, Jason -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080515/03a73107/attachment.html From susumu at mri.jhu.edu Thu May 15 18:03:17 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 15 May 2008 18:03:17 -0400 Subject: [Mristudio-users] Loading an Image and Changing Pixel Dimensions In-Reply-To: <849543.60976.qm@web32208.mail.mud.yahoo.com> Message-ID: <6i7deu$2ibe62@ipex1.johnshopkins.edu> Yes, I think the reason is these "minus" numbers. Please replace these bad numbers by activating the windows (choose "Raw Image" format), change them to any positive numbers, and choose "Analyze". This is an interesting bug,,,,, -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of darshan pai Sent: Thursday, May 15, 2008 3:50 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Loading an Image and Changing Pixel Dimensions I am still wondering why your width parameter says -0.9375 . I never seen a negative slice thickness. Does this Analyze file open in MRIcro? I think maybe u need to check ur Analyze header and change it to 0.9375 and check what happens --- Jason Stein wrote: > Hi Hangyi, > > Thanks very much. Unfortunately, when I downloaded > this new file and > changed the extension, I still get the same problem. > I attached a > screenshot if that helps. I think the problem may > be that the program is > storing information from the previously opened files > somewhere on my hard > drive and then using those values each time. I > think this because when I > downloaded your new program and went to the file > menu, there were some > previously opened files there. It did this even > when I deleted the program > and re-downloaded it. Do you think this could be > fooling the program into > thinking that the voxel dimensions were the same as > the previous image? > Where would this be stored so I could delete it and > try again? > > Thanks again very much for your help, > Jason > > On Thu, May 15, 2008 at 7:42 AM, Hangyi Jiang > wrote: > > > hi, jason, > > > > seems that your version has a bug. :)) > > > > you can got the latest version in our website. for > your convenience, I > > attached the program as a ".data" file. please > rename it back to > > "DtiStudio.exe" before you can play with it in you > PC. > > > > let me know if you have more questions. > > > > regards, > > > > hangyi > > > > > > > > > > >>> Jason Stein 05/14/08 7:37 > PM >>> > > Hello, > > > > I am new to DTIstudio so I apologize if this > question is too basic. > > > > I am trying to load an Analyze image into > DTIstudio. When I click on any > > image to open it, the image parameters screen > comes up in the DTI studio > > window. There, I make sure that Analyze radio > button is selected. The > > pixel dimensions are set to Pixel size - Width: > -0.9375 and Height: 0.9000. > > When I click OK, I get the error that "Please > enter a number between 0 and > > 4096". I think this might be because the pixel > dimension is set to be a > > negative number? However, I am unable to change > the values in the boxes. > > > > Also, if I try opening up an image with different > voxel sizes, the same > > pixel size and width are shown in the box. These > are incorrect, and I'm > > not > > sure why they do not change when I open a new > image. Also, why can I not > > change it manually? Any image I load brings the > same pixel width and > > height. > > > > Thanks in advance for any help, > > Jason > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From jasonlouisstein at gmail.com Thu May 15 18:18:14 2008 From: jasonlouisstein at gmail.com (Jason Stein) Date: Thu, 15 May 2008 15:18:14 -0700 Subject: [Mristudio-users] Loading an Image and Changing Pixel Dimensions In-Reply-To: <6i7deu$2ibdif@ipex1.johnshopkins.edu> References: <1bb422f90805150954x749a42e9s7075746716413611@mail.gmail.com> <6i7deu$2ibdif@ipex1.johnshopkins.edu> Message-ID: <1bb422f90805151518l53611760je9349482c92ce9e8@mail.gmail.com> Thank you! This works, and now I can see my image. On Thu, May 15, 2008 at 3:01 PM, susumu wrote: > Hi Jason, > > > > If you are reading Analyze data, I believe all the info about data > dimensions is read from the hdr file. The boxes for image dimensions and > pixel sizes are deactivated. It may show some numbers but they are not > meaningful and you can't change them. Only after you choose the "analyze" > format and data are read, correct dimension info is loaded from the hdr > file. > > > > Now, it is possible that the data input window still remembers old invalid > numbers, which interferes with the data loading. Please try following; > > > > 1) First choose the "raw" format and activate image dimensions and fov > windows. > > 2) Type in some meaningful numbers. This will erase prohibited numbers such > as minus values remain in the windows. > > 3) Then switch to the "analyze" format. All "voxel size" windows should be > deactivated > > 4) Click OK. > > > > I hope it will work. > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Jason Stein > *Sent:* Thursday, May 15, 2008 12:55 PM > *To:* Hangyi Jiang > *Cc:* mristudio-users at mristudio.org; Ilya Eckstein > *Subject:* Re: [Mristudio-users] Loading an Image and Changing Pixel > Dimensions > > > > Hi Hangyi, > > > Thanks very much. Unfortunately, when I downloaded this new file and > changed the extension, I still get the same problem. I attached a > screenshot if that helps. I think the problem may be that the program is > storing information from the previously opened files somewhere on my hard > drive and then using those values each time. I think this because when I > downloaded your new program and went to the file menu, there were some > previously opened files there. It did this even when I deleted the program > and re-downloaded it. Do you think this could be fooling the program into > thinking that the voxel dimensions were the same as the previous image? > Where would this be stored so I could delete it and try again? > > Thanks again very much for your help, > Jason > > On Thu, May 15, 2008 at 7:42 AM, Hangyi Jiang wrote: > > hi, jason, > > seems that your version has a bug. :)) > > you can got the latest version in our website. for your convenience, I > attached the program as a ".data" file. please rename it back to > "DtiStudio.exe" before you can play with it in you PC. > > let me know if you have more questions. > > regards, > > hangyi > > > > > >>> Jason Stein 05/14/08 7:37 PM >>> > Hello, > > I am new to DTIstudio so I apologize if this question is too basic. > > I am trying to load an Analyze image into DTIstudio. When I click on any > image to open it, the image parameters screen comes up in the DTI studio > window. There, I make sure that Analyze radio button is selected. The > pixel dimensions are set to Pixel size - Width: -0.9375 and Height: 0.9000. > When I click OK, I get the error that "Please enter a number between 0 and > 4096". I think this might be because the pixel dimension is set to be a > negative number? However, I am unable to change the values in the boxes. > > Also, if I try opening up an image with different voxel sizes, the same > pixel size and width are shown in the box. These are incorrect, and I'm > not > sure why they do not change when I open a new image. Also, why can I not > change it manually? Any image I load brings the same pixel width and > height. > > Thanks in advance for any help, > Jason > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080515/26066681/attachment-0001.html From Elizabeth.Finger at lhsc.on.ca Fri May 16 10:51:43 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Fri, 16 May 2008 10:51:43 -0400 Subject: [Mristudio-users] recalculating means with two AIR series? Message-ID: <482D673F020000A000003308@lhscgwiao.lhsc.on.ca> Hello- I have a large DTI data from GE in dicom format set that contains 3 B0 images plus 33 gradients, 50 slices, and two separate runs per subject. I am able to pull up both runs in DTI Mapping and to run the AIR. However, when I try to then calculate the means and STD for multiple runs, I run out of memory, as I do when trying to do the tensor calculation directly. I am able to proceed if I process just one run at a time. However, if possible, I would like to use the mean from the two series (it was from children, with a lot of movement and fair amount of scanner artifact). I have tried to save AIR files as raw and analyze format, but am only able to open up the analyze format in MRI 3dview, and not in DTI mapping (for the raw formats in DTI mapping, when I attempt to load them, it say "number of files in this fold is less than expected". Is there some way to load just the AIR files into DTI mapping to use for the means recalculation and tensor calculations? Many thanks, Elizabeth Finger -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From susumu at mri.jhu.edu Fri May 16 11:48:23 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 16 May 2008 11:48:23 -0400 Subject: [Mristudio-users] recalculating means with two AIR series? In-Reply-To: <482D673F020000A000003308@lhscgwiao.lhsc.on.ca> Message-ID: <6i7deu$2imibk@ipex1.johnshopkins.edu> I think you'd better run AIR, save the AIRed images, close the DtiStudio, open the AIRed images, and run DTI calculation. When you save the AIRed image, save the first 3+33 images into one file as the raw format. Then save the second 3+33 images is a separate files. In this way, you end up with two 4D AIRed files. To read these raw 4D files, please use "Philips REC" format. If you type in correct X, Y, and Z dimensions, you should see there are 36 images in your file. For DTI calculation, you can load the two 4D files for simultaneous fitting. Before the DTI calculation, it is good idea to calculate "mean and STD (actually subtraction in your case)" to get an idea about the quality of coregistration by AIR. However, this calculation would put extra burden to memory. So, after the quality check, you may need to close the window and load the data again before the tensor calculation. As a reminder, you need a 64bit system to use RAM bigger than 1GB. Hope this will help. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Elizabeth Finger Sent: Friday, May 16, 2008 10:52 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] recalculating means with two AIR series? Hello- I have a large DTI data from GE in dicom format set that contains 3 B0 images plus 33 gradients, 50 slices, and two separate runs per subject. I am able to pull up both runs in DTI Mapping and to run the AIR. However, when I try to then calculate the means and STD for multiple runs, I run out of memory, as I do when trying to do the tensor calculation directly. I am able to proceed if I process just one run at a time. However, if possible, I would like to use the mean from the two series (it was from children, with a lot of movement and fair amount of scanner artifact). I have tried to save AIR files as raw and analyze format, but am only able to open up the analyze format in MRI 3dview, and not in DTI mapping (for the raw formats in DTI mapping, when I attempt to load them, it say "number of files in this fold is less than expected". Is there some way to load just the AIR files into DTI mapping to use for the means recalculation and tensor calculations? Many thanks, Elizabeth Finger ---------------------------------------------------------------------------- ---- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From Elizabeth.Finger at lhsc.on.ca Fri May 16 12:26:29 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Fri, 16 May 2008 12:26:29 -0400 Subject: [Mristudio-users] recalculating means with two AIR series? Message-ID: <482D7D75020000A000003311@lhscgwiao.lhsc.on.ca> Thank you- that worked perfectly. My main mistake was not opening up the AIR files as .rec format. Thanks, Elizabeth Finger >>> susumu 05/16/08 11:48 AM >>> I think you'd better run AIR, save the AIRed images, close the DtiStudio, open the AIRed images, and run DTI calculation. When you save the AIRed image, save the first 3+33 images into one file as the raw format. Then save the second 3+33 images is a separate files. In this way, you end up with two 4D AIRed files. To read these raw 4D files, please use "Philips REC" format. If you type in correct X, Y, and Z dimensions, you should see there are 36 images in your file. For DTI calculation, you can load the two 4D files for simultaneous fitting. Before the DTI calculation, it is good idea to calculate "mean and STD (actually subtraction in your case)" to get an idea about the quality of coregistration by AIR. However, this calculation would put extra burden to memory. So, after the quality check, you may need to close the window and load the data again before the tensor calculation. As a reminder, you need a 64bit system to use RAM bigger than 1GB. Hope this will help. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Elizabeth Finger Sent: Friday, May 16, 2008 10:52 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] recalculating means with two AIR series? Hello- I have a large DTI data from GE in dicom format set that contains 3 B0 images plus 33 gradients, 50 slices, and two separate runs per subject. I am able to pull up both runs in DTI Mapping and to run the AIR. However, when I try to then calculate the means and STD for multiple runs, I run out of memory, as I do when trying to do the tensor calculation directly. I am able to proceed if I process just one run at a time. However, if possible, I would like to use the mean from the two series (it was from children, with a lot of movement and fair amount of scanner artifact). I have tried to save AIR files as raw and analyze format, but am only able to open up the analyze format in MRI 3dview, and not in DTI mapping (for the raw formats in DTI mapping, when I attempt to load them, it say "number of files in this fold is less than expected". Is there some way to load just the AIR files into DTI mapping to use for the means recalculation and tensor calculations? Many thanks, Elizabeth Finger ---------------------------------------------------------------------------- ---- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From susumu at mri.jhu.edu Fri May 16 18:36:37 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 16 May 2008 18:36:37 -0400 Subject: [Mristudio-users] comine the high resolution 3D image with the DTI image In-Reply-To: <484741.98701.qm@web32205.mail.mud.yahoo.com> Message-ID: <6i7deu$2itht1@ipex1.johnshopkins.edu> Hi Jinsong, I don't quite understand your question either, but do you mean how we can co-register 3D anatomical images such as MPRAGE and multi-slice DTI data? If that is the question, you first have to adjust the 3D anatomical image so that it has the same dimensions and pixel sizes as DTI. For example, suppose you have Sagittal MPRAGE with 256x256x120 with 1mm isotropic resolution and Axial DTI with 256x256x60 with 1x1x2.5mm. You have to change MPRAGE to 256x256x60 / 1x1x2.5 mm / Axial. You can do the opposite (change DTI to MPRAGE dimension), but this way is easier. You can use functions available in Landmarker to do this type of resampling. Also, make sure that the center and angles of the images are the same. Otherwise, even if the matrix dimensions are all adjusted, brain locations are not the same. You can read the center and orientation information from DICOM files and type in these numbers to Landmarker "translation" and "rotation" operation. Otherwise, you can use "AIR" to do rigid alignment between MPRAGE and DTI (you can use b0 or DWI). AIR can adjust matrix dimensions and brain locations all at once. So, this could be an easier way. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of darshan pai Sent: Friday, May 09, 2008 12:17 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] comine the high resolution 3D image with the DTI image What do you mean by 3D image ? There are actually various ways depending on what format you have. DICOM format will require you to key in the gradient values in the text area provided. dpf files is convenient which can be used for Analyze as well as RAW image. I am not sure abt 3D, but if you are referring to registration then DTIStudio dont do it . Not that i know of .. --- jinsong tang wrote: > Hello, > > I want to use DTIstudio to do fiber tracking. I > have 2 kinds of dada: DTI and 3D. So, how to comine > the high resolution 3D image with the DTI image? > > jinsong > > > --------------------------------- > ???????????????????????? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > ____________________________________________________________________________ ________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Fri May 16 18:52:06 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 16 May 2008 18:52:06 -0400 Subject: [Mristudio-users] [MRIstudio-users] ROIEditor-latest-x86.rar download In-Reply-To: <410205200.03855@bnu.edu.cn> Message-ID: <6i7deu$2itnh0@ipex1.johnshopkins.edu> Dear Yun, Sorry for the inconvenience. We'll test it from our side and find out what is happening. Xin, could you follow it up? Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of ?? Sent: Wednesday, May 07, 2008 8:07 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [MRIstudio-users] ROIEditor-latest-x86.rar download Hello, After registration, I have successfully downloaded all the required software offered by your website except ROIEditor-latest-x86.rar. For ROIEditor-latest-x86.rar, I couldn't get the saving prompt after entered my username and password, but a whole page of scrambled letters instead. And worst of all, each time my firefox has to be restarted to regain normal function. I've tried not only in my desktop but also my laptop, with both firefox and ie browser. Could you give me a hint on what I did was wrong? I am really eager to learn more about DTI and keen on getting all the preparing work done ASAP. Thanks very much for your help! Best, Yun TZDz5D at 4PEVPTx>-La5=: >From: susumu >Reply-To: "DTI Studio, ROI Editor, Landmarker Questions/Support" >To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" >Subject: Re: [Mristudio-users] [MRIstudio-users] script for map extraction >Date:Wed, 07 May 2008 11:32:59 -0400 > >Hi Benjamin, > >We are working with Pedro in MNI for the MINC format. Pedro and Hangyi, do >we have a version with MINC? > >Susumu > >________________________________________ >From: mristudio-users-bounces at mristudio.org >[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Benjamin D'hont >Sent: Tuesday, May 06, 2008 10:14 AM >To: mristudio-users at mristudio.org >Subject: [Mristudio-users] [MRIstudio-users] script for map extraction > >Hello, > >I would like to extract FA maps at MINC format from 110 DTI datasets. >Is there any possibility to get it done with a script or must I do it by >hand? > >Sincerely, > >Benjamin D'hont >McGill University / Montrial Neurological Institute > > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users From steinja at ucla.edu Wed May 21 12:25:19 2008 From: steinja at ucla.edu (Jason Stein) Date: Wed, 21 May 2008 09:25:19 -0700 Subject: [Mristudio-users] Fiber Tracking Saving Data Question Message-ID: <1bb422f90805210925g52392c27if4a440ec93f82ab6@mail.gmail.com> Hello, I ran some fibertracking on a DTI set and am trying to get the corticospinal tract. As per "Automated Fibertracking of Human Brain White Matter Using Diffusion Tensor Imaging", I placed seeds as follows, an cerebral peduncle AND motor cortex NOT contralateral hemisphere NOT cerebellum. After that I got a bundle which corresponds very well to the corticospinal tract. Now, I saved this dataset in both the Amira's format and the .dat format. When I reload the dataset into DTIstudio or using other code, it shows up in the wrong place (a few voxels off from where it originally started). I attached a screenshot of this problem where you can see that in OriginalFiberTract.jpg, the tract originates in the cerebral peduncle and in the ReloadedFiberTract.jpg, the tract originates in a place slightly posterior to the peduncle. Do you know why this happens and/or how we could fix it? Thanks in advance for any help! Jason -------------- next part -------------- An HTML attachment was scrubbed... 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Name: ReloadedFiberTract.jpg Type: image/jpeg Size: 223193 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080521/945506ef/attachment-0003.jpg From susumu at mri.jhu.edu Wed May 21 12:53:39 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 21 May 2008 12:53:39 -0400 Subject: [Mristudio-users] Fiber Tracking Saving Data Question In-Reply-To: <1bb422f90805210925g52392c27if4a440ec93f82ab6@mail.gmail.com> Message-ID: <6i7deu$2ladcq@ipex1.johnshopkins.edu> Hi Jason, It seems that you had a common problem of Radiology-Neurology display difference, which becomes an issue when you mix raw and Analyze formats. As you can see, the axial image of "reloaded" is inverted. This happens when you try to read images in the Neurology convention (left is left) to DtiStudio that follows the Radiology convention (left is right). As long as you stay with "raw" format within DtiStudio, this problem should not happen. However, if you try to load and save Analyze format, it may happen because the Analyze default is the Neurology convention. If you save image data by the Analyze format through DtiStudio, make sure to reload the image (not the fiber), by Analyze format so that DtiStudio knows what is happening and correct it to Radiology. The fiber information in *.dat is always the Radiology convention. So, first thing you have to do is to figure out the way to load your image upright in axial slice. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jason Stein Sent: Wednesday, May 21, 2008 12:25 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Cc: Ilya Eckstein Subject: [Mristudio-users] Fiber Tracking Saving Data Question Hello, I ran some fibertracking on a DTI set and am trying to get the corticospinal tract. As per "Automated Fibertracking of Human Brain White Matter Using Diffusion Tensor Imaging", I placed seeds as follows, an cerebral peduncle AND motor cortex NOT contralateral hemisphere NOT cerebellum. After that I got a bundle which corresponds very well to the corticospinal tract. Now, I saved this dataset in both the Amira's format and the .dat format. When I reload the dataset into DTIstudio or using other code, it shows up in the wrong place (a few voxels off from where it originally started). I attached a screenshot of this problem where you can see that in OriginalFiberTract.jpg, the tract originates in the cerebral peduncle and in the ReloadedFiberTract.jpg, the tract originates in a place slightly posterior to the peduncle. Do you know why this happens and/or how we could fix it? Thanks in advance for any help! Jason -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080521/2923ade2/attachment.html From Elizabeth.Finger at lhsc.on.ca Wed May 21 16:06:26 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Wed, 21 May 2008 16:06:26 -0400 Subject: [Mristudio-users] question on landmarker and tensor image Message-ID: <48344882020000A0000033F8@lhscgwiao.lhsc.on.ca> Hello- I have a data set in which I would like to compare the uncinate fasiculus in the patients vs. controls. Ideally, I would like to try both the automated white matter segmentation approach as well as a manual ROI approach. So far I have loaded the DTI data (2 runs), run AIR to register the runs together, and done the manual quality check and image flag file. I then reloaded the two AIR series as .rec format with the updated gradient table into DTI mapping and did the tensor calculation, saving the six tensors in one file (Dxx, Dyy, Dzz, etc.) as well as the FA, eigen vector, color maps, recalculated mean B0 and DWI separately as raw format. My next goal is to normalize the images so that I can use the LDDMM to use the automated white matter parcelation, to look at the statististics for the uncinate fasiculus and some control tracts. To do this, what I think needs to be done next (this is a question) is to choose an atlas, load the individual subject data and tensor, and perform the AIR transformation prior to LDDMM? To do this, I first resampled my images in Landmarker to fit the parameters of the atlas. I also did skull stripping in Landmarker, with the GUI button for skull stripping, and multiplied the resulting mask from the skull stripped B0 by the other images. Next, I am able to load the atlas images, and my own resampled images (FA, B0, DWI) successfully. However, when I try to load the tensor image using the Open.d file button, the image parameters of the atlas come up in the pop-up, and whether I load the tensor from DTI mapping, or a tensor which I attempted to resample, I receive an error message ?File size is smaller than expected value?. I would very much appreciate any suggestions as to the steps I have taken and what I should do in response to this error. I saw an email prior with the same error, but can not find how it was resolved. Thank you, Elizabeth Finger -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From susumu at mri.jhu.edu Wed May 21 16:36:43 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 21 May 2008 16:36:43 -0400 Subject: [Mristudio-users] question on landmarker and tensor image In-Reply-To: <48344882020000A0000033F8@lhscgwiao.lhsc.on.ca> Message-ID: <6i7deu$2lhm0e@ipex1.johnshopkins.edu> Hi Elizabeth, 1) First of all, the AIR-based linear transformation can take images with matrix and pixel sizes different from the atlas and save the normalized image in the atlas dimension. So you don't need the pre-processing, unless your data is sagittal and the atlas is axial. AIR would be confused with this 90-degree initial location difference. As long as the two images are reasonably close in terms of image orientation, you can just submit the two images to AIR directory. 2) AIR results are sensitive to the threshold values. Please make sure using the "landmarking" capability to see if the AIRed images are registered reasonably well. The brain height, width, length, and overall orientations should be well adjusted after the linear normalization. This will set all required conditions (matrix size, pixel size, and brain locations) for the next LDDMM. Once you set the good threshold value, that should be good for all other images (usually) using the same protocol. 3) If you use DWI (the sum of all DWIs) or b0 to drive AIR, you don't have to worry too much about skull stripping, because skull is well suppressed in these images and the simple threshold used in AIR can remove it. Sometimes, you can see some strong intensity from outside the brain such as sinus, which interfere with AIR linear registration and may need skull stripping. For skull stripping, you can test the skull-strip button in Landmarker or threshold/region growing x "masking" function (inside =/-* button) in RoiEditor. 4) When you load *.d, your *.d is still in the original dimension, while you said you already change the image dimensions of other images (FA, DWI, b0). Please use the original dimensions for all images (FA, DWI, b0, tensor) and submit them to AIR all together. You get normalized FA, DWI, b0, tensor in the atlas coordinates. AIR takes care for everything. I think you can resample *.d using the resampling function, save the resampled *.d, and reload with other resampled images, but it sounds too many steps.... Please let me know, if it doesn't work or you have further questions. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Elizabeth Finger Sent: Wednesday, May 21, 2008 4:06 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] question on landmarker and tensor image Hello- I have a data set in which I would like to compare the uncinate fasiculus in the patients vs. controls. Ideally, I would like to try both the automated white matter segmentation approach as well as a manual ROI approach. So far I have loaded the DTI data (2 runs), run AIR to register the runs together, and done the manual quality check and image flag file. I then reloaded the two AIR series as .rec format with the updated gradient table into DTI mapping and did the tensor calculation, saving the six tensors in one file (Dxx, Dyy, Dzz, etc.) as well as the FA, eigen vector, color maps, recalculated mean B0 and DWI separately as raw format. My next goal is to normalize the images so that I can use the LDDMM to use the automated white matter parcelation, to look at the statististics for the uncinate fasiculus and some control tracts. To do this, what I think needs to be done next (this is a question) is to choose an atlas, load the individual subject data and tensor, and perform the AIR transformation prior to LDDMM? To do this, I first resampled my images in Landmarker to fit the parameters of the atlas. I also did skull stripping in Landmarker, with the GUI button for skull stripping, and multiplied the resulting mask from the skull stripped B0 by the other images. Next, I am able to load the atlas images, and my own resampled images (FA, B0, DWI) successfully. However, when I try to load the tensor image using the Open.d file button, the image parameters of the atlas come up in the pop-up, and whether I load the tensor from DTI mapping, or a tensor which I attempted to resample, I receive an error message "File size is smaller than expected value". I would very much appreciate any suggestions as to the steps I have taken and what I should do in response to this error. I saw an email prior with the same error, but can not find how it was resolved. Thank you, Elizabeth Finger ---------------------------------------------------------------------------- ---- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From hkim at peds.uab.edu Wed May 21 16:54:19 2008 From: hkim at peds.uab.edu (Hyunmi Kim, M.D.) Date: Wed, 21 May 2008 15:54:19 -0500 Subject: [Mristudio-users] question on DTI protocol In-Reply-To: <48344882020000A0000033F8@lhscgwiao.lhsc.on.ca> References: <48344882020000A0000033F8@lhscgwiao.lhsc.on.ca> Message-ID: <66073DDBA72FF542AAA13469EF91E79E030BBDD4@ex1-777peds.peds.uab.edu> Dear sir/madam; I am on the way improving DTI protocol. We would like to have matrix scan reconstruction 256 and 3mm slice thickness without gap. When MRI tech tried to change it, We have to choose only one of the below; matrix scan reconstruction 128 and "0" gap OR matrix scan reconstruction 256 and "1" mm gap. Most our patients have epilepsy. Which parameter, do you think, is more important? Thank you for your help. Hyunmi Kim, MD, PhD Assistant Professor Division of Pediatric Neurology From susumu at mri.jhu.edu Wed May 21 17:08:44 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 21 May 2008 17:08:44 -0400 Subject: [Mristudio-users] question on DTI protocol In-Reply-To: <66073DDBA72FF542AAA13469EF91E79E030BBDD4@ex1-777peds.peds.uab.edu> Message-ID: <6i7deu$2lj0qu@ipex1.johnshopkins.edu> When you are talking about matrix size (128 or 256), do you mean the actual acquired data size is 128 and just interpolated to 256? Or do you want real 256 data acquisition? I would suggest data acquisition of 96 (with 240 mm FOV, 2.5 mm resolution) or 128 (with 256 mm FOV, 2 mm resolution), interpolated to 192 or 256. Real data acquisition of 256 is too much for DTI. Remember, we use single-shot EPI. After 96-128 echoes, there is not much signal left anymore. There is no point to keep sampling the noise. More data points (like 256) just give us more distortion without real gain of resolution. Also, gap should be 0. Anyway I would suggest first figuring out if you are dealing with interpolated 256 or real 256 datapoints. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hyunmi Kim, M.D. Sent: Wednesday, May 21, 2008 4:54 PM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] question on DTI protocol Dear sir/madam; I am on the way improving DTI protocol. We would like to have matrix scan reconstruction 256 and 3mm slice thickness without gap. When MRI tech tried to change it, We have to choose only one of the below; matrix scan reconstruction 128 and "0" gap OR matrix scan reconstruction 256 and "1" mm gap. Most our patients have epilepsy. Which parameter, do you think, is more important? Thank you for your help. Hyunmi Kim, MD, PhD Assistant Professor Division of Pediatric Neurology _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From SCopeland at mednet.ucla.edu Tue May 27 15:45:46 2008 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Tue, 27 May 2008 12:45:46 -0700 Subject: [Mristudio-users] gradient tables Message-ID: <96AC3D45F44CDC48A3A3201DCEF8B0CC0A96FF@admedmail4.ad.medctr.ucla.edu> Hello, In March, I received an e-mail about rotating gradient tables when using Siemens operating systems. I was glad to see it, since I was having this problem and didn't know how to solve it. I have one related question, though. Is it possible to get the corrected gradient table out of DTI studio? By this, I mean is the file written out somewhere, or can it be? I would love to have this information. Thanks for any help - Sarah Copeland ---------------------------------------------------------- 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 SCopeland at mednet.ucla.edu Tue May 27 15:48:17 2008 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Tue, 27 May 2008 12:48:17 -0700 Subject: [Mristudio-users] gradient tables Message-ID: <96AC3D45F44CDC48A3A3201DCEF8B0CC0A9700@admedmail4.ad.medctr.ucla.edu> Hello, In March I received the e-mail about rotating gradient tables for Siemens DTI data. I was happy to see it, since I have this problem and didn't know what to do to get the correct gradient table. I have one related question: is there a way to get the corrected gradient table out of DTI studio? By this I mean, is it written to a file, or can it be? I would like to have this information if I could. Thanks for any help - Sarah Copeland ---------------------------------------------------------- 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 mayuresh.korgaonkar at gmail.com Wed May 28 12:55:31 2008 From: mayuresh.korgaonkar at gmail.com (Mayuresh Korgaonkar) Date: Wed, 28 May 2008 12:55:31 -0400 Subject: [Mristudio-users] combining over DTI scans Message-ID: <66bddc1c0805280955g76e3ac5fx4abcf5ecd71e92df@mail.gmail.com> Hello all, I was wondering if you could suggest how to combine different DTI scans, each with a seperate gradient table, in DTI studio. Basically, I have two DTI scans and I have two sets of gradient tables for each scan (gradient table for each scan corrected separately for angulations and motion correction using the DTI gradient table creator code written by Johnathan Farrell). Next I want to use these separate gradient tables for each scan for further analyses. Can this be done using the dpf format? Thanks in advance, Mayuresh. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080528/3e60e448/attachment.html From susumu at mri.jhu.edu Wed May 28 14:06:39 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 28 May 2008 14:06:39 -0400 Subject: [Mristudio-users] gradient tables In-Reply-To: <96AC3D45F44CDC48A3A3201DCEF8B0CC0A96FF@admedmail4.ad.medctr.ucla.edu> Message-ID: <6u9t96$2oun5a@ipex1.johnshopkins.edu> Hi Sarah, I'm not sure if there is any way to export the re-calculated b-table based on oblique angles. Hangyi, is there such a function in DtiStudio? Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Copeland, Sarah A. Sent: Tuesday, May 27, 2008 3:46 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] gradient tables Hello, In March, I received an e-mail about rotating gradient tables when using Siemens operating systems. I was glad to see it, since I was having this problem and didn't know how to solve it. I have one related question, though. Is it possible to get the corrected gradient table out of DTI studio? By this, I mean is the file written out somewhere, or can it be? I would love to have this information. Thanks for any help - Sarah Copeland ---------------------------------------------------------- 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. ---------------------------------------------------------- _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Wed May 28 15:11:29 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 28 May 2008 15:11:29 -0400 Subject: [Mristudio-users] combining over DTI scans In-Reply-To: <66bddc1c0805280955g76e3ac5fx4abcf5ecd71e92df@mail.gmail.com> Message-ID: <6u9t96$2ovnf6@ipex1.johnshopkins.edu> If I understood your question correctly, you want to combine two DTI datasets with different b-table. For example one 30-orientation and one 15-orientation. You can load the 30-orientation data and 15-orientation data into one window. First open the 30-orientation using the "open" icon at the top left menu and then get a new viewing window. Then open the 15-orientation using another "open" icon at the right column of the viewing window. In this way, you get all 45 + b0s into one window. Then you can save all into one file using the "save" icon in the right column. In this way, you can create a concatenated file in which you have b0+30DWIs+b0+15DWIs. Next, combine the two b-table to create a 45-orientation file. Make sure that the order of the b-table is the same as the order of the stored images. In this way, you can combine the two. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Mayuresh Korgaonkar Sent: Wednesday, May 28, 2008 12:56 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] combining over DTI scans Hello all, I was wondering if you could suggest how to combine different DTI scans, each with a seperate gradient table, in DTI studio. Basically, I have two DTI scans and I have two sets of gradient tables for each scan (gradient table for each scan corrected separately for angulations and motion correction using the DTI gradient table creator code written by Johnathan Farrell). Next I want to use these separate gradient tables for each scan for further analyses. Can this be done using the dpf format? Thanks in advance, Mayuresh. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080528/ee265397/attachment.html From Shmuel.Miron at sheba.health.gov.il Wed Jun 4 09:15:49 2008 From: Shmuel.Miron at sheba.health.gov.il (Shmuel Miron Dr) Date: Wed, 04 Jun 2008 16:15:49 +0300 Subject: [Mristudio-users] reslicing DTI images Message-ID: Hello List members I have a large set of DTI data with a voxel dimension of 1 x 1 x 2.6 mm acquired in the axial position . However, In DTI studio the resolution on the sagital and coronal views is not satisfactory. Is there a way to re-slice the data (around 1900 dicom images) into voxels of 2.6 x 2.6 x 2.6 mm in DTI studio ? Is it possible to perform the job with a different software? Thanks Dr. Shmuel Miron Multiple Sclerosis Center ************************************************************************** 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 ***This email was scanned against viruses, vandals and malicious content*** ***Powered By Trend Micro - InterScan Messaging Security Suite1*** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080604/9fbc2d4c/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/jpeg Size: 3781 bytes Desc: image001.jpg Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080604/9fbc2d4c/attachment-0001.jpe From support at mristudio.org Wed Jun 4 09:58:56 2008 From: support at mristudio.org (support at mristudio.org) Date: Wed, 4 Jun 2008 09:58:56 -0400 (EDT) Subject: [Mristudio-users] reslicing DTI images In-Reply-To: References: Message-ID: <3834.162.129.28.194.1212587936.squirrel@webmail.mristudio.org> hello, don't know why the sagital and coronal views are not satisfactory. I guess that their width-height ratio looks incorrect, so you want to re-sample the images to cubic voxels (2.6 x 2.6 x 2.6). if this is the reason, please specify the image parameters (especially the pixel sizes, or FOV) correctly when you load the images in. the program will adjust the ratio for displaying. in DTI Studio, there is no function for re-slicing the images. regards, hangyi when you load the images in, please specify the image parameters > Hello List members > > > > I have a large set of DTI data with a voxel dimension of 1 x 1 x 2.6 mm > acquired in the axial position . > > However, In DTI studio the resolution on the sagital and coronal views > is not satisfactory. > > > > Is there a way to re-slice the data (around 1900 dicom images) into > voxels of 2.6 x 2.6 x 2.6 mm in DTI studio ? > > Is it possible to perform the job with a different software? > > > > Thanks > > > > > > Dr. Shmuel Miron > > Multiple Sclerosis Center > > > > > ************************************************************************** > 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 > ***This email was scanned against viruses, vandals and malicious content*** > ***Powered By Trend Micro - InterScan Messaging Security Suite1*** > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From susumu at mri.jhu.edu Wed Jun 4 10:02:48 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 04 Jun 2008 10:02:48 -0400 Subject: [Mristudio-users] reslicing DTI images In-Reply-To: Message-ID: <6ua0er$2cv9bg@ipex2.johnshopkins.edu> There are two ways to do the reslice. One is to reslice the raw DWIs or reslice images after tensor calculation. Either way, you can use the "reslice" function in Landmarker. 1) Reslice DWIs: Because you want z reslice, you first have to convert your 1,900 Dicom to a series of 3D volume data. You can easily do it by DtiStudio. Read all Dicom and save each 3D data as raw or analyze format (I recommend raw). You have to read each 3D volume to Landmarker and reslice it to the dimension and pixel size you want. The only problem of this approach is, you have to repeat it many times. For example, if you have 2 b0 and 30 DWIs, you have to do it 32 times. Landmarker can read text script, but it doesn't have butch processing capability. 2) Reslice after tensor calculation: Here you have two choices. You can read and reslice tensor elements by Landmarker. Then you can reload the resliced tensor into DtiStudio to recalculate eivenvalues, eigenvectors, and other maps like FA. The procedure is; > Calculate tensor by DtiStudio. Save each element (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) separately as a regular floating point image or save them into one file (so called *.d file in DtiStudio). > Load the image into Landmarker. If the 6 elements are saved separately, you have to read them individually. If you save them into one *.d file, you need to use "Open *.d" button to load all at once. (Please obtain the latest Landmarker because old versions can not interpolate tensor data. Also, the first image you open is always treated as a template in Landmarker and "Open *.d" is inactivated. You have to open the image you want to interpolate in the second window (first image can be anything because we don't use it for this interpolation operation). First please open a scalar image such as b0 or FA. Then you can find "Open *.d" in the right column of the window) > The interpolation button at in the bottom of "Image" section, second from the right. Type in the new dimensions and perform relice. > Save the 6 interpolated tensor elements into one file (new *.d file). Just for the sake of procedure, also reslice one scalar image such as b0 and save it. > Load the resliced scalar image (e.g. b0 with the new dimension) to DtiStudio. You can see "Open *.d" button in the right column of the viewing window. Load the new interpolated *.d into DtiStudio. In the dialog window, check "eigenvalues/vectors". The second option is, first calculate all the scalar maps such as FA and interpolate them. This can be easily done by Landmarker; > Load a FA map and interpolate using the button described above. These three ways lead to slightly different results. Visually the tensor interpolation tends to enhance FA contrast. For example, if there are two adjacent pixels with FA = 0.8 but fiber angles with 90 degree difference, FA interpolation between these two pixels gives FA = 0.8, but tensor interpolation gives FA < 0.8. Between two different fibers with different angles, there remain low FA regions with the tensor interpolation. I believe the raw DWI interpolation leads to image similar to the tensor interpolation, but not sure. This may give you impression that the tensor interpolation is the right thing to do. However, if the two adjacent pixels (FA = 0.8) belong to one continuous fiber with angle transition of 30 degree, you want to keep the same FA (FA = 0.8) between the two pixels. In this case, you don't want decrease in FA every time you interpolate pixels with slight angle difference. In reality, if you do fiber tracking, angle transition greater than 40-45 degree is rejected usually. Also, average angle transition is usually very small (<10), unless 2-2.5 mm image resolution is too large with respect to fiber curvature. So this may not pose a large practical issue. Anyway, as long as we don't know the exact neuroanatomy of each pixel, there is no single "right interpolation". You just have to stick with a consistent method. Or you can do both and apply the same manual ROI or voxel-based method to make sure there is no significant difference depending on the interpolation (and I doubt there would be). Hope it helps. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Shmuel Miron Dr Sent: Wednesday, June 04, 2008 9:16 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] reslicing DTI images Hello List members I have a large set of DTI data with a voxel dimension of 1 x 1 x 2.6 mm acquired in the axial position . However, In DTI studio the resolution on the sagital and coronal views is not satisfactory. Is there a way to re-slice the data (around 1900 dicom images) into voxels of 2.6 x 2.6 x 2.6 mm in DTI studio ? Is it possible to perform the job with a different software? Thanks Dr. Shmuel Miron Multiple Sclerosis Center ************************************************************************** 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 ***This email was scanned against viruses, vandals and malicious content*** ***Powered By Trend Micro - InterScan Messaging Security Suite1*** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080604/c9d9fd94/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/jpeg Size: 3781 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080604/c9d9fd94/attachment-0001.jpe From Weihong.Yuan at cchmc.org Thu Jun 5 15:22:21 2008 From: Weihong.Yuan at cchmc.org (Weihong Yuan) Date: Thu, 05 Jun 2008 15:22:21 -0400 Subject: [Mristudio-users] How to calculate a multi-b value tensor In-Reply-To: <6i7avk$nj4ae@ipex2.johnshopkins.edu> References: <6i7avk$nj4ae@ipex2.johnshopkins.edu> Message-ID: <484804AD.42F5.004B.0@cchmc.org> Dear all, If I have a DTI dataset acquired in 6 directions and 2 b-values (say, 100 and 800). How should I edit the gradient table? Is it something like: 0: 0, 0, 0 1: 1, 0, 1, 100 2: -1, 0,1, 100 3: 0,1,1, 100 4: 0,1, -1, 100 5: 1,1,0, 100 6: -1, 1, 0, 100 1: 1, 0, 1, 800 2: -1, 0,1, 800 3: 0,1,1, 800 4: 0,1, -1, 800 5: 1,1,0, 800 6: -1, 1, 0, 800 Thanks >>> susumu 2/18/2008 4:04 PM >>> Dear MriStudio_User subscribers, The tutorial in JHU will take place in Darner Conference Room / Ross Building basement on 2/25, 1-5 pm. I attached a map in which the Ross Building is indicated by a red asterisk (720 Rutland Ave., Baltimore, MD). One of the visitor parking lots is shown by a blue arrow. All users expressed their interest are welcome (currently we count 24 attendees). The tutorial is free. Please make sure that you follow the instruction in "Workshop" section of www.mristudio.org to pre-condition your laptop. We are trying to post the latest Landmarker this week that includes a new single-subject atlas that is required for non-linear image registration. If we can make it in time, I'll send you another email. The second (3/2) and third tutorial (5/4) are still scheduled as notified in the second announcement. Thanks, Susumu From hjiang at jhmi.edu Thu Jun 5 15:56:32 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Thu, 05 Jun 2008 15:56:32 -0400 Subject: [Mristudio-users] How to calculate a multi-b value tensor Message-ID: <48480CB00200006300012D08@cis27.hosts.jhmi.edu> yes, you are almost there; please re-write the 1st line as: 0: 0,0,0,0 so the program knows that this image's b-value is 0; hangyi >>> Weihong Yuan 06/05/08 3:22 PM >>> Dear all, If I have a DTI dataset acquired in 6 directions and 2 b-values (say, 100 and 800). How should I edit the gradient table? Is it something like: 0: 0, 0, 0 1: 1, 0, 1, 100 2: -1, 0,1, 100 3: 0,1,1, 100 4: 0,1, -1, 100 5: 1,1,0, 100 6: -1, 1, 0, 100 1: 1, 0, 1, 800 2: -1, 0,1, 800 3: 0,1,1, 800 4: 0,1, -1, 800 5: 1,1,0, 800 6: -1, 1, 0, 800 Thanks >>> susumu 2/18/2008 4:04 PM >>> Dear MriStudio_User subscribers, The tutorial in JHU will take place in Darner Conference Room / Ross Building basement on 2/25, 1-5 pm. I attached a map in which the Ross Building is indicated by a red asterisk (720 Rutland Ave., Baltimore, MD). One of the visitor parking lots is shown by a blue arrow. All users expressed their interest are welcome (currently we count 24 attendees). The tutorial is free. Please make sure that you follow the instruction in "Workshop" section of www.mristudio.org to pre-condition your laptop. We are trying to post the latest Landmarker this week that includes a new single-subject atlas that is required for non-linear image registration. If we can make it in time, I'll send you another email. The second (3/2) and third tutorial (5/4) are still scheduled as notified in the second announcement. Thanks, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From graeme.schwindt at gmail.com Tue Jun 17 12:56:31 2008 From: graeme.schwindt at gmail.com (Graeme Schwindt) Date: Tue, 17 Jun 2008 12:56:31 -0400 Subject: [Mristudio-users] Flipping eigen vectors in fiber tracking Message-ID: <8640b26c0806170956x6b81a522l76126540ab9f62ef@mail.gmail.com> Hello, >From the informative workshop here in Toronto, I have notes that indicate when performing fiber tracking, Siemens and GE data should have the eigen vector flipped in the X direction, and Philips in the Z direction. I have some GE dicom data, and have followed the protocol as in the workshop, loading in the AIRed FA map and eigenvector0 .vec file for fiber tracking. When I chose flip in the X direction, the results of tracking appeared wrong, with corpus callosum fibers projecting in clearly the wrong direction and projecting for very short distances. I then tried flipping in the other two directions, and found extremely good results when flipping in the Z direction, which I was happy with. But I want to make sure that these results are not spurious, though the fibers follow anatomical pathways properly and so seem to be real. I wondered if there may be some orientation label problem? Is it also correct to load in the eigenvector 0 as the principal vector? Has anyone else had experience with GE dicom data and used Z flipping? Thanks, Graeme -- Graeme C. Schwindt, HBSc MD/PhD Student University of Toronto graeme.schwindt at gmail.com 416.546.5453 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080617/6f0a5ccb/attachment.html From bjweiland at gmail.com Tue Jun 17 13:12:17 2008 From: bjweiland at gmail.com (Barbara Weiland) Date: Tue, 17 Jun 2008 13:12:17 -0400 Subject: [Mristudio-users] Flipping eigen vectors in fiber tracking In-Reply-To: <8640b26c0806170956x6b81a522l76126540ab9f62ef@mail.gmail.com> References: <8640b26c0806170956x6b81a522l76126540ab9f62ef@mail.gmail.com> Message-ID: <523a72ef0806171012s318d9503td7ce4d1843b03ecd@mail.gmail.com> Graeme - yes - we are using a GE system and are also flipping the z direction, Barbara -- Barbara Weiland, PhD Post Doc Fellow/MEG Physicist Neuromagnetism Laboratory Neurology Research Henry Ford Health System 2799 W. Grand Blvd., CFP 79 Detroit, MI 48202-2689 313-916-1075 bjweiland at gmail.com On 6/17/08, Graeme Schwindt wrote: > > Hello, > > From the informative workshop here in Toronto, I have notes that indicate > when performing fiber tracking, Siemens and GE data should have the eigen > vector flipped in the X direction, and Philips in the Z direction. I have > some GE dicom data, and have followed the protocol as in the workshop, > loading in the AIRed FA map and eigenvector0 .vec file for fiber tracking. > > When I chose flip in the X direction, the results of tracking appeared > wrong, with corpus callosum fibers projecting in clearly the wrong direction > and projecting for very short distances. I then tried flipping in the other > two directions, and found extremely good results when flipping in the Z > direction, which I was happy with. But I want to make sure that these > results are not spurious, though the fibers follow anatomical pathways > properly and so seem to be real. I wondered if there may be some orientation > label problem? Is it also correct to load in the eigenvector 0 as the > principal vector? Has anyone else had experience with GE dicom data and used > Z flipping? > > Thanks, > Graeme > > -- > Graeme C. Schwindt, HBSc > MD/PhD Student > University of Toronto > graeme.schwindt at gmail.com > 416.546.5453 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080617/29314d96/attachment.html From jmcentee at jhmi.edu Tue Jun 17 18:25:42 2008 From: jmcentee at jhmi.edu (JULIE E MCENTEE) Date: Tue, 17 Jun 2008 18:25:42 -0400 Subject: [Mristudio-users] how to get whole-brain FA Message-ID: Hello Group, Is there a way to get whole-brain FA statistics using DTI-Studio under Fber-Tracking? I am able to input my fa and eigenvector files, but when I click the Statistics button under the fiber tab and choose the fa file, I get "N/A". If anyone knows of another/better way to get whole-brain FA, please let me know. Also, is the a way to change the size of the images in the gui? The images of my data are VERY small, and zooming does not help. Thank-you for your help, 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 From SCopeland at mednet.ucla.edu Tue Jun 17 20:35:21 2008 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Tue, 17 Jun 2008 17:35:21 -0700 Subject: [Mristudio-users] loading anatomic images into ROIeditor Message-ID: <96AC3D45F44CDC48A3A3201DCEF8B0CC01D99E7C@admedmail4.ad.medctr.ucla.edu> Hello - I'm hoping someone can help me with loading MPRAGE images into ROIeditor. These are collected as part of the ICBM 30 direction protocol, and can be read as analyze images by fsl and mricro. When I try to load them into ROIeditor, I get the error message CMriView3DDoc()::CreatImgWithAnalyzeFile() Unrecognized Analyze Header File: Any suggestions? Thank you. Sarah Copeland ---------------------------------------------------------- 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 xli16 at jhmi.edu Wed Jun 18 14:23:37 2008 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 18 Jun 2008 14:23:37 -0400 Subject: [Mristudio-users] loading anatomic images into ROIeditor In-Reply-To: <96AC3D45F44CDC48A3A3201DCEF8B0CC01D99E7C@admedmail4.ad.medctr.ucla.edu> References: <96AC3D45F44CDC48A3A3201DCEF8B0CC01D99E7C@admedmail4.ad.medctr.ucla.edu> Message-ID: Hello, You may load your images in mricro and then save them as raw data. Then you should be able to load those raw data into ROIEditor. Xin ----- Original Message ----- From: "Copeland, Sarah A." Date: Tuesday, June 17, 2008 8:35 pm Subject: [Mristudio-users] loading anatomic images into ROIeditor To: mristudio-users at mristudio.org > Hello - > > I'm hoping someone can help me with loading MPRAGE images into > ROIeditor. These are collected as part of the ICBM 30 direction > protocol, and can be read as analyze images by fsl and mricro. When I > try to load them into ROIeditor, I get the error message > CMriView3DDoc()::CreatImgWithAnalyzeFile() > Unrecognized Analyze Header File: > > Any suggestions? > > Thank you. > > Sarah Copeland > > ---------------------------------------------------------- > 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. > ---------------------------------------------------------- > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From xli16 at jhmi.edu Wed Jun 18 14:27:19 2008 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 18 Jun 2008 14:27:19 -0400 Subject: [Mristudio-users] how to get whole-brain FA In-Reply-To: References: Message-ID: Hello, ROIEditor may help you get whole-brain FA statistics. Please check the online user manual. There is a function in Landmarker that can resample your images. Xin ----- Original Message ----- From: JULIE E MCENTEE Date: Tuesday, June 17, 2008 6:25 pm Subject: [Mristudio-users] how to get whole-brain FA To: mristudio-users at mristudio.org > Hello Group, > > Is there a way to get whole-brain FA statistics using DTI-Studio > under Fber-Tracking? I am able to input my fa and eigenvector files, > but when I click the Statistics button under the fiber tab and choose > the fa file, I get "N/A". > > If anyone knows of another/better way to get whole-brain FA, please > let me know. > > Also, is the a way to change the size of the images in the gui? The > images of my data are VERY small, and zooming does not help. > > Thank-you for your help, > > 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 > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From Hoptman at NKI.RFMH.ORG Mon Jun 23 10:42:20 2008 From: Hoptman at NKI.RFMH.ORG (Hoptman, Matthew) Date: Mon, 23 Jun 2008 10:42:20 -0400 Subject: [Mristudio-users] [Fwd: short course] Message-ID: <2586A1048152BE4D861E64A98700AD4266CE2F@nki-mail.NKI.rfmh.org> Hi all, How do I get an a measure of the length of each fiber? I'd like to do estimate the distribution of fiber lengths in some tracking that I'm doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080623/413fea07/attachment.html From llanyon at eyecarecentre.org Mon Jun 23 14:32:57 2008 From: llanyon at eyecarecentre.org (llanyon) Date: Mon, 23 Jun 2008 11:32:57 -0700 Subject: [Mristudio-users] left-right flipping Message-ID: <5CED06590F03DD459B340C608D68A85225CFF3124F@pc-vm-slserver.supportlink.ca> Hi everyone We are looking at the arcuate fasciculus (AF) with DTI Studio (version 2.40). Just about all the published literature says that the AF is larger in the left hemisphere than the right. However, we are seeing the reverse pattern, and are concerned about a possible flip of the data in the x direction. We have acquired our data on a 3T Philips Achieva Scanner. I have check L-R laterality using lesion patient data and there does not seem to be a flip, but I wondered whether anyone else has had any issues like this? Thanks Linda Lanyon ----------------------------------------------------------------------------------------------------- Linda Lanyon Post-doctoral Research Fellow, Michael Smith Foundation for Health Research University of British Columbia Human Vision & Eye Movement Laboratory Vancouver General Hospital Eye Care Centre 3rd Floor Research Labs - Rm 365 2550 Willow St, Vancouver, B.C., Canada Phone: +1-604-875-4111 x 69003 Fax: +1 604-875-4663 email: llanyon at eyecarecentre.org web: http://www.neuroophthalmology.ca/UBCNeuroOp/JBarton/labstaff/Linda.htm Director, Society for Canadian Women in Science and Technology: www.scwist.ca ----------------------------------------------------------------------------------------------------- The content of this e-mail, including any files attached, is confidential and may be privileged. Any unauthorized copying or distribution is strictly prohibited. If you receive this e-mail in error, please contact the sender immediately and delete this e-mail. From susumu at mri.jhu.edu Tue Jun 24 02:20:37 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 24 Jun 2008 02:20:37 -0400 Subject: [Mristudio-users] left-right flipping In-Reply-To: <5CED06590F03DD459B340C608D68A85225CFF3124F@pc-vm-slserver.supportlink.ca> References: <5CED06590F03DD459B340C608D68A85225CFF3124F@pc-vm-slserver.supportlink.ca> Message-ID: <168807F472574ED6826206595719F569@SusumuThinkPad> Hi Linda, Please note that DtiStudio follows the Radiological convention like all the scanners do; the right side of the image in axial and coronal slices are the patient's left. So far we haven't noticed any situations in which right-left is flipped in DtiStudio. If you want to confirm, you can put a syringe or a water bottle to one side of the brain during a scan. You need to be careful if your data went through other software programs. Many Neurology-oriented programs follow the Neurology convention. Default Analyze format also is Neurology convention. If the brain orientation is flipped, usually you can tell it immediately because the axial slice becomes inverted. As for the right-left, we are also one of them who published the right-left asymmetry based on tractography. However, we have to be careful. We know that the total white matter volume is almost the same between the right and the left hemisphere. Most white matter tracts should have the same sizes. The reason why tractography gives us the asymmetry results could be complicated; 1) There are regions with lower FA in one of the hemisphere. 2) The tract shape and size is more convoluted in one of the hemisphere (the size of the tractography is heavily influenced by the narrowest section of the entire path). 3) The SNR (or signal intensity) is inhomogeneous due to the nature of the RF coil. Please note that I've never seen that anybody (including myself) tested by scanning the same person twice; once with face up and once with face down, to reject the #3. Hope this helps. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of llanyon Sent: Monday, June 23, 2008 2:33 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] left-right flipping Hi everyone We are looking at the arcuate fasciculus (AF) with DTI Studio (version 2.40). Just about all the published literature says that the AF is larger in the left hemisphere than the right. However, we are seeing the reverse pattern, and are concerned about a possible flip of the data in the x direction. We have acquired our data on a 3T Philips Achieva Scanner. I have check L-R laterality using lesion patient data and there does not seem to be a flip, but I wondered whether anyone else has had any issues like this? Thanks Linda Lanyon ---------------------------------------------------------------------------- ------------------------- Linda Lanyon Post-doctoral Research Fellow, Michael Smith Foundation for Health Research University of British Columbia Human Vision & Eye Movement Laboratory Vancouver General Hospital Eye Care Centre 3rd Floor Research Labs - Rm 365 2550 Willow St, Vancouver, B.C., Canada Phone: +1-604-875-4111 x 69003 Fax: +1 604-875-4663 email: llanyon at eyecarecentre.org web: http://www.neuroophthalmology.ca/UBCNeuroOp/JBarton/labstaff/Linda.htm Director, Society for Canadian Women in Science and Technology: www.scwist.ca ---------------------------------------------------------------------------- ------------------------- The content of this e-mail, including any files attached, is confidential and may be privileged. Any unauthorized copying or distribution is strictly prohibited. If you receive this e-mail in error, please contact the sender immediately and delete this e-mail. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Tue Jun 24 04:02:31 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 24 Jun 2008 04:02:31 -0400 Subject: [Mristudio-users] [Fwd: short course] In-Reply-To: <2586A1048152BE4D861E64A98700AD4266CE2F@nki-mail.NKI.rfmh.org> Message-ID: <6u9t96$36c25v@ipex1.johnshopkins.edu> Dear Matt, I'm not sure if DtiSudio can provide a histogram of fiber length. It should be possible to extract such info from the stored tract file using IDL or Matlab codes. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Monday, June 23, 2008 10:42 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [Fwd: short course] Hi all, ??????????????? How do I get an a measure of the length of each fiber?? I?d like to do estimate the distribution of fiber lengths in some tracking that I?m doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine ________________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From Hoptman at NKI.RFMH.ORG Tue Jun 24 04:19:07 2008 From: Hoptman at NKI.RFMH.ORG (Hoptman, Matthew) Date: Tue, 24 Jun 2008 04:19:07 -0400 Subject: [Mristudio-users] [Fwd: short course] In-Reply-To: <6u9t96$36c25v@ipex1.johnshopkins.edu> References: <2586A1048152BE4D861E64A98700AD4266CE2F@nki-mail.NKI.rfmh.org> <6u9t96$36c25v@ipex1.johnshopkins.edu> Message-ID: <2586A1048152BE4D861E64A98700AD4201103949@nki-mail.NKI.rfmh.org> Hi again, I guess I'm asking a simpler question. Is there a way to get the length of each fiber? I can do the histogram part myself. --Matt -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:03 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] [Fwd: short course] Dear Matt, I'm not sure if DtiSudio can provide a histogram of fiber length. It should be possible to extract such info from the stored tract file using IDL or Matlab codes. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Monday, June 23, 2008 10:42 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [Fwd: short course] Hi all, ??????????????? How do I get an a measure of the length of each fiber?? I'd like to do estimate the distribution of fiber lengths in some tracking that I'm doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine ________________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From Hoptman at NKI.RFMH.ORG Tue Jun 24 04:22:05 2008 From: Hoptman at NKI.RFMH.ORG (Hoptman, Matthew) Date: Tue, 24 Jun 2008 04:22:05 -0400 Subject: [Mristudio-users] [Fwd: short course] In-Reply-To: <6u9t96$36c25v@ipex1.johnshopkins.edu> References: <2586A1048152BE4D861E64A98700AD4266CE2F@nki-mail.NKI.rfmh.org> <6u9t96$36c25v@ipex1.johnshopkins.edu> Message-ID: <2586A1048152BE4D861E64A98700AD420110394A@nki-mail.NKI.rfmh.org> PS> I mean the fiber length resulting from a given ROI. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:03 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] [Fwd: short course] Dear Matt, I'm not sure if DtiSudio can provide a histogram of fiber length. It should be possible to extract such info from the stored tract file using IDL or Matlab codes. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Monday, June 23, 2008 10:42 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [Fwd: short course] Hi all, ??????????????? How do I get an a measure of the length of each fiber?? I'd like to do estimate the distribution of fiber lengths in some tracking that I'm doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine ________________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From susumu at mri.jhu.edu Tue Jun 24 04:22:07 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 24 Jun 2008 04:22:07 -0400 Subject: [Mristudio-users] how to get whole-brain FA In-Reply-To: Message-ID: <6u9t96$36c7al@ipex1.johnshopkins.edu> Hi Julie, If you want the whole-brain FA, I assume it's not based on tractography. Then, as Xin suggested, I would recommend to use RoiEditor. You can delineate the entire brain using b0 image and intensity threshold or region growing tool. This (delineated brain) can be used as a masking. You can apply the mask to an FA map. Or, you can threshold FA directly using something like FA>0.25. In this way, you can get statistics within the masked area such as average FA of the whole brain. I believe you can export the data to a text file from which you can create a histogram using Exel. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of JULIE E MCENTEE Sent: Tuesday, June 17, 2008 6:26 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] how to get whole-brain FA Hello Group, Is there a way to get whole-brain FA statistics using DTI-Studio under Fber-Tracking? I am able to input my fa and eigenvector files, but when I click the Statistics button under the fiber tab and choose the fa file, I get "N/A". If anyone knows of another/better way to get whole-brain FA, please let me know. Also, is the a way to change the size of the images in the gui? The images of my data are VERY small, and zooming does not help. Thank-you for your help, 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 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Tue Jun 24 04:29:35 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 24 Jun 2008 04:29:35 -0400 Subject: [Mristudio-users] [Fwd: short course] In-Reply-To: <2586A1048152BE4D861E64A98700AD420110394A@nki-mail.NKI.rfmh.org> References: <2586A1048152BE4D861E64A98700AD4266CE2F@nki-mail.NKI.rfmh.org> <6u9t96$36c25v@ipex1.johnshopkins.edu> <2586A1048152BE4D861E64A98700AD420110394A@nki-mail.NKI.rfmh.org> Message-ID: <813A4A590FFB48099ED32F0F61BD7E37@SusumuThinkPad> I have to confirm Hangyi, but I believe a converter that can read a tract file, read the length of all stored tracts, and save the length of each tract, is needed. Luke, have you ever written such an IDL file before? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Tuesday, June 24, 2008 4:22 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] [Fwd: short course] PS> I mean the fiber length resulting from a given ROI. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:03 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] [Fwd: short course] Dear Matt, I'm not sure if DtiSudio can provide a histogram of fiber length. It should be possible to extract such info from the stored tract file using IDL or Matlab codes. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Monday, June 23, 2008 10:42 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [Fwd: short course] Hi all, ??????????????? How do I get an a measure of the length of each fiber?? I'd like to do estimate the distribution of fiber lengths in some tracking that I'm doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine ________________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From Hoptman at NKI.RFMH.ORG Tue Jun 24 04:31:11 2008 From: Hoptman at NKI.RFMH.ORG (Hoptman, Matthew) Date: Tue, 24 Jun 2008 04:31:11 -0400 Subject: [Mristudio-users] [Fwd: short course] In-Reply-To: <813A4A590FFB48099ED32F0F61BD7E37@SusumuThinkPad> References: <2586A1048152BE4D861E64A98700AD4266CE2F@nki-mail.NKI.rfmh.org> <6u9t96$36c25v@ipex1.johnshopkins.edu> <2586A1048152BE4D861E64A98700AD420110394A@nki-mail.NKI.rfmh.org> <813A4A590FFB48099ED32F0F61BD7E37@SusumuThinkPad> Message-ID: <2586A1048152BE4D861E64A98700AD420110394B@nki-mail.NKI.rfmh.org> That would be great! -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:30 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Cc: 'Hua KG' Subject: Re: [Mristudio-users] [Fwd: short course] I have to confirm Hangyi, but I believe a converter that can read a tract file, read the length of all stored tracts, and save the length of each tract, is needed. Luke, have you ever written such an IDL file before? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Tuesday, June 24, 2008 4:22 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] [Fwd: short course] PS> I mean the fiber length resulting from a given ROI. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:03 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] [Fwd: short course] Dear Matt, I'm not sure if DtiSudio can provide a histogram of fiber length. It should be possible to extract such info from the stored tract file using IDL or Matlab codes. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Monday, June 23, 2008 10:42 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [Fwd: short course] Hi all, ??????????????? How do I get an a measure of the length of each fiber?? I'd like to do estimate the distribution of fiber lengths in some tracking that I'm doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine ________________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From hjiang at jhmi.edu Tue Jun 24 08:23:57 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Tue, 24 Jun 2008 08:23:57 -0400 Subject: [Mristudio-users] [Fwd: short course] Message-ID: <4860AF1D02000063000137F8@cis27.hosts.jhmi.edu> hi, after fiber tracking, clicking "fiber statistics" button, you can find the fiber length in the pop-up windows. hangyi >>> "Hoptman, Matthew" 06/24/08 4:31 AM >>> That would be great! -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:30 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Cc: 'Hua KG' Subject: Re: [Mristudio-users] [Fwd: short course] I have to confirm Hangyi, but I believe a converter that can read a tract file, read the length of all stored tracts, and save the length of each tract, is needed. Luke, have you ever written such an IDL file before? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Tuesday, June 24, 2008 4:22 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] [Fwd: short course] PS> I mean the fiber length resulting from a given ROI. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:03 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] [Fwd: short course] Dear Matt, I'm not sure if DtiSudio can provide a histogram of fiber length. It should be possible to extract such info from the stored tract file using IDL or Matlab codes. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Monday, June 23, 2008 10:42 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [Fwd: short course] Hi all, How do I get an a measure of the length of each fiber? I'd like to do estimate the distribution of fiber lengths in some tracking that I'm doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine ________________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From Hoptman at NKI.RFMH.ORG Tue Jun 24 08:37:50 2008 From: Hoptman at NKI.RFMH.ORG (Hoptman, Matthew) Date: Tue, 24 Jun 2008 08:37:50 -0400 Subject: [Mristudio-users] [Fwd: short course] In-Reply-To: <4860AF1D02000063000137F8@cis27.hosts.jhmi.edu> References: <4860AF1D02000063000137F8@cis27.hosts.jhmi.edu> Message-ID: <2586A1048152BE4D861E64A98700AD420110394C@nki-mail.NKI.rfmh.org> Yes, but isn't that the mean fiber length? I'd like the length for each fiber. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hangyi Jiang Sent: Tuesday, June 24, 2008 8:24 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] [Fwd: short course] hi, after fiber tracking, clicking "fiber statistics" button, you can find the fiber length in the pop-up windows. hangyi >>> "Hoptman, Matthew" 06/24/08 4:31 AM >>> That would be great! -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:30 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Cc: 'Hua KG' Subject: Re: [Mristudio-users] [Fwd: short course] I have to confirm Hangyi, but I believe a converter that can read a tract file, read the length of all stored tracts, and save the length of each tract, is needed. Luke, have you ever written such an IDL file before? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Tuesday, June 24, 2008 4:22 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] [Fwd: short course] PS> I mean the fiber length resulting from a given ROI. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:03 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] [Fwd: short course] Dear Matt, I'm not sure if DtiSudio can provide a histogram of fiber length. It should be possible to extract such info from the stored tract file using IDL or Matlab codes. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Monday, June 23, 2008 10:42 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [Fwd: short course] Hi all, How do I get an a measure of the length of each fiber? I'd like to do estimate the distribution of fiber lengths in some tracking that I'm doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine ________________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From hjiang at jhmi.edu Tue Jun 24 08:49:04 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Tue, 24 Jun 2008 08:49:04 -0400 Subject: [Mristudio-users] [Fwd: short course] Message-ID: <4860B5000200006300013801@cis27.hosts.jhmi.edu> I see, you want a histogram of a group of fibers. please visit the website-FAQ, where you can find the fiber data file format; then you can read the fiber files, and get all infomation you needed. regards, hangyi >>> "Hoptman, Matthew" 06/24/08 8:37 AM >>> Yes, but isn't that the mean fiber length? I'd like the length for each fiber. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hangyi Jiang Sent: Tuesday, June 24, 2008 8:24 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] [Fwd: short course] hi, after fiber tracking, clicking "fiber statistics" button, you can find the fiber length in the pop-up windows. hangyi >>> "Hoptman, Matthew" 06/24/08 4:31 AM >>> That would be great! -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:30 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Cc: 'Hua KG' Subject: Re: [Mristudio-users] [Fwd: short course] I have to confirm Hangyi, but I believe a converter that can read a tract file, read the length of all stored tracts, and save the length of each tract, is needed. Luke, have you ever written such an IDL file before? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Tuesday, June 24, 2008 4:22 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] [Fwd: short course] PS> I mean the fiber length resulting from a given ROI. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:03 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] [Fwd: short course] Dear Matt, I'm not sure if DtiSudio can provide a histogram of fiber length. It should be possible to extract such info from the stored tract file using IDL or Matlab codes. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Monday, June 23, 2008 10:42 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [Fwd: short course] Hi all, How do I get an a measure of the length of each fiber? I'd like to do estimate the distribution of fiber lengths in some tracking that I'm doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine ________________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From Hoptman at NKI.RFMH.ORG Tue Jun 24 08:49:53 2008 From: Hoptman at NKI.RFMH.ORG (Hoptman, Matthew) Date: Tue, 24 Jun 2008 08:49:53 -0400 Subject: [Mristudio-users] [Fwd: short course] In-Reply-To: <4860B5000200006300013801@cis27.hosts.jhmi.edu> References: <4860B5000200006300013801@cis27.hosts.jhmi.edu> Message-ID: <2586A1048152BE4D861E64A98700AD420110394E@nki-mail.NKI.rfmh.org> Thanks!!! -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hangyi Jiang Sent: Tuesday, June 24, 2008 8:49 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] [Fwd: short course] I see, you want a histogram of a group of fibers. please visit the website-FAQ, where you can find the fiber data file format; then you can read the fiber files, and get all infomation you needed. regards, hangyi >>> "Hoptman, Matthew" 06/24/08 8:37 AM >>> Yes, but isn't that the mean fiber length? I'd like the length for each fiber. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hangyi Jiang Sent: Tuesday, June 24, 2008 8:24 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] [Fwd: short course] hi, after fiber tracking, clicking "fiber statistics" button, you can find the fiber length in the pop-up windows. hangyi >>> "Hoptman, Matthew" 06/24/08 4:31 AM >>> That would be great! -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:30 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Cc: 'Hua KG' Subject: Re: [Mristudio-users] [Fwd: short course] I have to confirm Hangyi, but I believe a converter that can read a tract file, read the length of all stored tracts, and save the length of each tract, is needed. Luke, have you ever written such an IDL file before? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Tuesday, June 24, 2008 4:22 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] [Fwd: short course] PS> I mean the fiber length resulting from a given ROI. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:03 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] [Fwd: short course] Dear Matt, I'm not sure if DtiSudio can provide a histogram of fiber length. It should be possible to extract such info from the stored tract file using IDL or Matlab codes. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Monday, June 23, 2008 10:42 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [Fwd: short course] Hi all, How do I get an a measure of the length of each fiber? I'd like to do estimate the distribution of fiber lengths in some tracking that I'm doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine ________________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From sjacobson at spokaneadvancedimaging.com Wed Jun 25 11:57:12 2008 From: sjacobson at spokaneadvancedimaging.com (sjacobson at spokaneadvancedimaging.com) Date: Wed, 25 Jun 2008 08:57:12 -0700 Subject: [Mristudio-users] question Message-ID: <20080625085712.e0f15dac35c4bf88aea872454247a5ef.cefdd42663.wbe@email.secureserver.net> An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080625/543d0783/attachment.html From llanyon at eyecarecentre.org Wed Jun 25 13:58:22 2008 From: llanyon at eyecarecentre.org (Linda Lanyon) Date: Wed, 25 Jun 2008 10:58:22 -0700 Subject: [Mristudio-users] left-right flipping In-Reply-To: <168807F472574ED6826206595719F569@SusumuThinkPad> References: <5CED06590F03DD459B340C608D68A85225CFF3124F@pc-vm-slserver.supportlink.ca> <168807F472574ED6826206595719F569@SusumuThinkPad> Message-ID: <001501c8d6ed$0fa4f040$54b75289@DC2NY2B1> Hi Susumu Thanks so much for your very helpful reply! Just to clarify, at #2 do you mean that a narrow section of the path might be too narrow for the fibers to significantly influence the overall diffusion in the voxel, so the tensor is not appropriately anisotropic, the FA value drops and tractography stops at that point? Best wishes Linda -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Monday, June 23, 2008 11:21 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] left-right flipping Hi Linda, Please note that DtiStudio follows the Radiological convention like all the scanners do; the right side of the image in axial and coronal slices are the patient's left. So far we haven't noticed any situations in which right-left is flipped in DtiStudio. If you want to confirm, you can put a syringe or a water bottle to one side of the brain during a scan. You need to be careful if your data went through other software programs. Many Neurology-oriented programs follow the Neurology convention. Default Analyze format also is Neurology convention. If the brain orientation is flipped, usually you can tell it immediately because the axial slice becomes inverted. As for the right-left, we are also one of them who published the right-left asymmetry based on tractography. However, we have to be careful. We know that the total white matter volume is almost the same between the right and the left hemisphere. Most white matter tracts should have the same sizes. The reason why tractography gives us the asymmetry results could be complicated; 1) There are regions with lower FA in one of the hemisphere. 2) The tract shape and size is more convoluted in one of the hemisphere (the size of the tractography is heavily influenced by the narrowest section of the entire path). 3) The SNR (or signal intensity) is inhomogeneous due to the nature of the RF coil. Please note that I've never seen that anybody (including myself) tested by scanning the same person twice; once with face up and once with face down, to reject the #3. Hope this helps. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of llanyon Sent: Monday, June 23, 2008 2:33 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] left-right flipping Hi everyone We are looking at the arcuate fasciculus (AF) with DTI Studio (version 2.40). Just about all the published literature says that the AF is larger in the left hemisphere than the right. However, we are seeing the reverse pattern, and are concerned about a possible flip of the data in the x direction. We have acquired our data on a 3T Philips Achieva Scanner. I have check L-R laterality using lesion patient data and there does not seem to be a flip, but I wondered whether anyone else has had any issues like this? Thanks Linda Lanyon ---------------------------------------------------------------------------- ------------------------- Linda Lanyon Post-doctoral Research Fellow, Michael Smith Foundation for Health Research University of British Columbia Human Vision & Eye Movement Laboratory Vancouver General Hospital Eye Care Centre 3rd Floor Research Labs - Rm 365 2550 Willow St, Vancouver, B.C., Canada Phone: +1-604-875-4111 x 69003 Fax: +1 604-875-4663 email: llanyon at eyecarecentre.org web: http://www.neuroophthalmology.ca/UBCNeuroOp/JBarton/labstaff/Linda.htm Director, Society for Canadian Women in Science and Technology: www.scwist.ca ---------------------------------------------------------------------------- ------------------------- The content of this e-mail, including any files attached, is confidential and may be privileged. Any unauthorized copying or distribution is strictly prohibited. If you receive this e-mail in error, please contact the sender immediately and delete this e-mail. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users The content of this e-mail, including any files attached, is confidential and may be privileged. Any unauthorized copying or distribution is strictly prohibited. If you receive this e-mail in error, please contact the sender immediately and delete this e-mail. From susumu at mri.jhu.edu Wed Jun 25 16:41:49 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 25 Jun 2008 16:41:49 -0400 Subject: [Mristudio-users] left-right flipping In-Reply-To: <001501c8d6ed$0fa4f040$54b75289@DC2NY2B1> References: <5CED06590F03DD459B340C608D68A85225CFF3124F@pc-vm-slserver.supportlink.ca> <168807F472574ED6826206595719F569@SusumuThinkPad> <001501c8d6ed$0fa4f040$54b75289@DC2NY2B1> Message-ID: Suppose you have a straight tract with 5-pixel diameter and 50-pixel long. If you do fiber tracking, you get 5 x 50-pixel tract. However, if there is one location where the diameter is only 3 pixel, it is likely that the tractography gives you 3 x 50 for the entire length. Does it make sense? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Linda Lanyon Sent: Wednesday, June 25, 2008 1:58 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] left-right flipping Hi Susumu Thanks so much for your very helpful reply! Just to clarify, at #2 do you mean that a narrow section of the path might be too narrow for the fibers to significantly influence the overall diffusion in the voxel, so the tensor is not appropriately anisotropic, the FA value drops and tractography stops at that point? Best wishes Linda -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Monday, June 23, 2008 11:21 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] left-right flipping Hi Linda, Please note that DtiStudio follows the Radiological convention like all the scanners do; the right side of the image in axial and coronal slices are the patient's left. So far we haven't noticed any situations in which right-left is flipped in DtiStudio. If you want to confirm, you can put a syringe or a water bottle to one side of the brain during a scan. You need to be careful if your data went through other software programs. Many Neurology-oriented programs follow the Neurology convention. Default Analyze format also is Neurology convention. If the brain orientation is flipped, usually you can tell it immediately because the axial slice becomes inverted. As for the right-left, we are also one of them who published the right-left asymmetry based on tractography. However, we have to be careful. We know that the total white matter volume is almost the same between the right and the left hemisphere. Most white matter tracts should have the same sizes. The reason why tractography gives us the asymmetry results could be complicated; 1) There are regions with lower FA in one of the hemisphere. 2) The tract shape and size is more convoluted in one of the hemisphere (the size of the tractography is heavily influenced by the narrowest section of the entire path). 3) The SNR (or signal intensity) is inhomogeneous due to the nature of the RF coil. Please note that I've never seen that anybody (including myself) tested by scanning the same person twice; once with face up and once with face down, to reject the #3. Hope this helps. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of llanyon Sent: Monday, June 23, 2008 2:33 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] left-right flipping Hi everyone We are looking at the arcuate fasciculus (AF) with DTI Studio (version 2.40). Just about all the published literature says that the AF is larger in the left hemisphere than the right. However, we are seeing the reverse pattern, and are concerned about a possible flip of the data in the x direction. We have acquired our data on a 3T Philips Achieva Scanner. I have check L-R laterality using lesion patient data and there does not seem to be a flip, but I wondered whether anyone else has had any issues like this? Thanks Linda Lanyon ---------------------------------------------------------------------------- ------------------------- Linda Lanyon Post-doctoral Research Fellow, Michael Smith Foundation for Health Research University of British Columbia Human Vision & Eye Movement Laboratory Vancouver General Hospital Eye Care Centre 3rd Floor Research Labs - Rm 365 2550 Willow St, Vancouver, B.C., Canada Phone: +1-604-875-4111 x 69003 Fax: +1 604-875-4663 email: llanyon at eyecarecentre.org web: http://www.neuroophthalmology.ca/UBCNeuroOp/JBarton/labstaff/Linda.htm Director, Society for Canadian Women in Science and Technology: www.scwist.ca ---------------------------------------------------------------------------- ------------------------- The content of this e-mail, including any files attached, is confidential and may be privileged. Any unauthorized copying or distribution is strictly prohibited. If you receive this e-mail in error, please contact the sender immediately and delete this e-mail. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users The content of this e-mail, including any files attached, is confidential and may be privileged. Any unauthorized copying or distribution is strictly prohibited. If you receive this e-mail in error, please contact the sender immediately and delete this e-mail. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From choisj70 at gmail.com Wed Jun 25 17:01:57 2008 From: choisj70 at gmail.com (Seongjin) Date: Wed, 25 Jun 2008 17:01:57 -0400 Subject: [Mristudio-users] Need help! Message-ID: I tried loading a set of DTI images acquired with philips achieva system. Total 320 slices (40 slices x 8: 8 = 6 gradients + 0 gradient + overall). I believe that I typed in correct image dimensions and parameters. And I got this result. (Note attached screen shot.) Any one know how to solve this problem? SJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080625/f17bec18/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: 2008-06-27.jpg Type: image/jpeg Size: 22285 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080625/f17bec18/attachment-0001.jpg From Shmuel.Miron at sheba.health.gov.il Thu Jun 26 07:28:07 2008 From: Shmuel.Miron at sheba.health.gov.il (Shmuel Miron Dr) Date: Thu, 26 Jun 2008 14:28:07 +0300 Subject: [Mristudio-users] indedxes and parameters In-Reply-To: Message-ID: Dear LIST Dear Prof Mori When a DTI map is created by DTI studio, we get automatically the following parameters, that we do not use Spherical index -Cs Planar index - Cp Linear Index - Cl Anisotropy - VR Anisotropy - RA Could you please indicate a reference paper that beside the mathematical formula explains these entities and maybe what they signify ? Thanks Dr. Shmuel Miron Multiple Sclerosis Center Sheba Medical - Israel Phone 972-3-5305962 Mobile 972-52-2958334 ************************************************************************** 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 ***This email was scanned against viruses, vandals and malicious content*** ***Powered By Trend Micro - InterScan Messaging Security Suite1*** From susumu at mri.jhu.edu Thu Jun 26 17:49:54 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 26 Jun 2008 17:49:54 -0400 Subject: [Mristudio-users] Need help! In-Reply-To: References: Message-ID: <11D22D0ACAFD40E28C9288624962D4E3@SusumuThinkPad> It seems you are trying to load a *.REC file? If so, please try to load using the "Philips REC" format. Also, x and y dimension you typed in seem to have a small error. Please check. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, June 25, 2008 5:02 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Need help! I tried loading a set of DTI images acquired with philips achieva system. Total 320 slices (40 slices x 8: 8 = 6 gradients + 0 gradient + overall). I believe that I typed in correct image dimensions and parameters. And I got this result. (Note attached screen shot.) Any one know how to solve this problem? SJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080626/0f52cb88/attachment.html From susumu at mri.jhu.edu Thu Jun 26 17:59:10 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 26 Jun 2008 17:59:10 -0400 Subject: [Mristudio-users] indedxes and parameters In-Reply-To: References: Message-ID: <298A2FAC53A945EA9A7E07BAF3AF2962@SusumuThinkPad> I believe you can find VR and RA in Pierpaoli et al, Magn. Reson. Med. 1996, 36, 893. For CP, CL, and CS, they are called Westin's indices. Please refer to Westin CF's paper. I don't have the exact reference now (I'm out of country now), but you can find relevant information in our paper, Zhang et al, Magn Reson. Med, 55, 439, 2006 -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Shmuel Miron Dr Sent: Thursday, June 26, 2008 7:28 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: [Mristudio-users] indedxes and parameters Dear LIST Dear Prof Mori When a DTI map is created by DTI studio, we get automatically the following parameters, that we do not use Spherical index -Cs Planar index - Cp Linear Index - Cl Anisotropy - VR Anisotropy - RA Could you please indicate a reference paper that beside the mathematical formula explains these entities and maybe what they signify ? Thanks Dr. Shmuel Miron Multiple Sclerosis Center Sheba Medical - Israel Phone 972-3-5305962 Mobile 972-52-2958334 ************************************************************************** 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 ***This email was scanned against viruses, vandals and malicious content*** ***Powered By Trend Micro - InterScan Messaging Security Suite1*** _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From nshu at nlpr.ia.ac.cn Fri Jun 27 00:54:41 2008 From: nshu at nlpr.ia.ac.cn (nshu) Date: Fri, 27 Jun 2008 12:54:41 +0800 Subject: [Mristudio-users] About DTIStudio 2.5 References: <11D22D0ACAFD40E28C9288624962D4E3@SusumuThinkPad> Message-ID: <200806271254414218815@nlpr.ia.ac.cn> Hi, Prof. Susumu Mori, I heard about DTIStudio 2.5 from a paper, but I can not find where to download it. I am always a fan of DTIStudio, and I want to know what is the difference in the new version. Could you kindly supply me the new version of DTIStudio? And I think it would be much helpful for my research. Thank you in advance! Best, Shu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080627/14ccd456/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: fox.gif Type: image/gif Size: 9519 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080627/14ccd456/attachment-0001.gif From susumu at mri.jhu.edu Fri Jun 27 01:10:29 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 27 Jun 2008 01:10:29 -0400 Subject: [Mristudio-users] About DTIStudio 2.5 In-Reply-To: <200806271254414218815@nlpr.ia.ac.cn> References: <11D22D0ACAFD40E28C9288624962D4E3@SusumuThinkPad> <200806271254414218815@nlpr.ia.ac.cn> Message-ID: <772818221D054749973F5359A0890A32@SusumuThinkPad> Dear Shu, We are about to release Version 3, which is in a final testing (well, it has been in final testing for half a year now,,,). If you want to test the beta version, please let us know. The manual is not ready but most of the new functions should be self-explanatory. One important new function is "outlier rejection". It has pixel-by-pixel and image-by-image rejection mode. The pixel mode takes a long time for computation and we haven't tested it. The image mode seems to work with a threshold value of 2-4%. The result can be seen by a big red cross in the image quality checking window. These results could be used as a suggestion for visual inspection (you can manually modify the result). We haven't done rigorous testing but most of the time, it seems working to detect obvious image corruption. I would appreciate your feedback. Thanks, Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of nshu Sent: Friday, June 27, 2008 12:55 AM To: DTI Studio, ROI Editor, Landmark Subject: [Mristudio-users] About DTIStudio 2.5 Hi, Prof. Susumu Mori, I heard about DTIStudio 2.5 from a paper, but I can not find where to download it. I am always a fan of DTIStudio, and I want to know what is the difference in the new version. Could you kindly supply me the new version of DTIStudio? And I think it would be much helpful for my research. Thank you in advance! Best, Shu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080627/c7c83c89/attachment.html From choisj70 at gmail.com Fri Jun 27 08:51:14 2008 From: choisj70 at gmail.com (Seongjin) Date: Fri, 27 Jun 2008 08:51:14 -0400 Subject: [Mristudio-users] About DTIStudio 2.5 In-Reply-To: <772818221D054749973F5359A0890A32@SusumuThinkPad> References: <11D22D0ACAFD40E28C9288624962D4E3@SusumuThinkPad> <200806271254414218815@nlpr.ia.ac.cn> <772818221D054749973F5359A0890A32@SusumuThinkPad> Message-ID: Dear Susumu, I am waiting for version 3. Could you let us know when will be the release time for version 3? Seongjin On Fri, Jun 27, 2008 at 1:10 AM, susumu wrote: > Dear Shu, > > > > We are about to release Version 3, which is in a final testing (well, it > has been in final testing for half a year now,,,). If you want to test the > beta version, please let us know. > > The manual is not ready but most of the new functions should be > self-explanatory. > > > > One important new function is "outlier rejection". It has pixel-by-pixel > and image-by-image rejection mode. The pixel mode takes a long time for > computation and we haven't tested it. The image mode seems to work with a > threshold value of 2-4%. The result can be seen by a big red cross in the > image quality checking window. These results could be used as a suggestion > for visual inspection (you can manually modify the result). We haven't done > rigorous testing but most of the time, it seems working to detect obvious > image corruption. I would appreciate your feedback. > > > > Thanks, > > > > Susumu > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *nshu > *Sent:* Friday, June 27, 2008 12:55 AM > *To:* DTI Studio, ROI Editor, Landmark > *Subject:* [Mristudio-users] About DTIStudio 2.5 > > > > Hi, Prof. Susumu Mori, > > > > I heard about DTIStudio 2.5 from a paper, but I can not find where to > download it. > > > > I am always a fan of DTIStudio, and I want to know what is the difference > in the new version. > > > > Could you kindly supply me the new version of DTIStudio? > > > > And I think it would be much helpful for my research. > > > > Thank you in advance! > > > > Best, > > Shu > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080627/345264a6/attachment.html From choisj70 at gmail.com Fri Jun 27 09:10:57 2008 From: choisj70 at gmail.com (Seongjin) Date: Fri, 27 Jun 2008 09:10:57 -0400 Subject: [Mristudio-users] Philips Achieva system gradient table Message-ID: Dear all, I am a Philips Achieva system user and recently started using DTI studio. A given gradient table for DTI_low is as follows: 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000 -0.7044 -0.0881 -0.7044 0.7044 0.7044 0.0881 0.0881 0.7044 0.7044 0.0000 0.0000 0.0000 So I use gradient table in DTI with following table. Somehow, b0 is located at the last. 0:1.0000, 0.0000, 0.0000 1:0.0000, 1.0000, 0.0000 2:0.0000, 0.0000, 1.0000 3:-0.7044, -0.0881, -0.7044 4:0.7044, 0.7044, 0.0881 5:0.0881, 0.7044, 0.7044 6:0.0000, 0.0000, 0.0000 Philips system DTI output image start with b0 image. I wonder if I am using the right table or in the right order for gradients. Best, Seongjin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080627/37e1399f/attachment.html From llanyon at eyecarecentre.org Fri Jun 27 11:55:06 2008 From: llanyon at eyecarecentre.org (llanyon) Date: Fri, 27 Jun 2008 08:55:06 -0700 Subject: [Mristudio-users] Philips Achieva system gradient table In-Reply-To: References: Message-ID: <5CED06590F03DD459B340C608D68A85225CFF3126E@pc-vm-slserver.supportlink.ca> Hi Seongjin You need to make sure the B0 line in the gradients table is in the same position as it is in the data - just move the line of zeros up to position zero and shift the rest down. cheers Linda ----------------------------------------------------------------------------------------------------- Linda Lanyon Post-doctoral Research Fellow, Michael Smith Foundation for Health Research University of British Columbia Human Vision & Eye Movement Laboratory Vancouver General Hospital Eye Care Centre 3rd Floor Research Labs - Rm 365 2550 Willow St, Vancouver, B.C., Canada Phone: +1-604-875-4111 x 69003 Fax: +1 604-875-4663 email: llanyon at eyecarecentre.org web: http://www.neuroophthalmology.ca/UBCNeuroOp/JBarton/labstaff/Linda.htm Director, Society for Canadian Women in Science and Technology: www.scwist.ca ----------------------------------------------------------------------------------------------------- ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] [choisj70 at gmail.com] Sent: 27 June 2008 06:10 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Philips Achieva system gradient table Dear all, I am a Philips Achieva system user and recently started using DTI studio. A given gradient table for DTI_low is as follows: 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000 -0.7044 -0.0881 -0.7044 0.7044 0.7044 0.0881 0.0881 0.7044 0.7044 0.0000 0.0000 0.0000 So I use gradient table in DTI with following table. Somehow, b0 is located at the last. 0:1.0000, 0.0000, 0.0000 1:0.0000, 1.0000, 0.0000 2:0.0000, 0.0000, 1.0000 3:-0.7044, -0.0881, -0.7044 4:0.7044, 0.7044, 0.0881 5:0.0881, 0.7044, 0.7044 6:0.0000, 0.0000, 0.0000 Philips system DTI output image start with b0 image. I wonder if I am using the right table or in the right order for gradients. Best, Seongjin ________________________________ The content of this e-mail, including any files attached, is confidential and may be privileged. Any unauthorized copying or distribution is strictly prohibited. If you receive this e-mail in error, please contact the sender immediately and delete this e-mail. The content of this e-mail, including any files attached, is confidential and may be privileged. Any unauthorized copying or distribution is strictly prohibited. If you receive this e-mail in error, please contact the sender immediately and delete this e-mail. From choisj70 at gmail.com Fri Jun 27 12:03:47 2008 From: choisj70 at gmail.com (Seongjin) Date: Fri, 27 Jun 2008 12:03:47 -0400 Subject: [Mristudio-users] Philips Achieva system gradient table In-Reply-To: <5CED06590F03DD459B340C608D68A85225CFF3126E@pc-vm-slserver.supportlink.ca> References: <5CED06590F03DD459B340C608D68A85225CFF3126E@pc-vm-slserver.supportlink.ca> Message-ID: Thank a lot. Linda. On Fri, Jun 27, 2008 at 11:55 AM, llanyon wrote: > Hi Seongjin > > You need to make sure the B0 line in the gradients table is in the same > position as it is in the data - just move the line of zeros up to position > zero and shift the rest down. > > cheers > Linda > > ----------------------------------------------------------------------------------------------------- > Linda Lanyon > Post-doctoral Research Fellow, Michael Smith Foundation for Health Research > University of British Columbia > Human Vision & Eye Movement Laboratory > Vancouver General Hospital Eye Care Centre > 3rd Floor Research Labs - Rm 365 > 2550 Willow St, Vancouver, B.C., Canada > Phone: +1-604-875-4111 x 69003 > Fax: +1 604-875-4663 > email: llanyon at eyecarecentre.org > web: > http://www.neuroophthalmology.ca/UBCNeuroOp/JBarton/labstaff/Linda.htm > Director, Society for Canadian Women in Science and Technology: > www.scwist.ca > > ----------------------------------------------------------------------------------------------------- > ________________________________________ > From: mristudio-users-bounces at mristudio.org [ > mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] [ > choisj70 at gmail.com] > Sent: 27 June 2008 06:10 > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: [Mristudio-users] Philips Achieva system gradient table > > Dear all, > > I am a Philips Achieva system user and recently started using DTI studio. > A given gradient table for DTI_low is as follows: > > 1.0000 0.0000 0.0000 > 0.0000 1.0000 0.0000 > 0.0000 0.0000 1.0000 > -0.7044 -0.0881 -0.7044 > 0.7044 0.7044 0.0881 > 0.0881 0.7044 0.7044 > 0.0000 0.0000 0.0000 > > So I use gradient table in DTI with following table. > Somehow, b0 is located at the last. > > 0:1.0000, 0.0000, 0.0000 > 1:0.0000, 1.0000, 0.0000 > 2:0.0000, 0.0000, 1.0000 > 3:-0.7044, -0.0881, -0.7044 > 4:0.7044, 0.7044, 0.0881 > 5:0.0881, 0.7044, 0.7044 > 6:0.0000, 0.0000, 0.0000 > > Philips system DTI output image start with b0 image. > I wonder if I am using the right table or in the right order for gradients. > > Best, > > Seongjin > > ________________________________ > The content of this e-mail, including any files attached, is confidential > and may be privileged. Any unauthorized copying or distribution is strictly > prohibited. If you receive this e-mail in error, please contact the sender > immediately and delete this e-mail. > > The content of this e-mail, including any files attached, is confidential > and may be privileged. Any unauthorized copying or distribution is strictly > prohibited. If you receive this e-mail in error, please contact the sender > immediately and delete this e-mail. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080627/8a8cf992/attachment.html From qianglf at xmzsh.com Fri Jul 4 04:31:14 2008 From: qianglf at xmzsh.com (=?gb2312?B?1PjHvw==?=) Date: Fri, 04 Jul 2008 16:31:14 +0800 Subject: [Mristudio-users] =?gb2312?b?ILTwuLQ6ICBbRndkOiBzaG9ydCBjb3Vyc2Vd?= References: <2586A1048152BE4D861E64A98700AD4266CE2F@nki-mail.NKI.rfmh.org> <6u9t96$36c25v@ipex1.johnshopkins.edu> <2586A1048152BE4D861E64A98700AD4201103949@nki-mail.NKI.rfmh.org> Message-ID: Dear madam or sir: I have a question that I don't know how to get the quatitaive of a fiber and the size of any fiber. wish your answer. thank you! ________________________________ From: mristudio-users-bounces at mristudio.org ?? Hoptman, Matthew Sent: 2008-6-24 (???) 16:19 To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] [Fwd: short course] Hi again, I guess I'm asking a simpler question. Is there a way to get the length of each fiber? I can do the histogram part myself. --Matt -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Tuesday, June 24, 2008 4:03 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] [Fwd: short course] Dear Matt, I'm not sure if DtiSudio can provide a histogram of fiber length. It should be possible to extract such info from the stored tract file using IDL or Matlab codes. Susumu ________________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hoptman, Matthew Sent: Monday, June 23, 2008 10:42 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] [Fwd: short course] Hi all, How do I get an a measure of the length of each fiber? I'd like to do estimate the distribution of fiber lengths in some tracking that I'm doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine ________________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 6048 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080704/d7314193/attachment.bin From JLaMarche at tams.com Fri Jul 4 07:01:44 2008 From: JLaMarche at tams.com (John LaMarche) Date: Fri, 04 Jul 2008 04:01:44 -0700 Subject: [Mristudio-users] John LaMarche is out of the office. Message-ID: I will be out of the office starting 07/03/2008 and will not return until 07/13/2008. I will respond to your message when I return. From graeme.schwindt at gmail.com Sun Jul 6 14:44:21 2008 From: graeme.schwindt at gmail.com (Graeme Schwindt) Date: Sun, 06 Jul 2008 12:44:21 -0600 Subject: [Mristudio-users] Results using analyze format in DTIStudio Message-ID: <8640b26c0807061144p6e4102f6j53c92c389aec4efc@mail.gmail.com> Hello, At the Toronto workshop, it was mentioned that loading analyze format images into dtistudio is not recommended as the images are loaded in flipped, and so the gradient tables will not apply properly, as I understood. We have analyzed a couple of subjects from two separate datasets using both the raw dicoms in dtistudio (following AIR), but also with some analyze format images that have been preprocessed in FSL (eddy-current correction). Surprisingly, the FA maps and colour maps are qualitatively very similar between the two methods, which is counterintuitive given the improper mapping between the gradient table and orientation of the analyze imgs. Also, the FA values are generally *higher* by 0.2 or so in the analyze version of the analysis. Is it possible that the analyze format is actually being read properly though its display is wrong? Any thoughts on the validity of using analyze format would be appreciated. Thanks, Graeme -- Graeme C. Schwindt, HBSc MD/PhD Student University of Toronto graeme.schwindt at gmail.com 416.546.5453 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080706/9b4620a8/attachment-0001.html From hjiang at jhmi.edu Mon Jul 7 09:53:21 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Mon, 07 Jul 2008 09:53:21 -0400 Subject: [Mristudio-users] [Fwd: short course] Message-ID: <4871E7920200006300013F0B@cis27.hosts.jhmi.edu> hi, matt, please save the fibers in a file and visit "MriStudio.org" for the fiber file format, so you can write your code to get the length of each fiber. thanks, hangyi >>> "Hoptman, Matthew" 06/23/08 10:42 AM >>> Hi all, How do I get an a measure of the length of each fiber? I'd like to do estimate the distribution of fiber lengths in some tracking that I'm doing. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. From susumu at mri.jhu.edu Mon Jul 7 21:24:21 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 07 Jul 2008 21:24:21 -0400 Subject: [Mristudio-users] Results using analyze format in DTIStudio In-Reply-To: <8640b26c0807061144p6e4102f6j53c92c389aec4efc@mail.gmail.com> References: <8640b26c0807061144p6e4102f6j53c92c389aec4efc@mail.gmail.com> Message-ID: <4E0061A7F6514FF6B965B9A81149237B@SusumuThinkPad> Hi Graeme, I believe FA, ADC, and color maps are insensitive to right-left, front-back, and up-down flip. It becomes in issue when you do fiber tracking. DtiStudio support the Analyze format to save 3D images after tensor calculation. If you save data as Analyze and read as Analyze, the orientation should be correct, but if it is saved as Analyze and read as Raw, you'd find that the axial image is upside-down, due to Neurology - Radiology conventions. In DtiStudio, we do not support tensor calculation of DWIs in the Analyze format. Also, it is difficult to confirm what would happen if DtiStudio processes data partially processed by other software programs because it is difficult for us to test many combinations of data processing by multiple programs. I would suggest to stick to single software for DWI - tensor calculation. It is indeed interesting that you saw 0.2 FA difference by going through the Analyze format, but again, it difficult for us to follow the results that were not processed by DtiStudio for the entire processing. If you experience 0.2 difference with and without AIR in DtiStudio, we would definitely look into the issue. If you mean difference is between; 1) raw DWI -> DtiStudio -> AIR in DtiStudio -> FA 2) raw DWI -> FSL (eddy correction) -> Analyze -> DtiStudio -> FA We first need to know 1) how did you read Analyze into DtiStudio? 2) Have you compared raw DWIs and Analyze (after FSL eddy correction) DWIs? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Graeme Schwindt Sent: Sunday, July 06, 2008 2:44 PM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] Results using analyze format in DTIStudio Hello, At the Toronto workshop, it was mentioned that loading analyze format images into dtistudio is not recommended as the images are loaded in flipped, and so the gradient tables will not apply properly, as I understood. We have analyzed a couple of subjects from two separate datasets using both the raw dicoms in dtistudio (following AIR), but also with some analyze format images that have been preprocessed in FSL (eddy-current correction). Surprisingly, the FA maps and colour maps are qualitatively very similar between the two methods, which is counterintuitive given the improper mapping between the gradient table and orientation of the analyze imgs. Also, the FA values are generally higher by 0.2 or so in the analyze version of the analysis. Is it possible that the analyze format is actually being read properly though its display is wrong? Any thoughts on the validity of using analyze format would be appreciated. Thanks, Graeme -- Graeme C. Schwindt, HBSc MD/PhD Student University of Toronto graeme.schwindt at gmail.com 416.546.5453 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080707/7d4c5d23/attachment.html From sjacobson at spokaneadvancedimaging.com Tue Jul 8 00:27:43 2008 From: sjacobson at spokaneadvancedimaging.com (sjacobson at spokaneadvancedimaging.com) Date: Mon, 07 Jul 2008 21:27:43 -0700 Subject: [Mristudio-users] Results using analyze format in DTIStudio Message-ID: <20080707212743.e0f15dac35c4bf88aea872454247a5ef.df55d535e1.wbe@email.secureserver.net> An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080707/fd0dc6ed/attachment-0001.html From icee41 at gmail.com Wed Jul 9 12:33:45 2008 From: icee41 at gmail.com (Tapan Jani) Date: Wed, 09 Jul 2008 11:33:45 -0500 Subject: [Mristudio-users] New to the program Message-ID: <43f2b0680807090933l61d03cf2s97ffcd77c12aa880@mail.gmail.com> Hello all, I've tried sending a couple of e-mails to the DtiStudio support staff, but they have yet to get back to me. While waiting for their reply, I was wondering if anyone in this newsletter would be able to answer my questions. Below, I have copy-pasted both my e-mails. I apologize for the length, I got a little carried away in my curiosity. If anyone can help, it would be greatly appreciated. Thank you very much, Tapan Jani tjani2 at uic.edu ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dear Support Team, I am writing you in reference to your program DTI Studio. Let me begin by stating that I am very new to diffusion tensor imaging, and am trying to use your program as a stepping stone into that field of study. For the record, I am a research assistant in a lab that is registered on your website ( dtistudio.org) under the username slee56. I write to you with only a few hours of experience with the program under my belt. The manual which you posted alongside the software is helpful in knowing how to open files and view them. For the purposes of learning how the program works, I downloaded the data set 01_020729_31.rec. Initially, I was able to boot up the program and load the data set via file -> dtimapping. Using the gradient posted next to the data set on your demo data database, and leaving all other settings as they were, I was able to bring up the axial, sagittal, coronal, and 3-d views of the .rec file. Next, under the dtimap tab, I clicked "tensor, color map, etc." to come up with the different maps. Once this was completed, I was able to view the different maps, but this is where my problems began. As I stated earlier, I am very new to this field, and thus am at a loss when it comes to actually *interpreting the data*. For this reason, I am contacting you to ask whether you have some documentation on how to "read" all the various DTI maps that this program is capable of creating, along with a glossary which explains every term used in the program. For me to create maps and not know what I am looking at presents a problem that, hopefully, you can help me with. I have looked through the user manual that is on your webpage, and while it is very helpful in utilizing the program itself, it does not help me interpret the images. For example, I am completely unaware how to find within what area of the brain the diffusion is higher or lower than normal, or even know what normal is for that matter. Finally, I was wondering if you could tell me that after creating the "tensor, color maps etc," where I can view the data this calculates, and what those figures mean. Also, just as a side note, under the dtimap whenever I click any of the buttons under "calculation," 40% of the time it causes the program to severely stall and/or crash altogether. I really appreciate your help in this matter, and hope to soon become knowledgeable in this area with your aid. So if there is some documentation explaining every single in and out of what DTI images are, show, and help with, it would be incredibly useful to me. Thank you for your time, Tapan Jani Tjani2 at uic.edu ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dear Support Team, This is the second e-mail that I am writing to you, and not being sure whether or not my first e-mail reached you, I've attached it below. This e-mail, however, is in reference to converting DICOM images to REC images. I was able to follow the user manual to perform the actual conversion, however, when I load the newly created REC, I am unable to perform any of the mapping functions. Does anyone know why this is happening? Thank you for your time, I hope to hear from you soon in regards to this e-mail and the one attached below. Tapan Jani tjani2 at uic.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080709/662530a5/attachment.html From icee41 at gmail.com Wed Jul 9 13:32:49 2008 From: icee41 at gmail.com (Tapan Jani) Date: Wed, 09 Jul 2008 12:32:49 -0500 Subject: [Mristudio-users] New to the program In-Reply-To: <43f2b0680807090933l61d03cf2s97ffcd77c12aa880@mail.gmail.com> References: <43f2b0680807090933l61d03cf2s97ffcd77c12aa880@mail.gmail.com> Message-ID: <43f2b0680807091032i6e506dbfv61674b83eb09c59f@mail.gmail.com> Sorry one final question, I have Siemens data in DICOM. I read the user manual for how to convert it to an REC file, but don't know what to use for my gradient table. Does anyone know how to generate one? Thank you again! Tapan tjani2 at uic.edu On Wed, Jul 9, 2008 at 11:33 AM, Tapan Jani wrote: > Hello all, > > I've tried sending a couple of e-mails to the DtiStudio support staff, but > they have yet to get back to me. While waiting for their reply, I was > wondering if anyone in this newsletter would be able to answer my questions. > Below, I have copy-pasted both my e-mails. I apologize for the length, I got > a little carried away in my curiosity. > > If anyone can help, it would be greatly appreciated. > > Thank you very much, > Tapan Jani > > tjani2 at uic.edu > > > ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > Dear Support Team, > > I am writing you in reference to your program DTI Studio. Let me begin by > stating that I am very new to diffusion tensor imaging, and am trying to use > your program as a stepping stone into that field of study. For the record, I > am a research assistant in a lab that is registered on your website ( > dtistudio.org) under the username slee56. > > I write to you with only a few hours of experience with the program under > my belt. The manual which you posted alongside the software is helpful in > knowing how to open files and view them. For the purposes of learning how > the program works, I downloaded the data set 01_020729_31.rec. > Initially, I was able to boot up the program and load the data set via file > -> dtimapping. Using the gradient posted next to the data set on your demo > data database, and leaving all other settings as they were, I was able to > bring up the axial, sagittal, coronal, and 3-d views of the .rec file. Next, > under the dtimap tab, I clicked "tensor, color map, etc." to come up with > the different maps. Once this was completed, I was able to view the > different maps, but this is where my problems began. > > As I stated earlier, I am very new to this field, and thus am at a loss > when it comes to actually *interpreting the data*. > > For this reason, I am contacting you to ask whether you have some > documentation on how to "read" all the various DTI maps that this program is > capable of creating, along with a glossary which explains every term used in > the program. For me to create maps and not know what I am looking at > presents a problem that, hopefully, you can help me with. I have looked > through the user manual that is on your webpage, and while it is very > helpful in utilizing the program itself, it does not help me interpret the > images. For example, I am completely unaware how to find within what area of > the brain the diffusion is higher or lower than normal, or even know what > normal is for that matter. > > Finally, I was wondering if you could tell me that after creating the > "tensor, color maps etc," where I can view the data this calculates, and > what those figures mean. > > Also, just as a side note, under the dtimap whenever I click any of the > buttons under "calculation," 40% of the time it causes the program to > severely stall and/or crash altogether. > > I really appreciate your help in this matter, and hope to soon become > knowledgeable in this area with your aid. So if there is some documentation > explaining every single in and out of what DTI images are, show, and help > with, it would be incredibly useful to me. > > > > Thank you for your time, > > > > Tapan Jani > > > > Tjani2 at uic.edu > > > ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > Dear Support Team, > > This is the second e-mail that I am writing to you, and not being sure > whether or not my first e-mail reached you, I've attached it below. This > e-mail, however, is in reference to converting DICOM images to REC images. I > was able to follow the user manual to perform the actual conversion, > however, when I load the newly created REC, I am unable to perform any of > the mapping functions. Does anyone know why this is happening? > > Thank you for your time, I hope to hear from you soon in regards to this > e-mail and the one attached below. > > > Tapan Jani > > tjani2 at uic.edu > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080709/a05cbcad/attachment.html From Elizabeth.Finger at lhsc.on.ca Wed Jul 9 15:39:36 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Wed, 09 Jul 2008 15:39:36 -0400 Subject: [Mristudio-users] error when calculating tensor with double gradient table Message-ID: <4874DBB8020000A0000040C8@lhscgwiao.lhsc.on.ca> Hello- I have running into an error- the DTI Mapping program is crashing out, when attempting to do a tensor calculation with an updated gradient table from the AIR Matrix calcuation that uses two series. We have two separate series with 3 b0 images and 33 graidents with the same DTI parameters per subject. We have used AIR to align them together, and generated an updated gradient table. When we reload the two AIR series into the DTI Mapping window with the new gradient table from AIRMatrix output (table pasted below, now with 72 lines, starting w/ 0 and ending w/ 71), the data load correctly. However, when we attempt to run the tensor calculation with automatic outlier rejection, as soon as the calculation starts the program crashes out. If we use the original gradient table there is no problem. Also, if we use half of the updated gradient tables (either first half w/ numbers from 0 to 35, or the second half w/ original airmatrix numbers from 36-71, the tensor calculation works. Is there something else we can do to use the revised gradient table for both series and include both series in the tensor calculation? Thank you, Elizabeth Finger *** New Gradient Table *** 0: 0.000000, 0.000000, 0.000000 1: 0.000000, 0.000000, 0.000000 2: 0.000000, 0.000000, 0.000000 3: 0.999999, 0.000434, -0.000390 4: 0.313706, 0.949767, -0.000230 5: -0.072833, 0.636259, 0.767252 6: 0.875411, -0.479757, 0.061399 7: -0.199675, -0.555806, 0.809540 8: -0.615266, -0.363411, 0.700719 9: 0.684460, 0.371145, 0.627016 10: -0.565897, 0.821968, 0.063204 11: 0.901326, 0.406546, 0.148179 12: 0.093208, -0.995034, -0.035177 13: 0.144608, -0.895242, -0.421890 14: 0.524194, -0.680821, -0.509454 15: -0.481128, -0.733741, 0.480656 16: -0.823076, 0.449965, 0.347979 17: -0.888253, -0.063133, -0.455690 18: -0.672102, -0.732741, 0.110781 19: 0.699453, -0.110723, -0.705987 20: 0.441389, -0.391523, -0.806244 21: -0.281831, -0.814184, -0.507885 22: -0.601632, -0.812283, -0.508305 23: 0.629421, 0.708171, 0.317496 24: -0.568210, 0.273148, -0.778529 25: 0.829784, -0.324714, 0.454091 26: 0.313490, 0.491775, 0.811144 27: 0.054139, -0.216170, -0.975053 28: 0.286972, -0.904461, 0.315101 29: 0.923529, -0.021970, -0.383806 30: 0.264165, -0.607207, 0.749858 31: 0.260233, -0.609104, 0.749834 32: 0.854475, 0.400779, -0.330854 33: -0.097884, 0.220989, -0.970907 34: -0.349784, -0.104215, 0.931861 35: -0.426056, -0.091100, -0.900897 36: 0.000000, 0.000000, 0.000000 37: 0.000000, 0.000000, 0.000000 38: 0.000000, 0.000000, 0.000000 39: 0.999991, -0.004224, -0.000249 40: 0.314415, 0.949532, -0.000519 41: -0.075562, 0.638964, 0.766869 42: 0.875203, -0.479650, 0.061976 43: -0.199274, -0.552859, 0.809863 44: -0.614361, -0.360801, 0.701046 45: 0.685615, 0.369276, 0.626992 46: -0.559605, 0.826597, 0.062539 47: 0.904448, 0.399873, 0.148048 48: 0.093181, -0.995075, -0.035007 49: 0.144334, -0.895057, -0.421964 50: 0.519135, -0.685870, -0.509212 51: -0.481587, -0.732226, 0.480938 52: -0.823207, 0.450559, 0.347815 53: -0.886639, -0.063294, -0.456166 54: -0.676109, -0.728467, 0.111361 55: 0.700883, -0.109309, -0.705804 56: 0.444573, -0.392454, -0.805908 57: -0.280834, -0.812282, -0.508434 58: -0.601365, -0.814664, -0.507772 59: 0.629210, 0.711182, 0.316532 60: -0.566986, 0.272640, -0.778692 61: 0.830525, -0.326559, 0.453683 62: 0.315200, 0.490945, 0.811119 63: 0.054672, -0.213494, -0.975138 64: 0.284283, -0.905688, 0.314935 65: 0.923751, -0.020852, -0.383734 66: 0.259252, -0.608233, 0.749993 67: 0.259508, -0.605161, 0.750359 68: 0.854059, 0.401502, -0.330884 69: -0.095633, 0.224934, -0.970803 70: -0.349293, -0.104589, 0.931882 71: -0.423139, -0.088227, -0.901151 -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From darshanp20 at yahoo.com Wed Jul 9 15:42:20 2008 From: darshanp20 at yahoo.com (darshan pai) Date: Wed, 09 Jul 2008 12:42:20 -0700 (PDT) Subject: [Mristudio-users] New to the program Message-ID: <50788.74007.qm@web30407.mail.mud.yahoo.com> The gradient table is the parameters of the data acquisition. You shld have it with u to actually make sense of the data. ----- Original Message ---- From: Tapan Jani To: Mristudio-users at mristudio.org Sent: Wednesday, July 9, 2008 1:32:49 PM Subject: Re: [Mristudio-users] New to the program Sorry one final question, I have Siemens data in DICOM. I read the user manual for how to convert it to an REC file, but don't know what to use for my gradient table. Does anyone know how to generate one? Thank you again! Tapan tjani2 at uic.edu On Wed, Jul 9, 2008 at 11:33 AM, Tapan Jani wrote: Hello all, I've tried sending a couple of e-mails to the DtiStudio support staff, but they have yet to get back to me. While waiting for their reply, I was wondering if anyone in this newsletter would be able to answer my questions. Below, I have copy-pasted both my e-mails. I apologize for the length, I got a little carried away in my curiosity. If anyone can help, it would be greatly appreciated. Thank you very much, Tapan Jani tjani2 at uic.edu ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dear Support Team, I am writing you in reference to your program DTI Studio. Let me begin by stating that I am very new to diffusion tensor imaging, and am trying to use your program as a stepping stone into that field of study. For the record, I am a research assistant in a lab that is registered on your website (dtistudio.org) under the username slee56. I write to you with only a few hours of experience with the program under my belt. The manual which you posted alongside the software is helpful in knowing how to open files and view them. For the purposes of learning how the program works, I downloaded the data set 01_020729_31.rec. Initially, I was able to boot up the program and load the data set via file -> dtimapping. Using the gradient posted next to the data set on your demo data database, and leaving all other settings as they were, I was able to bring up the axial, sagittal, coronal, and 3-d views of the .rec file. Next, under the dtimap tab, I clicked "tensor, color map, etc." to come up with the different maps. Once this was completed, I was able to view the different maps, but this is where my problems began. As I stated earlier, I am very new to this field, and thus am at a loss when it comes to actually interpreting the data. For this reason, I am contacting you to ask whether you have some documentation on how to "read" all the various DTI maps that this program is capable of creating, along with a glossary which explains every term used in the program. For me to create maps and not know what I am looking at presents a problem that, hopefully, you can help me with. I have looked through the user manual that is on your webpage, and while it is very helpful in utilizing the program itself, it does not help me interpret the images. For example, I am completely unaware how to find within what area of the brain the diffusion is higher or lower than normal, or even know what normal is for that matter. Finally, I was wondering if you could tell me that after creating the "tensor, color maps etc," where I can view the data this calculates, and what those figures mean. Also, just as a side note, under the dtimap whenever I click any of the buttons under "calculation," 40% of the time it causes the program to severely stall and/or crash altogether. I really appreciate your help in this matter, and hope to soon become knowledgeable in this area with your aid. So if there is some documentation explaining every single in and out of what DTI images are, show, and help with, it would be incredibly useful to me. Thank you for your time, Tapan Jani Tjani2 at uic.edu ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Dear Support Team, This is the second e-mail that I am writing to you, and not being sure whether or not my first e-mail reached you, I've attached it below. This e-mail, however, is in reference to converting DICOM images to REC images. I was able to follow the user manual to perform the actual conversion, however, when I load the newly created REC, I am unable to perform any of the mapping functions. Does anyone know why this is happening? Thank you for your time, I hope to hear from you soon in regards to this e-mail and the one attached below. Tapan Jani tjani2 at uic.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080709/5c0da376/attachment.html From choisj70 at gmail.com Wed Jul 9 16:40:14 2008 From: choisj70 at gmail.com (Seongjin) Date: Wed, 09 Jul 2008 16:40:14 -0400 Subject: [Mristudio-users] error when calculating tensor with double gradient table In-Reply-To: <4874DBB8020000A0000040C8@lhscgwiao.lhsc.on.ca> References: <4874DBB8020000A0000040C8@lhscgwiao.lhsc.on.ca> Message-ID: Dear Elizabeth, What vendor is this table for? Best, Seongjin Choi On Wed, Jul 9, 2008 at 3:39 PM, Elizabeth Finger < Elizabeth.Finger at lhsc.on.ca> wrote: > Hello- > > I have running into an error- the DTI Mapping program is crashing out, when > attempting to do a tensor calculation with an updated gradient table from > the AIR Matrix calcuation that uses two series. We have two separate series > with 3 b0 images and 33 graidents with the same DTI parameters per subject. > We have used AIR to align them together, and generated an updated gradient > table. When we reload the two AIR series into the DTI Mapping window with > the new gradient table from AIRMatrix output (table pasted below, now with > 72 lines, starting w/ 0 and ending w/ 71), the data load correctly. However, > when we attempt to run the tensor calculation with automatic outlier > rejection, as soon as the calculation starts the program crashes out. If we > use the original gradient table there is no problem. Also, if we use half of > the updated gradient tables (either first half w/ numbers from 0 to 35, or > the second half w/ original airmatrix numbers from 36-71, the tensor > calculation works. Is there something else we can do to use the revised > gradient table for both series and include both series in the tensor > calculation? > > Thank you, > Elizabeth Finger > > *** New Gradient Table *** > 0: 0.000000, 0.000000, 0.000000 > 1: 0.000000, 0.000000, 0.000000 > 2: 0.000000, 0.000000, 0.000000 > 3: 0.999999, 0.000434, -0.000390 > 4: 0.313706, 0.949767, -0.000230 > 5: -0.072833, 0.636259, 0.767252 > 6: 0.875411, -0.479757, 0.061399 > 7: -0.199675, -0.555806, 0.809540 > 8: -0.615266, -0.363411, 0.700719 > 9: 0.684460, 0.371145, 0.627016 > 10: -0.565897, 0.821968, 0.063204 > 11: 0.901326, 0.406546, 0.148179 > 12: 0.093208, -0.995034, -0.035177 > 13: 0.144608, -0.895242, -0.421890 > 14: 0.524194, -0.680821, -0.509454 > 15: -0.481128, -0.733741, 0.480656 > 16: -0.823076, 0.449965, 0.347979 > 17: -0.888253, -0.063133, -0.455690 > 18: -0.672102, -0.732741, 0.110781 > 19: 0.699453, -0.110723, -0.705987 > 20: 0.441389, -0.391523, -0.806244 > 21: -0.281831, -0.814184, -0.507885 > 22: -0.601632, -0.812283, -0.508305 > 23: 0.629421, 0.708171, 0.317496 > 24: -0.568210, 0.273148, -0.778529 > 25: 0.829784, -0.324714, 0.454091 > 26: 0.313490, 0.491775, 0.811144 > 27: 0.054139, -0.216170, -0.975053 > 28: 0.286972, -0.904461, 0.315101 > 29: 0.923529, -0.021970, -0.383806 > 30: 0.264165, -0.607207, 0.749858 > 31: 0.260233, -0.609104, 0.749834 > 32: 0.854475, 0.400779, -0.330854 > 33: -0.097884, 0.220989, -0.970907 > 34: -0.349784, -0.104215, 0.931861 > 35: -0.426056, -0.091100, -0.900897 > 36: 0.000000, 0.000000, 0.000000 > 37: 0.000000, 0.000000, 0.000000 > 38: 0.000000, 0.000000, 0.000000 > 39: 0.999991, -0.004224, -0.000249 > 40: 0.314415, 0.949532, -0.000519 > 41: -0.075562, 0.638964, 0.766869 > 42: 0.875203, -0.479650, 0.061976 > 43: -0.199274, -0.552859, 0.809863 > 44: -0.614361, -0.360801, 0.701046 > 45: 0.685615, 0.369276, 0.626992 > 46: -0.559605, 0.826597, 0.062539 > 47: 0.904448, 0.399873, 0.148048 > 48: 0.093181, -0.995075, -0.035007 > 49: 0.144334, -0.895057, -0.421964 > 50: 0.519135, -0.685870, -0.509212 > 51: -0.481587, -0.732226, 0.480938 > 52: -0.823207, 0.450559, 0.347815 > 53: -0.886639, -0.063294, -0.456166 > 54: -0.676109, -0.728467, 0.111361 > 55: 0.700883, -0.109309, -0.705804 > 56: 0.444573, -0.392454, -0.805908 > 57: -0.280834, -0.812282, -0.508434 > 58: -0.601365, -0.814664, -0.507772 > 59: 0.629210, 0.711182, 0.316532 > 60: -0.566986, 0.272640, -0.778692 > 61: 0.830525, -0.326559, 0.453683 > 62: 0.315200, 0.490945, 0.811119 > 63: 0.054672, -0.213494, -0.975138 > 64: 0.284283, -0.905688, 0.314935 > 65: 0.923751, -0.020852, -0.383734 > 66: 0.259252, -0.608233, 0.749993 > 67: 0.259508, -0.605161, 0.750359 > 68: 0.854059, 0.401502, -0.330884 > 69: -0.095633, 0.224934, -0.970803 > 70: -0.349293, -0.104589, 0.931882 > 71: -0.423139, -0.088227, -0.901151 > > -------------------------------------------------------------------------------- > This information is directed in confidence solely to the person named above > and may contain confidential and/or privileged material. This information > may not otherwise be distributed, copied or disclosed. If you have received > this e-mail in error, please notify the sender immediately via a return > e-mail and destroy original message. Thank you for your cooperation. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080709/711a8e33/attachment.html From s.lytle at sbcglobal.net Wed Jul 9 20:20:23 2008 From: s.lytle at sbcglobal.net (Scott Lytle) Date: Wed, 09 Jul 2008 17:20:23 -0700 (PDT) Subject: [Mristudio-users] Loading DICOM images Message-ID: <544426.27791.qm@web83407.mail.sp1.yahoo.com> I am having trouble loading my DICOM files into DTI Studio. I have Hitachi DICOM files, and Hitachi is not selectable in the list of DICOM files. Do I have to convert these files to a different format such as RAW? If so, is there a recommended "best way"? I do have all the gradient table data, just cannot load the DICOM files. Any suggestions would be great. Please let me know if you need any more info. Thank you, Scott -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080709/eea35296/attachment.html From s.lytle at sbcglobal.net Fri Jul 11 18:55:35 2008 From: s.lytle at sbcglobal.net (Scott Lytle) Date: Fri, 11 Jul 2008 15:55:35 -0700 (PDT) Subject: [Mristudio-users] MriView3D MFC Application Error when attemptin calculation Message-ID: <941391.84968.qm@web83404.mail.sp1.yahoo.com> After loading my DICOM files into DTI Studio's "DTI Mapping..." program, selecting the DtiMap tab, and then selecting any processing task, the error message "MriView3D MFC Application has stopped working" instantly appears. This error even occurs when performing a partial load of 1, 20, or 49 images, so I do not believe this to be a memory issue. I am running Windows Vista and have 2GB of RAM. I have tried using the sample data file provided "01_020729_31" with the same error message occurring, so I do not believe this to be an issue with my DICOM data. I have downloaded and ran the "vcredist_x86" file with no help. Any help would be great.... Thank you, Scott -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080711/7ba11a3c/attachment-0001.html From susumu at mri.jhu.edu Fri Jul 11 20:11:32 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 11 Jul 2008 20:11:32 -0400 Subject: [Mristudio-users] Loading DICOM images In-Reply-To: <544426.27791.qm@web83407.mail.sp1.yahoo.com> References: <544426.27791.qm@web83407.mail.sp1.yahoo.com> Message-ID: Dear Scott, If any of existing DICOM readers (Philips, GE, Siemens, Toshiba) doesn't work, please contact Hangyi and send one example file by email. We'll look into the header of Hitachi DICOM. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Scott Lytle Sent: Wednesday, July 09, 2008 8:20 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Loading DICOM images I am having trouble loading my DICOM files into DTI Studio. I have Hitachi DICOM files, and Hitachi is not selectable in the list of DICOM files. Do I have to convert these files to a different format such as RAW? If so, is there a recommended "best way"? I do have all the gradient table data, just cannot load the DICOM files. Any suggestions would be great. Please let me know if you need any more info. Thank you, Scott -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080711/c951f7b6/attachment.html From susumu at mri.jhu.edu Fri Jul 11 20:24:43 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 11 Jul 2008 20:24:43 -0400 Subject: [Mristudio-users] MriView3D MFC Application Error when attemptincalculation In-Reply-To: <941391.84968.qm@web83404.mail.sp1.yahoo.com> References: <941391.84968.qm@web83404.mail.sp1.yahoo.com> Message-ID: <22375DA662D945359129FA6DC05232BB@SusumuThinkPad> Hi Scott, After you load DICOM, please check what are in the pull-down image selector in "image" tab. If you use 21-axis gradient table, there should be 22 (21+b0) images. Make sure that all these images are loaded fine. Close the window and read the data (DTI Mapping) again. In the data input window, you can see the previous data parameters (matrix size, FoV, b-tables,,,). Carefully look at the b-table window and make sure that you have b0 + 21 rows. If you have any mistake in the syntax of the b-table, you can see how DtiStudio interpreted the previous table. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Scott Lytle Sent: Friday, July 11, 2008 6:56 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] MriView3D MFC Application Error when attemptincalculation After loading my DICOM files into DTI Studio's "DTI Mapping..." program, selecting the DtiMap tab, and then selecting any processing task, the error message "MriView3D MFC Application has stopped working" instantly appears. This error even occurs when performing a partial load of 1, 20, or 49 images, so I do not believe this to be a memory issue. I am running Windows Vista and have 2GB of RAM. I have tried using the sample data file provided "01_020729_31" with the same error message occurring, so I do not believe this to be an issue with my DICOM data. I have downloaded and ran the "vcredist_x86" file with no help. Any help would be great.... Thank you, Scott -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080711/6fb51562/attachment.html From susumu at mri.jhu.edu Fri Jul 11 21:55:56 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 11 Jul 2008 21:55:56 -0400 Subject: [Mristudio-users] error when calculating tensor with double gradient table In-Reply-To: References: <4874DBB8020000A0000040C8@lhscgwiao.lhsc.on.ca> Message-ID: <60A6FB1B9B0F4A21929C64D2B34DF1FF@SusumuThinkPad> Hi Elizabeth, There could be some bug. I must admit that we haven't rigorously tested the AIR-realigned table. In general if tensor calculation crushes after successful loading, following should be considered. 1) memory issue: Please try partial slice calculation (e.g. calculate only slice 1-20 instead of all slices). 2) Gradient table issue: Please load the data once, make sure that all images are loaded, close the window, and do "DTI Mapping" again. In the data input window, inspect the b-table, which is remember from the previous processing. If there is any mistake in the syntax, you can see how DtiStudio interpreted the table. 3) Also try no auto rejection and see if it works. Auto rejection is still a beta version. Please let us know the results of these tests. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, July 09, 2008 4:40 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] error when calculating tensor with double gradient table Dear Elizabeth, What vendor is this table for? Best, Seongjin Choi On Wed, Jul 9, 2008 at 3:39 PM, Elizabeth Finger wrote: Hello- I have running into an error- the DTI Mapping program is crashing out, when attempting to do a tensor calculation with an updated gradient table from the AIR Matrix calcuation that uses two series. We have two separate series with 3 b0 images and 33 graidents with the same DTI parameters per subject. We have used AIR to align them together, and generated an updated gradient table. When we reload the two AIR series into the DTI Mapping window with the new gradient table from AIRMatrix output (table pasted below, now with 72 lines, starting w/ 0 and ending w/ 71), the data load correctly. However, when we attempt to run the tensor calculation with automatic outlier rejection, as soon as the calculation starts the program crashes out. If we use the original gradient table there is no problem. Also, if we use half of the updated gradient tables (either first half w/ numbers from 0 to 35, or the second half w/ original airmatrix numbers from 36-71, the tensor calculation works. Is there something else we can do to use the revised gradient table for both series and include both series in the tensor calculation? Thank you, Elizabeth Finger *** New Gradient Table *** 0: 0.000000, 0.000000, 0.000000 1: 0.000000, 0.000000, 0.000000 2: 0.000000, 0.000000, 0.000000 3: 0.999999, 0.000434, -0.000390 4: 0.313706, 0.949767, -0.000230 5: -0.072833, 0.636259, 0.767252 6: 0.875411, -0.479757, 0.061399 7: -0.199675, -0.555806, 0.809540 8: -0.615266, -0.363411, 0.700719 9: 0.684460, 0.371145, 0.627016 10: -0.565897, 0.821968, 0.063204 11: 0.901326, 0.406546, 0.148179 12: 0.093208, -0.995034, -0.035177 13: 0.144608, -0.895242, -0.421890 14: 0.524194, -0.680821, -0.509454 15: -0.481128, -0.733741, 0.480656 16: -0.823076, 0.449965, 0.347979 17: -0.888253, -0.063133, -0.455690 18: -0.672102, -0.732741, 0.110781 19: 0.699453, -0.110723, -0.705987 20: 0.441389, -0.391523, -0.806244 21: -0.281831, -0.814184, -0.507885 22: -0.601632, -0.812283, -0.508305 23: 0.629421, 0.708171, 0.317496 24: -0.568210, 0.273148, -0.778529 25: 0.829784, -0.324714, 0.454091 26: 0.313490, 0.491775, 0.811144 27: 0.054139, -0.216170, -0.975053 28: 0.286972, -0.904461, 0.315101 29: 0.923529, -0.021970, -0.383806 30: 0.264165, -0.607207, 0.749858 31: 0.260233, -0.609104, 0.749834 32: 0.854475, 0.400779, -0.330854 33: -0.097884, 0.220989, -0.970907 34: -0.349784, -0.104215, 0.931861 35: -0.426056, -0.091100, -0.900897 36: 0.000000, 0.000000, 0.000000 37: 0.000000, 0.000000, 0.000000 38: 0.000000, 0.000000, 0.000000 39: 0.999991, -0.004224, -0.000249 40: 0.314415, 0.949532, -0.000519 41: -0.075562, 0.638964, 0.766869 42: 0.875203, -0.479650, 0.061976 43: -0.199274, -0.552859, 0.809863 44: -0.614361, -0.360801, 0.701046 45: 0.685615, 0.369276, 0.626992 46: -0.559605, 0.826597, 0.062539 47: 0.904448, 0.399873, 0.148048 48: 0.093181, -0.995075, -0.035007 49: 0.144334, -0.895057, -0.421964 50: 0.519135, -0.685870, -0.509212 51: -0.481587, -0.732226, 0.480938 52: -0.823207, 0.450559, 0.347815 53: -0.886639, -0.063294, -0.456166 54: -0.676109, -0.728467, 0.111361 55: 0.700883, -0.109309, -0.705804 56: 0.444573, -0.392454, -0.805908 57: -0.280834, -0.812282, -0.508434 58: -0.601365, -0.814664, -0.507772 59: 0.629210, 0.711182, 0.316532 60: -0.566986, 0.272640, -0.778692 61: 0.830525, -0.326559, 0.453683 62: 0.315200, 0.490945, 0.811119 63: 0.054672, -0.213494, -0.975138 64: 0.284283, -0.905688, 0.314935 65: 0.923751, -0.020852, -0.383734 66: 0.259252, -0.608233, 0.749993 67: 0.259508, -0.605161, 0.750359 68: 0.854059, 0.401502, -0.330884 69: -0.095633, 0.224934, -0.970803 70: -0.349293, -0.104589, 0.931882 71: -0.423139, -0.088227, -0.901151 ---------------------------------------------------------------------------- ---- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080711/ae7a654a/attachment-0001.html From susumu at mri.jhu.edu Sat Jul 12 08:01:18 2008 From: susumu at mri.jhu.edu (susumu) Date: Sat, 12 Jul 2008 08:01:18 -0400 Subject: [Mristudio-users] New to the program In-Reply-To: <43f2b0680807090933l61d03cf2s97ffcd77c12aa880@mail.gmail.com> References: <43f2b0680807090933l61d03cf2s97ffcd77c12aa880@mail.gmail.com> Message-ID: Dear Tapan, ********************************************************** I write to you with only a few hours of experience with the program under my belt. The manual which you posted alongside the software is helpful in knowing how to open files and view them. For the purposes of learning how the program works, I downloaded the data set 01_020729_31.rec. Initially, I was able to boot up the program and load the data set via file -> dtimapping. Using the gradient posted next to the data set on your demo data database, and leaving all other settings as they were, I was able to bring up the axial, sagittal, coronal, and 3-d views of the .rec file. Next, under the dtimap tab, I clicked "tensor, color map, etc." to come up with the different maps. Once this was completed, I was able to view the different maps, but this is where my problems began. As I stated earlier, I am very new to this field, and thus am at a loss when it comes to actually interpreting the data. For this reason, I am contacting you to ask whether you have some documentation on how to "read" all the various DTI maps that this program is capable of creating, along with a glossary which explains every term used in the program. For me to create maps and not know what I am looking at presents a problem that, hopefully, you can help me with. I have looked through the user manual that is on your webpage, and while it is very helpful in utilizing the program itself, it does not help me interpret the images. For example, I am completely unaware how to find within what area of the brain the diffusion is higher or lower than normal, or even know what normal is for that matter. ********************************************************* As you might have already noticed, the manual assumes that readers have a fair amount of knowledge about DTI. I recommend you to go over several papers or textbooks to familiarize yourself to the concept of DTI and tensor calculations. All the names such as FA, RA, VA, CL, CP, and trace follow widely used conventions. My recommendation is, of course, "Introduction to Diffusion Tensor Imaging", from Elsevier, which is written for people who do not have any background in DTI. There is detailed explanation about the meaning of the contrasts and how to interpret them. I hope it will be of help. ********************************************************** Finally, I was wondering if you could tell me that after creating the "tensor, color maps etc," where I can view the data this calculates, and what those figures mean. ********************************************************** After the tensor calculation, please go back to "image" tab in the right bottom corner. Within the tab, you can find a pull-down menu in which you can find a list of new images calculated by the tensor fitting. ********************************************************** Also, just as a side note, under the dtimap whenever I click any of the buttons under "calculation," 40% of the time it causes the program to severely stall and/or crash altogether. I really appreciate your help in this matter, and hope to soon become knowledgeable in this area with your aid. So if there is some documentation explaining every single in and out of what DTI images are, show, and help with, it would be incredibly useful to me. ********************************************************** Most of the clash is caused by memory shortage. The best way is to use the 64-bit operating system. Even if you have more than 2GB of RAM, the 32-bit system can allocate only up to 1.5GB to a single program. To check if the memory is the problem, you can limit the number of slices to be calculated. For example, if you have 50-slice data, you can divide the data into slice 0-24 and 25-49. If this approach works, it tells you have the memory problem. ? Susumu From susumu at mri.jhu.edu Sat Jul 12 08:05:40 2008 From: susumu at mri.jhu.edu (susumu) Date: Sat, 12 Jul 2008 08:05:40 -0400 Subject: [Mristudio-users] New to the program In-Reply-To: <43f2b0680807091032i6e506dbfv61674b83eb09c59f@mail.gmail.com> Message-ID: <6u9t96$3gkv3q@ipex1.johnshopkins.edu> This is a typical 12-orientation scheme used by Siemens. 0: 0.000, 0.000, 0.000 1: 1.000, 0.414, -0.414 2: 1.000, -0.414, -0.414 3: 1.000, -0.414, 0.414 4: 1.000, 0.414, 0.414 5: 0.414, 0.414, 1.000 6: 0.414, 1.000, 0.414 7: 0.414, 1.000, -0.414 8: 0.414, 0.414, -1.000 9: 0.414, -0.414, -1.000 10: 0.414, -1.000, -0.414 11: 0.414, -1.000, 0.414 12: 0.414, -0.414, 1.000 If it doesn't work, you may be using an old Siemens operating system. Please let me know. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Tapan Jani Sent: Wednesday, July 09, 2008 1:33 PM To: Mristudio-users at mristudio.org Subject: Re: [Mristudio-users] New to the program Sorry one final question, I have Siemens data in DICOM. I read the user manual for how to convert it to an REC file, but don't know what to use for my gradient table. Does anyone know how to generate one? Thank you again! Tapan tjani2 at uic.edu On Wed, Jul 9, 2008 at 11:33 AM, Tapan Jani wrote: Hello all, I've tried sending a couple of e-mails to the DtiStudio support staff, but they have yet to get back to me. While waiting for their reply, I was wondering if anyone in this newsletter would be able to answer my questions. Below, I have copy-pasted both my e-mails. I apologize for the length, I got a little carried away in my curiosity. If anyone can help, it would be greatly appreciated. Thank you very much, Tapan Jani tjani2 at uic.edu ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ---------------------- Dear Support Team, I am writing you in reference to your program DTI Studio. Let me begin by stating that I am very new to diffusion tensor imaging, and am trying to use your program as a stepping stone into that field of study. For the record, I am a research assistant in a lab that is registered on your website (dtistudio.org ) under the username slee56. I write to you with only a few hours of experience with the program under my belt. The manual which you posted alongside the software is helpful in knowing how to open files and view them. For the purposes of learning how the program works, I downloaded the data set 01_020729_31.rec. Initially, I was able to boot up the program and load the data set via file -> dtimapping. Using the gradient posted next to the data set on your demo data database, and leaving all other settings as they were, I was able to bring up the axial, sagittal, coronal, and 3-d views of the .rec file. Next, under the dtimap tab, I clicked "tensor, color map, etc." to come up with the different maps. Once this was completed, I was able to view the different maps, but this is where my problems began. As I stated earlier, I am very new to this field, and thus am at a loss when it comes to actually interpreting the data. For this reason, I am contacting you to ask whether you have some documentation on how to "read" all the various DTI maps that this program is capable of creating, along with a glossary which explains every term used in the program. For me to create maps and not know what I am looking at presents a problem that, hopefully, you can help me with. I have looked through the user manual that is on your webpage, and while it is very helpful in utilizing the program itself, it does not help me interpret the images. For example, I am completely unaware how to find within what area of the brain the diffusion is higher or lower than normal, or even know what normal is for that matter. Finally, I was wondering if you could tell me that after creating the "tensor, color maps etc," where I can view the data this calculates, and what those figures mean. Also, just as a side note, under the dtimap whenever I click any of the buttons under "calculation," 40% of the time it causes the program to severely stall and/or crash altogether. I really appreciate your help in this matter, and hope to soon become knowledgeable in this area with your aid. So if there is some documentation explaining every single in and out of what DTI images are, show, and help with, it would be incredibly useful to me. Thank you for your time, Tapan Jani Tjani2 at uic.edu ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ---------- Dear Support Team, This is the second e-mail that I am writing to you, and not being sure whether or not my first e-mail reached you, I've attached it below. This e-mail, however, is in reference to converting DICOM images to REC images. I was able to follow the user manual to perform the actual conversion, however, when I load the newly created REC, I am unable to perform any of the mapping functions. Does anyone know why this is happening? Thank you for your time, I hope to hear from you soon in regards to this e-mail and the one attached below. Tapan Jani tjani2 at uic.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080712/5ec5c2f6/attachment.html From susumu at mri.jhu.edu Sat Jul 12 08:57:17 2008 From: susumu at mri.jhu.edu (susumu) Date: Sat, 12 Jul 2008 08:57:17 -0400 Subject: [Mristudio-users] Results using analyze format in DTIStudio In-Reply-To: <20080707212743.e0f15dac35c4bf88aea872454247a5ef.df55d535e1.wbe@email.secureserver.net> References: <20080707212743.e0f15dac35c4bf88aea872454247a5ef.df55d535e1.wbe@email.secureserver.net> Message-ID: <3476732608CC454295A3A472332AB106@SusumuThinkPad> We are thinking about having another workshop in Hopkins. Hopefully sometime in August. We'll send everyone a notice once the date if fixed. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of sjacobson at spokaneadvancedimaging.com Sent: Tuesday, July 08, 2008 12:28 AM To: DTI Studio,ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] Results using analyze format in DTIStudio How can I get information on upcoming workshops for MRI studio? Susan Jacobson Spokane Advanced Imaging Institute 910 W. 5th Ave., Ste. 150 Spokane, Washington 99204 1-509-363-6502 1-509-863-3813 cell -------- Original Message -------- Subject: Re: [Mristudio-users] Results using analyze format in DTIStudio From: susumu Date: Mon, July 07, 2008 6:24 pm To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" Hi Graeme, I believe FA, ADC, and color maps are insensitive to right-left, front-back, and up-down flip. It becomes in issue when you do fiber tracking. DtiStudio support the Analyze format to save 3D images after tensor calculation. If you save data as Analyze and read as Analyze, the orientation should be correct, but if it is saved as Analyze and read as Raw, you'd find that the axial image is upside-down, due to Neurology - Radiology conventions. In DtiStudio, we do not support tensor calculation of DWIs in the Analyze format. Also, it is difficult to confirm what would happen if DtiStudio processes data partially processed by other software programs because it is difficult for us to test many combinations of data processing by multiple programs. I would suggest to stick to single software for DWI - tensor calculation. It is indeed interesting that you saw 0.2 FA difference by going through the Analyze format, but again, it difficult for us to follow the results that were not processed by DtiStudio for the entire processing. If you experience 0.2 difference with and without AIR in DtiStudio, we would definitely look into the issue. If you mean difference is between; 1) raw DWI -> DtiStudio -> AIR in DtiStudio -> FA 2) raw DWI -> FSL (eddy correction) -> Analyze -> DtiStudio -> FA We first need to know 1) how did you read Analyze into DtiStudio? 2) Have you compared raw DWIs and Analyze (after FSL eddy correction) DWIs? _____ From: mristudio-users-bounces at mristudio.org [ mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Graeme Schwindt Sent: Sunday, July 06, 2008 2:44 PM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] Results using analyze format in DTIStudio Hello, At the Toronto workshop, it was mentioned that loading analyze format images into dtistudio is not recommended as the images are loaded in flipped, and so the gradient tables will not apply properly, as I understood. We have analyzed a couple of subjects from two separate datasets using both the raw dicoms in dtistudio (following AIR), but also with some analyze format images that have been preprocessed in FSL (eddy-current correction). Surprisingly, the FA maps and colour maps are qualitatively very similar between the two methods, which is counterintuitive given the improper mapping between the gradient table and orientation of the analyze imgs. Also, the FA values are generally higher by 0.2 or so in the analyze version of the analysis. Is it possible that the analyze format is actually being read properly though its display is wrong? Any thoughts on the validity of using analyze format would be appreciated. Thanks, Graeme -- Graeme C. Schwindt, HBSc MD/PhD Student University of Toronto graeme.schwindt at gmail.com 416.546.5453 _____ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080712/8419bf41/attachment-0001.html From raj.jaswal at gmail.com Sun Jul 13 22:00:15 2008 From: raj.jaswal at gmail.com (Raj Jaswal) Date: Sun, 13 Jul 2008 22:00:15 -0400 Subject: [Mristudio-users] Loading NIfTI (.nii) format Message-ID: <32a27f2a0807131900i29d03dcbu909fa3a92a19f694@mail.gmail.com> Hello all, I'm having some problems loading the NIfTI (.nii) format using DTI Studio. First, when I decide to load a .nii file through MRI View3D...I do not find the appropriate format to select in the "Image Parameters" window. I tried to select the Analyze format because the .nii format is adapted from the Analyze format. But that does not work. I get the following error: * CMriView3DDoc()::CreateImgWithAnalyzeFile() Analyze Header File open error:* Next, if I want to load a .nii file through DTI Mapping...I do not find the appropriate format to select. The dataset that I have consists of one .nii file and one header file per subject. I am still relatively new to DTI Studio and am learning a lot as I go along! I would appreciate any help or input. Thank you very much. -- - RJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080713/9704b7d0/attachment.html From shig.t at kuhp.kyoto-u.ac.jp Mon Jul 14 01:47:33 2008 From: shig.t at kuhp.kyoto-u.ac.jp (Shigetoshi TAKAYA) Date: Mon, 14 Jul 2008 14:47:33 +0900 Subject: [Mristudio-users] Coregistration using AIR Message-ID: <007501c8e575$1cd1b960$8516ee0a@DellRIRC> Hello I have two scans of DWI with time interval for each patient (1st scan and 2nd scan). I would like to coregister the images in the 2nd scan onto those in the 1st scan in each subject using Automatic Image Registration (AIR) algorithm implemented in DTIStudio, for the purpose of drawing ROIs in the same brain regions in both scans. First, I did eddy current correction and motion correction using affine transformation in each scan (1st scan and 2nd scan). Then, I coregistered the B0 image in the 2nd scan onto that in the 1st scan. And I would like to adjust the same transformation matrix to the rest of the images in the 2nd scan. I know that the transformation matrix can be saved when conducting AIR. Can we use this file to transform the rest of the images in the 2nd scan? Many thanks, Shigetoshi Takaya -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080714/1234a908/attachment.html From icee41 at gmail.com Wed Jul 16 11:35:15 2008 From: icee41 at gmail.com (Tapan Jani) Date: Wed, 16 Jul 2008 10:35:15 -0500 Subject: [Mristudio-users] Gradient Table Message-ID: <43f2b0680807160835v55610425uba6521426774ee9b@mail.gmail.com> Hello all, I sent out an e-mail earlier about generating a gradient table and am still a little bit confused. 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 3T Excite GE scanner to perform our DTI scans, but we also have a Siemens scanner for which the following questions apply. Within the dicom header of the GE scanner, under the tag #DTI Diffusion Dir (0019, 01E0), we are able to tell the number of gradients, but not able to find the x,y,z information. Is there a program that can generate gradient tables to go along with our dicom data, or can it actually be found within the header - and if so, where? Finally I was curious as to whether there are standard gradient tables that go along with specific scanners every time a DTI scan is performed. Thank you very much for all of your help, it is much appreciated. Sincerely, Tapan Jani tjani2 at uic.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080716/bdc460ec/attachment.html From darshanp20 at yahoo.com Wed Jul 16 11:44:49 2008 From: darshanp20 at yahoo.com (darshan pai) Date: Wed, 16 Jul 2008 08:44:49 -0700 (PDT) Subject: [Mristudio-users] Gradient Table Message-ID: <892038.40382.qm@web30407.mail.mud.yahoo.com> Ur MRI personnel shld have that information . As far as i know there is no way to encode into DICOM ----- Original Message ---- From: Tapan Jani To: Mristudio-users at mristudio.org Sent: Wednesday, July 16, 2008 11:35:15 AM Subject: [Mristudio-users] Gradient Table Hello all, I sent out an e-mail earlier about generating a gradient table and am still a little bit confused. 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 3T Excite GE scanner to perform our DTI scans, but we also have a Siemens scanner for which the following questions apply. Within the dicom header of the GE scanner, under the tag #DTI Diffusion Dir (0019, 01E0), we are able to tell the number of gradients, but not able to find the x,y,z information. Is there a program that can generate gradient tables to go along with our dicom data, or can it actually be found within the header - and if so, where? Finally I was curious as to whether there are standard gradient tables that go along with specific scanners every time a DTI scan is performed. Thank you very much for all of your help, it is much appreciated. Sincerely, Tapan Jani tjani2 at uic.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080716/6c8d3665/attachment.html From hifreaks at gmail.com Wed Jul 16 20:54:31 2008 From: hifreaks at gmail.com (=?UTF-8?B?7KGw7JaR7KCc?=) Date: Thu, 17 Jul 2008 09:54:31 +0900 Subject: [Mristudio-users] Gradient Table In-Reply-To: <43f2b0680807160835v55610425uba6521426774ee9b@mail.gmail.com> References: <43f2b0680807160835v55610425uba6521426774ee9b@mail.gmail.com> Message-ID: <241cbec20807161754m2d4a2366vdefb927c54b943dc@mail.gmail.com> As I know, x,y,z information is not always necessary. I have succeeded to load Siemens (Trio, 20 dir) Mosaic files with gradient numbers You only have to not forget to write numbers of 100, 100, 100 and finally 0,0,0 at the end of table. Here is an example, 0: -1.000000, 0.000000, 0.000000 1: 0.000000, -1.000000, 0.000000 2: 0.031984, -0.799591, 0.599693 . . . 18: -0.111012, -0.264029, -0.958105 19: -0.031984, -0.799591, -0.599693 20: 100, 100, 100 21: 0,0,0 If you really want to find the x,y,z information, I'm afraid I can't answer it. But I have heard that the information is not technically necessary from the computer technologist working at the Siemens company. He have read the instructions and talked to me like that. Wish it would be helpful. Regards, YJ Cho 2008/7/17, Tapan Jani : > > Hello all, > > I sent out an e-mail earlier about generating a gradient table and am still > a little bit confused. 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 3T Excite GE scanner to perform our DTI scans, but we also have a > Siemens scanner for which the following questions apply. Within the dicom > header of the GE scanner, under the tag #DTI Diffusion Dir (0019, 01E0), we > are able to tell the number of gradients, but not able to find the x,y,z > information. > > Is there a program that can generate gradient tables to go along with our > dicom data, or can it actually be found within the header - and if so, > where? Finally I was curious as to whether there are standard gradient > tables that go along with specific scanners every time a DTI scan is > performed. > > Thank you very much for all of your help, it is much appreciated. > > Sincerely, > > Tapan Jani > > tjani2 at uic.edu > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Yang-Je Cho Dept of Neurology, Yonsei University College of Medicine, Seoul, Korea Phone: 82-2-2228-1600, Cell: 016-298-7456, Fax: 82-2-393-0705 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080717/6921ce8e/attachment.html From s.lytle at sbcglobal.net Wed Jul 16 23:04:05 2008 From: s.lytle at sbcglobal.net (Scott Lytle) Date: Wed, 16 Jul 2008 20:04:05 -0700 (PDT) Subject: [Mristudio-users] Gradient Table In-Reply-To: <241cbec20807161754m2d4a2366vdefb927c54b943dc@mail.gmail.com> Message-ID: <647190.8800.qm@web83403.mail.sp1.yahoo.com> The vendor (Siemens) should be able to provide the data for you. Every vendor is able to provide the gradient table, it's just a matter of getting in touch with the right person. Unfortunately for you, I don't work at Siemens, so I cannot help. Scott ??????? ? wrote: As I know, x,y,z information is not always necessary. I have succeeded to load Siemens (Trio, 20 dir) Mosaic files with gradient numbers You only have to not forget to write numbers of 100, 100, 100 and finally 0,0,0 at the end of table. Here is an example, 0: -1.000000, 0.000000, 0.000000 1: 0.000000, -1.000000, 0.000000 2: 0.031984, -0.799591, 0.599693 . . . 18: -0.111012, -0.264029, -0.958105 19: -0.031984, -0.799591, -0.599693 20: 100, 100, 100 21: 0,0,0 If you really want to find the x,y,z information, I'm afraid I can't answer it. But I have heard that the information is not technically necessary from the computer technologist working at the Siemens company. He have read the instructions and talked to me like that. Wish it would be helpful. Regards, YJ Cho 2008/7/17, Tapan Jani : Hello all, I sent out an e-mail earlier about generating a gradient table and am still a little bit confused. 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 3T Excite GE scanner to perform our DTI scans, but we also have a Siemens scanner for which the following questions apply. Within the dicom header of the GE scanner, under the tag #DTI Diffusion Dir (0019, 01E0), we are able to tell the number of gradients, but not able to find the x,y,z information. Is there a program that can generate gradient tables to go along with our dicom data, or can it actually be found within the header - and if so, where? Finally I was curious as to whether there are standard gradient tables that go along with specific scanners every time a DTI scan is performed. Thank you very much for all of your help, it is much appreciated. Sincerely, Tapan Jani tjani2 at uic.edu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Yang-Je Cho Dept of Neurology, Yonsei University College of Medicine, Seoul, Korea Phone: 82-2-2228-1600, Cell: 016-298-7456, Fax: 82-2-393-0705 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080716/b42ddebb/attachment-0001.html From jxu at wustl.edu Thu Jul 17 04:36:46 2008 From: jxu at wustl.edu (Junqian Gordon Xu) Date: Thu, 17 Jul 2008 03:36:46 -0500 Subject: [Mristudio-users] Gradient Table In-Reply-To: <241cbec20807161754m2d4a2366vdefb927c54b943dc@mail.gmail.com> References: <43f2b0680807160835v55610425uba6521426774ee9b@mail.gmail.com> <241cbec20807161754m2d4a2366vdefb927c54b943dc@mail.gmail.com> Message-ID: <487F049E.7050303@wustl.edu> 1) Siemens specify DTI table in lab coordinates (i.e. XYZ). 2) The where-abouts of the DTI table info is software version dependent VA25, VA21 and earlier: hard coded in the ep2d_diff.cpp source file. VB13, VB15 and later: if you use the standard MDDW (limits your max diffusion direction to 64?), the table is again hard coded. If you have the license to use diffusion FREE, the table is in a user supplied ASCII file (you probably know where it is). 3) You may find something like "diffusion direction" in DICOM headers if your scanner is VB13/VB15. One caveat is that this table is not the original table if your slices are oblique. In other words, this table has already been multiplied with "slice normal vector" which could also been found from the header. Siemens probably uses this for their color coded FA map. Hope this helps Gordon On 07/16/2008 07:54 PM, ??? wrote: > As I know, x,y,z information is not always necessary. > I have succeeded to load Siemens (Trio, 20 dir) Mosaic files with > gradient numbers > You only have to not forget to write numbers of 100, 100, 100 and > finally 0,0,0 at the end of table. > Here is an example, > > 0: -1.000000, 0.000000, 0.000000 > 1: 0.000000, -1.000000, 0.000000 > 2: 0.031984, -0.799591, 0.599693 > . > . > . > 18: -0.111012, -0.264029, -0.958105 > 19: -0.031984, -0.799591, -0.599693 > 20: 100, 100, 100 > 21: 0,0,0 > > If you really want to find the x,y,z information, I'm afraid I can't > answer it. > But I have heard that the information is not technically necessary from > the computer technologist > working at the Siemens company. He have read the instructions and talked > to me like that. > > Wish it would be helpful. > > Regards, > > YJ Cho > > > 2008/7/17, Tapan Jani >: > > Hello all, > > I sent out an e-mail earlier about generating a gradient table and > am still a little bit confused. 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 3T Excite GE scanner to perform > our DTI scans, but we also have a Siemens scanner for which the > following questions apply. Within the dicom header of the GE > scanner, under the tag #DTI Diffusion Dir (0019, 01E0), we are able > to tell the number of gradients, but not able to find the x,y,z > information. > > Is there a program that can generate gradient tables to go along > with our dicom data, or can it actually be found within the header - > and if so, where? Finally I was curious as to whether there are > standard gradient tables that go along with specific scanners every > time a DTI scan is performed. > > Thank you very much for all of your help, it is much appreciated. > > Sincerely, > > Tapan Jani > > tjani2 at uic.edu > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > -- > Yang-Je Cho > > Dept of Neurology, Yonsei University > College of Medicine, Seoul, Korea > Phone: 82-2-2228-1600, Cell: 016-298-7456, Fax: 82-2-393-0705 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users From darshanp20 at yahoo.com Fri Jul 18 16:45:54 2008 From: darshanp20 at yahoo.com (darshan pai) Date: Fri, 18 Jul 2008 13:45:54 -0700 (PDT) Subject: [Mristudio-users] The b matrix Message-ID: <334307.96121.qm@web30404.mail.mud.yahoo.com> Hello all, I just had a question regarding the Weighting matrix . I have always seen that the b value is usually set to be 1000 . Is there a specific reason to do that . I have seen literature which suggest that having b value to 1000 is appropriate to at least resolve two fiber populations. Which means that increasing the value should be advantageous for multiple orientations. Is there an SNR issue to take care of at higher b values ? Maybe the question is too basic and maybe a little too trivial . Just curious to know Regards Darshan From grojasy at puc.cl Sun Jul 20 11:57:54 2008 From: grojasy at puc.cl (Gonzalo Rojas) Date: Sun, 20 Jul 2008 08:57:54 -0700 Subject: [Mristudio-users] DTIStudio can read Analyze files ?... Message-ID: <48836082.5000009@puc.cl> Hi: In a course in UCLA (Summer School in Medical Imaging), I look a DTIStudio version that can read Analyze files... Which version is that?... How can I get it ?... Sincerely, -- Gonzalo Rojas Costa Laboratory of Medical Image Processing Department of Neuroradiology Institute of Neurosurgery Dr. Asenjo Jose Manuel Infante 553, Providencia, Santiago, Chile. Tel/Fax: 56-2-5754653 Cel: 56-9-97771785 www.neurorradiologia.cl From grojasy at puc.cl Mon Jul 21 00:14:41 2008 From: grojasy at puc.cl (Gonzalo Rojas) Date: Sun, 20 Jul 2008 21:14:41 -0700 Subject: [Mristudio-users] DTIStudio can read Analyze files ?... In-Reply-To: <85347.89159.qm@web30407.mail.mud.yahoo.com> References: <85347.89159.qm@web30407.mail.mud.yahoo.com> Message-ID: <48840D31.6030603@puc.cl> Hi: Yes... I downloaded the newest version from dtistudio.org, but it don't have the option to read Analyze files... for that reason I am asking that question.... Sincerely, Gonzalo Rojas Costa Laboratory of Medical Image Processing Department of Neuroradiology Institute of Neurosurgery Dr. Asenjo Jose Manuel Infante 553, Providencia, Santiago, Chile. Tel/Fax: 56-2-5754653 Cel: 56-9-97771785 www.neurorradiologia.cl darshan pai escribi?: > Get the latest version , :) > > > > ----- Original Message ---- > From: Gonzalo Rojas > To: mristudio-users at mristudio.org > Sent: Sunday, July 20, 2008 11:57:54 AM > Subject: [Mristudio-users] DTIStudio can read Analyze files ?... > > Hi: > > In a course in UCLA (Summer School in Medical Imaging), I look a > DTIStudio version that can read Analyze files... Which version is > that?... How can I get it ?... > > Sincerely, > > From susumu at mri.jhu.edu Mon Jul 21 18:26:23 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 21 Jul 2008 18:26:23 -0400 Subject: [Mristudio-users] DTIStudio can read Analyze files ?... In-Reply-To: <48836082.5000009@puc.cl> Message-ID: <6ua0er$33305n@ipex2.johnshopkins.edu> Hi Gonzalo, DtiStudio can read and write the Analyze format, except for raw DWIs for tensor calculation using "DtiMapping". For the tensor calculation, we need to import 4D data (3D DWIs x b-table). I'm not sure if the Analyze format can handle 4D. Unless we use 4D data, we have to specify, say, 30 DWI files for a 30-orientation study, which is not what we want to do usually. If the Analyze format can deal with 4D data and users want to use it, we are happy to incorporate it to DtiStudio. Please let us know. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Gonzalo Rojas Sent: Sunday, July 20, 2008 11:58 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] DTIStudio can read Analyze files ?... Hi: In a course in UCLA (Summer School in Medical Imaging), I look a DTIStudio version that can read Analyze files... Which version is that?... How can I get it ?... Sincerely, -- Gonzalo Rojas Costa Laboratory of Medical Image Processing Department of Neuroradiology Institute of Neurosurgery Dr. Asenjo Jose Manuel Infante 553, Providencia, Santiago, Chile. Tel/Fax: 56-2-5754653 Cel: 56-9-97771785 www.neurorradiologia.cl _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Mon Jul 21 19:10:08 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 21 Jul 2008 19:10:08 -0400 Subject: [Mristudio-users] The b matrix In-Reply-To: <334307.96121.qm@web30404.mail.mud.yahoo.com> Message-ID: <6ua0er$3337pu@ipex2.johnshopkins.edu> Hi Darshan, If we assume one tensor (one fiber population) in each pixel, b-value of 700 - 1,500 should provide similar results. If b-value is small, the image intensity is high, echo time shorter, less motion sensitive, and less eddy current. The downside is, you have less signal attenuation and determination of the slope (=D = proportional to Log(S/S0)) becomes unstable. For example, if there is only 5-10% expected signal loss while there is +/- 5% signal fluctuation by SNR, you have a problem. When b is higher than 1,000, you expect more than 50% of signal attenuation in average, which is enough to determine D, but the signal goes closer to the noise floor and have other practical issues such as longer TE (thus lower SNR), more motion sensitive, and eddy current. So too small b and too high b are not good from the SNR point of view. Empirically, the optimum b should be somewhere around 700 - 1,500. Here, the b - SNR relationship is the center of our interest when we use the simple tensor model. There are some simulation-based papers that tired to theoretically determine the optimum b, but it is not always straightforward because the impacts of TE/motion/eddy currents are difficult to model. Danny Alexander has the most comprehensive simulation paper in this regard. Our internal data with actual human data didn't show much difference between b = 750 to 1,500. Start to see problems with b-values lower than 500 and more than 2,000 . If you are interested in more than one tensor in each pixel, there is a totally different factor. First of all, the decay is not mono-exponential. An interesting feature of exponential decay is, if you want to differentiate bi-exponential and mono-exponential, you have to look at high-b range because they behave identical in low-b range. In other words, everything looks single-tensor if low b-values are used. This simulation can be seen in Larry Frank's HARDI paper, showing two-crossing-fiber pixel looks like a single pancake tensor, not "X" with a low b-value. The higher the b-value, the higher the power to delineate the "X" shape accurately. The smaller the crossing angle, the more difficult to resolve with smaller b. This is why the original Van Wedeen paper used b = 30,000. It is still under investigation by many researchers to figure out how much b is needed. Some say 3,000 is enough, but it should be a function of crossing angle, SNR, and the number of b-orientations. I don't know the answer. I hope this helps. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of darshan pai Sent: Friday, July 18, 2008 4:46 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] The b matrix Hello all, I just had a question regarding the Weighting matrix . I have always seen that the b value is usually set to be 1000 . Is there a specific reason to do that . I have seen literature which suggest that having b value to 1000 is appropriate to at least resolve two fiber populations. Which means that increasing the value should be advantageous for multiple orientations. Is there an SNR issue to take care of at higher b values ? Maybe the question is too basic and maybe a little too trivial . Just curious to know Regards Darshan _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From grojasy at puc.cl Mon Jul 21 21:55:03 2008 From: grojasy at puc.cl (Gonzalo Rojas) Date: Mon, 21 Jul 2008 18:55:03 -0700 Subject: [Mristudio-users] DTIStudio can read Analyze files ?... In-Reply-To: <6ua0er$33305n@ipex2.johnshopkins.edu> References: <6ua0er$33305n@ipex2.johnshopkins.edu> Message-ID: <48853DF7.5090709@puc.cl> susumu escribi?: > Hi Gonzalo, > > DtiStudio can read and write the Analyze format, except for raw DWIs for > tensor calculation using "DtiMapping". Hi Susumu: Ok... Thanks you very much for your answer... Yes... I am asking about read analyze files in DtiMapping only... I know that DtiStudio can read and write Analyze in other parts of the software (for example, DtiStudio could write Color-FA in Analyze)... > For the tensor calculation, we need > to import 4D data (3D DWIs x b-table). I'm not sure if the Analyze format > can handle 4D. Unless we use 4D data, we have to specify, say, 30 DWI files > for a 30-orientation study, which is not what we want to do usually. Yes... Analyze can handle 4D files... for example, in one Analyze file it could be included the 30 directions 3-D volumes... > If the Analyze format can deal with 4D data and users want to use it, we are > happy to incorporate it to DtiStudio. I think that it could be a good idea to add DtiStudio the option to read Analyze files for the tensor calculation because it is a widely used format in different medical software... Other question: sometime ago you mention a beta version of the newest 3.0 version of DtiStudio... I am very interested if I could be a beta tester of that sofware... Could you please tell me ?... Sincerely, > > Please let us know. > > Susumu Gonzalo Rojas Costa Laboratory of Medical Image Processing Department of Neuroradiology Institute of Neurosurgery Dr. Asenjo Jose Manuel Infante 553, Providencia, Santiago, Chile. Tel/Fax: 56-2-5754653 Cel: 56-9-97771785 www.neurorradiologia.cl From luut1 at yahoo.com Tue Jul 22 13:53:06 2008 From: luut1 at yahoo.com (paulina luu) Date: Tue, 22 Jul 2008 10:53:06 -0700 (PDT) Subject: [Mristudio-users] DTI STUDIO In-Reply-To: <6ua0er$3337pu@ipex2.johnshopkins.edu> Message-ID: <493321.24600.qm@web55813.mail.re3.yahoo.com> Dear Dr. Mori, I am a temporary research assistant who is currently learning about DTI and Difussion MRI. I recently downloaded the DTI studio software (John Hopkins) to upload your provided datas and be able to process the raw data. However, I want to know if the data format is 3D or 4D? I also would like to know if there is a tutorial available that provide steps to help me process the raw datas on my own. Thank You. Tieu Luu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080722/758bcf62/attachment-0001.html From c.bieck at T-Online.de Wed Jul 23 08:12:00 2008 From: c.bieck at T-Online.de (Christian Bieck) Date: Wed, 23 Jul 2008 12:12 +0000 (GMT) Subject: [Mristudio-users] Tensor matrix and the .d file Message-ID: <1KLdCk-1fupto0@fwd30.aul.t-online.de> Hello, Working on my DTI diploma thesis, I spent quite some time on getting acquainted with DTIStudio and even more on getting all those AIR .exe files compiled. I now have moved on to trying out Landmarker. To my dismay, the "getting started" section in the landmarker user manual talks about opening a .d file so you can normalize the tensor matrix. I would appreciate it *very* much if someone could provide information on what exactly the tensor matrix is (is it the tensor image I get after pressing on the "Tensor-Eigenvalue-etc." button under DtiMap?) and how I can save the tensor matrix as a .d file. Sorry for this rather elementary question. -Christian Bieck From susumu at mri.jhu.edu Wed Jul 23 10:55:14 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 23 Jul 2008 10:55:14 -0400 Subject: [Mristudio-users] Tensor matrix and the .d file In-Reply-To: <1KLdCk-1fupto0@fwd30.aul.t-online.de> Message-ID: <73alti$33nd08@ipex2.johnshopkins.edu> Hi Christian, the tensor file contains [dxx, dyy, dzz, dxy, dxz, dyz] values at each pixels. The dimension should be 6 x d1 x d2 x d3, where d1, d2, d3 are dimensions of 3d volume data. After you finish tensor calculation by DtiStudio, you get dxx, dyy, dzz, dxy, dxz, dyz images. You have to choose these 6 images and save in one file, which we call "tensor file". Hope it helps. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Christian Bieck Sent: Wednesday, July 23, 2008 8:12 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Tensor matrix and the .d file Hello, Working on my DTI diploma thesis, I spent quite some time on getting acquainted with DTIStudio and even more on getting all those AIR .exe files compiled. I now have moved on to trying out Landmarker. To my dismay, the "getting started" section in the landmarker user manual talks about opening a .d file so you can normalize the tensor matrix. I would appreciate it *very* much if someone could provide information on what exactly the tensor matrix is (is it the tensor image I get after pressing on the "Tensor-Eigenvalue-etc." button under DtiMap?) and how I can save the tensor matrix as a .d file. Sorry for this rather elementary question. -Christian Bieck _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Wed Jul 23 14:36:42 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 23 Jul 2008 14:36:42 -0400 Subject: [Mristudio-users] DTI STUDIO In-Reply-To: <493321.24600.qm@web55813.mail.re3.yahoo.com> Message-ID: <73alti$33pvlv@ipex2.johnshopkins.edu> Dear Tieu, If you donwloaded *.rec files, those are 4D files without headers. We are looking into 8/11 and 8/18 week to provide a tutorial in Baltimore. We'll make an announcement shortly. Meanwhile, please study the manual posted in www.mristudio.org. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of paulina luu Sent: Tuesday, July 22, 2008 1:53 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] DTI STUDIO Dear Dr. Mori, I am a temporary research assistant who is currently learning about DTI and Difussion MRI. I recently downloaded the DTI studio software (John Hopkins) to upload your provided datas and be able to process the raw data. However, I want to know if the data format is 3D or 4D? I also would like to know if there is a tutorial available that provide steps to help me process the raw datas on my own. Thank You. Tieu Luu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080723/81294db7/attachment.html From choisj70 at gmail.com Wed Jul 23 15:46:34 2008 From: choisj70 at gmail.com (Seongjin) Date: Wed, 23 Jul 2008 15:46:34 -0400 Subject: [Mristudio-users] Philips gradient tables Message-ID: Dear DTIstudio users, I wonder if you have gradient tables for Philips Achieva system. >From a source I have a gradient table for low resolution as follows: 0:1.0000, 0.0000, 0.0000 1:0.0000, 1.0000, 0.0000 2:0.0000, 0.0000, 1.0000 3:-0.7044, -0.0881, -0.7044 4:0.7044, 0.7044, 0.0881 5:0.0881, 0.7044, 0.7044 6:0.0000, 0.0000, 0.0000 For medium, 0: 0.7071 -0.7071 1.00 1: 0.7071 -0.7071 -1.00 2: 1.0000 1.0000 0.0000 3: 0.9999 -0.1561 0.9879 4: 0.9894 0.4091 0.9240 5: 0.4674 0.8874 0.9970 6: 0.3866 0.9297 0.9930 7: 0.7667 -0.9511 0.7124 8: 0.6945 0.9954 -0.7295 9: 0.3580 -0.9800 -0.9547 10: 1.0000 -0.9992 -0.0392 11: 0.9999 -0.3989 -0.9171 12: 0.9923 0.4082 -0.9213 13: 0.9989 0.9982 -0.0759 14: 0.2899 0.9919 -0.9655 15: 0.0000 0.0000 0.0000 For high, 0: 1.000, 0.000, 0.000 1: 0.000, 1.000, 0.000 2: 0.000, 0.000, 1.000 3: -0.042, -0.115, -0.993 4: 0.175, -0.200, -0.964 5: 0.232, -0.163, -0.959 6: 0.368, 0.026, -0.930 7: 0.190, 0.374, -0.908 8: -0.117, 0.833, -0.540 9: -0.200, 0.253, -0.947 10: -0.496, 0.134, -0.858 11: -0.014, -0.628, -0.778 12: -0.744, -0.148, -0.651 13: -0.761, 0.320, -0.564 14: -0.181, 0.925, -0.335 15: -0.680, -0.422, -0.600 16: 0.777, 0.471, -0.418 17: 0.924, -0.104, -0.368 18: 0.468, -0.767, -0.438 19: 0.882, -0.189, -0.432 20: 0.690, 0.706, -0.157 21: 0.239, 0.757, -0.608 22: -0.058, 0.984, 0.170 23: -0.537, 0.836, -0.113 24: -0.992, -0.121, -0.042 25: -0.997, 0.071, -0.038 26: -0.872, 0.478, -0.101 27: -0.249, 0.933, 0.258 28: 0.118, 0.992, -0.047 29: 0.338, 0.841, 0.422 30: 0.529, 0.841, 0.116 31: 0.997, 0.055, -0.057 32: 0.000, 0.000, 0.000 I wonder if the tables above are correct or not. Is there anything incorrect or partially incomplete, please let me know. Thanks in advance. Sincerely, Seongjin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080723/a716b665/attachment.html From susumu at mri.jhu.edu Fri Jul 25 07:12:32 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 25 Jul 2008 07:12:32 -0400 Subject: [Mristudio-users] Philips gradient tables In-Reply-To: Message-ID: <73alti$34bjq7@ipex2.johnshopkins.edu> Seongjin, In Philips, there are 3 types (low: 6, medium: 15, high: 32) x 2 (overplus on/off) = 6 gradient tables. The "gradient overplus = on" always use at least two gradients to enhance b efficiency and therefore gaining several millisecond of echo time. In your example, the low and high is "overplus = off" and the medium is "overplus = on". You can see "1, 0, 0" in the first two but not in the medium. The medium with "overplus = off" should look like; 0: 0, 0, 0 1: 1, 0, 0 2: 0, 1, 0 3: 0, 0, 1 4: -0.0424,-0.1146,-0.9925 5: 0.1749,-0.2005,-0.9639 6: 0.2323,-0.1626,-0.9590 7: 0.3675,0.0261,-0.9296 8: 0.1902,0.3744,-0.9076 9: -0.1168,0.8334,-0.5402 10: -0.2005,0.2527,-0.9466 11: -0.4958,0.1345,-0.8580 12: -0.0141,-0.6281,-0.7780 13: -0.7445,-0.1477,-0.6511 14: -0.7609,0.3204,-0.5643 15: -0.1809,0.9247,-0.33510 16: -0.6796,-0.4224,-0.5997 17: 0.7771,0.4707,-0.4178 18: 0.9242,-0.1036,-0.3677 19: 0.4685,-0.7674,-0.4378 20: 0.8817,-0.1893,-0.4322 21: 0.6904,0.7062,-0.1569 22: 0.2391,0.7571,-0.6080 23: -0.0578,0.9837,0.1703 24: -0.5368,0.8361,-0.1135 25: -0.9918,-0.1207,-0.0423 26: -0.9968,0.0709,-0.0379 27: -0.8724,0.4781,-0.1014 28: -0.2487,0.9335,0.2581 29: 0.1183,0.9919,-0.0471 30: 0.3376,0.8415,0.4218 31: 0.5286,0.8409,0.1163 32: 0.9969,0.0550,-0.0571 In general, I do not recommend to user "overplus = on", because tensor calculation get complicated when oblique planes are used. You have to recalculate the table based on the image angles. Also, please note that the "0, 0, 0" could be the first or the last image depending on how you specify the output files. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Wednesday, July 23, 2008 3:47 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Philips gradient tables Dear DTIstudio users, I wonder if you have gradient tables for Philips Achieva system. >From a source I have a gradient table for low resolution as follows: 0:1.0000, 0.0000, 0.0000 1:0.0000, 1.0000, 0.0000 2:0.0000, 0.0000, 1.0000 3:-0.7044, -0.0881, -0.7044 4:0.7044, 0.7044, 0.0881 5:0.0881, 0.7044, 0.7044 6:0.0000, 0.0000, 0.0000 For medium, 0: 0.7071 -0.7071 1.00 1: 0.7071 -0.7071 -1.00 2: 1.0000 1.0000 0.0000 3: 0.9999 -0.1561 0.9879 4: 0.9894 0.4091 0.9240 5: 0.4674 0.8874 0.9970 6: 0.3866 0.9297 0.9930 7: 0.7667 -0.9511 0.7124 8: 0.6945 0.9954 -0.7295 9: 0.3580 -0.9800 -0.9547 10: 1.0000 -0.9992 -0.0392 11: 0.9999 -0.3989 -0.9171 12: 0.9923 0.4082 -0.9213 13: 0.9989 0.9982 -0.0759 14: 0.2899 0.9919 -0.9655 15: 0.0000 0.0000 0.0000 For high, 0: 1.000, 0.000, 0.000 1: 0.000, 1.000, 0.000 2: 0.000, 0.000, 1.000 3: -0.042, -0.115, -0.993 4: 0.175, -0.200, -0.964 5: 0.232, -0.163, -0.959 6: 0.368, 0.026, -0.930 7: 0.190, 0.374, -0.908 8: -0.117, 0.833, -0.540 9: -0.200, 0.253, -0.947 10: -0.496, 0.134, -0.858 11: -0.014, -0.628, -0.778 12: -0.744, -0.148, -0.651 13: -0.761, 0.320, -0.564 14: -0.181, 0.925, -0.335 15: -0.680, -0.422, -0.600 16: 0.777, 0.471, -0.418 17: 0.924, -0.104, -0.368 18: 0.468, -0.767, -0.438 19: 0.882, -0.189, -0.432 20: 0.690, 0.706, -0.157 21: 0.239, 0.757, -0.608 22: -0.058, 0.984, 0.170 23: -0.537, 0.836, -0.113 24: -0.992, -0.121, -0.042 25: -0.997, 0.071, -0.038 26: -0.872, 0.478, -0.101 27: -0.249, 0.933, 0.258 28: 0.118, 0.992, -0.047 29: 0.338, 0.841, 0.422 30: 0.529, 0.841, 0.116 31: 0.997, 0.055, -0.057 32: 0.000, 0.000, 0.000 I wonder if the tables above are correct or not. Is there anything incorrect or partially incomplete, please let me know. Thanks in advance. Sincerely, Seongjin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080725/d057c875/attachment-0001.html From susumu at mri.jhu.edu Fri Jul 25 12:09:48 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 25 Jul 2008 12:09:48 -0400 Subject: [Mristudio-users] Coregistration using AIR In-Reply-To: <007501c8e575$1cd1b960$8516ee0a@DellRIRC> Message-ID: <73alti$34eaa4@ipex2.johnshopkins.edu> Dear Dr. Takaya, Do you want to coregister, combine two DTI scans and calculated a tensor? If that's the case, you can treat the two scans as two signal averaging. Load both of them, coregister the first scan to the second scan using the AIR in DtiStudio, and do tensor calculation. If you want to get separate tensor fields from the two datasets and then coregister for ROI drawing, I recommend you to use Landmarker. You first have to calculate all DTI-based images you need (tensor, FA, ADC, b0, etc). You can then bring b0 images from the two datasets into Landmarker and perform AIR. You can save the transformation matrix and apply it to other images. Alternatively, if you load all data at once, AIR is automatically applied to all loaded data (of course you have to specify which image you want to use to drive AIR). One important function of Landmarker is that it can apply the transformation matrix to tensor files too (it does tensor reorientations if rotation components are involved). Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Shigetoshi TAKAYA Sent: Monday, July 14, 2008 1:48 AM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] Coregistration using AIR Hello I have two scans of DWI with time interval for each patient (1st scan and 2nd scan). I would like to coregister the images in the 2nd scan onto those in the 1st scan in each subject using Automatic Image Registration (AIR) algorithm implemented in DTIStudio, for the purpose of drawing ROIs in the same brain regions in both scans. First, I did eddy current correction and motion correction using affine transformation in each scan (1st scan and 2nd scan). Then, I coregistered the B0 image in the 2nd scan onto that in the 1st scan. And I would like to adjust the same transformation matrix to the rest of the images in the 2nd scan. I know that the transformation matrix can be saved when conducting AIR. Can we use this file to transform the rest of the images in the 2nd scan? Many thanks, Shigetoshi Takaya -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080725/92196e02/attachment.html From susumu at mri.jhu.edu Fri Jul 25 12:15:39 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 25 Jul 2008 12:15:39 -0400 Subject: [Mristudio-users] Loading NIfTI (.nii) format In-Reply-To: <32a27f2a0807131900i29d03dcbu909fa3a92a19f694@mail.gmail.com> Message-ID: <73alti$34ec7a@ipex2.johnshopkins.edu> I don't think DtiStudio can read NIfTI, but we can look into it. If NIfTI is simply a header + data format and you know the exact size of the header, you can try "image offset" + raw or REC format. Once you could load it to MriView, you can convert the data to REC format (assuming you have 4D file), which can be used for tensor calculation (DtiMapping). _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Raj Jaswal Sent: Sunday, July 13, 2008 10:00 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Loading NIfTI (.nii) format Hello all, I'm having some problems loading the NIfTI (.nii) format using DTI Studio. First, when I decide to load a .nii file through MRI View3D...I do not find the appropriate format to select in the "Image Parameters" window. I tried to select the Analyze format because the .nii format is adapted from the Analyze format. But that does not work. I get the following error: CMriView3DDoc()::CreateImgWithAnalyzeFile() Analyze Header File open error: Next, if I want to load a .nii file through DTI Mapping...I do not find the appropriate format to select. The dataset that I have consists of one .nii file and one header file per subject. I am still relatively new to DTI Studio and am learning a lot as I go along! I would appreciate any help or input. Thank you very much. -- - RJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080725/34942a5b/attachment.html From choisj70 at gmail.com Fri Jul 25 17:48:19 2008 From: choisj70 at gmail.com (Seongjin) Date: Fri, 25 Jul 2008 17:48:19 -0400 Subject: [Mristudio-users] Philips gradient tables In-Reply-To: <73alti$34bjq7@ipex2.johnshopkins.edu> References: <73alti$34bjq7@ipex2.johnshopkins.edu> Message-ID: Thanks a lot. Seongjin On Fri, Jul 25, 2008 at 7:12 AM, susumu wrote: > Seongjin, > > > > In Philips, there are 3 types (low: 6, medium: 15, high: 32) x 2 (overplus > on/off) = 6 gradient tables. > > > > The "gradient overplus = on" always use at least two gradients to enhance b > efficiency and therefore gaining several millisecond of echo time. In your > example, the low and high is "overplus = off" and the medium is "overplus = > on". You can see "1, 0, 0" in the first two but not in the medium. > > > > The medium with "overplus = off" should look like; > > > > 0: 0, 0, 0 > > 1: 1, 0, 0 > > 2: 0, 1, 0 > > 3: 0, 0, 1 > > 4: -0.0424,-0.1146,-0.9925 > > 5: 0.1749,-0.2005,-0.9639 > > 6: 0.2323,-0.1626,-0.9590 > > 7: 0.3675,0.0261,-0.9296 > > 8: 0.1902,0.3744,-0.9076 > > 9: -0.1168,0.8334,-0.5402 > > 10: -0.2005,0.2527,-0.9466 > > 11: -0.4958,0.1345,-0.8580 > > 12: -0.0141,-0.6281,-0.7780 > > 13: -0.7445,-0.1477,-0.6511 > > 14: -0.7609,0.3204,-0.5643 > > 15: -0.1809,0.9247,-0.33510 > > 16: -0.6796,-0.4224,-0.5997 > > 17: 0.7771,0.4707,-0.4178 > > 18: 0.9242,-0.1036,-0.3677 > > 19: 0.4685,-0.7674,-0.4378 > > 20: 0.8817,-0.1893,-0.4322 > > 21: 0.6904,0.7062,-0.1569 > > 22: 0.2391,0.7571,-0.6080 > > 23: -0.0578,0.9837,0.1703 > > 24: -0.5368,0.8361,-0.1135 > > 25: -0.9918,-0.1207,-0.0423 > > 26: -0.9968,0.0709,-0.0379 > > 27: -0.8724,0.4781,-0.1014 > > 28: -0.2487,0.9335,0.2581 > > 29: 0.1183,0.9919,-0.0471 > > 30: 0.3376,0.8415,0.4218 > > 31: 0.5286,0.8409,0.1163 > > 32: 0.9969,0.0550,-0.0571 > > > > In general, I do not recommend to user "overplus = on", because tensor > calculation get complicated when oblique planes are used. You have to > recalculate the table based on the image angles. > > > > Also, please note that the "0, 0, 0" could be the first or the last image > depending on how you specify the output files. > > > > Susumu > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > *Sent:* Wednesday, July 23, 2008 3:47 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] Philips gradient tables > > > > Dear DTIstudio users, > > I wonder if you have gradient tables for Philips Achieva system. > > >From a source I have a gradient table for low resolution as follows: > > 0:1.0000, 0.0000, 0.0000 > 1:0.0000, 1.0000, 0.0000 > 2:0.0000, 0.0000, 1.0000 > 3:-0.7044, -0.0881, -0.7044 > 4:0.7044, 0.7044, 0.0881 > 5:0.0881, 0.7044, 0.7044 > 6:0.0000, 0.0000, 0.0000 > > > For medium, > > 0: 0.7071 -0.7071 1.00 > 1: 0.7071 -0.7071 -1.00 > 2: 1.0000 1.0000 0.0000 > 3: 0.9999 -0.1561 0.9879 > 4: 0.9894 0.4091 0.9240 > 5: 0.4674 0.8874 0.9970 > 6: 0.3866 0.9297 0.9930 > 7: 0.7667 -0.9511 0.7124 > 8: 0.6945 0.9954 -0.7295 > 9: 0.3580 -0.9800 -0.9547 > 10: 1.0000 -0.9992 -0.0392 > 11: 0.9999 -0.3989 -0.9171 > 12: 0.9923 0.4082 -0.9213 > 13: 0.9989 0.9982 -0.0759 > 14: 0.2899 0.9919 -0.9655 > 15: 0.0000 0.0000 0.0000 > > > For high, > > 0: 1.000, 0.000, 0.000 > 1: 0.000, 1.000, 0.000 > 2: 0.000, 0.000, 1.000 > 3: -0.042, -0.115, -0.993 > 4: 0.175, -0.200, -0.964 > 5: 0.232, -0.163, -0.959 > 6: 0.368, 0.026, -0.930 > 7: 0.190, 0.374, -0.908 > 8: -0.117, 0.833, -0.540 > 9: -0.200, 0.253, -0.947 > 10: -0.496, 0.134, -0.858 > 11: -0.014, -0.628, -0.778 > 12: -0.744, -0.148, -0.651 > 13: -0.761, 0.320, -0.564 > 14: -0.181, 0.925, -0.335 > 15: -0.680, -0.422, -0.600 > 16: 0.777, 0.471, -0.418 > 17: 0.924, -0.104, -0.368 > 18: 0.468, -0.767, -0.438 > 19: 0.882, -0.189, -0.432 > 20: 0.690, 0.706, -0.157 > 21: 0.239, 0.757, -0.608 > 22: -0.058, 0.984, 0.170 > 23: -0.537, 0.836, -0.113 > 24: -0.992, -0.121, -0.042 > 25: -0.997, 0.071, -0.038 > 26: -0.872, 0.478, -0.101 > 27: -0.249, 0.933, 0.258 > 28: 0.118, 0.992, -0.047 > 29: 0.338, 0.841, 0.422 > 30: 0.529, 0.841, 0.116 > 31: 0.997, 0.055, -0.057 > 32: 0.000, 0.000, 0.000 > > > I wonder if the tables above are correct or not. Is there anything > incorrect or partially incomplete, please let me know. > Thanks in advance. > > Sincerely, > Seongjin > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080725/eedeaebc/attachment-0001.html From jayashreemenon at gmail.com Fri Jul 25 23:30:41 2008 From: jayashreemenon at gmail.com (Jayasree) Date: Sat, 26 Jul 2008 09:00:41 +0530 Subject: [Mristudio-users] 3D reconstruction and gradient tables Message-ID: Dear DTIstudio users, I am a new user of the software. When I am loading the DICOM images using MRIview 3D, it is not reconstructing the 3D images , instead I am getting images as if we see on the film.Can any body give solution for this. Also please get me the gradient table for Siemens Magnetom Avanto TIM when 12, 20 and 30 gradient orientations are used. How do you get these tables? Please help. Thanks Jay -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080726/85a45a5d/attachment.html From darshanp20 at yahoo.com Sat Jul 26 11:12:41 2008 From: darshanp20 at yahoo.com (darshan pai) Date: Sat, 26 Jul 2008 08:12:41 -0700 (PDT) Subject: [Mristudio-users] The b matrix In-Reply-To: <6ua0er$3337pu@ipex2.johnshopkins.edu> Message-ID: <898987.89668.qm@web30401.mail.mud.yahoo.com> Thanx for the description Darshan --- On Mon, 7/21/08, susumu wrote: > From: susumu > Subject: Re: [Mristudio-users] The b matrix > To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > Date: Monday, July 21, 2008, 7:10 PM > Hi Darshan, > > If we assume one tensor (one fiber population) in each > pixel, b-value of 700 > - 1,500 should provide similar results. > > If b-value is small, the image intensity is high, echo time > shorter, less > motion sensitive, and less eddy current. The downside is, > you have less > signal attenuation and determination of the slope (=D = > proportional to > Log(S/S0)) becomes unstable. For example, if there is only > 5-10% expected > signal loss while there is +/- 5% signal fluctuation by > SNR, you have a > problem. > > When b is higher than 1,000, you expect more than 50% of > signal attenuation > in average, which is enough to determine D, but the signal > goes closer to > the noise floor and have other practical issues such as > longer TE (thus > lower SNR), more motion sensitive, and eddy current. > > So too small b and too high b are not good from the SNR > point of view. > Empirically, the optimum b should be somewhere around 700 - > 1,500. > > Here, the b - SNR relationship is the center of our > interest when we use the > simple tensor model. > > There are some simulation-based papers that tired to > theoretically determine > the optimum b, but it is not always straightforward because > the impacts of > TE/motion/eddy currents are difficult to model. Danny > Alexander has the most > comprehensive simulation paper in this regard. Our internal > data with actual > human data didn't show much difference between b = 750 > to 1,500. Start to > see problems with b-values lower than 500 and more than > 2,000 . > > If you are interested in more than one tensor in each > pixel, there is a > totally different factor. First of all, the decay is not > mono-exponential. > An interesting feature of exponential decay is, if you want > to differentiate > bi-exponential and mono-exponential, you have to look at > high-b range > because they behave identical in low-b range. In other > words, everything > looks single-tensor if low b-values are used. This > simulation can be seen in > Larry Frank's HARDI paper, showing two-crossing-fiber > pixel looks like a > single pancake tensor, not "X" with a low > b-value. The higher the b-value, > the higher the power to delineate the "X" shape > accurately. The smaller the > crossing angle, the more difficult to resolve with smaller > b. This is why > the original Van Wedeen paper used b = 30,000. > > It is still under investigation by many researchers to > figure out how much b > is needed. Some say 3,000 is enough, but it should be a > function of crossing > angle, SNR, and the number of b-orientations. I don't > know the answer. > > I hope this helps. > > Susumu > > > > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of > darshan pai > Sent: Friday, July 18, 2008 4:46 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] The b matrix > > Hello all, > > I just had a question regarding the Weighting matrix . I > have always seen > that the b value is usually set to be 1000 . Is there a > specific reason to > do that . I have seen literature which suggest that having > b value to 1000 > is appropriate to at least resolve two fiber populations. > Which means that > increasing the value should be advantageous for multiple > orientations. Is > there an SNR issue to take care of at higher b values ? > > Maybe the question is too basic and maybe a little too > trivial . Just > curious to know > > Regards > Darshan > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users From babimo at libero.it Mon Jul 28 13:11:35 2008 From: babimo at libero.it (babimo at libero.it) Date: Mon, 28 Jul 2008 19:11:35 +0200 Subject: [Mristudio-users] DTImapping Message-ID: Hi, i'm trying to use DTIMapping for fiber tracking, but the input format of the DICOM DWI must be in .dcm not in the native one, right? And if i load files in .dcm and i choose all slices to be processed, at the and of the calculation i have in sagittal and coronal view no one image but like a film. What parameter i have to choose in the module slice to be processed? the number of the slices for gradient direction? Thanks in advace, Babila Moroni From icee41 at gmail.com Mon Jul 28 13:17:23 2008 From: icee41 at gmail.com (Tapan Jani) Date: Mon, 28 Jul 2008 12:17:23 -0500 Subject: [Mristudio-users] DTImapping In-Reply-To: References: Message-ID: <43f2b0680807281017t39b6348elb0a8cf4c96df7e1d@mail.gmail.com> I had the same problem, all it was for me was properly adjusting the gradient table and the values therein. if you have those, it should help greatly. Tapan tjani2 at uic.edu p.s. my sagittal and coronal views are blurry and condensed, but my axial is stretched perfectly - any idea how to fix this? On Mon, Jul 28, 2008 at 12:11 PM, babimo at libero.it wrote: > Hi, > i'm trying to use DTIMapping for fiber tracking, but the input format of > the DICOM DWI > must be in .dcm not in the native one, right? > And if i load files in .dcm and i choose all slices to be processed, at the > and of the > calculation i have in sagittal and coronal view no one image but like a > film. > What parameter i have to choose in the module slice to be processed? the > number of the > slices for gradient direction? > Thanks in advace, > Babila Moroni > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080728/752b86e2/attachment.html From susumu at mri.jhu.edu Mon Jul 28 14:16:17 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 28 Jul 2008 14:16:17 -0400 Subject: [Mristudio-users] DTImapping In-Reply-To: Message-ID: <73alti$35den6@ipex2.johnshopkins.edu> Hi Babila, It happens if you try to read Siemens Mosaic as Dicom. If you are using Siemens, could you try Mosaic format? Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of babimo at libero.it Sent: Monday, July 28, 2008 1:12 PM To: mristudio-users Subject: [Mristudio-users] DTImapping Hi, i'm trying to use DTIMapping for fiber tracking, but the input format of the DICOM DWI must be in .dcm not in the native one, right? And if i load files in .dcm and i choose all slices to be processed, at the and of the calculation i have in sagittal and coronal view no one image but like a film. What parameter i have to choose in the module slice to be processed? the number of the slices for gradient direction? Thanks in advace, Babila Moroni _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From babila.moroni at mail.polimi.it Mon Jul 28 13:06:43 2008 From: babila.moroni at mail.polimi.it (babila.moroni at mail.polimi.it) Date: Mon, 28 Jul 2008 19:06:43 +0200 Subject: [Mristudio-users] DTIMapping Message-ID: <20080728190643.dkopww1mo4oos0k4@webmail-stud.polimi.it> Hi, i'm trying to use DTIMapping for fiber tracking, but the input format of the DICOM DWI must be in .dcm not in the native one, right? And if i load files in .dcm and i choose all slices to be processed, at the and of the calculation i have in sagittal and coronal view no one image but like a film. What parameter i have to choose in the module slice to be processed? the number of the slices for gradient direction? Thanks in advace, Babila Moroni From susumu at mri.jhu.edu Thu Jul 17 20:31:21 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 17 Jul 2008 20:31:21 -0400 Subject: [Mristudio-users] Gradient Table In-Reply-To: <487F049E.7050303@wustl.edu> Message-ID: <6u9t96$3k2q5t@ipex1.johnshopkins.edu> Hi all, Here I attached tables we are using. Please note that Siemens and GE changed gradient tables in the past. These should work for latest operating systems but may not for older versions. If gradient table is wrong, you can tell it immediately because color maps are not symmetric and the corpus callosum is not pure red. The best way is to contact the manufacturers, but we may help to locate the correct tables for older versions. As Gordon mentioned, Siemens users need to be EXTREMELY careful when they use oblique planes. Unless you are using the latest version of the operating system, the gradient table doesn't rotate with imaging place (it always stick with physical X/Y/Z gradient). That means, we need to recalculate gradient table based on the oblique information. If you are using Dicom/Mosaic, this can be automatically done by checking "Rotate table if applicable" check box. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users- bounces at mristudio.org] On Behalf Of Junqian Gordon Xu Sent: Thursday, July 17, 2008 4:37 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Gradient Table 1) Siemens specify DTI table in lab coordinates (i.e. XYZ). 2) The where-abouts of the DTI table info is software version dependent VA25, VA21 and earlier: hard coded in the ep2d_diff.cpp source file.VB13, VB15 and later: if you use the standard MDDW (limits your max diffusion direction to 64?), the table is again hard coded. If you have the license to use diffusion FREE, the table is in a user supplied ASCII file (you probably know where it is). 3) You may find something like "diffusion direction" in DICOM headers if your scanner is VB13/VB15. One caveat is that this table is not the original table if your slices are oblique. In other words, this table has already been multiplied with "slice normal vector" which could also been found from the header. Siemens probably uses this for their color coded FA map. Hope this helpsGordon On 07/16/2008 07:54 PM, ??? wrote:> As I know, x,y,z information is not always necessary.> I have succeeded to load Siemens (Trio, 20 dir) Mosaic files with > gradient numbers> You only have to not forget to write numbers of 100, 100, 100 and > finally 0,0,0 at the end of table.> Here is an example,> > 0: -1.000000, 0.000000, 0.000000> 1: 0.000000, -1.000000, 0.000000> 2: 0.031984, -0.799591, 0.599693> .> .> .> 18: -0.111012, - 0.264029, -0.958105> 19: -0.031984, -0.799591, -0.599693> 20: 100, 100, 100> 21: 0,0,0> > If you really want to find the x,y,z information, I'm afraid I can't > answer it.> But I have heard that the information is not technically necessary from > the computer technologist> working at the Siemens company. He have read the instructions and talked > to me like that. > > Wish it would be helpful.> > Regards,> > YJ Cho> > > 2008/7/17, Tapan Jani >:> > Hello all,> > I sent out an e-mail earlier about generating a gradient table and> am still a little bit confused. 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 3T Excite GE scanner to perform> our DTI scans, but we also have a Siemens scanner for which the> following questions apply. Within the dicom header of the GE> scanner, under the tag #DTI Diffusion Dir (0019, 01E0), we are able> to tell the number of gradients, but not able to find the x,y,z> information.> > Is there a program that can generate gradient tables to go along> with our dicom data, or can it actually be found within the header -> and if so, where? Finally I was curious as to whether there are> standard gradient tables that go along with specific scanners every> time a DTI scan is performed.> > Thank you very much for all of your help, it is much appreciated.> > Sincerely,> > Tapan Jani> > tjani2 at uic.edu > > > _______________________________________________> Mristudio-users mailing list> Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users> > > > > -- > Yang-Je Cho> > Dept of Neurology, Yonsei University> College of Medicine, Seoul, Korea> Phone: 82-2-2228-1600, Cell: 016-298-7456, Fax: 82-2-393- 0705> > > ------------------------------------------------------------------ ------> > _______________________________________________> Mristudio-users mailing list> Mristudio-users at mristudio.org> http://lists.mristudio.org/mailman/listinfo/mristudio- users_______________________________________________Mristudio-users mailing listMristudio- users at mristudio.orghttp://lists.mristudio.org/mailman/listinfo/mristudio- users -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: NewSiemens12.txt Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080717/2ea57cf6/attachment-0001.txt -------------- next part -------------- A non-text attachment was scrubbed... Name: GEtensor.doc Type: application/msword Size: 857088 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080717/2ea57cf6/attachment-0001.doc From babimo at libero.it Mon Jul 28 14:47:04 2008 From: babimo at libero.it (babimo at libero.it) Date: Mon, 28 Jul 2008 20:47:04 +0200 Subject: [Mristudio-users] DTImapping Message-ID: Hi, I have DICOM directly from the scanner SIEMENS Allegra they aren't with a .dcm extention so I convert them with a module in another program Slicer 3.2, I choose Siemens, GE or Philips DICOM and i load :a right gradient table 35 gradient direction with 5 B0 (T2 image); a .dcm files (805 files) and all slices to be processed; but DTIStudio build a 3D image in axial view with 805 slices, and the sagittal and coronal view like a film with 127 slices. I do not understand where mistake to load data. Thanks, Babila From susumu at mri.jhu.edu Mon Jul 28 15:09:32 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 28 Jul 2008 15:09:32 -0400 Subject: [Mristudio-users] DTImapping In-Reply-To: Message-ID: <73alti$35dvhe@ipex2.johnshopkins.edu> Hi Babila, Dicom formats do not always have *.dcm extension. DtiStudio can read it as long as it's dicom regardless of the extension. Did you try both Dicom and Mosaic directly from the original Siemens files? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of babimo at libero.it Sent: Monday, July 28, 2008 2:47 PM To: mristudio-users Subject: Re: [Mristudio-users] DTImapping Hi, I have DICOM directly from the scanner SIEMENS Allegra they aren't with a .dcm extention so I convert them with a module in another program Slicer 3.2, I choose Siemens, GE or Philips DICOM and i load :a right gradient table 35 gradient direction with 5 B0 (T2 image); a .dcm files (805 files) and all slices to be processed; but DTIStudio build a 3D image in axial view with 805 slices, and the sagittal and coronal view like a film with 127 slices. I do not understand where mistake to load data. Thanks, Babila _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From rajagov2 at ccf.org Mon Jul 28 17:18:06 2008 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Mon, 28 Jul 2008 17:18:06 -0400 Subject: [Mristudio-users] AIR files Message-ID: <77A88E90A851594AAEF830450587C39D01EDA8AB@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, I am having hard time in compiling the AIR files makeaheader.exe, alignlinear.exe and align_warp.exe. Is there any possibility that i can get these precompiled files. Thanks in Advance. Reagrds 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 (2008). 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/20080728/1d51a6db/attachment.html From susumu at mri.jhu.edu Mon Jul 28 17:43:38 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 28 Jul 2008 17:43:38 -0400 Subject: [Mristudio-users] 8/11 Tutorial Message-ID: <73alti$35fcad@ipex2.johnshopkins.edu> Hi all, It seems that we have the more than enough number of people (more than 40) expressing their interest to attend the tutorial. We are trying to find a room now and will get back to you tomorrow, hopefully. Some people asked about the level of the tutorial. We will try so that a person without any prior experience can at least manage to follow. Thanks, Susumu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080728/6f2e9ad2/attachment.html From choisj70 at gmail.com Mon Jul 28 18:16:49 2008 From: choisj70 at gmail.com (Seongjin) Date: Mon, 28 Jul 2008 18:16:49 -0400 Subject: [Mristudio-users] 8/11 Tutorial In-Reply-To: <73alti$35fcad@ipex2.johnshopkins.edu> References: <73alti$35fcad@ipex2.johnshopkins.edu> Message-ID: Do you have any plan put the tutorial on-line for people cannot attend the tutorial session? sincerely, Seongjin On Mon, Jul 28, 2008 at 5:43 PM, susumu wrote: > Hi all, > > > > It seems that we have the more than enough number of people (more than 40) > expressing their interest to attend the tutorial. We are trying to find a > room now and will get back to you tomorrow, hopefully. > > > > Some people asked about the level of the tutorial. We will try so that a > person without any prior experience can at least manage to follow. > > > > Thanks, > > > > Susumu > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080728/07885a1e/attachment.html From susumu at mri.jhu.edu Mon Jul 28 18:22:36 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 28 Jul 2008 18:22:36 -0400 Subject: [Mristudio-users] 8/11 Tutorial In-Reply-To: Message-ID: <73alti$35fl0t@ipex2.johnshopkins.edu> I can look into that option. Do you have any suggestions about how we can do it? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Monday, July 28, 2008 6:17 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] 8/11 Tutorial Do you have any plan put the tutorial on-line for people cannot attend the tutorial session? sincerely, Seongjin On Mon, Jul 28, 2008 at 5:43 PM, susumu wrote: Hi all, It seems that we have the more than enough number of people (more than 40) expressing their interest to attend the tutorial. We are trying to find a room now and will get back to you tomorrow, hopefully. Some people asked about the level of the tutorial. We will try so that a person without any prior experience can at least manage to follow. Thanks, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080728/c9e8e354/attachment-0001.html From fairywongyujia at gmail.com Mon Jul 28 22:59:27 2008 From: fairywongyujia at gmail.com (=?GB2312?B?zfXT6rzR?=) Date: Tue, 29 Jul 2008 10:59:27 +0800 Subject: [Mristudio-users] 8/11 Tutorial In-Reply-To: References: <73alti$35fcad@ipex2.johnshopkins.edu> Message-ID: Good suggestion ! 2008/7/29 [Seongjin] > Do you have any plan put the tutorial on-line for people cannot attend the > tutorial session? > > > sincerely, > > Seongjin > > On Mon, Jul 28, 2008 at 5:43 PM, susumu wrote: > >> Hi all, >> >> >> >> It seems that we have the more than enough number of people (more than 40) >> expressing their interest to attend the tutorial. We are trying to find a >> room now and will get back to you tomorrow, hopefully. >> >> >> >> Some people asked about the level of the tutorial. We will try so that a >> person without any prior experience can at least manage to follow. >> >> >> >> Thanks, >> >> >> >> Susumu >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Yujia Wang Department of Scientific & Engineering Computing School of Mathematical Sciences Peking University Phone: (86)-10-52769591 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080729/ab7f8ab8/attachment.html From chanlon at wfubmc.edu Mon Jul 28 23:04:10 2008 From: chanlon at wfubmc.edu (Colleen Hanlon) Date: Mon, 28 Jul 2008 23:04:10 -0400 Subject: [Mristudio-users] 8/11 Tutorial Message-ID: <4CCFAF32FB7B2C449A189C82198E4265108D9831@EXCHVS1.medctr.ad.wfubmc.edu> I agree! ----- Original Message ----- From: mristudio-users-bounces at mristudio.org To: DTI Studio, ROI Editor, Landmarker Questions/Support Sent: Mon Jul 28 22:59:27 2008 Subject: Re: [Mristudio-users] 8/11 Tutorial Good suggestion ! 2008/7/29 [Seongjin] Do you have any plan put the tutorial on-line for people cannot attend the tutorial session? sincerely, Seongjin On Mon, Jul 28, 2008 at 5:43 PM, susumu wrote: Hi all, It seems that we have the more than enough number of people (more than 40) expressing their interest to attend the tutorial. We are trying to find a room now and will get back to you tomorrow, hopefully. Some people asked about the level of the tutorial. We will try so that a person without any prior experience can at least manage to follow. Thanks, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Yujia Wang Department of Scientific & Engineering Computing School of Mathematical Sciences Peking University Phone: (86)-10-52769591 From smalone at tfs.psych.umn.edu Tue Jul 29 12:47:09 2008 From: smalone at tfs.psych.umn.edu (Steve Malone) Date: Tue, 29 Jul 2008 11:47:09 -0500 Subject: [Mristudio-users] streaming video of 8/11 Tutorial In-Reply-To: <73alti$35fl0t@ipex2.johnshopkins.edu> References: Message-ID: The UCLA Academic Technology Services web site has QuickTime movies of lectures on different topics in statistical analysis, which can be streamed to one's desktop over a high-speed connection. This page is for a seminar on making movies to be viewed over the web, with instructions: http://www.ats.ucla.edu/stat/seminars/MakingMovies/default.htm Regards, Steve On 28 Jul 08, at 18:22, susumu wrote: > This is a multi-part message in MIME format. > > --===============0640623822441498704== > Content-type: multipart/alternative; > boundary="----=_NextPart_000_03E1_01C8F0DE.E9509F00" > > This is a multi-part message in MIME format. > > ------=_NextPart_000_03E1_01C8F0DE.E9509F00 > Content-Type: text/plain; > charset="us-ascii" > Content-Transfer-Encoding: 7bit > > I can look into that option. Do you have any suggestions about how we can do > it? > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] > Sent: Monday, July 28, 2008 6:17 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] 8/11 Tutorial > > > > Do you have any plan put the tutorial on-line for people cannot attend the > tutorial session? > > > > > > sincerely, > > > > Seongjin > > On Mon, Jul 28, 2008 at 5:43 PM, susumu wrote: > > Hi all, > > > > It seems that we have the more than enough number of people (more than 40) > expressing their interest to attend the tutorial. We are trying to find a > room now and will get back to you tomorrow, hopefully. > > > > Some people asked about the level of the tutorial. We will try so that a > person without any prior experience can at least manage to follow. > > > > Thanks, > > > > Susumu > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > ------=_NextPart_000_03E1_01C8F0DE.E9509F00 > Content-Type: text/html; > charset="us-ascii" > Content-Transfer-Encoding: quoted-printable > > xmlns:o=3D"urn:schemas-microsoft-com:office:office" = > xmlns:w=3D"urn:schemas-microsoft-com:office:word" = > xmlns=3D"http://www.w3.org/TR/REC-html40"> > > > charset=3DUS-ASCII"> > > > > > > > > >
> >

style=3D'font-size: > 10.0pt;font-family:Arial;color:navy'>I can look into that option. Do you = > have > any suggestions about how we can do it?

> >

style=3D'font-size: > 10.0pt;font-family:Arial;color:navy'> 

> >
> >
size=3D3 > face=3D"Times New Roman"> > >
> >
> >

style=3D'font-size:10.0pt; > font-family:Tahoma;font-weight:bold'>From: size=3D2 > face=3DTahoma> > mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] style=3D'font-weight: > bold'>On Behalf Of [Seongjin]
> Sent: Monday, July 28, = > 2008 6:17 > PM
> To: DTI Studio, ROI = > Editor, > Landmarker Questions/Support
> Subject: Re: = > [Mristudio-users] > 8/11 Tutorial

> >
> >

style=3D'font-size: > 12.0pt'> 

> >
> >
> >

style=3D'font-size: > 12.0pt'>Do you have any plan put the tutorial on-line for people cannot = > attend > the tutorial session?

> >
> >
> >

style=3D'font-size: > 12.0pt'> 

> >
> >
> >

style=3D'font-size: > 12.0pt'> 

> >
> >
> >

style=3D'font-size: > 12.0pt'>sincerely,

> >
> >
> >

style=3D'font-size: > 12.0pt'> 

> >
> >
> >

face=3D"Times New Roman"> style=3D'font-size:12.0pt'>Seongjin

> >
> >
> >

style=3D'font-size: > 12.0pt'>On Mon, Jul 28, 2008 at 5:43 PM, susumu < href=3D"mailto:susumu at mri.jhu.edu">susumu at mri.jhu.edu> = > wrote:

> >
> >
> >

style=3D'font-size:10.0pt;font-family:Arial'>Hi > all,

> >

style=3D'font-size:10.0pt;font-family:Arial'>  :p>

> >

style=3D'font-size:10.0pt;font-family:Arial'>It > seems that we have the more than enough number of people (more than 40) > expressing their interest to attend the tutorial. We are trying to find = > a room > now and will get back to you tomorrow, hopefully. = >

> >

style=3D'font-size:10.0pt;font-family:Arial'>  :p>

> >

style=3D'font-size:10.0pt;font-family:Arial'>Some > people asked about the level of the tutorial. We will try so that a = > person > without any prior experience can at least manage to = > follow.

> >

style=3D'font-size:10.0pt;font-family:Arial'>  :p>

> >

style=3D'font-size:10.0pt;font-family:Arial'>Thanks, o:p>

> >

style=3D'font-size:10.0pt;font-family:Arial'>  :p>

> >

style=3D'font-size:10.0pt; > font-family:Arial;color:#888888'>Susumu color=3D"#888888"> style=3D'color:#888888'>

> >
> >
> >

face=3D"Times New Roman">
> _______________________________________________
> Mristudio-users mailing list
> href=3D"mailto:Mristudio-users at mristudio.org">Mristudio-users at mristudio.o= > rg
> target=3D"_blank">http://lists.mristudio.org/mailman/listinfo/mristudio-u= > sers

> >
> >

style=3D'font-size: > 12.0pt'> 

> >
> >
> > > > > > ------=_NextPart_000_03E1_01C8F0DE.E9509F00-- > > --===============0640623822441498704== > Content-Type: text/plain; charset="us-ascii" > MIME-Version: 1.0 > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > --===============0640623822441498704==-- From haoyihui3 at yahoo.com.cn Tue Jul 29 23:28:57 2008 From: haoyihui3 at yahoo.com.cn (yihui hao) Date: Wed, 30 Jul 2008 11:28:57 +0800 (CST) Subject: [Mristudio-users] =?gb2312?b?ILvYuLSjuiBSZTogIHN0cmVhbWluZyB2aWRl?= =?gb2312?b?byBvZiA4LzExIFR1dG9yaWFs?= In-Reply-To: Message-ID: <801985.65923.qm@web15003.mail.cnb.yahoo.com> Thanks, very pretty. Steve Malone ??? The UCLA Academic Technology Services web site has QuickTime movies of lectures on different topics in statistical analysis, which can be streamed to one's desktop over a high-speed connection. This page is for a seminar on making movies to be viewed over the web, with instructions: http://www.ats.ucla.edu/stat/seminars/MakingMovies/default.htm Regards, Steve On 28 Jul 08, at 18:22, susumu wrote: > This is a multi-part message in MIME format. > > --===============0640623822441498704== > Content-type: multipart/alternative; > boundary="----=_NextPart_000_03E1_01C8F0DE.E9509F00" > > This is a multi-part message in MIME format. > > ------=_NextPart_000_03E1_01C8F0DE.E9509F00 > Content-Type: text/plain; > charset="us-ascii" > Content-Transfer-Encoding: 7bit > > I can look into that option. Do you have any suggestions about how we can do > it? > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] > Sent: Monday, July 28, 2008 6:17 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] 8/11 Tutorial > > > > Do you have any plan put the tutorial on-line for people cannot attend the > tutorial session? > > > > > > sincerely, > > > > Seongjin > > On Mon, Jul 28, 2008 at 5:43 PM, susumu wrote: > > Hi all, > > > > It seems that we have the more than enough number of people (more than 40) > expressing their interest to attend the tutorial. We are trying to find a > room now and will get back to you tomorrow, hopefully. > > > > Some people asked about the level of the tutorial. We will try so that a > person without any prior experience can at least manage to follow. > > > > Thanks, > > > > Susumu > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > ------=_NextPart_000_03E1_01C8F0DE.E9509F00 > Content-Type: text/html; > charset="us-ascii" > Content-Transfer-Encoding: quoted-printable > > > xmlns:o=3D"urn:schemas-microsoft-com:office:office" = > xmlns:w=3D"urn:schemas-microsoft-com:office:word" = > xmlns=3D"http://www.w3.org/TR/REC-html40"> > > > > charset=3DUS-ASCII"> > > > > v\:* {behavior:url(#default#VML);} > o\:* {behavior:url(#default#VML);} > w\:* {behavior:url(#default#VML);} > .shape {behavior:url(#default#VML);} > > > > > /* Font Definitions */ > @font-face > {font-family:"MS Mincho"; > panose-1:2 2 6 9 4 2 5 8 3 4;} > @font-face > {font-family:Tahoma; > panose-1:2 11 6 4 3 5 4 4 2 4;} > @font-face > {font-family:"\@MS Mincho"; > panose-1:2 2 6 9 4 2 5 8 3 4;} > /* Style Definitions */ > p.MsoNormal, li.MsoNormal, div.MsoNormal > {margin:0in; > margin-bottom:.0001pt; > font-size:12.0pt; > font-family:"Times New Roman";} > a:link, span.MsoHyperlink > {color:blue; > text-decoration:underline;} > a:visited, span.MsoHyperlinkFollowed > {color:blue; > text-decoration:underline;} > p > {mso-margin-top-alt:auto; > margin-right:0in; > mso-margin-bottom-alt:auto; > margin-left:0in; > font-size:12.0pt; > font-family:"Times New Roman";} > span.EmailStyle18 > {mso-style-type:personal-reply; > font-family:Arial; > color:navy;} > @page Section1 > {size:8.5in 11.0in; > margin:1.0in 1.25in 1.0in 1.25in;} > div.Section1 > {page:Section1;} > --> > > > > > > > > > > style=3D'font-size: > 10.0pt;font-family:Arial;color:navy'>I can look into that option. Do you = > have > any suggestions about how we can do it? > > > style=3D'font-size: > 10.0pt;font-family:Arial;color:navy'> > > > > > size=3D3 > face=3D"Times New Roman"> > > --------------------------------- > > > > > style=3D'font-size:10.0pt; > font-family:Tahoma;font-weight:bold'>From:> size=3D2 > face=3DTahoma> > mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] > style=3D'font-weight: > bold'>On Behalf Of [Seongjin] > Sent: Monday, July 28, = > 2008 6:17 > PM > To: DTI Studio, ROI = > Editor, > Landmarker Questions/Support > Subject: Re: = > [Mristudio-users] > 8/11 Tutorial > > > > > style=3D'font-size: > 12.0pt'> > > > > > > > style=3D'font-size: > 12.0pt'>Do you have any plan put the tutorial on-line for people cannot = > attend > the tutorial session? > > > > > > > style=3D'font-size: > 12.0pt'> > > > > > > > style=3D'font-size: > 12.0pt'> > > > > > > > style=3D'font-size: > 12.0pt'>sincerely, > > > > > > > style=3D'font-size: > 12.0pt'> > > > > > > > face=3D"Times New Roman">> style=3D'font-size:12.0pt'>Seongjin > > > > > > > style=3D'font-size: > 12.0pt'>On Mon, Jul 28, 2008 at 5:43 PM, susumu <> href=3D"mailto:susumu at mri.jhu.edu">susumu at mri.jhu.edu> = > wrote: > > > > > > > style=3D'font-size:10.0pt;font-family:Arial'>Hi > all, > > > style=3D'font-size:10.0pt;font-family:Arial'> > :p> > > > style=3D'font-size:10.0pt;font-family:Arial'>It > seems that we have the more than enough number of people (more than 40) > expressing their interest to attend the tutorial. We are trying to find = > a room > now and will get back to you tomorrow, hopefully. = > > > > style=3D'font-size:10.0pt;font-family:Arial'> > :p> > > > style=3D'font-size:10.0pt;font-family:Arial'>Some > people asked about the level of the tutorial. We will try so that a = > person > without any prior experience can at least manage to = > follow. > > > style=3D'font-size:10.0pt;font-family:Arial'> > :p> > > > style=3D'font-size:10.0pt;font-family:Arial'>Thanks,> o:p> > > > style=3D'font-size:10.0pt;font-family:Arial'> > :p> > > > style=3D'font-size:10.0pt; > font-family:Arial;color:#888888'>Susumu> color=3D"#888888">> style=3D'color:#888888'> > > > > > > > face=3D"Times New Roman"> > _______________________________________________ > Mristudio-users mailing list > > href=3D"mailto:Mristudio-users at mristudio.org">Mristudio-users at mristudio.o= > rg > > target=3D"_blank">http://lists.mristudio.org/mailman/listinfo/mristudio-u= > sers > > > > > style=3D'font-size: > 12.0pt'> > > > > > > > > > > ------=_NextPart_000_03E1_01C8F0DE.E9509F00-- > > --===============0640623822441498704== > Content-Type: text/plain; charset="us-ascii" > MIME-Version: 1.0 > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > --===============0640623822441498704==-- _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080730/4279f632/attachment-0001.html From susumu at mri.jhu.edu Wed Jul 30 09:05:01 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 30 Jul 2008 09:05:01 -0400 Subject: [Mristudio-users] 8/11 tutorial Message-ID: <73alti$36095k@ipex2.johnshopkins.edu> Dear MriStudio Users, We reserved a room for 40 people. So this is a confirmation email that we WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about the room will be posted in www.mristudio.org -> Workshop shortly. Because there are already 41 people expressing the interest, we have to stop taking further registration. For those who already expressed were all registered. We are looking for a larger room. If we can find it, we will notify. The attendants are required to bring their own laptops which have all the software and sample data loaded from www.mristudio.org -> Workshop. Please follow the instruction in this site. The tutorial will start at 10:00 and end around 5:00. We will go over DtiStudio, RoiEditor, and Landmarker for DTI calculation, image quantification, and normalization. We will try to provide donuts and coffee but not lunch. Please feel free to ask questions. Sincerely, Susumu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080730/eff2ea25/attachment.html From meggersw at gmail.com Wed Jul 30 11:16:44 2008 From: meggersw at gmail.com (Megan Walsh) Date: Wed, 30 Jul 2008 11:16:44 -0400 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Message-ID: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> Hey- I already replied saying I was interested. I downloaded the latests versions of DTI studio, ROI editor, and Landmarker. I know I need to download AIR and make files. BUT I can't seem to access the webpage. Is the link down? or do I need to use a different web browser (I am using I.E.) Meg On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: > Dear MriStudio Users, > > > > We reserved a room for 40 people. So this is a confirmation email that we > WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about > the room will be posted in www.mristudio.org -> Workshop shortly. > > > > Because there are already 41 people expressing the interest, we have to > stop taking further registration. For those who already expressed were all > registered. We are looking for a larger room. If we can find it, we will > notify. > > > > The attendants are required to bring their own laptops which have all the > software and sample data loaded from www.mristudio.org -> Workshop. > Please follow the instruction in this site. > > > > The tutorial will start at 10:00 and end around 5:00. We will go over > DtiStudio, RoiEditor, and Landmarker for DTI calculation, image > quantification, and normalization. We will try to provide donuts and coffee > but not lunch. > > > > Please feel free to ask questions. > > > > Sincerely, > > > > Susumu > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080730/bb765a21/attachment.html From jack.vanhorn at loni.ucla.edu Wed Jul 30 12:04:50 2008 From: jack.vanhorn at loni.ucla.edu (Jack Van Horn) Date: Wed, 30 Jul 2008 09:04:50 -0700 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> Message-ID: You may download AIR from http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 Best, Jack Van Horn From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Megan Walsh Sent: Wednesday, July 30, 2008 8:17 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Hey- I already replied saying I was interested. I downloaded the latests versions of DTI studio, ROI editor, and Landmarker. I know I need to download AIR and make files. BUT I can't seem to access the webpage. Is the link down? or do I need to use a different web browser (I am using I.E.) Meg On Wed, Jul 30, 2008 at 9:05 AM, susumu > wrote: Dear MriStudio Users, We reserved a room for 40 people. So this is a confirmation email that we WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about the room will be posted in www.mristudio.org -> Workshop shortly. Because there are already 41 people expressing the interest, we have to stop taking further registration. For those who already expressed were all registered. We are looking for a larger room. If we can find it, we will notify. The attendants are required to bring their own laptops which have all the software and sample data loaded from www.mristudio.org -> Workshop. Please follow the instruction in this site. The tutorial will start at 10:00 and end around 5:00. We will go over DtiStudio, RoiEditor, and Landmarker for DTI calculation, image quantification, and normalization. We will try to provide donuts and coffee but not lunch. Please feel free to ask questions. Sincerely, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080730/4cb9d1b5/attachment-0001.html From evangelouI at ninds.nih.gov Wed Jul 30 12:49:53 2008 From: evangelouI at ninds.nih.gov (Evangelou, Iordanis (NIH/NINDS) [F]) Date: Wed, 30 Jul 2008 12:49:53 -0400 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> Message-ID: <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> I have compiled AIR on Windows XP so if anyone is interested I can email them copies ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Postdoctoral Fellow Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- ________________________________ From: Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] Sent: Wednesday, July 30, 2008 12:05 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial You may download AIR from http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 Best, Jack Van Horn From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Megan Walsh Sent: Wednesday, July 30, 2008 8:17 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Hey- I already replied saying I was interested. I downloaded the latests versions of DTI studio, ROI editor, and Landmarker. I know I need to download AIR and make files. BUT I can't seem to access the webpage. Is the link down? or do I need to use a different web browser (I am using I.E.) Meg On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: Dear MriStudio Users, We reserved a room for 40 people. So this is a confirmation email that we WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about the room will be posted in www.mristudio.org -> Workshop shortly. Because there are already 41 people expressing the interest, we have to stop taking further registration. For those who already expressed were all registered. We are looking for a larger room. If we can find it, we will notify. The attendants are required to bring their own laptops which have all the software and sample data loaded from www.mristudio.org -> Workshop. Please follow the instruction in this site. The tutorial will start at 10:00 and end around 5:00. We will go over DtiStudio, RoiEditor, and Landmarker for DTI calculation, image quantification, and normalization. We will try to provide donuts and coffee but not lunch. Please feel free to ask questions. Sincerely, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080730/a770f766/attachment.html From ankrishn at seas.rochester.edu Wed Jul 30 12:53:07 2008 From: ankrishn at seas.rochester.edu (Anitha Priya K) Date: Wed, 30 Jul 2008 12:53:07 -0400 Subject: [Mristudio-users] tractography in ex-vivo rat brain Message-ID: <771875ef0807300953o7c422e3pe04038ecf8fae2e7@mail.gmail.com> Hi We are trying to do tractography in an ex-vivo rat brain using DTI Studio. The imaging parameters were: Gradient directions image 0 : [0,0,0] image 1 : [.707,.707,0] image 2 : [.707,0,.707] image 3 : [0,.707,.707] image 4 : [-.707,.707,0] image 5 : [.707,0,-.707] image 6 : [0,-.707,.707] diffusion weighting b = ~996 image resolution: 128 *128*128 voxel size: 0.164 * 0.117* 0.117 mm Coronal sections The images are saved as unsigned int - 16 bit raw images. When we analyzed the data with DTIStudio, all the fibers seem to be running longitudinally (superior-inferior) and there are no fibers in the transverse direction (radially). Does your experience imaging rodent brains match these outcomes, and if not could you provide us information on whether additional or specialized processing is required when analyzing ex-vivo datasets for rodents? thanks Anitha Priya Krishnan, PhD graduate student in Biomedical Engineering Walter O'Dell, PhD, Assistant Professor of Radiation Oncology, and Biomedical Engineering Delphine Davis, PhD, Assistant Professor of Imaging Sciences, and Radiation Oncology University of Rochester Rochester, NY 14642 From icee41 at gmail.com Wed Jul 30 13:00:20 2008 From: icee41 at gmail.com (Tapan Jani) Date: Wed, 30 Jul 2008 12:00:20 -0500 Subject: [Mristudio-users] DTI-Studio Zoom in Message-ID: <43f2b0680807301000h4c01ad94y6756c31112e349f5@mail.gmail.com> Is there any way to zoom in on the axial, sag, or coronal views? I know I can zoom the 3-D image, but since I can't make ROIs on that one, I was trying to figure out what to do. I'm trying to really specify my ROIs, so any help would be much appreciated. Thanks, Tapan tjani2 at uic.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080730/cb49ce92/attachment.html From choisj70 at gmail.com Wed Jul 30 13:10:17 2008 From: choisj70 at gmail.com (Seongjin) Date: Wed, 30 Jul 2008 13:10:17 -0400 Subject: [Mristudio-users] DTI-Studio Zoom in In-Reply-To: <43f2b0680807301000h4c01ad94y6756c31112e349f5@mail.gmail.com> References: <43f2b0680807301000h4c01ad94y6756c31112e349f5@mail.gmail.com> Message-ID: You can find two magnifying glass buttons with + and - sign on the same line where save and delete buttons are in the "Orthogonal view" box. That buttons work for zoom in and out. For coronal, axial, sagittal views. Seongjin On Wed, Jul 30, 2008 at 1:00 PM, Tapan Jani wrote: > Is there any way to zoom in on the axial, sag, or coronal views? I know I > can zoom the 3-D image, but since I can't make ROIs on that one, I was > trying to figure out what to do. > I'm trying to really specify my ROIs, so any help would be much > appreciated. > > Thanks, > Tapan > > tjani2 at uic.edu > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080730/dbf933fd/attachment.html From susumu at mri.jhu.edu Wed Jul 30 13:13:01 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 30 Jul 2008 13:13:01 -0400 Subject: [Mristudio-users] tractography in ex-vivo rat brain In-Reply-To: <771875ef0807300953o7c422e3pe04038ecf8fae2e7@mail.gmail.com> Message-ID: <73alti$362svt@ipex2.johnshopkins.edu> First check the color map. If all are running along the same orientation, it should have only one color (like all blue). Then there is something wrong. The most common mistake is, forgot to turn off auto-scaling of the 7 images in the scanner. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Anitha Priya K Sent: Wednesday, July 30, 2008 12:53 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] tractography in ex-vivo rat brain Hi We are trying to do tractography in an ex-vivo rat brain using DTI Studio. The imaging parameters were: Gradient directions image 0 : [0,0,0] image 1 : [.707,.707,0] image 2 : [.707,0,.707] image 3 : [0,.707,.707] image 4 : [-.707,.707,0] image 5 : [.707,0,-.707] image 6 : [0,-.707,.707] diffusion weighting b = ~996 image resolution: 128 *128*128 voxel size: 0.164 * 0.117* 0.117 mm Coronal sections The images are saved as unsigned int - 16 bit raw images. When we analyzed the data with DTIStudio, all the fibers seem to be running longitudinally (superior-inferior) and there are no fibers in the transverse direction (radially). Does your experience imaging rodent brains match these outcomes, and if not could you provide us information on whether additional or specialized processing is required when analyzing ex-vivo datasets for rodents? thanks Anitha Priya Krishnan, PhD graduate student in Biomedical Engineering Walter O'Dell, PhD, Assistant Professor of Radiation Oncology, and Biomedical Engineering Delphine Davis, PhD, Assistant Professor of Imaging Sciences, and Radiation Oncology University of Rochester Rochester, NY 14642 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From rajagov2 at ccf.org Wed Jul 30 15:40:14 2008 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Wed, 30 Jul 2008 15:40:14 -0400 Subject: [Mristudio-users] skull stripping Message-ID: <77A88E90A851594AAEF830450587C39D01EDA8B5@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, I have only ROI editor manual for version 1.1 where i couldn't find information regarding how to use skull stripping (ROI editor version 1.2) i.e. to fill in values in options Predownsample, Gamma, segment Downsample, seed etc. It will be of great help to me if someone could please direct me where i can find manual or details to use skull stripping. Thanks in advance Regards 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 (2008). 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/20080730/d578c516/attachment.html From babimo at libero.it Wed Jul 30 16:03:42 2008 From: babimo at libero.it (babimo at libero.it) Date: Wed, 30 Jul 2008 22:03:42 +0200 Subject: [Mristudio-users] DTImapping Message-ID: Hi, thanks for your quicky reply. unfortunately I have no data in the Mosaic format but DICOM files from the scanner in the ima format. You might suggest me some program that transforms in.dcm my data? Thanks , Babila ---------- Initial Header ----------- >From : mristudio-users-bounces at mristudio.org To : "DTI Studio, ROI Editor, Landmarker Questions/Support" mristudio-users at mristudio.org Cc : Date : Mon, 28 Jul 2008 14:16:17 -0400 Subject : Re: [Mristudio-users] DTImapping > Hi Babila, > > It happens if you try to read Siemens Mosaic as Dicom. If you are using > Siemens, could you try Mosaic format? > > Susumu > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of babimo at libero.it > Sent: Monday, July 28, 2008 1:12 PM > To: mristudio-users > Subject: [Mristudio-users] DTImapping > > Hi, > i'm trying to use DTIMapping for fiber tracking, but the input format of the > DICOM DWI > must be in .dcm not in the native one, right? > And if i load files in .dcm and i choose all slices to be processed, at the > and of the > calculation i have in sagittal and coronal view no one image but like a > film. > What parameter i have to choose in the module slice to be processed? the > number of the > slices for gradient direction? > Thanks in advace, > Babila Moroni > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From jayashreemenon at gmail.com Wed Jul 30 23:59:25 2008 From: jayashreemenon at gmail.com (Jayasree) Date: Thu, 31 Jul 2008 09:29:25 +0530 Subject: [Mristudio-users] Fwd: 3D reconstruction and gradient tables In-Reply-To: References: Message-ID: Hi all, I am resending my mail as i haven't received any reply. can somebody help me? regards jay Dear DTIstudio users, I am a new user of the software. When I am loading the DICOM images using MRIview 3D, it is not reconstructing the 3D images , instead I am getting images as if we see on the film.Can any body give solution for this. Also please get me the gradient table for Siemens Magnetom Avanto TIM when 12, 20 and 30 gradient orientations are used. How do you get these tables? Please help. Thanks Jay -- R.S.Jayasree, Ph.D Scientist Department of Imaging Sciences and Interventional Radiology SCTIMST, Trivandrum-695011,Kerala, India, Phone:+91 471 2443152(O), +91 471 2524124(O-direct), +91 471 2478792(R), +91 9495948221(Mob) Fax:+91 471 2446433 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080731/f7981b33/attachment.html From Elizabeth.Finger at lhsc.on.ca Thu Jul 31 17:03:47 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Thu, 31 Jul 2008 17:03:47 -0400 Subject: [Mristudio-users] question on getting to byte data format for LDDMM References: <4891EF0B.51BC.00A0.0@lhsc.on.ca> Message-ID: <4891F073.51BC.00A0.0@lhsc.on.ca> Hello- I am at the step of sending an individual subject's data to LDDMM for automatic tract segementation, and have run into the following questions: 1. For single subjects, do you recommend normalizing to the ICBM group atlas or to the JHU-MNI single subject atlas? 2. After loading the template B0 and FA images, and then our subject mean B0, FA, DWI, eigenvalue and tensor, we did the AIR linear transformation in Landmarker using the template B0 and the subject B0 images. We then saved each 'updated files' files (and the tensors together)in the raw image format following the normalization. When I then attempt to use histogram buttons or the the single channel LDDMM button, an error pops up that says the subject data must be in byte format. Clicking on the multple channel LDDMM, we can see the input screen, but once we load up the template BO and FA and the subject B) and FA and try to submit, we get the same error message that the subject data must be in byte format. We are not sure how to convert the updated-normalized images from Landmarker to byte format for LDDMM? Thank you, Elizabeth Finger -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From susumu at mri.jhu.edu Thu Jul 31 17:15:28 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 31 Jul 2008 17:15:28 -0400 Subject: [Mristudio-users] question on getting to byte data format for LDDMM In-Reply-To: <4891F073.51BC.00A0.0@lhsc.on.ca> Message-ID: <73alti$36fff1@ipex2.johnshopkins.edu> 1: For LDDMM, definitely the single-subject. LDDMM aggressively identifies and matches structures. The population-averaged maps have very blur structural definitions, which confuses LDDMM. For linear and low-order non-linear, the population averaged is better because it maximizes the matching between the normalized subject and atlas after such low-level transformations. 2: Yes, all images have to be converted to byte. This can be easily done by the "BWF" button in the top section. Please note that once the images such as FA is converted to byte, it is usable to drive LDDMM, but not usable for the subsequent quantification (who wants FA values 0 - 255?). So, you have to apply the resultant transformation matrix to FA later. Related to this issue, we are testing ADC (trace) not b0 image to drive LDDMM (I mean FA + ADC dual channel). The reason is, FA and ADC maps are quantitative maps and do not require histogram (intensity) matching. When you convert FA&ADC to byte, you can specify the absolute range for the conversion (for example, byte 0 = FA 0 or ADC 0 / byte 255 = FA 1 or ADC 3.5 (trace 10)). The latest version can specify the absolute range conversion. This makes our life easier. Because LDDMM operates on intensity, intensity matching is important. Our single subject atlas is from Philips which has a certain degree of intensity distribution, which is different from Siemens. Without intensity matching, LDDMM won't work. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Elizabeth Finger Sent: Thursday, July 31, 2008 5:04 PM To: dti studio help Subject: [Mristudio-users] question on getting to byte data format for LDDMM Hello- I am at the step of sending an individual subject's data to LDDMM for automatic tract segementation, and have run into the following questions: 1. For single subjects, do you recommend normalizing to the ICBM group atlas or to the JHU-MNI single subject atlas? 2. After loading the template B0 and FA images, and then our subject mean B0, FA, DWI, eigenvalue and tensor, we did the AIR linear transformation in Landmarker using the template B0 and the subject B0 images. We then saved each 'updated files' files (and the tensors together)in the raw image format following the normalization. When I then attempt to use histogram buttons or the the single channel LDDMM button, an error pops up that says the subject data must be in byte format. Clicking on the multple channel LDDMM, we can see the input screen, but once we load up the template BO and FA and the subject B) and FA and try to submit, we get the same error message that the subject data must be in byte format. We are not sure how to convert the updated-normalized images from Landmarker to byte format for LDDMM? Thank you, Elizabeth Finger ---------------------------------------------------------------------------- ---- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Thu Jul 31 17:20:02 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 31 Jul 2008 17:20:02 -0400 Subject: [Mristudio-users] Fwd: 3D reconstruction and gradient tables In-Reply-To: Message-ID: <73alti$36fgpu@ipex2.johnshopkins.edu> Hi Jay, We get this symptom when we try to read Siemens Mosaic using Dicom format. Mosaic has to be read as Mosaic. Have you tried to read it as Mosaic? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jayasree Sent: Wednesday, July 30, 2008 11:59 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Fwd: 3D reconstruction and gradient tables Hi all, I am resending my mail as i haven't received any reply. can somebody help me? regards jay Dear DTIstudio users, I am a new user of the software. When I am loading the DICOM images using MRIview 3D, it is not reconstructing the 3D images , instead I am getting images as if we see on the film.Can any body give solution for this. Also please get me the gradient table for Siemens Magnetom Avanto TIM when 12, 20 and 30 gradient orientations are used. How do you get these tables? Please help. Thanks Jay -- R.S.Jayasree, Ph.D Scientist Department of Imaging Sciences and Interventional Radiology SCTIMST, Trivandrum-695011,Kerala, India, Phone:+91 471 2443152(O), +91 471 2524124(O-direct), +91 471 2478792(R), +91 9495948221(Mob) Fax:+91 471 2446433 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080731/8fe30674/attachment-0001.html From xli16 at jhmi.edu Thu Jul 31 17:27:57 2008 From: xli16 at jhmi.edu (XIN LI) Date: Thu, 31 Jul 2008 17:27:57 -0400 Subject: [Mristudio-users] question on getting to byte data format for LDDMM In-Reply-To: <4891F073.51BC.00A0.0@lhsc.on.ca> References: <4891EF0B.51BC.00A0.0@lhsc.on.ca> <4891F073.51BC.00A0.0@lhsc.on.ca> Message-ID: Hello Elizabeth, For the second question, Landmarker has the function that can change the data format of images to byte. The button is below the check box "Slice Marker". Xin ----- Original Message ----- From: Elizabeth Finger Date: Thursday, July 31, 2008 5:04 pm Subject: [Mristudio-users] question on getting to byte data format for LDDMM To: dti studio help > Hello- > > I am at the step of sending an individual subject's data to LDDMM for > automatic tract segementation, and have run into the following questions: > > 1. For single subjects, do you recommend normalizing to the ICBM > group atlas or to the JHU-MNI single subject atlas? > > 2. After loading the template B0 and FA images, and then our subject > mean B0, FA, DWI, eigenvalue and tensor, we did the AIR linear > transformation in Landmarker using the template B0 and the subject B0 > images. We then saved each 'updated files' files (and the tensors > together)in the raw image format following the normalization. When I > then attempt to use histogram buttons or the the single channel LDDMM > button, an error pops up that says the subject data must be in byte > format. Clicking on the multple channel LDDMM, we can see the input > screen, but once we load up the template BO and FA and the subject B) > and FA and try to submit, we get the same error message that the > subject data must be in byte format. We are not sure how to convert > the updated-normalized images from Landmarker to byte format for LDDMM? > > Thank you, > > Elizabeth Finger > > -------------------------------------------------------------------------------- > This information is directed in confidence solely to the person named > above and may contain confidential and/or privileged material. This > information may not otherwise be distributed, copied or disclosed. If > you have received this e-mail in error, please notify the sender > immediately via a return e-mail and destroy original message. Thank > you for your cooperation. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From haoyihui3 at yahoo.com.cn Thu Jul 31 21:17:44 2008 From: haoyihui3 at yahoo.com.cn (yihui hao) Date: Fri, 01 Aug 2008 09:17:44 +0800 (CST) Subject: [Mristudio-users] =?gb2312?b?ILvYuLSjuiBSZTogIEFJUi0tPz8/IFJlOiAg?= =?gb2312?b?OC8xMSB0dXRvcmlhbA==?= In-Reply-To: <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> Message-ID: <290208.94252.qm@web15005.mail.cnb.yahoo.com> Dear, Please email it to me. Thank you. Email?haoyihui3 at yahoo.com.cn Yihui "Evangelou, Iordanis (NIH/NINDS) [F]" ??? @font-face { font-family: Cambria Math; } @font-face { font-family: Calibri; } @font-face { font-family: Tahoma; } @page Section1 {size: 8.5in 11.0in; margin: 1.0in 1.0in 1.0in 1.0in; } P.MsoNormal { FONT-SIZE: 12pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: "Times New Roman","serif" } LI.MsoNormal { FONT-SIZE: 12pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: "Times New Roman","serif" } DIV.MsoNormal { FONT-SIZE: 12pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: "Times New Roman","serif" } A:link { COLOR: blue; TEXT-DECORATION: underline; mso-style-priority: 99 } SPAN.MsoHyperlink { COLOR: blue; TEXT-DECORATION: underline; mso-style-priority: 99 } A:visited { COLOR: purple; TEXT-DECORATION: underline; mso-style-priority: 99 } SPAN.MsoHyperlinkFollowed { COLOR: purple; TEXT-DECORATION: underline; mso-style-priority: 99 } P { FONT-SIZE: 12pt; MARGIN-LEFT: 0in; MARGIN-RIGHT: 0in; FONT-FAMILY: "Times New Roman","serif"; mso-style-priority: 99; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto } SPAN.EmailStyle18 { COLOR: #1f497d; FONT-FAMILY: "Calibri","sans-serif"; mso-style-type: personal-reply } .MsoChpDefault { mso-style-type: export-only } DIV.Section1 { page: Section1 } I have compiled AIR on Windows XP so if anyone is interested I can email them copies ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Postdoctoral Fellow Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- --------------------------------- From: Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] Sent: Wednesday, July 30, 2008 12:05 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial You may download AIR from http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 Best, Jack Van Horn From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Megan Walsh Sent: Wednesday, July 30, 2008 8:17 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Hey- I already replied saying I was interested. I downloaded the latests versions of DTI studio, ROI editor, and Landmarker. I know I need to download AIR and make files. BUT I can't seem to access the webpage. Is the link down? or do I need to use a different web browser (I am using I.E.) Meg On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: Dear MriStudio Users, We reserved a room for 40 people. So this is a confirmation email that we WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about the room will be posted in www.mristudio.org -> Workshop shortly. Because there are already 41 people expressing the interest, we have to stop taking further registration. For those who already expressed were all registered. We are looking for a larger room. If we can find it, we will notify. The attendants are required to bring their own laptops which have all the software and sample data loaded from www.mristudio.org -> Workshop. Please follow the instruction in this site. The tutorial will start at 10:00 and end around 5:00. We will go over DtiStudio, RoiEditor, and Landmarker for DTI calculation, image quantification, and normalization. We will try to provide donuts and coffee but not lunch. Please feel free to ask questions. Sincerely, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080801/b6f6b516/attachment.html From cvidal at usc.edu Thu Jul 31 21:36:47 2008 From: cvidal at usc.edu (Christine Vidal) Date: Thu, 31 Jul 2008 18:36:47 -0700 Subject: [Mristudio-users] =?big5?b?pl7OYKFHIFJlOiAgQUlSLS0/Pz8gUmU6ICA4?= =?big5?b?LzExIHR1dG9yaWFs?= In-Reply-To: <290208.94252.qm@web15005.mail.cnb.yahoo.com> References: <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> <290208.94252.qm@web15005.mail.cnb.yahoo.com> Message-ID: Please, email it to me too! My email: cvidal at usc.edu Thanks a lot! Christine N. Vidal, Ph.D. University of Southern California Postdoctoral Fellow at the Brain and Creativity Institute Dana and David Dornsife Cognitive Neuroscience Imaging Center 3520A McClintock Avenue Los Angeles, CA 90089 Phone: (213)-821-4263 Fax: (213) 821-4270 Email: cvidal at usc.edu ----- Original Message ----- From: yihui hao Date: Thursday, July 31, 2008 6:18 pm Subject: [Mristudio-users] ??? Re: AIR--??? Re: 8/11 tutorial To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > Dear, > Please email it to me. Thank you. > Email?haoyihui3 at yahoo.com.cn > > Yihui > > "Evangelou, Iordanis (NIH/NINDS) [F]" ??? > @font-face { font-family: Cambria Math; } @font-face { > font-family: Calibri; } @font-face { font-family: Tahoma; } > @page Section1 {size: 8.5in 11.0in; margin: 1.0in 1.0in 1.0in > 1.0in; } P.MsoNormal { FONT-SIZE: 12pt; MARGIN: 0in 0in 0pt; > FONT-FAMILY: "Times New Roman","serif" } LI.MsoNormal { FONT- > SIZE: 12pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: "Times New > Roman","serif" } DIV.MsoNormal { FONT-SIZE: 12pt; MARGIN: 0in > 0in 0pt; FONT-FAMILY: "Times New Roman","serif" } A:link { > COLOR: blue; TEXT-DECORATION: underline; mso-style-priority: 99 } > SPAN.MsoHyperlink { COLOR: blue; TEXT-DECORATION: underline; mso- > style-priority: 99 } A:visited { COLOR: purple; TEXT- > DECORATION: underline; mso-style-priority: 99 } > SPAN.MsoHyperlinkFollowed { COLOR: purple; TEXT-DECORATION: > underline; mso-style-priority: 99 } P { FONT-SIZE: 12pt; MARGIN- > LEFT: 0in; MARGIN-RIGHT: 0in; FONT-FAMILY: "Times New > Roman","serif"; mso-style-priority: 99; > mso-margin-top-alt: auto; mso-margin-bottom-alt: auto } > SPAN.EmailStyle18 { COLOR: #1f497d; FONT-FAMILY: "Calibri","sans- > serif"; mso-style-type: personal-reply } .MsoChpDefault { mso- > style-type: export-only } DIV.Section1 { page: Section1 } > I have compiled AIR on Windows XP so if anyone is interested I can > email them copies > > -------------------------------------------------------------- > ----- > Iordanis E. Evangelou, DPhil > Postdoctoral Fellow > Neuroimmunology Branch > National Institute of Neurological Disorders and Stroke > National Institutes of Health > Building 10, Room 5C203B > Bethesda, MD 20892 > USA > ------------------------------------------------------------------ > - > > > > > > --------------------------------- > From: Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] > Sent: Wednesday, July 30, 2008 12:05 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > You may download AIR from > http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 > > Best, > > Jack Van Horn > > From: mristudio-users-bounces at mristudio.org [mailto:mristudio- > users-bounces at mristudio.org] On Behalf Of Megan Walsh > Sent: Wednesday, July 30, 2008 8:17 AM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > Hey- > > > > I already replied saying I was interested. I downloaded the > latests versions of DTI studio, ROI editor, and Landmarker. I know > I need to download AIR and make files. BUT I can't seem to access > the webpage. Is the link down? or do I need to use a different > web browser (I am using I.E.) > > > > Meg > > On Wed, Jul 30, 2008 at 9:05 AM, susumu > wrote: Dear MriStudio Users, > > We reserved a room for 40 people. So this is a confirmation email > that we WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. > The detail about the room will be posted in www.mristudio.org -> > Workshop shortly. > > Because there are already 41 people expressing the interest, we > have to stop taking further registration. For those who already > expressed were all registered. We are looking for a larger room. If > we can find it, we will notify. > > The attendants are required to bring their own laptops which have > all the software and sample data loaded from www.mristudio.org -> > Workshop. Please follow the instruction in this site. > > The tutorial will start at 10:00 and end around 5:00. We will go > over DtiStudio, RoiEditor, and Landmarker for DTI calculation, > image quantification, and normalization. We will try to provide > donuts and coffee but not lunch. > > Please feel free to ask questions. > > Sincerely, > > Susumu > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > -- > Megan Kay Walsh > Graduate Student > Johns Hopkins University > Psychological & Brain Sciences > 204 Ames Hall > 3400 N. Charles St. > Baltimore, MD 21218 > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > --------------------------------- > ???????????? > From chenqin8124 at gmail.com Thu Jul 31 23:47:29 2008 From: chenqin8124 at gmail.com (June.Chen) Date: Fri, 01 Aug 2008 11:47:29 +0800 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> Message-ID: Thanks a lot. Pleas email to me chenqin8124 at gmail.com June 2008/7/31, Evangelou, Iordanis (NIH/NINDS) [F] : > > I have compiled AIR on Windows XP so if anyone is interested I can email > them copies > > ------------------------------------------------------------------- > *Iordanis E. Evangelou, DPhil* > Postdoctoral Fellow > Neuroimmunology Branch > National Institute of Neurological Disorders and Stroke > National Institutes of Health > Building 10, Room 5C203B > Bethesda, MD 20892 > USA > ------------------------------------------------------------------- > > > ------------------------------ > *From:* Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] > *Sent:* Wednesday, July 30, 2008 12:05 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > You may download AIR from > http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 > > > > Best, > > > > Jack Van Horn > > > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Megan Walsh > *Sent:* Wednesday, July 30, 2008 8:17 AM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > Hey- > > > > I already replied saying I was interested. I downloaded the latests > versions of DTI studio, ROI editor, and Landmarker. I know I need to > download AIR and make files. BUT I can't seem to access the webpage. Is > the link down? or do I need to use a different web browser (I am using > I.E.) > > > > Meg > > On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: > > Dear MriStudio Users, > > > > We reserved a room for 40 people. So this is a confirmation email that we > WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about > the room will be posted in www.mristudio.org -> Workshop shortly. > > > > Because there are already 41 people expressing the interest, we have to > stop taking further registration. For those who already expressed were all > registered. We are looking for a larger room. If we can find it, we will > notify. > > > > The attendants are required to bring their own laptops which have all the > software and sample data loaded from www.mristudio.org -> Workshop. > Please follow the instruction in this site. > > > > The tutorial will start at 10:00 and end around 5:00. We will go over > DtiStudio, RoiEditor, and Landmarker for DTI calculation, image > quantification, and normalization. We will try to provide donuts and coffee > but not lunch. > > > > Please feel free to ask questions. > > > > Sincerely, > > > > Susumu > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > -- > Megan Kay Walsh > Graduate Student > Johns Hopkins University > Psychological & Brain Sciences > 204 Ames Hall > 3400 N. Charles St. > Baltimore, MD 21218 > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Qin Chen M.D. Department of Neurology West China Hospital Sichuan University Wai Nan Guo Xue Lane 37# Chengdu,P.R.China,610041 Tel: +86 8542 3960 (Lab) Fax: +86 8542 2549 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080801/44abcf96/attachment-0001.html From nbulak at gata.edu.tr Fri Aug 1 00:31:40 2008 From: nbulak at gata.edu.tr (=?ISO-8859-9?Q?Nail_Bulakba=FE=FD?=) Date: Fri, 01 Aug 2008 07:31:40 +0300 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Message-ID: <6D516B4B9E363E4DAFB7DB856A55F3EA01F9730F@gatamailsrv.gatadomain.com.tr> Hello, Please email to me. nbulak at gata.edu.tr ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Evangelou, Iordanis (NIH/NINDS) [F] Sent: Wednesday, July 30, 2008 7:50 PM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial I have compiled AIR on Windows XP so if anyone is interested I can email them copies ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Postdoctoral Fellow Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- ________________________________ From: Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] Sent: Wednesday, July 30, 2008 12:05 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial You may download AIR from http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 Best, Jack Van Horn From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Megan Walsh Sent: Wednesday, July 30, 2008 8:17 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Hey- I already replied saying I was interested. I downloaded the latests versions of DTI studio, ROI editor, and Landmarker. I know I need to download AIR and make files. BUT I can't seem to access the webpage. Is the link down? or do I need to use a different web browser (I am using I.E.) Meg On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: Dear MriStudio Users, We reserved a room for 40 people. So this is a confirmation email that we WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about the room will be posted in www.mristudio.org -> Workshop shortly. Because there are already 41 people expressing the interest, we have to stop taking further registration. For those who already expressed were all registered. We are looking for a larger room. If we can find it, we will notify. The attendants are required to bring their own laptops which have all the software and sample data loaded from www.mristudio.org -> Workshop. Please follow the instruction in this site. The tutorial will start at 10:00 and end around 5:00. We will go over DtiStudio, RoiEditor, and Landmarker for DTI calculation, image quantification, and normalization. We will try to provide donuts and coffee but not lunch. Please feel free to ask questions. Sincerely, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080801/30f3b753/attachment.html From jojo55 at 163.com Fri Aug 1 03:45:00 2008 From: jojo55 at 163.com (shasha Li) Date: Fri, 01 Aug 2008 15:45:00 +0800 (CST) Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> Message-ID: <32802503.328871217576700965.JavaMail.coremail@bj163app125.163.com> Thanks and send to jojo55 at 163.com all the best -- ?2008-08-01?"June.Chen" ??? Thanks a lot. Pleas email to me chenqin8124 at gmail.com June 2008/7/31, Evangelou, Iordanis (NIH/NINDS) [F] : I have compiled AIR on Windows XP so if anyone is interested I can email them copies ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Postdoctoral Fellow Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- From: Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] Sent: Wednesday, July 30, 2008 12:05 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial You may download AIR from http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 Best, Jack Van Horn From:mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Megan Walsh Sent: Wednesday, July 30, 2008 8:17 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Hey- I already replied saying I was interested. I downloaded the latests versions of DTI studio, ROI editor, and Landmarker. I know I need to download AIR and make files. BUT I can't seem to access the webpage. Is the link down? or do I need to use a different web browser (I am using I.E.) Meg On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: Dear MriStudio Users, We reserved a room for 40 people. So this is a confirmation email that we WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about the room will be posted in www.mristudio.org -> Workshop shortly. Because there are already 41 people expressing the interest, we have to stop taking further registration. For those who already expressed were all registered. We are looking for a larger room. If we can find it, we will notify. The attendants are required to bring their own laptops which have all the software and sample data loaded from www.mristudio.org -> Workshop. Please follow the instruction in this site. The tutorial will start at 10:00 and end around 5:00. We will go over DtiStudio, RoiEditor, and Landmarker for DTI calculation, image quantification, and normalization. We will try to provide donuts and coffee but not lunch. Please feel free to ask questions. Sincerely, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Qin Chen M.D. Department of Neurology West China Hospital Sichuan University Wai Nan Guo Xue Lane 37# Chengdu,P.R.China,610041 Tel: +86 8542 3960 (Lab) Fax: +86 8542 2549 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080801/5dff44f8/attachment-0001.html From aprats at ub.edu Fri Aug 1 04:34:37 2008 From: aprats at ub.edu (ALBERTO PRATS GALINO) Date: Fri, 01 Aug 2008 10:34:37 +0200 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <32802503.328871217576700965.JavaMail.coremail@bj163app125.163.com> References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> <32802503.328871217576700965.JavaMail.coremail@bj163app125.163.com> Message-ID: <1217579677.4892ca9dc1292@webmail3.ub.edu> Please, can you also send to aprats at ub.edu? Thanks Alberto Missatge de shasha Li : > Thanks and send to jojo55 at 163.com > > all the best > -- > > > ??2008-08-01??"June.Chen" ?????? > > Thanks a lot. > Pleas email to me > chenqin8124 at gmail.com > > June > > > 2008/7/31, Evangelou, Iordanis (NIH/NINDS) [F] : > I have compiled AIR on Windows XP so if anyone is interested I can email them > copies > > ------------------------------------------------------------------- > Iordanis E. Evangelou, DPhil > Postdoctoral Fellow > Neuroimmunology Branch > National Institute of Neurological Disorders and Stroke > National Institutes of Health > Building 10, Room 5C203B > Bethesda, MD 20892 > USA > ------------------------------------------------------------------- > > > > From: Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] > Sent: Wednesday, July 30, 2008 12:05 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > You may download AIR from > http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 > > > > Best, > > > > Jack Van Horn > > > > From:mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Megan Walsh > Sent: Wednesday, July 30, 2008 8:17 AM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > Hey- > > > > I already replied saying I was interested. I downloaded the latests versions > of DTI studio, ROI editor, and Landmarker. I know I need to download AIR and > make files. BUT I can't seem to access the webpage. Is the link down? or > do I need to use a different web browser (I am using I.E.) > > > > Meg > > On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: > > Dear MriStudio Users, > > > > We reserved a room for 40 people. So this is a confirmation email that we > WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about the > room will be posted in www.mristudio.org -> Workshop shortly. > > > > Because there are already 41 people expressing the interest, we have to stop > taking further registration. For those who already expressed were all > registered. We are looking for a larger room. If we can find it, we will > notify. > > > > The attendants are required to bring their own laptops which have all the > software and sample data loaded from www.mristudio.org -> Workshop. Please > follow the instruction in this site. > > > > The tutorial will start at 10:00 and end around 5:00. We will go over > DtiStudio, RoiEditor, and Landmarker for DTI calculation, image > quantification, and normalization. We will try to provide donuts and coffee > but not lunch. > > > > Please feel free to ask questions. > > > > Sincerely, > > > > Susumu > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > -- > Megan Kay Walsh > Graduate Student > Johns Hopkins University > Psychological & Brain Sciences > 204 Ames Hall > 3400 N. Charles St. > Baltimore, MD 21218 > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > > -- > Qin Chen M.D. > Department of Neurology > West China Hospital > Sichuan University > Wai Nan Guo Xue Lane 37# > Chengdu,P.R.China,610041 > Tel: +86 8542 3960 (Lab) > Fax: +86 8542 2549 ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From meggersw at gmail.com Fri Aug 1 09:46:23 2008 From: meggersw at gmail.com (Megan Walsh) Date: Fri, 01 Aug 2008 09:46:23 -0400 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> Message-ID: <254662fa0808010646w680057f1qd03b7bc17dd2e72c@mail.gmail.com> Yes, Please send me copies!!! Thanks meg On Wed, Jul 30, 2008 at 12:49 PM, Evangelou, Iordanis (NIH/NINDS) [F] < evangelouI at ninds.nih.gov> wrote: > I have compiled AIR on Windows XP so if anyone is interested I can email > them copies > > ------------------------------------------------------------------- > *Iordanis E. Evangelou, DPhil* > Postdoctoral Fellow > Neuroimmunology Branch > National Institute of Neurological Disorders and Stroke > National Institutes of Health > Building 10, Room 5C203B > Bethesda, MD 20892 > USA > ------------------------------------------------------------------- > > > ------------------------------ > *From:* Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] > *Sent:* Wednesday, July 30, 2008 12:05 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > You may download AIR from > http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 > > > > Best, > > > > Jack Van Horn > > > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Megan Walsh > *Sent:* Wednesday, July 30, 2008 8:17 AM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > Hey- > > > > I already replied saying I was interested. I downloaded the latests > versions of DTI studio, ROI editor, and Landmarker. I know I need to > download AIR and make files. BUT I can't seem to access the webpage. Is > the link down? or do I need to use a different web browser (I am using > I.E.) > > > > Meg > > On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: > > Dear MriStudio Users, > > > > We reserved a room for 40 people. So this is a confirmation email that we > WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about > the room will be posted in www.mristudio.org -> Workshop shortly. > > > > Because there are already 41 people expressing the interest, we have to > stop taking further registration. For those who already expressed were all > registered. We are looking for a larger room. If we can find it, we will > notify. > > > > The attendants are required to bring their own laptops which have all the > software and sample data loaded from www.mristudio.org -> Workshop. > Please follow the instruction in this site. > > > > The tutorial will start at 10:00 and end around 5:00. We will go over > DtiStudio, RoiEditor, and Landmarker for DTI calculation, image > quantification, and normalization. We will try to provide donuts and coffee > but not lunch. > > > > Please feel free to ask questions. > > > > Sincerely, > > > > Susumu > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > -- > Megan Kay Walsh > Graduate Student > Johns Hopkins University > Psychological & Brain Sciences > 204 Ames Hall > 3400 N. Charles St. > Baltimore, MD 21218 > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080801/31f577af/attachment.html From choisj70 at gmail.com Fri Aug 1 11:02:14 2008 From: choisj70 at gmail.com (Seongjin) Date: Fri, 01 Aug 2008 11:02:14 -0400 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> Message-ID: Please send a copy. Thanks in advance. On Wed, Jul 30, 2008 at 12:49 PM, Evangelou, Iordanis (NIH/NINDS) [F] < evangelouI at ninds.nih.gov> wrote: > I have compiled AIR on Windows XP so if anyone is interested I can email > them copies > > ------------------------------------------------------------------- > *Iordanis E. Evangelou, DPhil* > Postdoctoral Fellow > Neuroimmunology Branch > National Institute of Neurological Disorders and Stroke > National Institutes of Health > Building 10, Room 5C203B > Bethesda, MD 20892 > USA > ------------------------------------------------------------------- > > > ------------------------------ > *From:* Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] > *Sent:* Wednesday, July 30, 2008 12:05 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > You may download AIR from > http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 > > > > Best, > > > > Jack Van Horn > > > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Megan Walsh > *Sent:* Wednesday, July 30, 2008 8:17 AM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > Hey- > > > > I already replied saying I was interested. I downloaded the latests > versions of DTI studio, ROI editor, and Landmarker. I know I need to > download AIR and make files. BUT I can't seem to access the webpage. Is > the link down? or do I need to use a different web browser (I am using > I.E.) > > > > Meg > > On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: > > Dear MriStudio Users, > > > > We reserved a room for 40 people. So this is a confirmation email that we > WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about > the room will be posted in www.mristudio.org -> Workshop shortly. > > > > Because there are already 41 people expressing the interest, we have to > stop taking further registration. For those who already expressed were all > registered. We are looking for a larger room. If we can find it, we will > notify. > > > > The attendants are required to bring their own laptops which have all the > software and sample data loaded from www.mristudio.org -> Workshop. > Please follow the instruction in this site. > > > > The tutorial will start at 10:00 and end around 5:00. We will go over > DtiStudio, RoiEditor, and Landmarker for DTI calculation, image > quantification, and normalization. We will try to provide donuts and coffee > but not lunch. > > > > Please feel free to ask questions. > > > > Sincerely, > > > > Susumu > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > -- > Megan Kay Walsh > Graduate Student > Johns Hopkins University > Psychological & Brain Sciences > 204 Ames Hall > 3400 N. Charles St. > Baltimore, MD 21218 > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080801/bd6b1868/attachment-0001.html From choisj70 at gmail.com Fri Aug 1 12:28:36 2008 From: choisj70 at gmail.com (Seongjin) Date: Fri, 01 Aug 2008 12:28:36 -0400 Subject: [Mristudio-users] Mulitiple b-values Message-ID: I have some DTI data have 5 b-values: 0, 250, 500, 750, 1000. (Philips 3T) For each b-value, low directional resolution was applied and all the data were saved in a single file. Is DTI studio capable of handling this data? Is there anyone who worked on this types of data? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080801/cac66344/attachment.html From raj.jaswal at gmail.com Fri Aug 1 13:05:17 2008 From: raj.jaswal at gmail.com (Raj Jaswal) Date: Fri, 01 Aug 2008 13:05:17 -0400 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> Message-ID: <32a27f2a0808011005k439cf941ja5ef997be55de7d6@mail.gmail.com> If you can, I would appreciate a copy as well. Thank you very much! - RJ On Wed, Jul 30, 2008 at 12:49 PM, Evangelou, Iordanis (NIH/NINDS) [F] < evangelouI at ninds.nih.gov> wrote: > I have compiled AIR on Windows XP so if anyone is interested I can email > them copies > > ------------------------------------------------------------------- > *Iordanis E. Evangelou, DPhil* > Postdoctoral Fellow > Neuroimmunology Branch > National Institute of Neurological Disorders and Stroke > National Institutes of Health > Building 10, Room 5C203B > Bethesda, MD 20892 > USA > ------------------------------------------------------------------- > > > ------------------------------ > *From:* Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] > *Sent:* Wednesday, July 30, 2008 12:05 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > You may download AIR from > http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 > > > > Best, > > > > Jack Van Horn > > > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Megan Walsh > *Sent:* Wednesday, July 30, 2008 8:17 AM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > Hey- > > > > I already replied saying I was interested. I downloaded the latests > versions of DTI studio, ROI editor, and Landmarker. I know I need to > download AIR and make files. BUT I can't seem to access the webpage. Is > the link down? or do I need to use a different web browser (I am using > I.E.) > > > > Meg > > On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: > > Dear MriStudio Users, > > > > We reserved a room for 40 people. So this is a confirmation email that we > WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about > the room will be posted in www.mristudio.org -> Workshop shortly. > > > > Because there are already 41 people expressing the interest, we have to > stop taking further registration. For those who already expressed were all > registered. We are looking for a larger room. If we can find it, we will > notify. > > > > The attendants are required to bring their own laptops which have all the > software and sample data loaded from www.mristudio.org -> Workshop. > Please follow the instruction in this site. > > > > The tutorial will start at 10:00 and end around 5:00. We will go over > DtiStudio, RoiEditor, and Landmarker for DTI calculation, image > quantification, and normalization. We will try to provide donuts and coffee > but not lunch. > > > > Please feel free to ask questions. > > > > Sincerely, > > > > Susumu > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > -- > Megan Kay Walsh > Graduate Student > Johns Hopkins University > Psychological & Brain Sciences > 204 Ames Hall > 3400 N. Charles St. > Baltimore, MD 21218 > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- - RJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080801/ad58d381/attachment.html From harishs at illinois.edu Fri Aug 1 13:15:01 2008 From: harishs at illinois.edu (Sharma, Harish) Date: Fri, 01 Aug 2008 12:15:01 -0500 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> References: <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> Message-ID: <87D63F6D93DB14418272BF5859FFF2C9080A5DA3@BI-ADMEX.beckman-admin.uiuc.edu> Could you please send me a copy? Thanks, Harish harishs at illinois.edu ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Evangelou, Iordanis (NIH/NINDS) [F] Sent: Wednesday, July 30, 2008 11:50 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial I have compiled AIR on Windows XP so if anyone is interested I can email them copies ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Postdoctoral Fellow Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- ________________________________ From: Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] Sent: Wednesday, July 30, 2008 12:05 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial You may download AIR from http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 Best, Jack Van Horn From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Megan Walsh Sent: Wednesday, July 30, 2008 8:17 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Hey- I already replied saying I was interested. I downloaded the latests versions of DTI studio, ROI editor, and Landmarker. I know I need to download AIR and make files. BUT I can't seem to access the webpage. Is the link down? or do I need to use a different web browser (I am using I.E.) Meg On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: Dear MriStudio Users, We reserved a room for 40 people. So this is a confirmation email that we WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about the room will be posted in www.mristudio.org -> Workshop shortly. Because there are already 41 people expressing the interest, we have to stop taking further registration. For those who already expressed were all registered. We are looking for a larger room. If we can find it, we will notify. The attendants are required to bring their own laptops which have all the software and sample data loaded from www.mristudio.org -> Workshop. Please follow the instruction in this site. The tutorial will start at 10:00 and end around 5:00. We will go over DtiStudio, RoiEditor, and Landmarker for DTI calculation, image quantification, and normalization. We will try to provide donuts and coffee but not lunch. Please feel free to ask questions. Sincerely, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080801/14abd478/attachment-0001.html From hjiang at jhmi.edu Fri Aug 1 13:41:47 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Fri, 01 Aug 2008 13:41:47 -0400 Subject: [Mristudio-users] Mulitiple b-values Message-ID: <4893129B0200006300014D72@cis27.hosts.jhmi.edu> hi, you can process the multiple b-values' dataset by defining the gradient table in this way: #: X, Y, Z, b-value for example, if you have 2 dataset (6 directional DWI), one is acquired with b-value=800, another one is 1000; the gradent table might be: 1: 1, 0, 0, 800 2: 0, 1, 0, 800 3: 0, 0, 1, 800 4: 1, 1, 0, 800 ...... 7: 1, 0, 0, 1000 8: 0, 1, 0, 1000 9: 0, 0, 1, 1000 10: 1, 1, 0, 1000 .... regards, hangyi >>> "[Seongjin]" 08/01/08 12:28 PM >>> I have some DTI data have 5 b-values: 0, 250, 500, 750, 1000. (Philips 3T) For each b-value, low directional resolution was applied and all the data were saved in a single file. Is DTI studio capable of handling this data? Is there anyone who worked on this types of data? From choisj70 at gmail.com Fri Aug 1 13:47:23 2008 From: choisj70 at gmail.com (Seongjin) Date: Fri, 01 Aug 2008 13:47:23 -0400 Subject: [Mristudio-users] Mulitiple b-values In-Reply-To: <4893129B0200006300014D72@cis27.hosts.jhmi.edu> References: <4893129B0200006300014D72@cis27.hosts.jhmi.edu> Message-ID: I appreciate it! On Fri, Aug 1, 2008 at 1:41 PM, Hangyi Jiang wrote: > hi, > > you can process the multiple b-values' dataset by defining the gradient > table in this way: > > #: X, Y, Z, b-value > > for example, if you have 2 dataset (6 directional DWI), one is acquired > with b-value=800, another one is 1000; the gradent table might be: > > 1: 1, 0, 0, 800 > 2: 0, 1, 0, 800 > 3: 0, 0, 1, 800 > 4: 1, 1, 0, 800 > ...... > 7: 1, 0, 0, 1000 > 8: 0, 1, 0, 1000 > 9: 0, 0, 1, 1000 > 10: 1, 1, 0, 1000 > .... > > regards, > > hangyi > > > > > > > > > >>> "[Seongjin]" 08/01/08 12:28 PM >>> > I have some DTI data have 5 b-values: 0, 250, 500, 750, 1000. (Philips 3T) > For each b-value, low directional resolution was applied and all the data > were saved in a single file. > Is DTI studio capable of handling this data? > Is there anyone who worked on this types of data? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080801/7885516c/attachment.html From hifreaks at gmail.com Fri Aug 1 16:21:54 2008 From: hifreaks at gmail.com (=?UTF-8?B?7KGw7JaR7KCc?=) Date: Fri, 01 Aug 2008 22:21:54 +0200 Subject: [Mristudio-users] 3D reconstruction and gradient tables In-Reply-To: References: Message-ID: <241cbec20808011321j33e64bdcg88db3d2ba2297732@mail.gmail.com> Hello, Here is a 20 gradient table for our Siemens Trio, I'm sure. 0: -1.000000, 0.000000, 0.000000 1: 0.000000, -1.000000, 0.000000 2: 0.031984, -0.799591, 0.599693 3: -0.856706, -0.493831, -0.148949 4: -0.834429, -0.309159, 0.456234 5: -0.834429 0.309159 0.456234 6: -0.856706, 0.493831, -0.148949 7: -0.822228, -0.000000, -0.569158 8: -0.550834, -0.425872, -0.717784 9: -0.468173, -0.834308, -0.291108 10: -0.515933, -0.808894, 0.281963 11: -0.391890, -0.515855, 0.761785 12: -0.478151, -0.000000, 0.878278 13: -0.391890, 0.515855, 0.761785 14: -0.515933, 0.808894, 0.281963 15: -0.468173, 0.834308, -0.291108 16: -0.550834, 0.425872, -0.717784 17: -0.111012, 0.264029, -0.958105 18: -0.111012, -0.264029, -0.958105 19: -0.031984, -0.799591, -0.599693 20: 100, 100, 100 21: 0,0,0 But I don't know it will work with your Avanto. You should contact your vender company for getting the table. And also I use the mosaic files (a bit big files). Wish you good luck! Yang-Je Cho 2008/7/26 Jayasree > Dear DTIstudio users, > I am a new user of the software. When I am loading the DICOM images > using MRIview 3D, it is not reconstructing the 3D images , instead I am > getting images as if we see on the film.Can any body give solution for this. > Also please get me the gradient table for Siemens Magnetom Avanto TIM > when 12, 20 and 30 gradient orientations are used. How do you get these > tables? Please help. > > Thanks > > Jay > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Yang-Je Cho Dept of Neurology, Yonsei University College of Medicine, Seoul, Korea Phone: 82-2-2228-1600, Cell: 016-298-7456, Fax: 82-2-393-0705 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080801/27af95e9/attachment.html From c.bieck at T-Online.de Fri Aug 1 16:42:00 2008 From: c.bieck at T-Online.de (Christian Bieck) Date: Fri, 01 Aug 2008 20:42 +0000 (GMT) Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Message-ID: <1KP1SH-1y9Z0S0@fwd27.aul.t-online.de> I'd appreciate a copy as well. Thank you. :) Christian Bieck > Please send a copy. > Thanks in advance. > > > On Wed, Jul 30, 2008 at 12:49 PM, Evangelou, Iordanis (NIH/NINDS) [F] < > evangelouI at ninds.nih.gov> wrote: > > > I have compiled AIR on Windows XP so if anyone is interested I can email > > them copies > > > > ------------------------------------------------------------------- > > *Iordanis E. Evangelou, DPhil* > > Postdoctoral Fellow > > Neuroimmunology Branch > > National Institute of Neurological Disorders and Stroke > > National Institutes of Health > > Building 10, Room 5C203B > > Bethesda, MD 20892 > > USA > > ------------------------------------------------------------------- > > > > > > ------------------------------ > > *From:* Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] > > *Sent:* Wednesday, July 30, 2008 12:05 PM > > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > > *Subject:* Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > You may download AIR from > > http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 > > > > > > > > Best, > > > > > > > > Jack Van Horn > > > > > > > > *From:* mristudio-users-bounces at mristudio.org [mailto: > > mristudio-users-bounces at mristudio.org] *On Behalf Of *Megan Walsh > > *Sent:* Wednesday, July 30, 2008 8:17 AM > > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > > *Subject:* [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > > > > > Hey- > > > > > > > > I already replied saying I was interested. I downloaded the latests > > versions of DTI studio, ROI editor, and Landmarker. I know I need to > > download AIR and make files. BUT I can't seem to access the webpage. Is > > the link down? or do I need to use a different web browser (I am using > > I.E.) > > > > > > > > Meg > > > > On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: > > > > Dear MriStudio Users, > > > > > > > > We reserved a room for 40 people. So this is a confirmation email that we > > WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about > > the room will be posted in www.mristudio.org -> Workshop shortly. > > > > > > > > Because there are already 41 people expressing the interest, we have to > > stop taking further registration. For those who already expressed were all > > registered. We are looking for a larger room. If we can find it, we will > > notify. > > > > > > > > The attendants are required to bring their own laptops which have all the > > software and sample data loaded from www.mristudio.org -> Workshop. > > Please follow the instruction in this site. > > > > > > > > The tutorial will start at 10:00 and end around 5:00. We will go over > > DtiStudio, RoiEditor, and Landmarker for DTI calculation, image > > quantification, and normalization. We will try to provide donuts and coffee > > but not lunch. > > > > > > > > Please feel free to ask questions. > > > > > > > > Sincerely, > > > > > > > > Susumu > > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > > > > > > -- > > Megan Kay Walsh > > Graduate Student > > Johns Hopkins University > > Psychological & Brain Sciences > > 204 Ames Hall > > 3400 N. Charles St. > > Baltimore, MD 21218 > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > From zackowski at kennedykrieger.org Fri Aug 1 17:02:24 2008 From: zackowski at kennedykrieger.org (Kathy Zackowski) Date: Fri, 01 Aug 2008 17:02:24 -0400 Subject: [Mristudio-users] 8/11 Tutorial In-Reply-To: <73alti$35fcad@ipex2.johnshopkins.edu> References: <73alti$35fcad@ipex2.johnshopkins.edu> Message-ID: <489341A0.D104.0003.0@kennedykrieger.org> Hi Susumu, I am sorry but my research coordinator can not make it to the 8/11 tutorial. So, please fill his spot with someone else. Thanks for having the tutorial, I will have him attend the next one you offer if possible. -Kathy Kathy Zackowski, PhD, OTR Motion Analysis Laboratory Kennedy Krieger Institute Assistant Professor Depts PM&R, Neurology Johns Hopkins University School of Medicine 707 North Broadway Baltimore, MD 21224 443-923-2717 >>> susumu 7/28/2008 5:43 PM >>> Hi all, It seems that we have the more than enough number of people (more than 40) expressing their interest to attend the tutorial. We are trying to find a room now and will get back to you tomorrow, hopefully. Some people asked about the level of the tutorial. We will try so that a person without any prior experience can at least manage to follow. Thanks, Susumu 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/20080801/9588b2a8/attachment.html From jameen2006 at gmail.com Fri Aug 1 21:57:16 2008 From: jameen2006 at gmail.com (jameen ARM) Date: Sat, 02 Aug 2008 11:57:16 +1000 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <1KP1SH-1y9Z0S0@fwd27.aul.t-online.de> References: <1KP1SH-1y9Z0S0@fwd27.aul.t-online.de> Message-ID: <5f2dd9ad0808011857m586a25d7rf01980ae77a9aaca@mail.gmail.com> I would like to have a copy too. Thanks Jameen On Fri, 01 Aug 2008 20:42 +0000 (GMT), Christian Bieck wrote: > > I'd appreciate a copy as well. Thank you. :) > > Christian Bieck > > > > Please send a copy. > > Thanks in advance. > > > > > > On Wed, Jul 30, 2008 at 12:49 PM, Evangelou, Iordanis (NIH/NINDS) [F] < > > evangelouI at ninds.nih.gov> wrote: > > > > > I have compiled AIR on Windows XP so if anyone is interested I can > email > > > them copies > > > > > > ------------------------------------------------------------------- > > > *Iordanis E. Evangelou, DPhil* > > > Postdoctoral Fellow > > > Neuroimmunology Branch > > > National Institute of Neurological Disorders and Stroke > > > National Institutes of Health > > > Building 10, Room 5C203B > > > Bethesda, MD 20892 > > > USA > > > ------------------------------------------------------------------- > > > > > > > > > ------------------------------ > > > *From:* Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] > > > *Sent:* Wednesday, July 30, 2008 12:05 PM > > > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > > > *Subject:* Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > > > You may download AIR from > > > http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 > > > > > > > > > > > > Best, > > > > > > > > > > > > Jack Van Horn > > > > > > > > > > > > *From:* mristudio-users-bounces at mristudio.org [mailto: > > > mristudio-users-bounces at mristudio.org] *On Behalf Of *Megan Walsh > > > *Sent:* Wednesday, July 30, 2008 8:17 AM > > > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > > > *Subject:* [Mristudio-users] AIR--??? Re: 8/11 tutorial > > > > > > > > > > > > Hey- > > > > > > > > > > > > I already replied saying I was interested. I downloaded the latests > > > versions of DTI studio, ROI editor, and Landmarker. I know I need to > > > download AIR and make files. BUT I can't seem to access the > webpage. Is > > > the link down? or do I need to use a different web browser (I am using > > > I.E.) > > > > > > > > > > > > Meg > > > > > > On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: > > > > > > Dear MriStudio Users, > > > > > > > > > > > > We reserved a room for 40 people. So this is a confirmation email that > we > > > WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail > about > > > the room will be posted in www.mristudio.org -> Workshop shortly. > > > > > > > > > > > > Because there are already 41 people expressing the interest, we have to > > > stop taking further registration. For those who already expressed were > all > > > registered. We are looking for a larger room. If we can find it, we > will > > > notify. > > > > > > > > > > > > The attendants are required to bring their own laptops which have all > the > > > software and sample data loaded from www.mristudio.org -> Workshop. > > > Please follow the instruction in this site. > > > > > > > > > > > > The tutorial will start at 10:00 and end around 5:00. We will go over > > > DtiStudio, RoiEditor, and Landmarker for DTI calculation, image > > > quantification, and normalization. We will try to provide donuts and > coffee > > > but not lunch. > > > > > > > > > > > > Please feel free to ask questions. > > > > > > > > > > > > Sincerely, > > > > > > > > > > > > Susumu > > > > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > > > > > > > > > > > -- > > > Megan Kay Walsh > > > Graduate Student > > > Johns Hopkins University > > > Psychological & Brain Sciences > > > 204 Ames Hall > > > 3400 N. Charles St. > > > Baltimore, MD 21218 > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080802/e5d9ae96/attachment-0001.html From jayashreemenon at gmail.com Fri Aug 1 23:05:27 2008 From: jayashreemenon at gmail.com (Jayasree) Date: Sat, 02 Aug 2008 08:35:27 +0530 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <5f2dd9ad0808011857m586a25d7rf01980ae77a9aaca@mail.gmail.com> References: <1KP1SH-1y9Z0S0@fwd27.aul.t-online.de> <5f2dd9ad0808011857m586a25d7rf01980ae77a9aaca@mail.gmail.com> Message-ID: Please send me a copy Thanks in advance jayashreemenon at gmail.com Jay -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080802/afade8f0/attachment.html From grojasy at puc.cl Sat Aug 2 16:12:23 2008 From: grojasy at puc.cl (Gonzalo Rojas) Date: Sat, 02 Aug 2008 16:12:23 -0400 Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files... Message-ID: <4894BFA7.2010402@puc.cl> Hi: I have DWI DICOM files from a Philips Achieva 3T... They are 4D DICOM file with all the slices and directions in that file... How can I read with DTIStudio, or convert it to 3D DICOM files ?... Sincerely, -- Gonzalo Rojas Costa Laboratory of Medical Image Processing Department of Neuroradiology Institute of Neurosurgery Dr. Asenjo Jose Manuel Infante 553, Providencia, Santiago, Chile. Tel/Fax: 56-2-5754653 Cel: 56-9-97771785 www.neurorradiologia.cl From susumu at mri.jhu.edu Sun Aug 3 08:08:41 2008 From: susumu at mri.jhu.edu (susumu) Date: Sun, 03 Aug 2008 08:08:41 -0400 Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files... In-Reply-To: <4894BFA7.2010402@puc.cl> References: <4894BFA7.2010402@puc.cl> Message-ID: Hi Gonzalo, When you said "4D DICOM", does it mean you have only one DICOM file, in which all 4D data are stored? Then, it must be a new format and DtiStudio can't read it. In this case, we are happy to look into it. Please let me know. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Gonzalo Rojas Sent: Saturday, August 02, 2008 4:12 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files... Hi: I have DWI DICOM files from a Philips Achieva 3T... They are 4D DICOM file with all the slices and directions in that file... How can I read with DTIStudio, or convert it to 3D DICOM files ?... Sincerely, -- Gonzalo Rojas Costa Laboratory of Medical Image Processing Department of Neuroradiology Institute of Neurosurgery Dr. Asenjo Jose Manuel Infante 553, Providencia, Santiago, Chile. Tel/Fax: 56-2-5754653 Cel: 56-9-97771785 www.neurorradiologia.cl _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From grojasy at puc.cl Sun Aug 3 20:39:08 2008 From: grojasy at puc.cl (Gonzalo Rojas) Date: Sun, 03 Aug 2008 20:39:08 -0400 Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files... In-Reply-To: References: <4894BFA7.2010402@puc.cl> Message-ID: <48964FAC.6030905@puc.cl> Hi Susumu: Yes... It is a DICOM file that I got from a Philips Achieva 3T... It is a unique DICOM file with all the slices and gradient directions on it (32 gradient directions)... If you want, I could send you an example of such a file... Sincerely, Gonzalo Rojas Costa susumu escribi?: > Hi Gonzalo, > > When you said "4D DICOM", does it mean you have only one DICOM file, in > which all 4D data are stored? Then, it must be a new format and DtiStudio > can't read it. In this case, we are happy to look into it. > > Please let me know. > > Susumu From jayashreemenon at gmail.com Sun Aug 3 23:50:30 2008 From: jayashreemenon at gmail.com (Jayasree) Date: Mon, 04 Aug 2008 09:20:30 +0530 Subject: [Mristudio-users] 3D reconstruction and gradient tables In-Reply-To: <241cbec20808011321j33e64bdcg88db3d2ba2297732@mail.gmail.com> References: <241cbec20808011321j33e64bdcg88db3d2ba2297732@mail.gmail.com> Message-ID: Thank you very much for the gradient table information Jay On 8/2/08, ??? wrote: > > Hello, > > Here is a 20 gradient table for our Siemens Trio, I'm sure. > > 0: -1.000000, 0.000000, 0.000000 > 1: 0.000000, -1.000000, 0.000000 > 2: 0.031984, -0.799591, 0.599693 > 3: -0.856706, -0.493831, -0.148949 > 4: -0.834429, -0.309159, 0.456234 > 5: -0.834429 0.309159 0.456234 > 6: -0.856706, 0.493831, -0.148949 > 7: -0.822228, -0.000000, -0.569158 > 8: -0.550834, -0.425872, -0.717784 > 9: -0.468173, -0.834308, -0.291108 > 10: -0.515933, -0.808894, 0.281963 > 11: -0.391890, -0.515855, 0.761785 > 12: -0.478151, -0.000000, 0.878278 > 13: -0.391890, 0.515855, 0.761785 > 14: -0.515933, 0.808894, 0.281963 > 15: -0.468173, 0.834308, -0.291108 > 16: -0.550834, 0.425872, -0.717784 > 17: -0.111012, 0.264029, -0.958105 > 18: -0.111012, -0.264029, -0.958105 > 19: -0.031984, -0.799591, -0.599693 > 20: 100, 100, 100 > 21: 0,0,0 > > But I don't know it will work with your Avanto. > You should contact your vender company for getting the table. > And also I use the mosaic files (a bit big files). > > Wish you good luck! > > Yang-Je Cho > > 2008/7/26 Jayasree > >> Dear DTIstudio users, >> I am a new user of the software. When I am loading the DICOM images >> using MRIview 3D, it is not reconstructing the 3D images , instead I am >> getting images as if we see on the film.Can any body give solution for this. >> Also please get me the gradient table for Siemens Magnetom Avanto TIM >> when 12, 20 and 30 gradient orientations are used. How do you get these >> tables? Please help. >> >> Thanks >> >> Jay >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > > -- > Yang-Je Cho > > Dept of Neurology, Yonsei University > College of Medicine, Seoul, Korea > Phone: 82-2-2228-1600, Cell: 016-298-7456, Fax: 82-2-393-0705 > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080804/92c61ca5/attachment.html From jayashreemenon at gmail.com Sun Aug 3 23:53:16 2008 From: jayashreemenon at gmail.com (Jayasree) Date: Mon, 04 Aug 2008 09:23:16 +0530 Subject: [Mristudio-users] Thank you Message-ID: Hi Susumu, Thank you for the information. Now it is working. Jay On 8/1/08, susumu wrote: > > Hi Jay, > > > > We get this symptom when we try to read Siemens Mosaic using Dicom format. > Mosaic has to be read as Mosaic. Have you tried to read it as Mosaic? > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *Jayasree > *Sent:* Wednesday, July 30, 2008 11:59 PM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] Fwd: 3D reconstruction and gradient tables > > > > > > Hi all, > > I am resending my mail as i haven't received any reply. can somebody help > me? > > regards > > jay > > > > > > > > > Dear DTIstudio users, > > I am a new user of the software. When I am loading the DICOM images > using MRIview 3D, it is not reconstructing the 3D images , instead I am > getting images as if we see on the film.Can any body give solution for this. > > Also please get me the gradient table for Siemens Magnetom Avanto TIM > when 12, 20 and 30 gradient orientations are used. How do you get these > tables? Please help. > > > > Thanks > > > > Jay > > > > > > -- > R.S.Jayasree, Ph.D > Scientist > Department of Imaging Sciences and Interventional Radiology > SCTIMST, Trivandrum-695011,Kerala, India, > Phone:+91 471 2443152(O), +91 471 2524124(O-direct), +91 471 2478792(R), > +91 9495948221(Mob) > Fax:+91 471 2446433 > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- R.S.Jayasree, Ph.D Scientist Department of Imaging Sciences and Interventional Radiology SCTIMST, Trivandrum-695011,Kerala, India, Phone:+91 471 2443152(O), +91 471 2524124(O-direct), +91 471 2478792(R), +91 9495948221(Mob) Fax:+91 471 2446433 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080804/5e3d6f7a/attachment-0001.html From daniel.harrison78 at gmail.com Mon Aug 4 09:03:50 2008 From: daniel.harrison78 at gmail.com (Daniel Harrison) Date: Mon, 04 Aug 2008 09:03:50 -0400 Subject: [Mristudio-users] 8/11 Tutorial In-Reply-To: <73alti$35fcad@ipex2.johnshopkins.edu> References: <73alti$35fcad@ipex2.johnshopkins.edu> Message-ID: <460dfa830808040603p7a80ec30q2df231af830d1936@mail.gmail.com> Dear Susumu, I am one of the clinical and research fellows in the neurology department at Johns Hopkins. I am currently working with Danny Reich and Peter Calabresi on clinical correlations for diffusion tensor imaging in patients with Multiple Sclerosis. I will be using DTI studio for my research, and would appreciate being involved in the tutorial. I know space is tight, but if there are any cancellations, please let me know. Thank you. Sincerely, Daniel Harrison, MD Postdoctoral Fellow Neuroimmunology and Neuroinfectious Disease daniel.harrison78 at gmail.com dharri90 at jhmi.edu On Mon, Jul 28, 2008 at 5:43 PM, susumu wrote: > Hi all, > > > > It seems that we have the more than enough number of people (more than 40) > expressing their interest to attend the tutorial. We are trying to find a > room now and will get back to you tomorrow, hopefully. > > > > Some people asked about the level of the tutorial. We will try so that a > person without any prior experience can at least manage to follow. > > > > Thanks, > > > > Susumu > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080804/d2a9eba7/attachment.html From valalik at hu.inter.net Sun Aug 3 02:56:04 2008 From: valalik at hu.inter.net (=?iso-8859-1?Q?dr.Val=E1lik_Istv=E1n?=) Date: Sun, 03 Aug 2008 08:56:04 +0200 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> Message-ID: <005f01c8f535$ffa45250$0201a8c0@agy> Dear Iordanis, Please, can you also send to valalik at hu.inter.net Thanks a lot in advance Istvan Valalik -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080803/1cb23eae/attachment.html From susumu at mri.jhu.edu Mon Aug 4 10:32:41 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 04 Aug 2008 10:32:41 -0400 Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files... In-Reply-To: <4894BFA7.2010402@puc.cl> Message-ID: <73ap56$3rncqq@ipex1.johnshopkins.edu> We can take a look. Could you post it somewhere so that we can retrieve? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Gonzalo Rojas Sent: Saturday, August 02, 2008 4:12 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] read 4D DWI Philips Achieva 3T DICOM files... Hi: I have DWI DICOM files from a Philips Achieva 3T... They are 4D DICOM file with all the slices and directions in that file... How can I read with DTIStudio, or convert it to 3D DICOM files ?... Sincerely, -- Gonzalo Rojas Costa Laboratory of Medical Image Processing Department of Neuroradiology Institute of Neurosurgery Dr. Asenjo Jose Manuel Infante 553, Providencia, Santiago, Chile. Tel/Fax: 56-2-5754653 Cel: 56-9-97771785 www.neurorradiologia.cl _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From c.bieck at T-Online.de Mon Aug 4 14:37:00 2008 From: c.bieck at T-Online.de (Christian Bieck) Date: Mon, 04 Aug 2008 18:37 +0000 (GMT) Subject: [Mristudio-users] Landmarker Image File Create Eroor Message-ID: <1KQ4vT-0o8Oqe0@fwd33.aul.t-online.de> Hello, I'm trying to normalize the files (DWI, B0s, Color Map etc.) I made via DTI Studio by using the AIR "Linear" option in Landmarker. However, when I press the button, I get a message saying "Image File Create Error" even though the correct Atlas sample images were opened. I got this error message both with using my own compiled .exe files and the .exe files Dr Evangelou was so kind to send me, so I'm somewhat at a loss as to what went wrong. I'd very much appreciate it if you could shed some light on what might be the possible sources of the Image File Create Error and how I could fix it. Thank you in advance, Christian Bieck -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080804/81138afc/attachment.html From choisj70 at gmail.com Mon Aug 4 14:52:06 2008 From: choisj70 at gmail.com (Seongjin) Date: Mon, 04 Aug 2008 14:52:06 -0400 Subject: [Mristudio-users] Mulitiple b-values In-Reply-To: <4893129B0200006300014D72@cis27.hosts.jhmi.edu> References: <4893129B0200006300014D72@cis27.hosts.jhmi.edu> Message-ID: What I found while I was trying your recommendation, somehow DTI data did not work with image sequence option "gradient by gradient". When I selected the option with "slice-by-slice", I had a good 3D view. Do you have any recommendation on selecting options on this? Regards, Seongjin On Fri, Aug 1, 2008 at 1:41 PM, Hangyi Jiang wrote: > hi, > > you can process the multiple b-values' dataset by defining the gradient > table in this way: > > #: X, Y, Z, b-value > > for example, if you have 2 dataset (6 directional DWI), one is acquired > with b-value=800, another one is 1000; the gradent table might be: > > 1: 1, 0, 0, 800 > 2: 0, 1, 0, 800 > 3: 0, 0, 1, 800 > 4: 1, 1, 0, 800 > ...... > 7: 1, 0, 0, 1000 > 8: 0, 1, 0, 1000 > 9: 0, 0, 1, 1000 > 10: 1, 1, 0, 1000 > .... > > regards, > > hangyi > > > > > > > > > >>> "[Seongjin]" 08/01/08 12:28 PM >>> > I have some DTI data have 5 b-values: 0, 250, 500, 750, 1000. (Philips 3T) > For each b-value, low directional resolution was applied and all the data > were saved in a single file. > Is DTI studio capable of handling this data? > Is there anyone who worked on this types of data? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080804/7fcdfc3f/attachment.html From xli16 at jhmi.edu Mon Aug 4 15:03:33 2008 From: xli16 at jhmi.edu (XIN LI) Date: Mon, 04 Aug 2008 15:03:33 -0400 Subject: [Mristudio-users] Landmarker Image File Create Eroor In-Reply-To: <1KQ4vT-0o8Oqe0@fwd33.aul.t-online.de> References: <1KQ4vT-0o8Oqe0@fwd33.aul.t-online.de> Message-ID: Dr. Bieck, When AIR alignlinear function is applied, two temporary images are generated in the Landmarker folder. The message you got means that these two images cannot be generated. Actually this error rarely happens. Could you please give me more details about how you did? What's the path of the Landmarker folder on your machine? What's the operating system you use? Could you please give me a few screenshots to decribe your problem? Thanks! Xin ----- Original Message ----- From: Christian Bieck Date: Monday, August 4, 2008 2:37 pm Subject: [Mristudio-users] Landmarker Image File Create Eroor To: mristudio-users at mristudio.org > Hello, > > I'm trying to normalize the files (DWI, B0s, Color Map etc.) I made > via DTI Studio by using the AIR "Linear" option in Landmarker. > However, when I press the button, I get a message saying "Image File > Create Error" even though the correct Atlas sample images were opened. > I got this error message both with using my own compiled .exe files > and the .exe files Dr Evangelou was so kind to send me, so I'm > somewhat at a loss as to what went wrong. > I'd very much appreciate it if you could shed some light on what > might be the possible sources of the Image File Create Error and how I > could fix it. > > Thank you in advance, > Christian Bieck > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From hjiang at jhmi.edu Mon Aug 4 16:55:24 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Mon, 04 Aug 2008 16:55:24 -0400 Subject: [Mristudio-users] Mulitiple b-values Message-ID: <4897347C0200006300014E68@cis27.hosts.jhmi.edu> hi, seems that your dataset is from Philips, right? as we known, the old Philips software (before version 4.xx? i'm not exactly sure) export the DWIs by "slice-by-slice" format, while new versions use "gradient by gradient" format. regards, hangyi >>> "[Seongjin]" 08/04/08 2:52 PM >>> What I found while I was trying your recommendation, somehow DTI data did not work with image sequence option "gradient by gradient". When I selected the option with "slice-by-slice", I had a good 3D view. Do you have any recommendation on selecting options on this? Regards, Seongjin On Fri, Aug 1, 2008 at 1:41 PM, Hangyi Jiang wrote: > hi, > > you can process the multiple b-values' dataset by defining the gradient > table in this way: > > #: X, Y, Z, b-value > > for example, if you have 2 dataset (6 directional DWI), one is acquired > with b-value=800, another one is 1000; the gradent table might be: > > 1: 1, 0, 0, 800 > 2: 0, 1, 0, 800 > 3: 0, 0, 1, 800 > 4: 1, 1, 0, 800 > ...... > 7: 1, 0, 0, 1000 > 8: 0, 1, 0, 1000 > 9: 0, 0, 1, 1000 > 10: 1, 1, 0, 1000 > .... > > regards, > > hangyi > > > > > > > > > >>> "[Seongjin]" 08/01/08 12:28 PM >>> > I have some DTI data have 5 b-values: 0, 250, 500, 750, 1000. (Philips 3T) > For each b-value, low directional resolution was applied and all the data > were saved in a single file. > Is DTI studio capable of handling this data? > Is there anyone who worked on this types of data? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From susumu at mri.jhu.edu Mon Aug 4 17:22:39 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 04 Aug 2008 17:22:39 -0400 Subject: [Mristudio-users] 8/11 Tutorial Message-ID: <73ap56$3rrv2v@ipex1.johnshopkins.edu> Dear Users, Sorry for our slow response to inquiries about the detail of the tutorial. We could finally reserve a bigger room and I would like to lift the restriction for the registration. If you are interested in joining the tutorial, please send us an email at support at mristudio.org. The tutorial will start from 10:00 am on 8/11 at Mountcastle Auditorium in the1st floor of the PCTB building. In the attached map, the building is #20. If you will drive, you can park your car in the McElderry Visitor Parking of North Caroline St (the left end of the map). If you come by an airplane or Amtrak, you can take a cab ($30 from BWI airport and $10 from Baltimore Penn Station) to Main Hopkins Hospital in the East Baltimore Campus. Most likely, you will be dropped at the Main entrance indicated by the red color in the map. The Mountcastle Auditorium is right after the entrance of the PCTB building (you can't miss). It is the other side of a cafeteria where you can buy lunch. Please let us know if you have any questions about the tutorial. Thanks, Susumu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080804/71fbf554/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: parking-map.pdf Type: application/pdf Size: 156616 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080804/71fbf554/attachment-0001.pdf From choisj70 at gmail.com Mon Aug 4 18:52:23 2008 From: choisj70 at gmail.com (Seongjin) Date: Mon, 04 Aug 2008 18:52:23 -0400 Subject: [Mristudio-users] Mulitiple b-values In-Reply-To: <4897347C0200006300014E68@cis27.hosts.jhmi.edu> References: <4897347C0200006300014E68@cis27.hosts.jhmi.edu> Message-ID: Thanks for your reply. That's why 3T and 7T data did not work with DTI studio with the same options. Thanks again. Seongjin On Mon, Aug 4, 2008 at 4:55 PM, Hangyi Jiang wrote: > hi, > > seems that your dataset is from Philips, right? > > as we known, the old Philips software (before version 4.xx? i'm not exactly > sure) export the DWIs by "slice-by-slice" format, while new versions use > "gradient by gradient" format. > > regards, > > hangyi > > > > > > >>> "[Seongjin]" 08/04/08 2:52 PM >>> > What I found while I was trying your recommendation, somehow DTI data > did not work with image sequence option "gradient by gradient". > When I selected the option with "slice-by-slice", I had a good 3D view. > Do you have any recommendation on selecting options on this? > > Regards, > > Seongjin > > On Fri, Aug 1, 2008 at 1:41 PM, Hangyi Jiang wrote: > > > hi, > > > > you can process the multiple b-values' dataset by defining the gradient > > table in this way: > > > > #: X, Y, Z, b-value > > > > for example, if you have 2 dataset (6 directional DWI), one is acquired > > with b-value=800, another one is 1000; the gradent table might be: > > > > 1: 1, 0, 0, 800 > > 2: 0, 1, 0, 800 > > 3: 0, 0, 1, 800 > > 4: 1, 1, 0, 800 > > ...... > > 7: 1, 0, 0, 1000 > > 8: 0, 1, 0, 1000 > > 9: 0, 0, 1, 1000 > > 10: 1, 1, 0, 1000 > > .... > > > > regards, > > > > hangyi > > > > > > > > > > > > > > > > > > >>> "[Seongjin]" 08/01/08 12:28 PM >>> > > I have some DTI data have 5 b-values: 0, 250, 500, 750, 1000. (Philips > 3T) > > For each b-value, low directional resolution was applied and all the data > > were saved in a single file. > > Is DTI studio capable of handling this data? > > Is there anyone who worked on this types of data? > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080804/071c0a52/attachment.html From jayashreemenon at gmail.com Mon Aug 4 22:58:50 2008 From: jayashreemenon at gmail.com (Jayasree) Date: Tue, 05 Aug 2008 08:28:50 +0530 Subject: [Mristudio-users] 8/11 Tutorial In-Reply-To: <73ap56$3rrv2v@ipex1.johnshopkins.edu> References: <73ap56$3rrv2v@ipex1.johnshopkins.edu> Message-ID: Dear Dr.Susumu, is there any possibilityof making the tutorial material available online? Jay -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080805/c81381cb/attachment.html From mustela at mce.hggm.es Mon Aug 4 14:30:53 2008 From: mustela at mce.hggm.es (mustela at mce.hggm.es) Date: Mon, 04 Aug 2008 20:30:53 +0200 Subject: [Mristudio-users] non isometric voxels Message-ID: <20080804183118.79BA82C4011@dns.hggm.es> Hi, I wonder if someone has experience in DTI analysis using scans from a 1.5 GE Signa. The problem is that images were acquired for 33 directions but with a pixel size of 1.1 x 1.1 x 5 mm (x,y,z) aquired in axial (x,y) plane. Far for being isometric, as recommended by the experts... Before doing all the preprocessing, do you think that those images would be too noisy for tracktography or FA analysis?? The data is intended to investigate group comparison patients /controls using ADC and RA values, and sample size is not very large. Thanks in advance, Santiago ><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?> `?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.?? Santiago Reig Hospital General Universitario Gregorio Mara??n Unidad de Medicina y Cirug?a Experimental c/ Dr. Esquerdo 46, 28007 Madrid Tel: 34 91 426 5067 Fax: 34 91 426 5108 mustela at mce.hggm.es http://www.hggm.es/image From junyiwang2002 at yahoo.com Tue Aug 5 09:54:37 2008 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Tue, 05 Aug 2008 06:54:37 -0700 (PDT) Subject: [Mristudio-users] non isometric voxels Message-ID: <951272.57488.qm@web50512.mail.re2.yahoo.com> Hi Santiago, We also have DTI images with 1x1x5 mm voxel size.? We tried tractography using DTI Studio, but the fibers fell to propagate to next slices.? I don't know whether reslicing to thinner slices will help or not.? But even it works, the quality of the tractography will not be good. Jun Yi Wang Predoc., University of Texas at Dallas Research assistant, University of Texast Southwestern Medical Center ----- Original Message ---- From: "mustela at mce.hggm.es" To: mristudio-users at mristudio.org Sent: Monday, August 4, 2008 1:30:53 PM Subject: [Mristudio-users] non isometric voxels Hi, I wonder if someone has experience in DTI analysis using scans from a 1.5 GE Signa. The problem is that images were acquired for 33 directions but with a pixel size of 1.1 x 1.1 x 5 mm? (x,y,z) aquired in axial (x,y) plane. Far for being isometric, as recommended by the experts... Before doing all the preprocessing, do you think that those images would be too noisy for tracktography or FA analysis?? The data is intended to investigate group comparison patients /controls using ADC and RA values, and sample size is not very large. Thanks in advance, Santiago ><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?> ? `?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.?? Santiago Reig ? ? Hospital General Universitario Gregorio Mara??n ? ? Unidad de Medicina y Cirug?a Experimental ? ? c/ Dr. Esquerdo 46, 28007 Madrid ? ? ? ? ? Tel:? 34 91 426 5067 Fax: 34 91 426 5108 mustela at mce.hggm.es? http://www.hggm.es/image? _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080805/d5c1bce9/attachment.html From albrecht at psychiatrie.klinik.uni-mainz.de Tue Aug 5 10:05:32 2008 From: albrecht at psychiatrie.klinik.uni-mainz.de (albrecht) Date: Tue, 05 Aug 2008 16:05:32 +0200 Subject: [Mristudio-users] cancel me from mailing list please Message-ID: <48985E2C.6050807@psychiatrie.klinik.uni-mainz.de> Dear all, would you please cancel me from your mailing list!! Thanx a lot, Juliane From c.bieck at T-Online.de Tue Aug 5 15:00:00 2008 From: c.bieck at T-Online.de (Christian Bieck) Date: Tue, 05 Aug 2008 19:00 +0000 (GMT) Subject: [Mristudio-users] Landmarker Image File Create Eroor Message-ID: <1KQRm2-1pfnUm0@fwd33.aul.t-online.de> Hello, As far as DTI Studio went, I did a regular DTI Mapping as described in the User's Manual with the Siemens Mosaic files I have, calculating all relevant images (Color Map, Eigenvector, Mean DWIs, B0, etc.) and then saving them as seperate Raw Data files. Then, prior to starting Landmarker, I compiled the .exe files as instructed and put them into the Landmarker folder, whose path is C:\Users\CBieck\DTI_Studio\Landmarker . Then, starting Landmarker, I opened the JHU_Talairach_SS_DWI to use as template and then opened my DWI file (96x96x60, Field of View 192x192, Slice thickness 2, Pixel size 2,0x2,0) and all other files I wanted to normalize, finally loading the .d file in the form of a Raw Data file that contained the six tensor images Dxx, Dyy, Dzz, Dxy, Dxz, Dyz. It did not have a .d file extension, however. The loading itself worked without any problems so far, though. Making sure that the correct DWI template image was loaded, I then clicked the "Automatic Image Registration Linear" button when the error message "Image File Create Error" popped up. Now I get this error message for all DWI template images JHU_MNI_GA, JHU_MNI_SS, JHU_Talairach_SS and ICBM_DTI_81 and both with my own .exe files and those that Dr. Evangelou kindly sent to me, so I'm somewhat perplexed at it all. Could it be that Windows Vista has something to do with it? DTI Studio worked very fine so far on Vista, but maybe Vista has a problem with Landmarker? Anyways, I hope I could provide enough information. If not, I'd be happy to elaborate a bit further as I'm looking very much forward to get this problem solved. Thank you for your time, Christian Bieck > Dr. Bieck, > > When AIR alignlinear function is applied, two temporary images are generated in the Landmarker folder. The message you got means that these two images cannot be generated. Actually this error rarely happens. > > Could you please give me more details about how you did? What's the path of the Landmarker folder on your machine? What's the operating system you use? Could you please give me a few screenshots to decribe your problem? > > Thanks! > > > > Xin > > > > ----- Original Message ----- > From: Christian Bieck > Date: Monday, August 4, 2008 2:37 pm > Subject: [Mristudio-users] Landmarker Image File Create Eroor > To: mristudio-users at mristudio.org > > > > Hello, > > > > I'm trying to normalize the files (DWI, B0s, Color Map etc.) I made > > via DTI Studio by using the AIR "Linear" option in Landmarker. > > However, when I press the button, I get a message saying "Image File > > Create Error" even though the correct Atlas sample images were opened. > > I got this error message both with using my own compiled .exe files > > and the .exe files Dr Evangelou was so kind to send me, so I'm > > somewhat at a loss as to what went wrong. > > I'd very much appreciate it if you could shed some light on what > > might be the possible sources of the Image File Create Error and how I > > could fix it. > > > > Thank you in advance, > > Christian Bieck > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080805/a280bbb8/attachment-0001.html From susumu at mri.jhu.edu Tue Aug 5 17:52:45 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 05 Aug 2008 17:52:45 -0400 Subject: [Mristudio-users] Landmarker Image File Create Eroor In-Reply-To: <1KQRm2-1pfnUm0@fwd33.aul.t-online.de> Message-ID: <73alti$380jd7@ipex2.johnshopkins.edu> Hmmm, that's an interesting error message. Xin, is it something we expect when AIR.exe is not right? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Christian Bieck Sent: Tuesday, August 05, 2008 3:00 PM To: XIN LI; mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Landmarker Image File Create Eroor Hello, As far as DTI Studio went, I did a regular DTI Mapping as described in the User's Manual with the Siemens Mosaic files I have, calculating all relevant images (Color Map, Eigenvector, Mean DWIs, B0, etc.) and then saving them as seperate Raw Data files. Then, prior to starting Landmarker, I compiled the .exe files as instructed and put them into the Landmarker folder, whose path is C:UsersCBieckDTI_StudioLandmarker . Then, starting Landmarker, I opened the JHU_Talairach_SS_DWI to use as template and then opened my DWI file (96x96x60, Field of View 192x192, Slice thickness 2, Pixel size 2,0x2,0) and all other files I wanted to normalize, finally loading the .d file in the form of a Raw Data file that contained the six tensor images Dxx, Dyy, Dzz, Dxy, Dxz, Dyz. It did not have a .d file extension, however. The loading itself worked without any problems so far, though. Making sure that the correct DWI template image was loaded, I then clicked the "Automatic Image Registration Linear" button when the error message "Image File Create Error" popped up. Now I get this error message for all DWI template images JHU_MNI_GA, JHU_MNI_SS, JHU_Talairach_SS and ICBM_DTI_81 and both with my own .exe files and those that Dr. Evangelou kindly sent to me, so I'm somewhat perplexed at it all. Could it be that Windows Vista has something to do with it? DTI Studio worked very fine so far on Vista, but maybe Vista has a problem with Landmarker? Anyways, I hope I could provide enough information. If not, I'd be happy to elaborate a bit further as I'm looking very much forward to get this problem solved. Thank you for your time, Christian Bieck > Dr. Bieck, > > When AIR alignlinear function is applied, two temporary images are generated in the Landmarker folder. The message you got means that these two images cannot be generated. Actually this error rarely happens. > > Could you please give me more details about how you did? What's the path of the Landmarker folder on your machine? What's the operating system you use? Could you please give me a few screenshots to decribe your problem? > > Thanks! > > > > Xin > > > > ----- Original Message ----- > From: Christian Bieck > Date: Monday, August 4, 2008 2:37 pm > Subject: [Mristudio-users] Landmarker Image File Create Eroor > To: mristudio-users at mristudio.org > > > > Hello, > > > > I'm trying to normalize the files (DWI, B0s, Color Map etc.) I made > > via DTI Studio by using the AIR "Linear" option in Landmarker. > > However, when I press the button, I get a message saying "Image File > > Create Error" even though the correct Atlas sample images were opened. > > I got this error message both with using my own compiled .exe files > > and the .exe files Dr Evangelou was so kind to send me, so I'm > > somewhat at a loss as to what went wrong. > > I'd very much appreciate it if you could shed some light on what > > might be the possible sources of the Image File Create Error and how I > > could fix it. > > > > Thank you in advance, > > Christian Bieck > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080805/0498b47d/attachment.html From susumu at mri.jhu.edu Tue Aug 5 18:19:44 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 05 Aug 2008 18:19:44 -0400 Subject: [Mristudio-users] non isometric voxels In-Reply-To: <951272.57488.qm@web50512.mail.re2.yahoo.com> Message-ID: <73alti$380opl@ipex2.johnshopkins.edu> It is difficult to set a threshold and say, "you can do tractography if your pixel size is like this". Of course, isotropic resolution is better than anisotropic pixels in general, but if the fiber of your interest has a tubular shape along the longest axis of the anisotropy pixel (e.g. the corticospinal tract + axial imaging), then you do not have much partial volume problem. On the other hand, you'd have irreproducible results for the corpus callosum reconstruction with 5 mm axial slice. If you do tractography for all subjects and get reproducible results, you may be able to use the data. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang Sent: Tuesday, August 05, 2008 9:55 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] non isometric voxels Hi Santiago, We also have DTI images with 1x1x5 mm voxel size. We tried tractography using DTI Studio, but the fibers fell to propagate to next slices. I don't know whether reslicing to thinner slices will help or not. But even it works, the quality of the tractography will not be good. Jun Yi Wang Predoc., University of Texas at Dallas Research assistant, University of Texast Southwestern Medical Center ----- Original Message ---- From: "mustela at mce.hggm.es" To: mristudio-users at mristudio.org Sent: Monday, August 4, 2008 1:30:53 PM Subject: [Mristudio-users] non isometric voxels Hi, I wonder if someone has experience in DTI analysis using scans from a 1.5 GE Signa. The problem is that images were acquired for 33 directions but with a pixel size of 1.1 x 1.1 x 5 mm (x,y,z) aquired in axial (x,y) plane. Far for being isometric, as recommended by the experts... Before doing all the preprocessing, do you think that those images would be too noisy for tracktography or FA analysis?? The data is intended to investigate group comparison patients /controls using ADC and RA values, and sample size is not very large. Thanks in advance, Santiago ><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?> `?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.?? Santiago Reig Hospital General Universitario Gregorio Mara??n Unidad de Medicina y Cirug?a Experimental c/ Dr. Esquerdo 46, 28007 Madrid Tel: 34 91 426 5067 Fax: 34 91 426 5108 mustela at mce.hggm.es http://www.hggm.es/image _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080805/bc4a5bbd/attachment-0001.html From susumu at mri.jhu.edu Tue Aug 5 18:27:29 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 05 Aug 2008 18:27:29 -0400 Subject: [Mristudio-users] 8/11 Tutorial In-Reply-To: Message-ID: <73alti$380q54@ipex2.johnshopkins.edu> There are several requests about the online tutorial. We've been going over several options. In the past, I video recorded the tutorials but the recording quality of the consumer-grade camcorder has not been very great especially under the low right conditions (and of course I always had problems like forgot to turn off, turn on, battery runs out, etc). This time, we will try to record the events in my computer using Wink. If it works, we will post the entire tutorial after some editing. Another option is the real-time broadcasting. This won't be free of us and don't know how many people would sit in their office and follow the tutorial in real time. So, let's see if the second option (Wink) works. We would welcome any suggestions regarding this. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jayasree Sent: Monday, August 04, 2008 10:59 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] 8/11 Tutorial Dear Dr.Susumu, is there any possibilityof making the tutorial material available online? Jay -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080805/2bcc4af5/attachment.html From grojasy at puc.cl Tue Aug 5 21:26:02 2008 From: grojasy at puc.cl (Gonzalo Rojas) Date: Tue, 05 Aug 2008 21:26:02 -0400 Subject: [Mristudio-users] 8/11 Tutorial In-Reply-To: <73alti$380q54@ipex2.johnshopkins.edu> References: <73alti$380q54@ipex2.johnshopkins.edu> Message-ID: <4898FDAA.6060608@puc.cl> Susumu: Other idea... Russ Poldrack's in his "UCLA Advanced Neuroimaging Summer School 2008" put for some talks a Podcast file (.m4a)... That file have the PPT with the sound of the talk live... You can view some examples in http://summercourse.poldracklab.org/index.php/Schedule_2008 Sincerely, Gonzalo Rojas Costa Laboratory of Medical Image Processing Department of Neuroradiology Institute of Neurosurgery Dr. Asenjo Jose Manuel Infante 553, Providencia, Santiago, Chile. Tel/Fax: 56-2-5754653 Cel: 56-9-97771785 www.neurorradiologia.cl susumu escribi?: > There are several requests about the online tutorial. We've been going > over several options. In the past, I video recorded the tutorials but > the recording quality of the consumer-grade camcorder has not been very > great especially under the low right conditions (and of course I always > had problems like forgot to turn off, turn on, battery runs out, etc). > > > > This time, we will try to record the events in my computer using Wink. > If it works, we will post the entire tutorial after some editing. > > > > Another option is the real-time broadcasting. This won't be free of us > and don't know how many people would sit in their office and follow the > tutorial in real time. > > > > So, let's see if the second option (Wink) works. > > > > We would welcome any suggestions regarding this. > > > > Susumu > > > > ------------------------------------------------------------------------ > > *From:* mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] *On Behalf Of *Jayasree > *Sent:* Monday, August 04, 2008 10:59 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] 8/11 Tutorial > > > > Dear Dr.Susumu, > > is there any possibilityof making the tutorial material available > online? > > Jay > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users From grojasy at puc.cl Tue Aug 5 21:36:12 2008 From: grojasy at puc.cl (Gonzalo Rojas) Date: Tue, 05 Aug 2008 21:36:12 -0400 Subject: [Mristudio-users] 8/11 Tutorial In-Reply-To: <73alti$380q54@ipex2.johnshopkins.edu> References: <73alti$380q54@ipex2.johnshopkins.edu> Message-ID: <4899000C.1070801@puc.cl> Dear Susumu: I don't know which software Russ Poldrack's uses to create that Podcast files (.m4a)... Sincerely, Gonzalo Rojas Costa Laboratory of Medical Image Processing Department of Neuroradiology Institute of Neurosurgery Dr. Asenjo Jose Manuel Infante 553, Providencia, Santiago, Chile. Tel/Fax: 56-2-5754653 Cel: 56-9-97771785 www.neurorradiologia.cl susumu escribi?: > There are several requests about the online tutorial. We've been going > over several options. In the past, I video recorded the tutorials but > the recording quality of the consumer-grade camcorder has not been very > great especially under the low right conditions (and of course I always > had problems like forgot to turn off, turn on, battery runs out, etc). > > > > This time, we will try to record the events in my computer using Wink. > If it works, we will post the entire tutorial after some editing. > > > > Another option is the real-time broadcasting. This won't be free of us > and don't know how many people would sit in their office and follow the > tutorial in real time. > > > > So, let's see if the second option (Wink) works. > > > > We would welcome any suggestions regarding this. > > > > Susumu > > > > ------------------------------------------------------------------------ > > *From:* mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] *On Behalf Of *Jayasree > *Sent:* Monday, August 04, 2008 10:59 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] 8/11 Tutorial > > > > Dear Dr.Susumu, > > is there any possibilityof making the tutorial material available > online? > > Jay > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users From steinja at ucla.edu Wed Aug 6 00:27:44 2008 From: steinja at ucla.edu (Jason Stein) Date: Tue, 05 Aug 2008 21:27:44 -0700 Subject: [Mristudio-users] 8/11 Tutorial In-Reply-To: <4899000C.1070801@puc.cl> References: <73alti$380q54@ipex2.johnshopkins.edu> <4899000C.1070801@puc.cl> Message-ID: <1bb422f90808052127w17778696ne82f36481d088d84@mail.gmail.com> Hi, I believe he used profcast: http://www.profcast.com/public/index.php. Looks like it's not free though... Jason On Tue, Aug 5, 2008 at 6:36 PM, Gonzalo Rojas wrote: > Dear Susumu: > > I don't know which software Russ Poldrack's uses to create that > Podcast files (.m4a)... > > Sincerely, > > > Gonzalo Rojas Costa > Laboratory of Medical Image Processing > Department of Neuroradiology > Institute of Neurosurgery Dr. Asenjo > Jose Manuel Infante 553, Providencia, Santiago, Chile. > Tel/Fax: 56-2-5754653 > Cel: 56-9-97771785 > www.neurorradiologia.cl > > susumu escribi?: > > There are several requests about the online tutorial. We've been going > > over several options. In the past, I video recorded the tutorials but > > the recording quality of the consumer-grade camcorder has not been very > > great especially under the low right conditions (and of course I always > > had problems like forgot to turn off, turn on, battery runs out, etc). > > > > > > > > This time, we will try to record the events in my computer using Wink. > > If it works, we will post the entire tutorial after some editing. > > > > > > > > Another option is the real-time broadcasting. This won't be free of us > > and don't know how many people would sit in their office and follow the > > tutorial in real time. > > > > > > > > So, let's see if the second option (Wink) works. > > > > > > > > We would welcome any suggestions regarding this. > > > > > > > > Susumu > > > > > > > > ------------------------------------------------------------------------ > > > > *From:* mristudio-users-bounces at mristudio.org > > [mailto:mristudio-users-bounces at mristudio.org] *On Behalf Of *Jayasree > > *Sent:* Monday, August 04, 2008 10:59 PM > > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > > *Subject:* Re: [Mristudio-users] 8/11 Tutorial > > > > > > > > Dear Dr.Susumu, > > > > is there any possibilityof making the tutorial material available > > online? > > > > Jay > > > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/mristudio-users > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080805/cbd70dab/attachment.html From mustela at mce.hggm.es Wed Aug 6 10:54:56 2008 From: mustela at mce.hggm.es (mustela at mce.hggm.es) Date: Wed, 06 Aug 2008 16:54:56 +0200 Subject: [Mristudio-users] non isometric voxels (susumu) In-Reply-To: References: Message-ID: <20080806145459.017802C400B@dns.hggm.es> Thank you for your suggestions! regards, Santiago At 00:19 06/08/2008, you wrote: >Date: Tue, 05 Aug 2008 18:19:44 -0400 >From: susumu >Subject: Re: [Mristudio-users] non isometric voxels >To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" > >Message-ID: <73alti$380opl at ipex2.johnshopkins.edu> >Content-Type: text/plain; charset="iso-8859-1" > >It is difficult to set a threshold and say, "you can do tractography if your >pixel size is like this". Of course, isotropic resolution is better than >anisotropic pixels in general, but if the fiber of your interest has a >tubular shape along the longest axis of the anisotropy pixel (e.g. the >corticospinal tract + axial imaging), then you do not have much partial >volume problem. On the other hand, you'd have irreproducible results for the >corpus callosum reconstruction with 5 mm axial slice. If you do tractography >for all subjects and get reproducible results, you may be able to use the >data. > > > > _____ > >From: mristudio-users-bounces at mristudio.org >[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang >Sent: Tuesday, August 05, 2008 9:55 AM >To: DTI Studio, ROI Editor, Landmarker Questions/Support >Subject: Re: [Mristudio-users] non isometric voxels > > > >Hi Santiago, > > > >We also have DTI images with 1x1x5 mm voxel size. We tried tractography >using DTI Studio, but the fibers fell to propagate to next slices. I don't >know whether reslicing to thinner slices will help or not. But even it >works, the quality of the tractography will not be good. > > > >Jun Yi Wang > >Predoc., University of Texas at Dallas > >Research assistant, University of Texast Southwestern Medical Center > > > >----- Original Message ---- >From: "mustela at mce.hggm.es" >To: mristudio-users at mristudio.org >Sent: Monday, August 4, 2008 1:30:53 PM >Subject: [Mristudio-users] non isometric voxels > >Hi, > >I wonder if someone has experience in DTI analysis using scans from a >1.5 GE Signa. The problem is that images were acquired for 33 >directions but with a pixel size of 1.1 x 1.1 x 5 mm (x,y,z) aquired >in axial (x,y) plane. Far for being isometric, as recommended by the >experts... > >Before doing all the preprocessing, do you think that those images >would be too noisy for tracktography or FA analysis?? >The data is intended to investigate group comparison patients >/controls using ADC and RA values, and sample size is not very large. > >Thanks in advance, > >Santiago > > ><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?> > `?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.?? >Santiago Reig > Hospital General Universitario Gregorio Mara??n > Unidad de Medicina y Cirug?a Experimental > c/ Dr. Esquerdo 46, 28007 Madrid > Tel: 34 91 426 5067 Fax: 34 91 426 5108 >mustela at mce.hggm.es http://www.hggm.es/image From fanglucy.liu at utoronto.ca Wed Aug 6 17:30:36 2008 From: fanglucy.liu at utoronto.ca (Fang Liu) Date: Wed, 06 Aug 2008 17:30:36 -0400 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> Message-ID: <20080806173036.dh65k00ajsooco4w@webmail.utoronto.ca> Thanks a lot. Please email to me fanglucy.liu at utoronto.ca Fang > > > 2008/7/31, Evangelou, Iordanis (NIH/NINDS) [F] : >> >> I have compiled AIR on Windows XP so if anyone is interested I can email >> them copies >> >> ------------------------------------------------------------------- >> *Iordanis E. Evangelou, DPhil* >> Postdoctoral Fellow >> Neuroimmunology Branch >> National Institute of Neurological Disorders and Stroke >> National Institutes of Health >> Building 10, Room 5C203B >> Bethesda, MD 20892 >> USA >> ------------------------------------------------------------------- >> >> >> ------------------------------ >> *From:* Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] >> *Sent:* Wednesday, July 30, 2008 12:05 PM >> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support >> *Subject:* Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial >> >> >> >> You may download AIR from >> http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 >> >> >> >> Best, >> >> >> >> Jack Van Horn >> >> >> >> *From:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *On Behalf Of *Megan Walsh >> *Sent:* Wednesday, July 30, 2008 8:17 AM >> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support >> *Subject:* [Mristudio-users] AIR--??? Re: 8/11 tutorial >> >> >> >> Hey- >> >> >> >> I already replied saying I was interested. I downloaded the latests >> versions of DTI studio, ROI editor, and Landmarker. I know I need to >> download AIR and make files. BUT I can't seem to access the webpage. Is >> the link down? or do I need to use a different web browser (I am using >> I.E.) >> >> >> >> Meg >> >> On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: >> >> Dear MriStudio Users, >> >> >> >> We reserved a room for 40 people. So this is a confirmation email that we >> WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about >> the room will be posted in www.mristudio.org -> Workshop shortly. >> >> >> >> Because there are already 41 people expressing the interest, we have to >> stop taking further registration. For those who already expressed were all >> registered. We are looking for a larger room. If we can find it, we will >> notify. >> >> >> >> The attendants are required to bring their own laptops which have all the >> software and sample data loaded from www.mristudio.org -> Workshop. >> Please follow the instruction in this site. >> >> >> >> The tutorial will start at 10:00 and end around 5:00. We will go over >> DtiStudio, RoiEditor, and Landmarker for DTI calculation, image >> quantification, and normalization. We will try to provide donuts and coffee >> but not lunch. >> >> >> >> Please feel free to ask questions. >> >> >> >> Sincerely, >> >> >> >> Susumu >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> >> >> >> -- >> Megan Kay Walsh >> Graduate Student >> Johns Hopkins University >> Psychological & Brain Sciences >> 204 Ames Hall >> 3400 N. Charles St. >> Baltimore, MD 21218 >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > > -- > Qin Chen M.D. > Department of Neurology > West China Hospital > Sichuan University > Wai Nan Guo Xue Lane 37# > Chengdu,P.R.China,610041 > Tel: +86 8542 3960 (Lab) > Fax: +86 8542 2549 > From basketballmouse at 163.com Wed Aug 6 19:59:27 2008 From: basketballmouse at 163.com (basketballmouse) Date: Thu, 07 Aug 2008 07:59:27 +0800 (CST) Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <20080806173036.dh65k00ajsooco4w@webmail.utoronto.ca> References: <20080806173036.dh65k00ajsooco4w@webmail.utoronto.ca> <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> Message-ID: <28809508.20541218067167824.JavaMail.coremail@bj163app105.163.com> Please email to me Thank you very much basketballmouse at 163.com Huang ?2008-08-07?"Fang Liu" ??? >Thanks a lot. >Please email to me >fanglucy.liu at utoronto.ca > >Fang >> >> >> 2008/7/31, Evangelou, Iordanis (NIH/NINDS) [F] -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080807/8b552098/attachment.html From JLaMarche at tams.com Thu Aug 7 01:05:56 2008 From: JLaMarche at tams.com (John LaMarche) Date: Wed, 06 Aug 2008 22:05:56 -0700 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <20080806173036.dh65k00ajsooco4w@webmail.utoronto.ca> Message-ID: Please send me a copy. Thank you John LaMarche Clinical Marketing Manger, MR TOSHIBA AMERICA MEDICAL SYSTEMS Phone: 714-669-7552 Cell Phone: 805-680-5015 Fax: 714-832-2570 Voice Mail: 800-621-1968 x7552 E-Mail: jlamarche at tams.com Web: medical.toshiba.com Fang Liu Sent by: mristudio-users-bounces at mristudio.org 08/06/2008 02:31 PM Please respond to "DTI Studio, ROI Editor, Landmarker Questions/Support" To "DTI Studio, ROI Editor, Landmarker Questions/Support" cc Subject Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial Thanks a lot. Please email to me fanglucy.liu at utoronto.ca Fang > > > 2008/7/31, Evangelou, Iordanis (NIH/NINDS) [F] : >> >> I have compiled AIR on Windows XP so if anyone is interested I can email >> them copies >> >> ------------------------------------------------------------------- >> *Iordanis E. Evangelou, DPhil* >> Postdoctoral Fellow >> Neuroimmunology Branch >> National Institute of Neurological Disorders and Stroke >> National Institutes of Health >> Building 10, Room 5C203B >> Bethesda, MD 20892 >> USA >> ------------------------------------------------------------------- >> >> >> ------------------------------ >> *From:* Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] >> *Sent:* Wednesday, July 30, 2008 12:05 PM >> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support >> *Subject:* Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial >> >> >> >> You may download AIR from >> http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 >> >> >> >> Best, >> >> >> >> Jack Van Horn >> >> >> >> *From:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *On Behalf Of *Megan Walsh >> *Sent:* Wednesday, July 30, 2008 8:17 AM >> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support >> *Subject:* [Mristudio-users] AIR--??? Re: 8/11 tutorial >> >> >> >> Hey- >> >> >> >> I already replied saying I was interested. I downloaded the latests >> versions of DTI studio, ROI editor, and Landmarker. I know I need to >> download AIR and make files. BUT I can't seem to access the webpage. Is >> the link down? or do I need to use a different web browser (I am using >> I.E.) >> >> >> >> Meg >> >> On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: >> >> Dear MriStudio Users, >> >> >> >> We reserved a room for 40 people. So this is a confirmation email that we >> WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about >> the room will be posted in www.mristudio.org -> Workshop shortly. >> >> >> >> Because there are already 41 people expressing the interest, we have to >> stop taking further registration. For those who already expressed were all >> registered. We are looking for a larger room. If we can find it, we will >> notify. >> >> >> >> The attendants are required to bring their own laptops which have all the >> software and sample data loaded from www.mristudio.org -> Workshop. >> Please follow the instruction in this site. >> >> >> >> The tutorial will start at 10:00 and end around 5:00. We will go over >> DtiStudio, RoiEditor, and Landmarker for DTI calculation, image >> quantification, and normalization. We will try to provide donuts and coffee >> but not lunch. >> >> >> >> Please feel free to ask questions. >> >> >> >> Sincerely, >> >> >> >> Susumu >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> >> >> >> -- >> Megan Kay Walsh >> Graduate Student >> Johns Hopkins University >> Psychological & Brain Sciences >> 204 Ames Hall >> 3400 N. Charles St. >> Baltimore, MD 21218 >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > > -- > Qin Chen M.D. > Department of Neurology > West China Hospital > Sichuan University > Wai Nan Guo Xue Lane 37# > Chengdu,P.R.China,610041 > Tel: +86 8542 3960 (Lab) > Fax: +86 8542 2549 > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080806/2cf0dd67/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 3111 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080806/2cf0dd67/attachment-0001.gif From ajay at pet.wayne.edu Fri Aug 8 09:43:26 2008 From: ajay at pet.wayne.edu (Ajay Kumar, MD,PhD,DNB,MNAMS) Date: Fri, 08 Aug 2008 09:43:26 -0400 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial In-Reply-To: <20080806173036.dh65k00ajsooco4w@webmail.utoronto.ca> References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> <20080806173036.dh65k00ajsooco4w@webmail.utoronto.ca> Message-ID: <00eb01c8f95c$bff856d0$3fe90470$@wayne.edu> Thanks a lot. Can you please email to me also. Ajay ajay at pet.wayne.edu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Fang Liu Sent: Wednesday, August 06, 2008 5:31 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial Thanks a lot. Please email to me fanglucy.liu at utoronto.ca Fang > > > 2008/7/31, Evangelou, Iordanis (NIH/NINDS) [F] : >> >> I have compiled AIR on Windows XP so if anyone is interested I can email >> them copies >> >> ------------------------------------------------------------------- >> *Iordanis E. Evangelou, DPhil* >> Postdoctoral Fellow >> Neuroimmunology Branch >> National Institute of Neurological Disorders and Stroke >> National Institutes of Health >> Building 10, Room 5C203B >> Bethesda, MD 20892 >> USA >> ------------------------------------------------------------------- >> >> >> ------------------------------ >> *From:* Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] >> *Sent:* Wednesday, July 30, 2008 12:05 PM >> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support >> *Subject:* Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial >> >> >> >> You may download AIR from >> http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 >> >> >> >> Best, >> >> >> >> Jack Van Horn >> >> >> >> *From:* mristudio-users-bounces at mristudio.org [mailto: >> mristudio-users-bounces at mristudio.org] *On Behalf Of *Megan Walsh >> *Sent:* Wednesday, July 30, 2008 8:17 AM >> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support >> *Subject:* [Mristudio-users] AIR--??? Re: 8/11 tutorial >> >> >> >> Hey- >> >> >> >> I already replied saying I was interested. I downloaded the latests >> versions of DTI studio, ROI editor, and Landmarker. I know I need to >> download AIR and make files. BUT I can't seem to access the webpage. Is >> the link down? or do I need to use a different web browser (I am using >> I.E.) >> >> >> >> Meg >> >> On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: >> >> Dear MriStudio Users, >> >> >> >> We reserved a room for 40 people. So this is a confirmation email that we >> WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about >> the room will be posted in www.mristudio.org -> Workshop shortly. >> >> >> >> Because there are already 41 people expressing the interest, we have to >> stop taking further registration. For those who already expressed were all >> registered. We are looking for a larger room. If we can find it, we will >> notify. >> >> >> >> The attendants are required to bring their own laptops which have all the >> software and sample data loaded from www.mristudio.org -> Workshop. >> Please follow the instruction in this site. >> >> >> >> The tutorial will start at 10:00 and end around 5:00. We will go over >> DtiStudio, RoiEditor, and Landmarker for DTI calculation, image >> quantification, and normalization. We will try to provide donuts and coffee >> but not lunch. >> >> >> >> Please feel free to ask questions. >> >> >> >> Sincerely, >> >> >> >> Susumu >> >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> >> >> >> -- >> Megan Kay Walsh >> Graduate Student >> Johns Hopkins University >> Psychological & Brain Sciences >> 204 Ames Hall >> 3400 N. Charles St. >> Baltimore, MD 21218 >> >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> >> > > > -- > Qin Chen M.D. > Department of Neurology > West China Hospital > Sichuan University > Wai Nan Guo Xue Lane 37# > Chengdu,P.R.China,610041 > Tel: +86 8542 3960 (Lab) > Fax: +86 8542 2549 > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From meggersw at gmail.com Fri Aug 8 12:00:53 2008 From: meggersw at gmail.com (Megan Walsh) Date: Fri, 08 Aug 2008 12:00:53 -0400 Subject: [Mristudio-users] Downloading sample data Re: 8/11 tutorial Message-ID: <254662fa0808080900g9ac13bcib73e73533695debd@mail.gmail.com> Hey everyone- I tried to download the sample data for monday. And i was able to get the par/rec files fine. And then I proceeded to download the processed data zip file and the sample data zip file. But for some reason I can't seem to find the Siemens data that is instructed in the "tutorial" that we need to run through before monday. Any hints? Thanks meg On Fri, Aug 8, 2008 at 9:43 AM, Ajay Kumar, MD,PhD,DNB,MNAMS < ajay at pet.wayne.edu> wrote: > Thanks a lot. > > Can you please email to me also. > > Ajay > > ajay at pet.wayne.edu > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Fang Liu > Sent: Wednesday, August 06, 2008 5:31 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > Thanks a lot. > Please email to me > fanglucy.liu at utoronto.ca > > Fang > > > > > > 2008/7/31, Evangelou, Iordanis (NIH/NINDS) [F] >: > >> > >> I have compiled AIR on Windows XP so if anyone is interested I can > email > >> them copies > >> > >> ------------------------------------------------------------------- > >> *Iordanis E. Evangelou, DPhil* > >> Postdoctoral Fellow > >> Neuroimmunology Branch > >> National Institute of Neurological Disorders and Stroke > >> National Institutes of Health > >> Building 10, Room 5C203B > >> Bethesda, MD 20892 > >> USA > >> ------------------------------------------------------------------- > >> > >> > >> ------------------------------ > >> *From:* Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] > >> *Sent:* Wednesday, July 30, 2008 12:05 PM > >> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > >> *Subject:* Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > >> > >> > >> > >> You may download AIR from > >> http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 > >> > >> > >> > >> Best, > >> > >> > >> > >> Jack Van Horn > >> > >> > >> > >> *From:* mristudio-users-bounces at mristudio.org [mailto: > >> mristudio-users-bounces at mristudio.org] *On Behalf Of *Megan Walsh > >> *Sent:* Wednesday, July 30, 2008 8:17 AM > >> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > >> *Subject:* [Mristudio-users] AIR--??? Re: 8/11 tutorial > >> > >> > >> > >> Hey- > >> > >> > >> > >> I already replied saying I was interested. I downloaded the latests > >> versions of DTI studio, ROI editor, and Landmarker. I know I need to > >> download AIR and make files. BUT I can't seem to access the webpage. > Is > >> the link down? or do I need to use a different web browser (I am using > >> I.E.) > >> > >> > >> > >> Meg > >> > >> On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: > >> > >> Dear MriStudio Users, > >> > >> > >> > >> We reserved a room for 40 people. So this is a confirmation email that > we > >> WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail > about > >> the room will be posted in www.mristudio.org -> Workshop shortly. > >> > >> > >> > >> Because there are already 41 people expressing the interest, we have to > >> stop taking further registration. For those who already expressed were > all > >> registered. We are looking for a larger room. If we can find it, we will > >> notify. > >> > >> > >> > >> The attendants are required to bring their own laptops which have all > the > >> software and sample data loaded from www.mristudio.org -> Workshop. > >> Please follow the instruction in this site. > >> > >> > >> > >> The tutorial will start at 10:00 and end around 5:00. We will go over > >> DtiStudio, RoiEditor, and Landmarker for DTI calculation, image > >> quantification, and normalization. We will try to provide donuts and > coffee > >> but not lunch. > >> > >> > >> > >> Please feel free to ask questions. > >> > >> > >> > >> Sincerely, > >> > >> > >> > >> Susumu > >> > >> > >> _______________________________________________ > >> Mristudio-users mailing list > >> Mristudio-users at mristudio.org > >> http://lists.mristudio.org/mailman/listinfo/mristudio-users > >> > >> > >> > >> > >> -- > >> Megan Kay Walsh > >> Graduate Student > >> Johns Hopkins University > >> Psychological & Brain Sciences > >> 204 Ames Hall > >> 3400 N. Charles St. > >> Baltimore, MD 21218 > >> > >> _______________________________________________ > >> Mristudio-users mailing list > >> Mristudio-users at mristudio.org > >> http://lists.mristudio.org/mailman/listinfo/mristudio-users > >> > >> > > > > > > -- > > Qin Chen M.D. > > Department of Neurology > > West China Hospital > > Sichuan University > > Wai Nan Guo Xue Lane 37# > > Chengdu,P.R.China,610041 > > Tel: +86 8542 3960 (Lab) > > Fax: +86 8542 2549 > > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080808/cae7de34/attachment.html From espieker at mprc.umaryland.edu Fri Aug 8 13:36:25 2008 From: espieker at mprc.umaryland.edu (Elena Spieker) Date: Fri, 08 Aug 2008 13:36:25 -0400 Subject: [Mristudio-users] Downloading sample data Re: 8/11 tutorial Message-ID: If you downloaded the 2 zipped files for sample data and processed data you have what you need. Make sure these files are all extracted before you try to open them in DTIStudio. Go into DTIStudio and paste the gradient table for the Siemens. Then add the folder NEW1 then NEW2 because that is where the needed files. When you extract you may get a single folder with subfolders inside, there should be the above named folders (when u open your zip file window you will see on the far right the name of the folder to which each file belongs so you can doublecheck). If you still do not have these i recommend redownloading the zip files and opening them to be certain you have the dicom files. Hope this helps. Elena Elena Spieker Research Coordinator Maryland Psychiatric Research Center PO Box 21247 Baltimore, MD 21228 443-848-7672 410-402-6031 >>> meggersw at gmail.com 8/8/2008 12:00:53 PM >>> Hey everyone- I tried to download the sample data for monday. And i was able to get the par/rec files fine. And then I proceeded to download the processed data zip file and the sample data zip file. But for some reason I can't seem to find the Siemens data that is instructed in the "tutorial" that we need to run through before monday. Any hints? Thanks meg On Fri, Aug 8, 2008 at 9:43 AM, Ajay Kumar, MD,PhD,DNB,MNAMS < ajay at pet.wayne.edu> wrote: > Thanks a lot. > > Can you please email to me also. > > Ajay > > ajay at pet.wayne.edu > > -----Original Message----- > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Fang Liu > Sent: Wednesday, August 06, 2008 5:31 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > > Thanks a lot. > Please email to me > fanglucy.liu at utoronto.ca > > Fang > > > > > > 2008/7/31, Evangelou, Iordanis (NIH/NINDS) [F] >: > >> > >> I have compiled AIR on Windows XP so if anyone is interested I can > email > >> them copies > >> > >> ------------------------------------------------------------------- > >> *Iordanis E. Evangelou, DPhil* > >> Postdoctoral Fellow > >> Neuroimmunology Branch > >> National Institute of Neurological Disorders and Stroke > >> National Institutes of Health > >> Building 10, Room 5C203B > >> Bethesda, MD 20892 > >> USA > >> ------------------------------------------------------------------- > >> > >> > >> ------------------------------ > >> *From:* Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] > >> *Sent:* Wednesday, July 30, 2008 12:05 PM > >> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > >> *Subject:* Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial > >> > >> > >> > >> You may download AIR from > >> http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 > >> > >> > >> > >> Best, > >> > >> > >> > >> Jack Van Horn > >> > >> > >> > >> *From:* mristudio-users-bounces at mristudio.org [mailto: > >> mristudio-users-bounces at mristudio.org] *On Behalf Of *Megan Walsh > >> *Sent:* Wednesday, July 30, 2008 8:17 AM > >> *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > >> *Subject:* [Mristudio-users] AIR--??? Re: 8/11 tutorial > >> > >> > >> > >> Hey- > >> > >> > >> > >> I already replied saying I was interested. I downloaded the latests > >> versions of DTI studio, ROI editor, and Landmarker. I know I need to > >> download AIR and make files. BUT I can't seem to access the webpage. > Is > >> the link down? or do I need to use a different web browser (I am using > >> I.E.) > >> > >> > >> > >> Meg > >> > >> On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: > >> > >> Dear MriStudio Users, > >> > >> > >> > >> We reserved a room for 40 people. So this is a confirmation email that > we > >> WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail > about > >> the room will be posted in www.mristudio.org -> Workshop shortly. > >> > >> > >> > >> Because there are already 41 people expressing the interest, we have to > >> stop taking further registration. For those who already expressed were > all > >> registered. We are looking for a larger room. If we can find it, we will > >> notify. > >> > >> > >> > >> The attendants are required to bring their own laptops which have all > the > >> software and sample data loaded from www.mristudio.org -> Workshop. > >> Please follow the instruction in this site. > >> > >> > >> > >> The tutorial will start at 10:00 and end around 5:00. We will go over > >> DtiStudio, RoiEditor, and Landmarker for DTI calculation, image > >> quantification, and normalization. We will try to provide donuts and > coffee > >> but not lunch. > >> > >> > >> > >> Please feel free to ask questions. > >> > >> > >> > >> Sincerely, > >> > >> > >> > >> Susumu > >> > >> > >> _______________________________________________ > >> Mristudio-users mailing list > >> Mristudio-users at mristudio.org > >> http://lists.mristudio.org/mailman/listinfo/mristudio-users > >> > >> > >> > >> > >> -- > >> Megan Kay Walsh > >> Graduate Student > >> Johns Hopkins University > >> Psychological & Brain Sciences > >> 204 Ames Hall > >> 3400 N. Charles St. > >> Baltimore, MD 21218 > >> > >> _______________________________________________ > >> Mristudio-users mailing list > >> Mristudio-users at mristudio.org > >> http://lists.mristudio.org/mailman/listinfo/mristudio-users > >> > >> > > > > > > -- > > Qin Chen M.D. > > Department of Neurology > > West China Hospital > > Sichuan University > > Wai Nan Guo Xue Lane 37# > > Chengdu,P.R.China,610041 > > Tel: +86 8542 3960 (Lab) > > Fax: +86 8542 2549 > > > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 From susumu at mri.jhu.edu Fri Aug 8 14:50:12 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 08 Aug 2008 14:50:12 -0400 Subject: [Mristudio-users] 8/11 Tutorial Message-ID: <73alti$38tgmh@ipex2.johnshopkins.edu> For those who will come to the tutorial on 8/11; If you had a hard time in downloading software and sample data, I encourage to come 30 min earlier. We have DVDs and a hard drive ready in the Mountcastle auditorium. See you soon. Susumu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080808/cb78476b/attachment.html From johnlsherman at hotmail.com Sat Aug 9 22:30:25 2008 From: johnlsherman at hotmail.com (John Sherman) Date: Sat, 09 Aug 2008 20:30:25 -0600 Subject: [Mristudio-users] mailing list In-Reply-To: <18897347.1218334383562.JavaMail.servappsprod@aragon-rs1.loni.ucla.edu> References: <18897347.1218334383562.JavaMail.servappsprod@aragon-rs1.loni.ucla.edu> Message-ID: I have not been able to get onto the mailing list although I have tried several time. I will be at the workshop on Monday morning (early). Thanks John Sherman M.D. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080809/ff014c85/attachment.html From evangelouI at ninds.nih.gov Sun Aug 10 22:47:36 2008 From: evangelouI at ninds.nih.gov (Evangelou, Iordanis (NIH/NINDS) [F]) Date: Sun, 10 Aug 2008 22:47:36 -0400 Subject: [Mristudio-users] AIR for XP References: <18897347.1218334383562.JavaMail.servappsprod@aragon-rs1.loni.ucla.edu> Message-ID: <9A3BEE43EE449840B003538CCC88903088647E@nihcesmlbx2.nih.gov> Dear all since most of you will need this tomorrow here it is http://www.geocities.com/iordanis_evangelou/pub/ ------------------------------------------------------- Iordanis E. Evangelou, DPhil Postdoctoral Fellow Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Bethesda, MD 20892 ------------------------------------------------------- From budha at nbrc.res.in Mon Aug 11 05:27:08 2008 From: budha at nbrc.res.in (budha) Date: Mon, 11 Aug 2008 14:57:08 +0530 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> Message-ID: <006301c8fb94$6d053ad0$3600a8c0@nbrc.ac.in> Please send me a copy also. Thanking you in advance, Yours sincerely, Kh. Budhachandra Senior Research Fellow National NeuroImaging Facility National Brain Research Centre Gurgaon, Manesar, India Email # budha at nbrc.res.in ----- Original Message ----- From: Evangelou, Iordanis (NIH/NINDS) [F] To: DTI Studio, ROI Editor,Landmarker Questions/Support Sent: Wednesday, July 30, 2008 10:19 PM Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial I have compiled AIR on Windows XP so if anyone is interested I can email them copies ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Postdoctoral Fellow Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- ------------------------------------------------------------------------------ From: Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] Sent: Wednesday, July 30, 2008 12:05 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial You may download AIR from http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 Best, Jack Van Horn From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Megan Walsh Sent: Wednesday, July 30, 2008 8:17 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Hey- I already replied saying I was interested. I downloaded the latests versions of DTI studio, ROI editor, and Landmarker. I know I need to download AIR and make files. BUT I can't seem to access the webpage. Is the link down? or do I need to use a different web browser (I am using I.E.) Meg On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: Dear MriStudio Users, We reserved a room for 40 people. So this is a confirmation email that we WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about the room will be posted in www.mristudio.org -> Workshop shortly. Because there are already 41 people expressing the interest, we have to stop taking further registration. For those who already expressed were all registered. We are looking for a larger room. If we can find it, we will notify. The attendants are required to bring their own laptops which have all the software and sample data loaded from www.mristudio.org -> Workshop. Please follow the instruction in this site. The tutorial will start at 10:00 and end around 5:00. We will go over DtiStudio, RoiEditor, and Landmarker for DTI calculation, image quantification, and normalization. We will try to provide donuts and coffee but not lunch. Please feel free to ask questions. Sincerely, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 ------------------------------------------------------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080811/2a201686/attachment-0001.html From support at mristudio.org Mon Aug 11 06:38:27 2008 From: support at mristudio.org (support at mristudio.org) Date: Mon, 11 Aug 2008 06:38:27 -0400 (EDT) Subject: [Mristudio-users] mailing list In-Reply-To: References: <18897347.1218334383562.JavaMail.servappsprod@aragon-rs1.loni.ucla.edu> Message-ID: <34345.128.220.140.158.1218451107.squirrel@webmail.mristudio.org> You have been added to the mailing list. > I have not been able to get onto the mailing list although I have tried several > time. > I will be at the workshop on Monday morning (early). > > Thanks > > John Sherman M.D. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From evangelouI at ninds.nih.gov Mon Aug 11 06:50:09 2008 From: evangelouI at ninds.nih.gov (Evangelou, Iordanis (NIH/NINDS) [F]) Date: Mon, 11 Aug 2008 06:50:09 -0400 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial References: <254662fa0807300816l40654e2dm5f52db0e1a253d16@mail.gmail.com> <9A3BEE43EE449840B003538CCC889030BCBDA9@nihcesmlbx2.nih.gov> <006301c8fb94$6d053ad0$3600a8c0@nbrc.ac.in> Message-ID: <9A3BEE43EE449840B003538CCC889030886481@nihcesmlbx2.nih.gov> here it is http://www.geocities.com/iordanis_evangelou/pub/ ------------------------------------------------------- Iordanis E. Evangelou, DPhil Postdoctoral Fellow Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Bethesda, MD 20892 ------------------------------------------------------- ________________________________ From: budha [mailto:budha at nbrc.res.in] Sent: Mon 8/11/2008 5:27 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial Please send me a copy also. Thanking you in advance, Yours sincerely, Kh. Budhachandra Senior Research Fellow National NeuroImaging Facility National Brain Research Centre Gurgaon, Manesar, India Email # budha at nbrc.res.in ----- Original Message ----- From: Evangelou, Iordanis (NIH/NINDS) [F] To: DTI Studio, ROI Editor,Landmarker Questions/Support Sent: Wednesday, July 30, 2008 10:19 PM Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial I have compiled AIR on Windows XP so if anyone is interested I can email them copies ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Postdoctoral Fellow Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- ________________________________ From: Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] Sent: Wednesday, July 30, 2008 12:05 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial You may download AIR from http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 Best, Jack Van Horn From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Megan Walsh Sent: Wednesday, July 30, 2008 8:17 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Hey- I already replied saying I was interested. I downloaded the latests versions of DTI studio, ROI editor, and Landmarker. I know I need to download AIR and make files. BUT I can't seem to access the webpage. Is the link down? or do I need to use a different web browser (I am using I.E.) Meg On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: Dear MriStudio Users, We reserved a room for 40 people. So this is a confirmation email that we WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about the room will be posted in www.mristudio.org -> Workshop shortly. Because there are already 41 people expressing the interest, we have to stop taking further registration. For those who already expressed were all registered. We are looking for a larger room. If we can find it, we will notify. The attendants are required to bring their own laptops which have all the software and sample data loaded from www.mristudio.org -> Workshop. Please follow the instruction in this site. The tutorial will start at 10:00 and end around 5:00. We will go over DtiStudio, RoiEditor, and Landmarker for DTI calculation, image quantification, and normalization. We will try to provide donuts and coffee but not lunch. Please feel free to ask questions. Sincerely, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 ________________________________ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 10922 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080811/6afd23c1/attachment.bin From TGould at amirad.com Mon Aug 11 08:36:17 2008 From: TGould at amirad.com (Tim Gould) Date: Mon, 11 Aug 2008 07:36:17 -0500 Subject: [Mristudio-users] mailing list In-Reply-To: <34345.128.220.140.158.1218451107.squirrel@webmail.mristudio.org> References: <18897347.1218334383562.JavaMail.servappsprod@aragon-rs1.loni.ucla.edu> <34345.128.220.140.158.1218451107.squirrel@webmail.mristudio.org> Message-ID: <3969D7174FE35949BD0D8881AEE426C001267E11@DOC.RASAPA09.local> Could you please remove me from the list Thank You, Timothy L. Gould R.T. R MR PACS Administrator Radiology Associates of San Antonio, PA Advanced Medical Imaging Centers Telephone: (210) 918-8626, cell 838-8999 E-mail: TGould at AMIRAD.com Confidentiality E-mail Notice This e-mail is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential or otherwise protected from disclosure. Dissemination, distribution or copying of this e-mail or the information herein by anyone other than the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, is prohibited and unauthorized. If you have received this e-mail in error, please call me and destroy the original message and all copies immediately. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of support at mristudio.org Sent: Monday, August 11, 2008 5:38 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] mailing list You have been added to the mailing list. > I have not been able to get onto the mailing list although I have > tried several time. > I will be at the workshop on Monday morning (early). > > Thanks > > John Sherman M.D. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From espieker at mprc.umaryland.edu Mon Aug 11 08:54:23 2008 From: espieker at mprc.umaryland.edu (Elena Spieker) Date: Mon, 11 Aug 2008 08:54:23 -0400 Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Message-ID: please forward a copy if you do not mind. I will be at the workshop early if you have a cd copy and that is easier to you. >>> budha at nbrc.res.in 8/11/2008 5:27 AM >>> Please send me a copy also. Thanking you in advance, Yours sincerely, Kh. Budhachandra Senior Research Fellow National NeuroImaging Facility National Brain Research Centre Gurgaon, Manesar, India Email # budha at nbrc.res.in ----- Original Message ----- From: Evangelou, Iordanis (NIH/NINDS) [F] To: DTI Studio, ROI Editor,Landmarker Questions/Support Sent: Wednesday, July 30, 2008 10:19 PM Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial I have compiled AIR on Windows XP so if anyone is interested I can email them copies ------------------------------------------------------------------- Iordanis E. Evangelou, DPhil Postdoctoral Fellow Neuroimmunology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health Building 10, Room 5C203B Bethesda, MD 20892 USA ------------------------------------------------------------------- ------------------------------------------------------------------------------ From: Jack Van Horn [mailto:jack.vanhorn at loni.ucla.edu] Sent: Wednesday, July 30, 2008 12:05 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR--??? Re: 8/11 tutorial You may download AIR from http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=8 Best, Jack Van Horn From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Megan Walsh Sent: Wednesday, July 30, 2008 8:17 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] AIR--??? Re: 8/11 tutorial Hey- I already replied saying I was interested. I downloaded the latests versions of DTI studio, ROI editor, and Landmarker. I know I need to download AIR and make files. BUT I can't seem to access the webpage. Is the link down? or do I need to use a different web browser (I am using I.E.) Meg On Wed, Jul 30, 2008 at 9:05 AM, susumu wrote: Dear MriStudio Users, We reserved a room for 40 people. So this is a confirmation email that we WILL HAVE THE TUTORIAL on 8/11 from 10:00 am in Hopkins. The detail about the room will be posted in www.mristudio.org -> Workshop shortly. Because there are already 41 people expressing the interest, we have to stop taking further registration. For those who already expressed were all registered. We are looking for a larger room. If we can find it, we will notify. The attendants are required to bring their own laptops which have all the software and sample data loaded from www.mristudio.org -> Workshop. Please follow the instruction in this site. The tutorial will start at 10:00 and end around 5:00. We will go over DtiStudio, RoiEditor, and Landmarker for DTI calculation, image quantification, and normalization. We will try to provide donuts and coffee but not lunch. Please feel free to ask questions. Sincerely, Susumu _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 ------------------------------------------------------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From dna4rna at hotmail.com Tue Aug 12 09:29:56 2008 From: dna4rna at hotmail.com (Javier) Date: Tue, 12 Aug 2008 08:29:56 -0500 Subject: [Mristudio-users] (no subject) Message-ID: Could you please remove me from the list Thank You Javier logo_2 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080812/cd2ba177/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 80690 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080812/cd2ba177/attachment-0001.png From Moustafa.Nouali at erasme.ulb.ac.be Mon Aug 11 09:59:26 2008 From: Moustafa.Nouali at erasme.ulb.ac.be (Nouali Moustafa) Date: Mon, 11 Aug 2008 15:59:26 +0200 Subject: [Mristudio-users] mailing list In-Reply-To: <3969D7174FE35949BD0D8881AEE426C001267E11@DOC.RASAPA09.local> Message-ID: Could you please remove me from the list Thank You, Timothy L. Gould R.T. R MR PACS Administrator Radiology Associates of San Antonio, PA Advanced Medical Imaging Centers Telephone: (210) 918-8626, cell 838-8999 E-mail: TGould at AMIRAD.com Confidentiality E-mail Notice This e-mail is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential or otherwise protected from disclosure. Dissemination, distribution or copying of this e-mail or the information herein by anyone other than the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, is prohibited and unauthorized. If you have received this e-mail in error, please call me and destroy the original message and all copies immediately. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of support at mristudio.org Sent: Monday, August 11, 2008 5:38 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] mailing list You have been added to the mailing list. > I have not been able to get onto the mailing list although I have > tried several time. > I will be at the workshop on Monday morning (early). > > Thanks > > John Sherman M.D. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From John.Woo at uphs.upenn.edu Wed Aug 13 14:52:16 2008 From: John.Woo at uphs.upenn.edu (Woo, John) Date: Wed, 13 Aug 2008 14:52:16 -0400 Subject: [Mristudio-users] cut operation Message-ID: <4BFD060857263F43AEA4C10586DDE446058DF039@uphsmbx8.UPHS.PENNHEALTH.PRV> Hi, I've been trying to understand the "cut" operation of defining the voxels between two ROIs. Each fiber intersects both ROIs. I can see that "nSelectFiberStartPoint" and "nSelectFiberEndPoint" determine the indices of the cut points. If the fiber intersects each ROI in exactly one point, I can confirm that these are precisely the points. But if say ROI 1 intersects the fiber in two points, it is not entirely clear to me which point is chosen. It seems that sometimes the first is chosen, sometimes the second. Interestingly, in an attempt to elucidate the process further, I tried swapping the two ROIs of the cut operation (by altering the ".map" file). The resulting fiber depends on the order of the ROIs. That is, cut(ROI1,ROI2) does not always equal cut(ROI2,ROI1), although they are almost identical. Thanks to anyone who can help. -John. 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080813/badb3d50/attachment.html From hkim at peds.uab.edu Wed Aug 13 15:53:06 2008 From: hkim at peds.uab.edu (Hyunmi Kim, M.D.) Date: Wed, 13 Aug 2008 14:53:06 -0500 Subject: [Mristudio-users] FW: DTI Gradiant Orientation table (matrix) Message-ID: <66073DDBA72FF542AAA13469EF91E79E04D53C14@ex1-777peds.peds.uab.edu> Dear Sir; I would like to have DTI Gradiant Orientation table. Our MRI model is GE HDMR 1.5 SignaXciteHD. 25 directions DTI. GE persons could not provide it... I am also forwarding our current DTI portocol. Thank you for your earliest attention. Sincerely, Hyunmi Kim, MD, PhD Assistant Professor Division of Pediatric Neurology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080813/8e919578/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: DTI-Protocol-GE.pdf Type: application/octet-stream Size: 60685 bytes Desc: DTI-Protocol-GE.pdf Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080813/8e919578/attachment-0001.obj From johnlsherman at hotmail.com Thu Aug 14 02:16:36 2008 From: johnlsherman at hotmail.com (John Sherman) Date: Thu, 14 Aug 2008 00:16:36 -0600 Subject: [Mristudio-users] FW: DTI Gradiant Orientation table (matrix) In-Reply-To: <66073DDBA72FF542AAA13469EF91E79E04D53C14@ex1-777peds.peds.uab.edu> References: <66073DDBA72FF542AAA13469EF91E79E04D53C14@ex1-777peds.peds.uab.edu> Message-ID: Ask you service rep for a file named "tensor.dat". They can provide this to you. I am attaching a file that I got from G.E. for our 3.0 T. It will be different for your scanner but it will give you an idea of what you are looking for. I had to switch my x and y values and reformat the table to fit the DTI Studio format but then it worked. Good Luck. John Sherman, M.D. Neuroradiology Pueblo Imaging Center Date: Wed, 13 Aug 2008 14:53:06 -0500From: hkim at peds.uab.eduTo: mristudio-users at mristudio.orgSubject: [Mristudio-users] FW: DTI Gradiant Orientation table (matrix) Dear Sir; I would like to have DTI Gradiant Orientation table. Our MRI model is GE HDMR 1.5 SignaXciteHD. 25 directions DTI. GE persons could not provide it? I am also forwarding our current DTI portocol. Thank you for your earliest attention. Sincerely, Hyunmi Kim, MD, PhD Assistant Professor Division of Pediatric Neurology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080814/170a68b4/attachment-0001.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: tensor_dat.txt Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080814/170a68b4/attachment-0001.txt From chelmick at dal.ca Thu Aug 14 08:03:43 2008 From: chelmick at dal.ca (Carl Helmick) Date: Thu, 14 Aug 2008 09:03:43 -0300 Subject: [Mristudio-users] FW: DTI Gradient Orientation table (matrix) In-Reply-To: References: Message-ID: <23BF172F-20C8-4341-9E82-F74394220FC8@dal.ca> The gradient orientation table is an ASCII text file and is located on the scanner. It is called "tensor.dat" and is located in /usr/g/bin. The file is made up such that there is a line with a single number indicating number of directions, then a line for each gradient combination to get that number of directions. For example, for 6, 7, and 8 directions you will see: 6 0.707 0.0 0.707 -0.707 0.0 0.707 0.0 0.707 0.707 0.0 0.707 -0.707 0.707 0.707 0.0 -0.707 0.707 0.0 7 1.0 0.0 0.0 0.333 0.943 0.0 -0.333 0.472 0.817 0.577 -0.817 0.0 0.333 -0.472 0.817 -0.577 -0.407 0.707 0.577 0.407 0.707 8 1.0 0.0 0.0 0.333 0.943 0.0 -0.333 0.472 0.817 0.577 -0.817 0.0 0.333 -0.472 0.817 -0.577 -0.407 0.707 0.577 0.407 0.707 0.0 1.0 0.0 This corresponds to gradient amplitudes in X, Y, and Z directions. Here is the one from a GE Signa 1.5T (v.12): -------------- next part -------------- A non-text attachment was scrubbed... Name: tensor.dat.zip Type: application/zip Size: 178881 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080814/2a1d8a11/attachment-0001.zip -------------- next part -------------- Cheers, -------------------------------------------- Carl Helmick, B.C.S. Manager, System Administrator, & Computer Programmer Brain Imaging Laboratory Department of Psychiatry Dalhousie University -------------------------------------------- On 14-Aug-08, at 7:26 AM, mristudio-users-request at mristudio.org wrote: > Send Mristudio-users mailing list submissions to > mristudio-users at mristudio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.mristudio.org/mailman/listinfo/mristudio-users > or, via email, send a message with subject or body 'help' to > mristudio-users-request at mristudio.org > > You can reach the person managing the list at > mristudio-users-owner at mristudio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Mristudio-users digest..." > > > Today's Topics: > > 1. Re: FW: DTI Gradiant Orientation table (matrix) (John Sherman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 14 Aug 2008 00:16:36 -0600 > From: John Sherman > Subject: Re: [Mristudio-users] FW: DTI Gradiant Orientation table > (matrix) > To: "DTI Studio, ROI Editor, Landmarker Questions/Support" > > Message-ID: > Content-Type: text/plain; charset="windows-1252" > > Ask you service rep for a file named "tensor.dat". They can provide > this to you. > I am attaching a file that I got from G.E. for our 3.0 T. It will be > different for your scanner but it will give you an idea of what you > are looking for. > I had to switch my x and y values and reformat the table to fit the > DTI Studio format but then it worked. > > Good Luck. > > John Sherman, M.D. > Neuroradiology > Pueblo Imaging Center > > > > > > > Date: Wed, 13 Aug 2008 14:53:06 -0500From: hkim at peds.uab.eduTo: mristudio-users at mristudio.orgSubject > : [Mristudio-users] FW: DTI Gradiant Orientation table (matrix) > > > > > Dear Sir; > > I would like to have DTI Gradiant Orientation table. > Our MRI model is GE HDMR 1.5 SignaXciteHD. > 25 directions DTI. > GE persons could not provide it? > > I am also forwarding our current DTI portocol. > Thank you for your earliest attention. > > Sincerely, > > > Hyunmi Kim, MD, PhD > Assistant Professor > Division of Pediatric Neurology > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080814/170a68b4/attachment.html > -------------- next part -------------- > An embedded and charset-unspecified text was scrubbed... > Name: tensor_dat.txt > Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080814/170a68b4/attachment.txt > > ------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > End of Mristudio-users Digest, Vol 7, Issue 17 > ********************************************** From hkim at peds.uab.edu Thu Aug 14 10:08:52 2008 From: hkim at peds.uab.edu (Hyunmi Kim, M.D.) Date: Thu, 14 Aug 2008 09:08:52 -0500 Subject: [Mristudio-users] FW: DTI Gradient Orientation table (matrix) In-Reply-To: <23BF172F-20C8-4341-9E82-F74394220FC8@dal.ca> References: <23BF172F-20C8-4341-9E82-F74394220FC8@dal.ca> Message-ID: <66073DDBA72FF542AAA13469EF91E79E04D53C19@ex1-777peds.peds.uab.edu> Dear Sir; You have my many thanks! Hyunmi -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Carl Helmick Sent: Thursday, August 14, 2008 7:04 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] FW: DTI Gradient Orientation table (matrix) The gradient orientation table is an ASCII text file and is located on the scanner. It is called "tensor.dat" and is located in /usr/g/bin. The file is made up such that there is a line with a single number indicating number of directions, then a line for each gradient combination to get that number of directions. For example, for 6, 7, and 8 directions you will see: 6 0.707 0.0 0.707 -0.707 0.0 0.707 0.0 0.707 0.707 0.0 0.707 -0.707 0.707 0.707 0.0 -0.707 0.707 0.0 7 1.0 0.0 0.0 0.333 0.943 0.0 -0.333 0.472 0.817 0.577 -0.817 0.0 0.333 -0.472 0.817 -0.577 -0.407 0.707 0.577 0.407 0.707 8 1.0 0.0 0.0 0.333 0.943 0.0 -0.333 0.472 0.817 0.577 -0.817 0.0 0.333 -0.472 0.817 -0.577 -0.407 0.707 0.577 0.407 0.707 0.0 1.0 0.0 This corresponds to gradient amplitudes in X, Y, and Z directions. Here is the one from a GE Signa 1.5T (v.12): From susumu at mri.jhu.edu Thu Aug 14 10:32:16 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 14 Aug 2008 10:32:16 -0400 Subject: [Mristudio-users] cut operation In-Reply-To: <4BFD060857263F43AEA4C10586DDE446058DF039@uphsmbx8.UPHS.PENNHEALTH.PRV> Message-ID: <73alti$3also7@ipex2.johnshopkins.edu> Hi John, That is a good question. I need Hangyi's answer for more detail, but my guess is the following points are related to this issue; 1) As you know, in DtiStudio fiber tracking is completed in the beginning from the center of all pixels with FA values above the threshold. 2) If we draw two ROIs and select fibers that penetrate the both ROIs, there are two classes of fibers; a) The seed pixels are within the two ROIs b) The seed pixels are outside the two ROIs 3) If there are fibers that penetrate one ROI twice, the (a) and (b) class may pick up different points for the crossing. Also, it may become sensitive to the order of ROI drawing. Of course, this becomes an issue only when we use the "CUT" operation. Hangyi, do you think this is really the case? I hope these differences cause only minor problems, but if not please let us know. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Woo, John Sent: Wednesday, August 13, 2008 2:52 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] cut operation Hi, I've been trying to understand the "cut" operation of defining the voxels between two ROIs. Each fiber intersects both ROIs. I can see that "nSelectFiberStartPoint" and "nSelectFiberEndPoint" determine the indices of the cut points. If the fiber intersects each ROI in exactly one point, I can confirm that these are precisely the points. But if say ROI 1 intersects the fiber in two points, it is not entirely clear to me which point is chosen. It seems that sometimes the first is chosen, sometimes the second. Interestingly, in an attempt to elucidate the process further, I tried swapping the two ROIs of the cut operation (by altering the ".map" file). The resulting fiber depends on the order of the ROIs. That is, cut(ROI1,ROI2) does not always equal cut(ROI2,ROI1), although they are almost identical. Thanks to anyone who can help. -John. 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080814/583b85c0/attachment.html From hkim at peds.uab.edu Thu Aug 14 10:40:08 2008 From: hkim at peds.uab.edu (Hyunmi Kim, M.D.) Date: Thu, 14 Aug 2008 09:40:08 -0500 Subject: [Mristudio-users] FW: DTI Gradiant Orientation table (matrix) In-Reply-To: References: <66073DDBA72FF542AAA13469EF91E79E04D53C14@ex1-777peds.peds.uab.edu> Message-ID: <66073DDBA72FF542AAA13469EF91E79E04D53C1C@ex1-777peds.peds.uab.edu> Dear Sir; Thank you so much! Hyunmi ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of John Sherman Sent: Thursday, August 14, 2008 1:17 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] FW: DTI Gradiant Orientation table (matrix) Ask you service rep for a file named "tensor.dat". They can provide this to you. I am attaching a file that I got from G.E. for our 3.0 T. It will be different for your scanner but it will give you an idea of what you are looking for. I had to switch my x and y values and reformat the table to fit the DTI Studio format but then it worked. Good Luck. John Sherman, M.D. Neuroradiology Pueblo Imaging Center ________________________________ Date: Wed, 13 Aug 2008 14:53:06 -0500 From: hkim at peds.uab.edu To: mristudio-users at mristudio.org Subject: [Mristudio-users] FW: DTI Gradiant Orientation table (matrix) Dear Sir; I would like to have DTI Gradiant Orientation table. Our MRI model is GE HDMR 1.5 SignaXciteHD. 25 directions DTI. GE persons could not provide it... I am also forwarding our current DTI portocol. Thank you for your earliest attention. Sincerely, Hyunmi Kim, MD, PhD Assistant Professor Division of Pediatric Neurology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080814/94332768/attachment-0001.html From support at mristudio.org Thu Aug 14 11:42:34 2008 From: support at mristudio.org (support at mristudio.org) Date: Thu, 14 Aug 2008 11:42:34 -0400 (EDT) Subject: [Mristudio-users] cut operation In-Reply-To: <73alti$3also7@ipex2.johnshopkins.edu> References: <73alti$3also7@ipex2.johnshopkins.edu> Message-ID: <1500.162.129.28.138.1218728554.squirrel@webmail.mristudio.org> Hi John, when a fiber passing through a voxel, there are usually 2 intersection points, one is for entering, one is for exiting. if what you said "ROI intersects the fiber in two points" means this situation, the result of cut operation depends on the 2D-slice direction where the ROI was drawn. take a 2D as a example: | A / | ------/------- | / | | / | B / | -/------------- / | | | | if you drawing the ROI in horizontal slicing direction, the "cut operation" will result point A. on the other hand, if the ROI was drawn in vertical slicing direction, the result is B. when you dealing with digital grid, this happens all the time. this is something related to digitizing error. hangyi > Hi John, > > > > That is a good question. I need Hangyi's answer for more detail, but my > guess is the following points are related to this issue; > > > > 1) As you know, in DtiStudio fiber tracking is completed in the beginning > from the center of all pixels with FA values above the threshold. > > 2) If we draw two ROIs and select fibers that penetrate the both ROIs, there > are two classes of fibers; > > a) The seed pixels are within the two ROIs > > b) The seed pixels are outside the two ROIs > > 3) If there are fibers that penetrate one ROI twice, the (a) and (b) class > may pick up different points for the crossing. Also, it may become sensitive > to the order of ROI drawing. Of course, this becomes an issue only when we > use the "CUT" operation. > > > > Hangyi, do you think this is really the case? > > > > I hope these differences cause only minor problems, but if not please let us > know. > > > > Susumu > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Woo, John > Sent: Wednesday, August 13, 2008 2:52 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] cut operation > > > > Hi, I've been trying to understand the "cut" operation of defining the > voxels between two ROIs. > > > > Each fiber intersects both ROIs. I can see that "nSelectFiberStartPoint" > and "nSelectFiberEndPoint" determine the indices of the cut points. If the > fiber intersects each ROI in exactly one point, I can confirm that these are > precisely the points. > > > > But if say ROI 1 intersects the fiber in two points, it is not entirely > clear to me which point is chosen. It seems that sometimes the first is > chosen, sometimes the second. > > > > Interestingly, in an attempt to elucidate the process further, I tried > swapping the two ROIs of the cut operation (by altering the ".map" file). > The resulting fiber depends on the order of the ROIs. That is, > cut(ROI1,ROI2) does not always equal cut(ROI2,ROI1), although they are > almost identical. > > > > Thanks to anyone who can help. > > > > -John. > > > > > 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/mristudio-users > From darshanp20 at yahoo.com Fri Aug 15 16:04:07 2008 From: darshanp20 at yahoo.com (darshan pai) Date: Fri, 15 Aug 2008 13:04:07 -0700 (PDT) Subject: [Mristudio-users] DTIStudio:Adding fibers Message-ID: <478059.36340.qm@web30704.mail.mud.yahoo.com> In DTIStudio, Fibers that are generated can be saved as a Dat file which is very convenient. But later when I visualize the fibers by loading the Dat file, I dont have an option of clearing these fibers from the screen unless ofcourse I do some processing like not operation for example. And also i cannot save these fibers again after say a not operation. Is this some functionality that is needed or maybe I am not getting it Regards Darshan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080815/47cc406f/attachment.html From hjiang at jhmi.edu Mon Aug 18 10:11:03 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Mon, 18 Aug 2008 10:11:03 -0400 Subject: [Mristudio-users] DTIStudio:Adding fibers Message-ID: <48A94AB8020000630001552E@cis27.hosts.jhmi.edu> hi, Darshan, you can simply choose "None" of the fiber display options if you don't want see the fibers. hangyi >>> darshan pai 08/15/08 4:04 PM >>> In DTIStudio, Fibers that are generated can be saved as a Dat file which is very convenient. But later when I visualize the fibers by loading the Dat file, I dont have an option of clearing these fibers from the screen unless ofcourse I do some processing like not operation for example. And also i cannot save these fibers again after say a not operation. Is this some functionality that is needed or maybe I am not getting it Regards Darshan From cvidal at usc.edu Mon Aug 18 17:11:13 2008 From: cvidal at usc.edu (Christine Vidal) Date: Mon, 18 Aug 2008 14:11:13 -0700 Subject: [Mristudio-users] Question about format - Siemens DCM Message-ID: Dear All, I am having some problems opening my DTI data in DTIStudio. I work on a Siemens scanner that has the TIM system. The output from the scanner are dicom files that each contains one volume (1 volume /direction). As an example, if I acquire data with an angular resolution of 64, I will get 65 dicom volumes (1 more for b0 volume). It looks like all the examples shown in DTIStudio are examples using dicom that contain 1 slice of brain only. When I open my dicom volumes in DTI studio, the 3D shows the 2D cuts in a panel. Has anyone had the same problem? Any idea on what to do? Thanks Christine Christine N. Vidal, Ph.D. University of Southern California Postdoctoral Fellow at the Brain and Creativity Institute Dana and David Dornsife Cognitive Neuroscience Imaging Center 3520A McClintock Avenue Los Angeles, CA 90089 Phone: (213)-821-4263 Fax: (213) 821-4270 Email: cvidal at usc.edu From jayashreemenon at gmail.com Mon Aug 18 23:56:42 2008 From: jayashreemenon at gmail.com (Jayasree) Date: Tue, 19 Aug 2008 09:26:42 +0530 Subject: [Mristudio-users] Question about format - Siemens DCM In-Reply-To: References: Message-ID: Hi Christine, I had a similar problem earlier. Susumu has adviced me in this regard. Now it is working. Instead of selecting DICOM, select the mosaic files for Siemens. Try it All the best Jay -- R.S.Jayasree, Ph.D Scientist Department of Imaging Sciences and Interventional Radiology SCTIMST, Trivandrum-695011,Kerala, India, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080819/aaa70470/attachment.html From John.Woo at uphs.upenn.edu Thu Aug 21 11:35:08 2008 From: John.Woo at uphs.upenn.edu (Woo, John) Date: Thu, 21 Aug 2008 11:35:08 -0400 Subject: [Mristudio-users] cut operation In-Reply-To: <1500.162.129.28.138.1218728554.squirrel@webmail.mristudio.org> References: <73alti$3also7@ipex2.johnshopkins.edu> <1500.162.129.28.138.1218728554.squirrel@webmail.mristudio.org> Message-ID: <4BFD060857263F43AEA4C10586DDE44605A1938F@uphsmbx8.UPHS.PENNHEALTH.PRV> Susumu and Hangyi - Thank you for both your responses. I'll have to think about them a little more deeply. All my ROIs were drawn in the axial plane, so I'm not sure if Hangyi's explanation applies. However, Susumu's response is interesting, and certainly seems to be a plausible explanation why there sometimes may be an asymmetry between cut(ROI1,ROI2) and cut(ROI2,ROI1). The effect of the seed point and its relation to the fiber hadn't occurred to me. At any rate, the differences are very minor (usually no difference, or at most one pixel). I was only interested in getting a more "exact" understanding of the process. - John. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of support at mristudio.org Sent: Thursday, August 14, 2008 11:43 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: Re: [Mristudio-users] cut operation Hi John, when a fiber passing through a voxel, there are usually 2 intersection points, one is for entering, one is for exiting. if what you said "ROI intersects the fiber in two points" means this situation, the result of cut operation depends on the 2D-slice direction where the ROI was drawn. take a 2D as a example: | A / | ------/------- | / | | / | B / | -/------------- / | | | | if you drawing the ROI in horizontal slicing direction, the "cut operation" will result point A. on the other hand, if the ROI was drawn in vertical slicing direction, the result is B. when you dealing with digital grid, this happens all the time. this is something related to digitizing error. hangyi > Hi John, > > > > That is a good question. I need Hangyi's answer for more detail, but my > guess is the following points are related to this issue; > > > > 1) As you know, in DtiStudio fiber tracking is completed in the beginning > from the center of all pixels with FA values above the threshold. > > 2) If we draw two ROIs and select fibers that penetrate the both ROIs, there > are two classes of fibers; > > a) The seed pixels are within the two ROIs > > b) The seed pixels are outside the two ROIs > > 3) If there are fibers that penetrate one ROI twice, the (a) and (b) class > may pick up different points for the crossing. Also, it may become sensitive > to the order of ROI drawing. Of course, this becomes an issue only when we > use the "CUT" operation. > > > > Hangyi, do you think this is really the case? > > > > I hope these differences cause only minor problems, but if not please let us > know. > > > > Susumu > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Woo, John > Sent: Wednesday, August 13, 2008 2:52 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] cut operation > > > > Hi, I've been trying to understand the "cut" operation of defining the > voxels between two ROIs. > > > > Each fiber intersects both ROIs. I can see that "nSelectFiberStartPoint" > and "nSelectFiberEndPoint" determine the indices of the cut points. If the > fiber intersects each ROI in exactly one point, I can confirm that these are > precisely the points. > > > > But if say ROI 1 intersects the fiber in two points, it is not entirely > clear to me which point is chosen. It seems that sometimes the first is > chosen, sometimes the second. > > > > Interestingly, in an attempt to elucidate the process further, I tried > swapping the two ROIs of the cut operation (by altering the ".map" file). > The resulting fiber depends on the order of the ROIs. That is, > cut(ROI1,ROI2) does not always equal cut(ROI2,ROI1), although they are > almost identical. > > > > Thanks to anyone who can help. > > > > -John. > > > > > 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/mristudio-users > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users 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 choisj70 at gmail.com Wed Aug 27 16:09:05 2008 From: choisj70 at gmail.com (Seongjin) Date: Wed, 27 Aug 2008 16:09:05 -0400 Subject: [Mristudio-users] Nrrd file format Message-ID: Dear DTI users, I was trying to convert a part of multi b-valued DTI ParRec data into Nrrd file format on DTIstudio. File converted without any error and gave me a set of Nrrd-formatted files. However, the file could not be read-in by other analysis tool, even by DTI studio. Is anyone who experienced this issue before? Thanks. Regards, S. Choi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080827/ad3abe11/attachment-0001.html From Shan.Shen at surrey.ac.uk Thu Aug 28 06:31:57 2008 From: Shan.Shen at surrey.ac.uk (Shan.Shen at surrey.ac.uk) Date: Thu, 28 Aug 2008 11:31:57 +0100 Subject: [Mristudio-users] Save ROIs in fibre tracking Message-ID: <49F2A9E7CD49B24AAC16C3C5D38CFD0B0F6AD8@EVS-EC1-NODE1.surrey.ac.uk> Hi, I would like to use the 'cut' operation to track fibres between two ROIs. I did the fibre tracking first, then drew the two ROIs, the fibres displayed were those between the two ROIs. However, if I save the ROIs and load them again, this time the fibres displayed are not the ones between the ROIs anymore, but are fibres passing through one of the ROIs. Could anyone tell me what the possible problem is? I tried saving the ROIs as different formats, but the problem is the same. Many thanks shan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080828/8c87d8ec/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/jpeg Size: 2950 bytes Desc: image001.jpg Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080828/8c87d8ec/attachment.jpe From meggersw at gmail.com Fri Sep 5 10:07:19 2008 From: meggersw at gmail.com (Megan Walsh) Date: Fri, 05 Sep 2008 10:07:19 -0400 Subject: [Mristudio-users] When Fibers Aren't there Message-ID: <254662fa0809050707m2a12ae3bif1cd6c961ca9c8fa@mail.gmail.com> Hey DTI Studio experts!!! So in my project I'm tracking 3 frontal-striatal white matter tracts, and also track the CST. Our population is patients with Multiple Sclerosis. One of our patients has such bad damage that there are no fibers that make it through the CST ROIS. This is obviously important to include in the analysis. BUT. When I go to save the file, it will not let me save an empty file. So what do I do? To clarify what I'm doing: DTISTUDIO: Fiber Tracking Create 3 ROIS to define CST Save fibers: as binary images, as both a .dat file and a .bin file. Now I haven't had this issue with any other subjects (they've all had fibers). Does any one know how to just make an empty .dat or .bin file that is the same dimensions? Thanks Meg -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080905/a476f756/attachment.html From susumu at mri.jhu.edu Fri Sep 5 12:40:15 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 05 Sep 2008 12:40:15 -0400 Subject: [Mristudio-users] Save ROIs in fibre tracking In-Reply-To: <49F2A9E7CD49B24AAC16C3C5D38CFD0B0F6AD8@EVS-EC1-NODE1.surrey.ac.uk> References: <49F2A9E7CD49B24AAC16C3C5D38CFD0B0F6AD8@EVS-EC1-NODE1.surrey.ac.uk> Message-ID: Hi Shan, Hangyi may have a more "official" answer to your question, but I want to introduce you to the "Binary Map" option. When you store your ROI, there are several options for the format and one of them is the "Binary Map". If you click it, you get 3 files. Two 3D binary files (your ROI pixels are 1 and all other pixels are 0) and one text file. You get the two binary files because you drew 2 ROIs. If you drew 3 ROIs, you get 3 binary files. Please open the text file and study what's inside. It is like a header file containing information about the ROI binary file paths and image dimensions. There you can also find "operation" fields, in which you can specify how to use each ROI files. If one ROI have operation "0", then it is used as "OR". "1" is for "AND". There is an explanation at the end of the file. You can specify the two ROI files for CUT#1 and CUT#2 too. This format is much more powerful because you can import any 1/0 binary maps, such as fMRI activation maps, and combine them with different operators (OR, AND, NOT, CUT etc). Also in this way, you should not have the problem you reported. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Shan.Shen at surrey.ac.uk Sent: Thursday, August 28, 2008 6:32 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Save ROIs in fibre tracking Hi, I would like to use the 'cut' operation to track fibres between two ROIs. I did the fibre tracking first, then drew the two ROIs, the fibres displayed were those between the two ROIs. However, if I save the ROIs and load them again, this time the fibres displayed are not the ones between the ROIs anymore, but are fibres passing through one of the ROIs. Could anyone tell me what the possible problem is? I tried saving the ROIs as different formats, but the problem is the same. Many thanks shan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080905/6ffaf8e7/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/jpeg Size: 2950 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080905/6ffaf8e7/attachment-0001.jpe From rajagov2 at ccf.org Fri Sep 5 12:49:43 2008 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Fri, 05 Sep 2008 12:49:43 -0400 Subject: [Mristudio-users] tensor calculation - automatic outlier rejection Message-ID: <77A88E90A851594AAEF830450587C39D01EDA8DB@CCHSCLEXMB56.cc.ad.cchs.net> Dear All, Recently i downloaded latest version of DTI studio. When i tried to do Tensor calculation the usual DTI- map options appear first and when fill in the details and say ok another window pops up asking for outlier rejection and when i say yes another window pops up where there are many options to fill in. It will be of great help to me if anyone could please tell me what this new automatic outlier rejection option is for and where i can get details regarding how to choose these different options and under what circumstances should i go for this as i couldn't find their details in the manual. Thanks 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 (2008). 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/20080905/5d4f18c5/attachment.html From susumu at mri.jhu.edu Fri Sep 5 13:25:28 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 05 Sep 2008 13:25:28 -0400 Subject: [Mristudio-users] tensor calculation - automatic outlier rejection In-Reply-To: <77A88E90A851594AAEF830450587C39D01EDA8DB@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D01EDA8DB@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Hi Venkateswaran, The outlier rejection is still work-in-progress. We are about to post Version 3, in which there will be only one threshold to simplify the function. Meanwhile please use very large numbers for all thresholds to avoid the software to reject any images. However, there are two very handy functions in "verify the results" section of the window, which are two checkboxes with "create images of ,,,,". After the calculation, please click the "Original-ADC-Mean-STD" button. In this window, you can see your raw data and "theory image", which tells how the image should look like calculated from all data, and "error image", which is the difference between the raw and theory data. These images can be very informative to detect corrupted images, typically observed around the forth ventricle (brainstem, cerebellum, and often up to the splenium of the corpus callosum). For the corrupted images, you can simply click the bad image and large red X mark appears. These images won't be included for tensor calculation. In our experience, maybe well more than 50% of DTI data do not have significantly corrupted images and you don't need to worry. There are, however, sometimes subjects who have several corrupted images. Once affected, it is common to see multiple severely corrupted ones. My experience says pediatric brains are more prone to the artifacts. There are sometimes signal leak from outside MRI that causes a spike in the k-space and produce "zebra" patterns. This should also be eliminated. The "error images" also sensitively detect subject motions and eddy current issues. These problems appear as a ring around the brain. If the subject moved in the middle of the scan, half the error images show bright edge in one side of the brain and dark edge in the other side. The rest of the images have the same edges but with the opposite bright/dark edge locations. You can try different threshold levels to see if the software can automatically detect the one you thought bad. The version 3 has better automatic detection, but these functions are still beta. Hope this helps. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Rajagopalan, Venkateswaran Sent: Friday, September 05, 2008 12:50 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] tensor calculation - automatic outlier rejection Dear All, Recently i downloaded latest version of DTI studio. When i tried to do Tensor calculation the usual DTI- map options appear first and when fill in the details and say ok another window pops up asking for outlier rejection and when i say yes another window pops up where there are many options to fill in. It will be of great help to me if anyone could please tell me what this new automatic outlier rejection option is for and where i can get details regarding how to choose these different options and under what circumstances should i go for this as i couldn't find their details in the manual. Thanks 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 (2008). 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/20080905/cf6ed3a8/attachment.html From hjiang at jhmi.edu Fri Sep 5 13:49:09 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Fri, 05 Sep 2008 13:49:09 -0400 Subject: [Mristudio-users] Save ROIs in fibre tracking Message-ID: <48C138D50200006300015E55@cis27.hosts.jhmi.edu> hi, Shan, you should save the ROIs as "Graphic compatible (default)" or, as Susumu said, "Binary Maps" format. these formats will both work for you. regards, hangyi >>> 08/28/08 6:31 AM >>> Hi, I would like to use the 'cut' operation to track fibres between two ROIs. I did the fibre tracking first, then drew the two ROIs, the fibres displayed were those between the two ROIs. However, if I save the ROIs and load them again, this time the fibres displayed are not the ones between the ROIs anymore, but are fibres passing through one of the ROIs. Could anyone tell me what the possible problem is? I tried saving the ROIs as different formats, but the problem is the same. Many thanks shan From icee41 at gmail.com Fri Sep 5 16:10:52 2008 From: icee41 at gmail.com (Tapan Jani) Date: Fri, 05 Sep 2008 15:10:52 -0500 Subject: [Mristudio-users] ROIEditor and LandMarker Installation Message-ID: <43f2b0680809051310x4e56bf50q229ff37b390e51a8@mail.gmail.com> Hello all, In order to access the 81 patient database incorporated in LandMarker and ROIEditor, I downloaded both in 64 bit version because it matches the configuration of my computer. The version of DTIStudio that I use is the 64-bit one. At any rate, when I try to open both programs I get the same error message: "This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem." This is curious because I never officially "installed" either program. Any ideas on how to fix this? Thank you, Tapan tjani2 at uic.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080905/279b6975/attachment.html From susumu at mri.jhu.edu Fri Sep 5 16:18:29 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 05 Sep 2008 16:18:29 -0400 Subject: [Mristudio-users] ROIEditor and LandMarker Installation In-Reply-To: <43f2b0680809051310x4e56bf50q229ff37b390e51a8@mail.gmail.com> References: <43f2b0680809051310x4e56bf50q229ff37b390e51a8@mail.gmail.com> Message-ID: <8DE0244555D04A02AB3C1F3C092E1C06@SusumuThinkPad> I believe it's because you are missing one program called "vcredist", which you can download from the same site. You have to run this program once before you install Landmarker and RoiEditor. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Tapan Jani Sent: Friday, September 05, 2008 4:11 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ROIEditor and LandMarker Installation Hello all, In order to access the 81 patient database incorporated in LandMarker and ROIEditor, I downloaded both in 64 bit version because it matches the configuration of my computer. The version of DTIStudio that I use is the 64-bit one. At any rate, when I try to open both programs I get the same error message: "This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem." This is curious because I never officially "installed" either program. Any ideas on how to fix this? Thank you, Tapan tjani2 at uic.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080905/3156c731/attachment.html From xli16 at jhmi.edu Fri Sep 5 16:40:36 2008 From: xli16 at jhmi.edu (XIN LI) Date: Fri, 05 Sep 2008 16:40:36 -0400 Subject: [Mristudio-users] ROIEditor and LandMarker Installation In-Reply-To: <8DE0244555D04A02AB3C1F3C092E1C06@SusumuThinkPad> References: <43f2b0680809051310x4e56bf50q229ff37b390e51a8@mail.gmail.com> <8DE0244555D04A02AB3C1F3C092E1C06@SusumuThinkPad> Message-ID: Yes. As Susumu said, please download vcredist_x64.exe from https://www.mristudio.org/wiki/installation and run this executable file first. Xin ----- Original Message ----- From: susumu Date: Friday, September 5, 2008 4:18 pm Subject: RE: [Mristudio-users] ROIEditor and LandMarker Installation To: "'DTI Studio, ROI Editor, Landmarker Questions/Support'" Cc: 'XIN LI' > I believe it's because you are missing one program called "vcredist", > which > you can download from the same site. You have to run this program once > before you install Landmarker and RoiEditor. > > > > _____ > > From: mristudio-users-bounces at mristudio.org > [ On Behalf Of Tapan Jani > Sent: Friday, September 05, 2008 4:11 PM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] ROIEditor and LandMarker Installation > > > > Hello all, > > In order to access the 81 patient database incorporated in LandMarker > and > ROIEditor, I downloaded both in 64 bit version because it matches the > configuration of my computer. The version of DTIStudio that I use is > the > 64-bit one. At any rate, when I try to open both programs I get the same > error message: "This application has failed to start because the application > configuration is incorrect. Reinstalling the application may fix this > problem." > > This is curious because I never officially "installed" either > program. > > Any ideas on how to fix this? > > Thank you, > Tapan > > tjani2 at uic.edu > From junyiwang2002 at yahoo.com Fri Sep 5 17:03:29 2008 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Fri, 05 Sep 2008 14:03:29 -0700 (PDT) Subject: [Mristudio-users] Coregistration using AIR Message-ID: <120222.28676.qm@web50507.mail.re2.yahoo.com> Hi All, ? I have followup questions regarding the AIR program in DTI Studio. ? 1).?The instruction stated that AIR in DTI Studio is for motion correction and eddy current correction for multiple DTI aquisitions.? So if I have DTI sequences already averaged by the scanner, can I use the AIR to correct for motion and eddy current? ? 2). After the AIR process in DTI Studio, the saved matrix has corrected gradient table.? If I proceed to calculate tensor, etc., is the modified gradient table or the original one used in the calculation?? If the corrected table is not used, should I calculate tensor by closing the DTI Studio, loading all images, and use the modified gradient table for tensor calculation? ? 3).?I have been using FSL's eddy_correct program, and I can hardly find any discription for the program.? Has anyone compared it with the AIR? ? Thank you for your wonderful tools and timely support! Jun Yi Wang ----- Original Message ---- From: susumu To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Friday, July 25, 2008 11:09:48 AM Subject: Re: [Mristudio-users] Coregistration using AIR Dear Dr. Takaya, ? Do you want to coregister, combine two DTI scans and calculated a tensor? If that's the case, you can treat the two scans as two signal averaging. Load both of them, coregister the first scan to the second scan using the AIR in DtiStudio, and do tensor calculation. ? If you want to get separate tensor fields from the two datasets and then coregister for ROI drawing, I recommend you to use Landmarker. You first have to calculate all DTI-based images you need (tensor, FA, ADC, b0, etc). You can then bring b0 images from the two datasets into Landmarker and perform AIR. You can save the transformation matrix and apply it to other images. Alternatively, if you load all data at once, AIR is automatically applied to all loaded data (of course you have to specify which image you want to use to drive AIR). ? One important function of Landmarker is that it can apply the transformation matrix to tensor files too (it does tensor reorientations if rotation components are involved). ? Susumu ? ________________________________ From:mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Shigetoshi TAKAYA Sent: Monday, July 14, 2008 1:48 AM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] Coregistration using AIR ? Hello ? I have two scans of DWI with time interval for each patient (1st scan and 2nd scan). I would like to coregister the?images in the 2nd scan?onto?those in the?1st?scan in each subject using Automatic Image Registration (AIR) algorithm implemented in DTIStudio, for the purpose of drawing ROIs in the same brain regions in both scans. ? First, I?did eddy current correction and motion correction using affine transformation in each scan (1st scan and 2nd scan). Then, I coregistered?the B0 image?in the 2nd scan?onto that?in the?1st scan. And I would like to adjust the same transformation matrix to the rest of the?images in the 2nd scan. ? I know that the transformation matrix can be saved when conducting AIR. Can we use this file to transform the rest of the images in the 2nd scan? ? Many thanks, ? Shigetoshi Takaya -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080905/7b873e95/attachment-0001.html From susumu at mri.jhu.edu Tue Sep 9 13:18:04 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 09 Sep 2008 13:18:04 -0400 Subject: [Mristudio-users] When Fibers Aren't there In-Reply-To: <254662fa0809050707m2a12ae3bif1cd6c961ca9c8fa@mail.gmail.com> Message-ID: <73ap56$47pti7@ipex1.johnshopkins.edu> Hi Meg, I've been thinking how we can do this but could not come up with a way with our programs. I think you need to create one using Matlab or IDL, which requires only one line. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Megan Walsh Sent: Friday, September 05, 2008 10:07 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] When Fibers Aren't there Hey DTI Studio experts!!! So in my project I'm tracking 3 frontal-striatal white matter tracts, and also track the CST. Our population is patients with Multiple Sclerosis. One of our patients has such bad damage that there are no fibers that make it through the CST ROIS. This is obviously important to include in the analysis. BUT. When I go to save the file, it will not let me save an empty file. So what do I do? To clarify what I'm doing: DTISTUDIO: Fiber Tracking Create 3 ROIS to define CST Save fibers: as binary images, as both a .dat file and a .bin file. Now I haven't had this issue with any other subjects (they've all had fibers). Does any one know how to just make an empty .dat or .bin file that is the same dimensions? Thanks Meg -- Megan Kay Walsh Graduate Student Johns Hopkins University Psychological & Brain Sciences 204 Ames Hall 3400 N. Charles St. Baltimore, MD 21218 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080909/b7d55948/attachment.html From susumu at mri.jhu.edu Tue Sep 9 13:50:58 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 09 Sep 2008 13:50:58 -0400 Subject: [Mristudio-users] Coregistration using AIR In-Reply-To: <120222.28676.qm@web50507.mail.re2.yahoo.com> References: <120222.28676.qm@web50507.mail.re2.yahoo.com> Message-ID: Hi Jun, Please see my response below. 1). The instruction stated that AIR in DTI Studio is for motion correction and eddy current correction for multiple DTI aquisitions. So if I have DTI sequences already averaged by the scanner, can I use the AIR to correct for motion and eddy current? >I recommend not to average scans inside the scanner. Eddy current should be correctable even if the images are already averaged. Motion correction is a tricky question. It depends on when the second set is acquired and when the motion happens. In the worst case, second scan take place after the first complete DTI is finished so that there is ? of scanning time lapsed between the averaging (typically several minutes). If the motion happens between the first and second scans, then motion correction may not work well. 2). After the AIR process in DTI Studio, the saved matrix has corrected gradient table. If I proceed to calculate tensor, etc., is the modified gradient table or the original one used in the calculation? If the corrected table is not used, should I calculate tensor by closing the DTI Studio, loading all images, and use the modified gradient table for tensor calculation? >Good question. I need Hangyi to answer this. My guess is the corrected table is applied by default if you choose this option. Please remember, unless you uncheck the ?create new image after registration?, AIR simply creates corrected images. The subsequent calculation still uses the uncorrected original data. In this case, you do have to save the corrected images & table and reload them to use them. If you unckeck this button, then the original images are overwritten by the AIRed images. In this case, the subsequent tensor calculation will be based on the AIRed images. Then the gradient table should be automatically corrected (although I have to confirm this point with Hangyi). 3). I have been using FSL's eddy_correct program, and I can hardly find any discription for the program. Has anyone compared it with the AIR? > I heard FLIRT in FSL works better than AIR. One of the AIR?s weak points is its sensitivity to the threshold setting. The ?create image ? functions in the ?outlier rejection? and calculation of subtracted images when there are more than two repeated measurements provide very good interface to visually inspect the existence of the mis-registration. At this point, I recommend you to confirm the results of AIR using these functions and the the inspection window (?Original-ADC-Mean-STD? button). Thank you for your wonderful tools and timely support! Jun Yi Wang ----- Original Message ---- From: susumu To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Friday, July 25, 2008 11:09:48 AM Subject: Re: [Mristudio-users] Coregistration using AIR Dear Dr. Takaya, Do you want to coregister, combine two DTI scans and calculated a tensor? If that's the case, you can treat the two scans as two signal averaging. Load both of them, coregister the first scan to the second scan using the AIR in DtiStudio, and do tensor calculation. If you want to get separate tensor fields from the two datasets and then coregister for ROI drawing, I recommend you to use Landmarker. You first have to calculate all DTI-based images you need (tensor, FA, ADC, b0, etc). You can then bring b0 images from the two datasets into Landmarker and perform AIR. You can save the transformation matrix and apply it to other images. Alternatively, if you load all data at once, AIR is automatically applied to all loaded data (of course you have to specify which image you want to use to drive AIR). One important function of Landmarker is that it can apply the transformation matrix to tensor files too (it does tensor reorientations if rotation components are involved). Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Shigetoshi TAKAYA Sent: Monday, July 14, 2008 1:48 AM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] Coregistration using AIR Hello I have two scans of DWI with time interval for each patient (1st scan and 2nd scan). I would like to coregister the images in the 2nd scan onto those in the 1st scan in each subject using Automatic Image Registration (AIR) algorithm implemented in DTIStudio, for the purpose of drawing ROIs in the same brain regions in both scans. First, I did eddy current correction and motion correction using affine transformation in each scan (1st scan and 2nd scan). Then, I coregistered the B0 image in the 2nd scan onto that in the 1st scan. And I would like to adjust the same transformation matrix to the rest of the images in the 2nd scan. I know that the transformation matrix can be saved when conducting AIR. Can we use this file to transform the rest of the images in the 2nd scan? Many thanks, Shigetoshi Takaya -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080909/c15875a4/attachment-0001.html From mgold51 at gmail.com Tue Sep 9 17:02:09 2008 From: mgold51 at gmail.com (mark gold) Date: Tue, 09 Sep 2008 16:02:09 -0500 Subject: [Mristudio-users] ROIEditor and LandMarker data format Message-ID: <55aa985a0809091402u7e4adb48y75a84448c38a346d@mail.gmail.com> Hi, This is my first time to use ROIEditor and LandMarker. Follow the manual I installed these two software. But I don't know what kind of data should import to ROIEditor or LandMarker. The raw data? or FA and b0 image from MRIstudio. Thanks. Best, Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080909/7231b86b/attachment.html From xli16 at jhmi.edu Tue Sep 9 17:15:06 2008 From: xli16 at jhmi.edu (XIN LI) Date: Tue, 09 Sep 2008 17:15:06 -0400 Subject: [Mristudio-users] ROIEditor and LandMarker data format In-Reply-To: <55aa985a0809091402u7e4adb48y75a84448c38a346d@mail.gmail.com> References: <55aa985a0809091402u7e4adb48y75a84448c38a346d@mail.gmail.com> Message-ID: Mark, You can load raw data files or analyze images into these two softwares. The data format can be byte, word, float, color and so on. Xin ----- Original Message ----- From: mark gold Date: Tuesday, September 9, 2008 5:02 pm Subject: [Mristudio-users] ROIEditor and LandMarker data format To: mristudio-users at mristudio.org > Hi, > > This is my first time to use ROIEditor and LandMarker. Follow the > manual I > installed these two software. But I don't know what kind of data should > import to ROIEditor or LandMarker. The raw data? or FA and b0 image from > MRIstudio. Thanks. > > Best, > > Mark > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From Elizabeth.Finger at lhsc.on.ca Wed Sep 10 14:12:53 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Wed, 10 Sep 2008 14:12:53 -0400 Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio Message-ID: <48C7D5E5020000A000004F76@lhscgwiao.lhsc.on.ca> Hello- I have been following the proior posts on this topic but cannot seem to open up in DTI studio the ROI's saved as a binary map which I created in ROI Editor. I have attached the binary map file that I created in ROI Editor and then edited to include the Operation: 1 to each binary file to signify AND. Then in DTI-Studio- Fibertracking, I load my FA map and eigenvector_0 and complete the fiber tracking. When I then in the fiber tab under ROI Operation click on load, binary map, and select my file, nothing (no ROIs nor fibers) appear on the screen, and no ROI statistics are available. I have tried this with several subjects and with several different ROIs. Perhaps there is a step I have missed? Thank you, Elizabeth Finger -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. -------------- next part -------------- A non-text attachment was scrubbed... Name: ROIMap_motor_map.dat Type: application/octet-stream Size: 638 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080910/44aa8bc0/attachment.obj From xli16 at jhmi.edu Wed Sep 10 14:45:12 2008 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 10 Sep 2008 14:45:12 -0400 Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio In-Reply-To: <48C7D5E5020000A000004F76@lhscgwiao.lhsc.on.ca> References: <48C7D5E5020000A000004F76@lhscgwiao.lhsc.on.ca> Message-ID: Elizabeth, Please change the file name from "ROIMap_motor_map.dat" to "ROIMap_motor_map.map" and try again. Xin ----- Original Message ----- From: Elizabeth Finger Date: Wednesday, September 10, 2008 2:13 pm Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio To: mristudio-users at mristudio.org > Hello- > > I have been following the proior posts on this topic but cannot seem > to open up in DTI studio the ROI's saved as a binary map which I > created in ROI Editor. I have attached the binary map file that I > created in ROI Editor and then edited to include the Operation: 1 to > each binary file to signify AND. Then in DTI-Studio- Fibertracking, I > load my FA map and eigenvector_0 and complete the fiber tracking. > When I then in the fiber tab under ROI Operation click on load, binary > map, and select my file, nothing (no ROIs nor fibers) appear on the > screen, and no ROI statistics are available. I have tried this with > several subjects and with several different ROIs. Perhaps there is a > step I have missed? > > Thank you, > Elizabeth Finger > -------------------------------------------------------------------------------- > This information is directed in confidence solely to the person named > above and may contain confidential and/or privileged material. This > information may not otherwise be distributed, copied or disclosed. If > you have received this e-mail in error, please notify the sender > immediately via a return e-mail and destroy original message. Thank > you for your cooperation. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From Elizabeth.Finger at lhsc.on.ca Wed Sep 10 15:00:28 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Wed, 10 Sep 2008 15:00:28 -0400 Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio Message-ID: <48C7E10C020000A000004F7A@lhscgwiao.lhsc.on.ca> Thanks - I have tried that as well but still have the same problem. Elizabeth >>> XIN LI 09/10/08 2:45 PM >>> Elizabeth, Please change the file name from "ROIMap_motor_map.dat" to "ROIMap_motor_map.map" and try again. Xin ----- Original Message ----- From: Elizabeth Finger Date: Wednesday, September 10, 2008 2:13 pm Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio To: mristudio-users at mristudio.org > Hello- > > I have been following the proior posts on this topic but cannot seem > to open up in DTI studio the ROI's saved as a binary map which I > created in ROI Editor. I have attached the binary map file that I > created in ROI Editor and then edited to include the Operation: 1 to > each binary file to signify AND. Then in DTI-Studio- Fibertracking, I > load my FA map and eigenvector_0 and complete the fiber tracking. > When I then in the fiber tab under ROI Operation click on load, binary > map, and select my file, nothing (no ROIs nor fibers) appear on the > screen, and no ROI statistics are available. I have tried this with > several subjects and with several different ROIs. Perhaps there is a > step I have missed? > > Thank you, > Elizabeth Finger > -------------------------------------------------------------------------------- > This information is directed in confidence solely to the person named > above and may contain confidential and/or privileged material. This > information may not otherwise be distributed, copied or disclosed. If > you have received this e-mail in error, please notify the sender > immediately via a return e-mail and destroy original message. Thank > you for your cooperation. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From xli16 at jhmi.edu Wed Sep 10 17:45:36 2008 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 10 Sep 2008 17:45:36 -0400 Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio In-Reply-To: <48C7E10C020000A000004F7A@lhscgwiao.lhsc.on.ca> References: <48C7E10C020000A000004F7A@lhscgwiao.lhsc.on.ca> Message-ID: Elizabeth, Please try the following: 1. Set the operation of the first fiber as "0" not "1". 2. Add one more line for each fiber: ColorMode: 0 Xin ----- Original Message ----- From: Elizabeth Finger Date: Wednesday, September 10, 2008 3:00 pm Subject: Re: [Mristudio-users] ROI uploading and viewing in DTI Studio To: mristudio-users at mristudio.org > Thanks - I have tried that as well but still have the same problem. > > Elizabeth > > >>> XIN LI 09/10/08 2:45 PM >>> > Elizabeth, > > Please change the file name from "ROIMap_motor_map.dat" to > "ROIMap_motor_map.map" and try again. > > Xin > > > > ----- Original Message ----- > From: Elizabeth Finger > Date: Wednesday, September 10, 2008 2:13 pm > Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio > To: mristudio-users at mristudio.org > > > > Hello- > > > > I have been following the proior posts on this topic but cannot > seem > > to open up in DTI studio the ROI's saved as a binary map which I > > created in ROI Editor. I have attached the binary map file that I > > > created in ROI Editor and then edited to include the Operation: 1 > to > > each binary file to signify AND. Then in DTI-Studio- > Fibertracking, I > > load my FA map and eigenvector_0 and complete the fiber tracking. > > > When I then in the fiber tab under ROI Operation click on load, > binary > > map, and select my file, nothing (no ROIs nor fibers) appear on the > > > screen, and no ROI statistics are available. I have tried this > with > > several subjects and with several different ROIs. Perhaps there is > a > > step I have missed? > > > > Thank you, > > Elizabeth Finger > > -------------------------------------------------------------------------------- > > This information is directed in confidence solely to the person > named > > above and may contain confidential and/or privileged material. This > > > information may not otherwise be distributed, copied or disclosed. > If > > you have received this e-mail in error, please notify the sender > > immediately via a return e-mail and destroy original message. Thank > > > you for your cooperation. > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > > -------------------------------------------------------------------------------- > This information is directed in confidence solely to the person named > above and may contain confidential and/or privileged material. This > information may not otherwise be distributed, copied or disclosed. If > you have received this e-mail in error, please notify the sender > immediately via a return e-mail and destroy original message. Thank > you for your cooperation. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From sumita.rachapudi at duke.edu Thu Sep 11 11:48:00 2008 From: sumita.rachapudi at duke.edu (Sumita P Rachapudi) Date: Thu, 11 Sep 2008 11:48:00 -0400 Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio In-Reply-To: Message-ID: Please remove me from your mailing list. XIN LI Sent by: mristudio-users-bounces at mristudio.org 09/10/2008 05:46 PM Please respond to "DTI Studio, ROI Editor, Landmarker Questions/Support" To "DTI Studio, ROI Editor, Landmarker Questions/Support" cc Subject Re: [Mristudio-users] ROI uploading and viewing in DTI Studio Elizabeth, Please try the following: 1. Set the operation of the first fiber as "0" not "1". 2. Add one more line for each fiber: ColorMode: 0 Xin ----- Original Message ----- From: Elizabeth Finger Date: Wednesday, September 10, 2008 3:00 pm Subject: Re: [Mristudio-users] ROI uploading and viewing in DTI Studio To: mristudio-users at mristudio.org > Thanks - I have tried that as well but still have the same problem. > > Elizabeth > > >>> XIN LI 09/10/08 2:45 PM >>> > Elizabeth, > > Please change the file name from "ROIMap_motor_map.dat" to > "ROIMap_motor_map.map" and try again. > > Xin > > > > ----- Original Message ----- > From: Elizabeth Finger > Date: Wednesday, September 10, 2008 2:13 pm > Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio > To: mristudio-users at mristudio.org > > > > Hello- > > > > I have been following the proior posts on this topic but cannot > seem > > to open up in DTI studio the ROI's saved as a binary map which I > > created in ROI Editor. I have attached the binary map file that I > > > created in ROI Editor and then edited to include the Operation: 1 > to > > each binary file to signify AND. Then in DTI-Studio- > Fibertracking, I > > load my FA map and eigenvector_0 and complete the fiber tracking. > > > When I then in the fiber tab under ROI Operation click on load, > binary > > map, and select my file, nothing (no ROIs nor fibers) appear on the > > > screen, and no ROI statistics are available. I have tried this > with > > several subjects and with several different ROIs. Perhaps there is > a > > step I have missed? > > > > Thank you, > > Elizabeth Finger > > -------------------------------------------------------------------------------- > > This information is directed in confidence solely to the person > named > > above and may contain confidential and/or privileged material. This > > > information may not otherwise be distributed, copied or disclosed. > If > > you have received this e-mail in error, please notify the sender > > immediately via a return e-mail and destroy original message. Thank > > > you for your cooperation. > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > > -------------------------------------------------------------------------------- > This information is directed in confidence solely to the person named > above and may contain confidential and/or privileged material. This > information may not otherwise be distributed, copied or disclosed. If > you have received this e-mail in error, please notify the sender > immediately via a return e-mail and destroy original message. Thank > you for your cooperation. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080911/13c632ed/attachment-0001.html From basarsarikayamd at yahoo.com Thu Sep 11 23:05:17 2008 From: basarsarikayamd at yahoo.com (Basar Sarikaya) Date: Thu, 11 Sep 2008 20:05:17 -0700 (PDT) Subject: [Mristudio-users] How to save the image file after coregistration Message-ID: <210019.49085.qm@web56404.mail.re3.yahoo.com> Hi, my question may seem?a little absurd. I've used AIR to coregister two CT angio data sets (which were preconverted to image file with MRIcro) now I can see the file with the name beginning with AIR... But I can not save it. Either "save" or "save as" only saves a filesize of 0 kbyte. I would really appreciate any answer or help to my rather unrelated question. ? ? Basar Sarikaya, M. D. Assistant Professor of Radiology Gaziosmanpasa University Medical Faculty, Tokat, Turkey Visiting Research Scholar to Duke University Medical Center, Durham, NC, US ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080911/d9833aff/attachment.html From choisj70 at gmail.com Fri Sep 12 16:40:27 2008 From: choisj70 at gmail.com (Seongjin) Date: Fri, 12 Sep 2008 16:40:27 -0400 Subject: [Mristudio-users] Directional fiber coloring Message-ID: Dear all, Philips console provides directional fiber coloring and it is nice feature to have for fiber tractography. I wonder if this is possible on DTIstudio. I would appreciate if anyone let me know this. S.C. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080912/538a8d64/attachment.html From choisj70 at gmail.com Mon Sep 15 12:12:50 2008 From: choisj70 at gmail.com (Seongjin) Date: Mon, 15 Sep 2008 12:12:50 -0400 Subject: [Mristudio-users] Mac version? Message-ID: Dear DTI studio users, One of my colleagues want to use DTI studio on her Mac book. I wonder if there is any Mac version of DTI studio? Best, S.C. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080915/62435044/attachment.html From rajagov2 at ccf.org Tue Sep 16 10:45:31 2008 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Tue, 16 Sep 2008 10:45:31 -0400 Subject: [Mristudio-users] tensor calculation - automatic outlier rejection References: <77A88E90A851594AAEF830450587C39D01EDA8DB@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: <77A88E90A851594AAEF830450587C39D01EDA8E7@CCHSCLEXMB56.cc.ad.cchs.net> Dear Dr.Mori, Thank you very much for your kind information. Thanks again, Regards venkateswaran ________________________________ From: mristudio-users-bounces at mristudio.org on behalf of susumu Sent: Fri 9/5/2008 1:25 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] tensor calculation - automatic outlier rejection Hi Venkateswaran, The outlier rejection is still work-in-progress. We are about to post Version 3, in which there will be only one threshold to simplify the function. Meanwhile please use very large numbers for all thresholds to avoid the software to reject any images. However, there are two very handy functions in "verify the results" section of the window, which are two checkboxes with "create images of ,,,,". After the calculation, please click the "Original-ADC-Mean-STD" button. In this window, you can see your raw data and "theory image", which tells how the image should look like calculated from all data, and "error image", which is the difference between the raw and theory data. These images can be very informative to detect corrupted images, typically observed around the forth ventricle (brainstem, cerebellum, and often up to the splenium of the corpus callosum). For the corrupted images, you can simply click the bad image and large red X mark appears. These images won't be included for tensor calculation. In our experience, maybe well more than 50% of DTI data do not have significantly corrupted images and you don't need to worry. There are, however, sometimes subjects who have several corrupted images. Once affected, it is common to see multiple severely corrupted ones. My experience says pediatric brains are more prone to the artifacts. There are sometimes signal leak from outside MRI that causes a spike in the k-space and produce "zebra" patterns. This should also be eliminated. The "error images" also sensitively detect subject motions and eddy current issues. These problems appear as a ring around the brain. If the subject moved in the middle of the scan, half the error images show bright edge in one side of the brain and dark edge in the other side. The rest of the images have the same edges but with the opposite bright/dark edge locations. You can try different threshold levels to see if the software can automatically detect the one you thought bad. The version 3 has better automatic detection, but these functions are still beta. Hope this helps. Susumu ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Rajagopalan, Venkateswaran Sent: Friday, September 05, 2008 12:50 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] tensor calculation - automatic outlier rejection Dear All, Recently i downloaded latest version of DTI studio. When i tried to do Tensor calculation the usual DTI- map options appear first and when fill in the details and say ok another window pops up asking for outlier rejection and when i say yes another window pops up where there are many options to fill in. It will be of great help to me if anyone could please tell me what this new automatic outlier rejection option is for and where i can get details regarding how to choose these different options and under what circumstances should i go for this as i couldn't find their details in the manual. Thanks 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 (2008). 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. 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 (2008). 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: 11059 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080916/ab4113f4/attachment-0001.bin From choisj70 at gmail.com Tue Sep 16 13:47:14 2008 From: choisj70 at gmail.com (Seongjin) Date: Tue, 16 Sep 2008 13:47:14 -0400 Subject: [Mristudio-users] Version 3 beta Message-ID: Version 3 beta seems to work strangely. This may be because of my mistake or still under developing. I selected default options for fiber tracking without changing any numbers, it gives me very strange images. Is there any know issue or some changes in process? S.C. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080916/bec4311f/attachment.html From Elizabeth.Finger at lhsc.on.ca Tue Sep 16 14:47:49 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Tue, 16 Sep 2008 14:47:49 -0400 Subject: [Mristudio-users] viewing automated tract details from LDMM Message-ID: <48CFC715020000A0000050F2@lhscgwiao.lhsc.on.ca> Hello- Are there any step- by step instructions available after retrieving results from the LDMM remote processing? I was able to retrieve my results, but it is not clear to me which templates and files should be loaded next into Landmarker and how I can view the automated white matter tracts and associated stastistics? Thank you, Elizabeth Finger -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From xli16 at jhmi.edu Tue Sep 16 15:21:03 2008 From: xli16 at jhmi.edu (XIN LI) Date: Tue, 16 Sep 2008 15:21:03 -0400 Subject: [Mristudio-users] viewing automated tract details from LDMM In-Reply-To: <48CFC715020000A0000050F2@lhscgwiao.lhsc.on.ca> References: <48CFC715020000A0000050F2@lhscgwiao.lhsc.on.ca> Message-ID: Elizabeth, There are two image files in the LDDMM processing result, "Template" and "Target". Please load them to Landmarker, "Template" as a template and "Target" as a subject. Please click the button "Load Transformation Matrix" in the subject window, select the radio box "LDDMM Matrix (VTK Format)" and load the file "Kimap.vtk" that is in the LDDMM processing result. Landmarker will show you a new subject image updated based on the LDDMM matrix. Xin ----- Original Message ----- From: Elizabeth Finger Date: Tuesday, September 16, 2008 2:48 pm Subject: [Mristudio-users] viewing automated tract details from LDMM To: mristudio-users at mristudio.org > Hello- > > Are there any step- by step instructions available after retrieving > results from the LDMM remote processing? I was able to retrieve my > results, but it is not clear to me which templates and files should be > loaded next into Landmarker and how I can view the automated white > matter tracts and associated stastistics? > > Thank you, > Elizabeth Finger > -------------------------------------------------------------------------------- > This information is directed in confidence solely to the person named > above and may contain confidential and/or privileged material. This > information may not otherwise be distributed, copied or disclosed. If > you have received this e-mail in error, please notify the sender > immediately via a return e-mail and destroy original message. Thank > you for your cooperation. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From Elizabeth.Finger at lhsc.on.ca Tue Sep 16 15:45:33 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Tue, 16 Sep 2008 15:45:33 -0400 Subject: [Mristudio-users] viewing automated tract details from LDMM Message-ID: <48CFD49D020000A0000050FC@lhscgwiao.lhsc.on.ca> Thank you Xin- That has seemingly worked so far. Can you tell me after the new subject image is updated (it shows up as Updated_Target.img in Landmarker, how I then can visualize the automated tracts which have been segmented, and how to find the # fibers and FA values for those tracts? Elizabeth >>> XIN LI 09/16/08 3:21 PM >>> Elizabeth, There are two image files in the LDDMM processing result, "Template" and "Target". Please load them to Landmarker, "Template" as a template and "Target" as a subject. Please click the button "Load Transformation Matrix" in the subject window, select the radio box "LDDMM Matrix (VTK Format)" and load the file "Kimap.vtk" that is in the LDDMM processing result. Landmarker will show you a new subject image updated based on the LDDMM matrix. Xin ----- Original Message ----- From: Elizabeth Finger Date: Tuesday, September 16, 2008 2:48 pm Subject: [Mristudio-users] viewing automated tract details from LDMM To: mristudio-users at mristudio.org > Hello- > > Are there any step- by step instructions available after retrieving > results from the LDMM remote processing? I was able to retrieve my > results, but it is not clear to me which templates and files should be > loaded next into Landmarker and how I can view the automated white > matter tracts and associated stastistics? > > Thank you, > Elizabeth Finger > -------------------------------------------------------------------------------- > This information is directed in confidence solely to the person named > above and may contain confidential and/or privileged material. This > information may not otherwise be distributed, copied or disclosed. If > you have received this e-mail in error, please notify the sender > immediately via a return e-mail and destroy original message. Thank > you for your cooperation. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From xli16 at jhmi.edu Wed Sep 17 11:13:00 2008 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 17 Sep 2008 11:13:00 -0400 Subject: [Mristudio-users] viewing automated tract details from LDMM In-Reply-To: <48CFD49D020000A0000050FC@lhscgwiao.lhsc.on.ca> References: <48CFD49D020000A0000050FC@lhscgwiao.lhsc.on.ca> Message-ID: Elizabeth, Please also apply the Kimap to the fiber file to get the updated fiber file. Then load the updated target image into ROIEditor and load the updated fiber file as a raw ROI data file. In that way, you can get what you want. Xin ----- Original Message ----- From: Elizabeth Finger Date: Tuesday, September 16, 2008 3:45 pm Subject: Re: [Mristudio-users] viewing automated tract details from LDMM To: mristudio-users at mristudio.org > Thank you Xin- > > That has seemingly worked so far. Can you tell me after the new > subject image is updated (it shows up as Updated_Target.img in > Landmarker, how I then can visualize the automated tracts which have > been segmented, and how to find the # fibers and FA values for those tracts? > > Elizabeth > > >>> XIN LI 09/16/08 3:21 PM >>> > Elizabeth, > > There are two image files in the LDDMM processing result, "Template" > and "Target". Please load them to Landmarker, "Template" as a template > and "Target" as a subject. Please click the button "Load > Transformation Matrix" in the subject window, select the radio box > "LDDMM Matrix (VTK Format)" and load the file "Kimap.vtk" that is in > the LDDMM processing result. Landmarker will show you a new subject > image updated based on the LDDMM matrix. > > > Xin > > > > ----- Original Message ----- > From: Elizabeth Finger > Date: Tuesday, September 16, 2008 2:48 pm > Subject: [Mristudio-users] viewing automated tract details from LDMM > To: mristudio-users at mristudio.org > > > > Hello- > > > > Are there any step- by step instructions available after > retrieving > > results from the LDMM remote processing? I was able to retrieve my > > > results, but it is not clear to me which templates and files should > be > > loaded next into Landmarker and how I can view the automated white > > > matter tracts and associated stastistics? > > > > Thank you, > > Elizabeth Finger > > -------------------------------------------------------------------------------- > > This information is directed in confidence solely to the person > named > > above and may contain confidential and/or privileged material. This > > > information may not otherwise be distributed, copied or disclosed. > If > > you have received this e-mail in error, please notify the sender > > immediately via a return e-mail and destroy original message. Thank > > > you for your cooperation. > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > > -------------------------------------------------------------------------------- > This information is directed in confidence solely to the person named > above and may contain confidential and/or privileged material. This > information may not otherwise be distributed, copied or disclosed. If > you have received this e-mail in error, please notify the sender > immediately via a return e-mail and destroy original message. Thank > you for your cooperation. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From Elizabeth.Finger at lhsc.on.ca Wed Sep 17 11:57:31 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Wed, 17 Sep 2008 11:57:31 -0400 Subject: [Mristudio-users] viewing automated tract details from LDMM Message-ID: <48D0F0AB020000A000005141@lhscgwiao.lhsc.on.ca> Thanks Xin- I have completed fiber tracking and saved the file with all fibers in DTI studio. When I try to load this file into Landmarker, no matter the image parameters or Image data format I enter, I cannot pull up the correct image. If I draw an ROI in fiber tracking and save this in binary format, I can open up the fiber file in Landmarker, however when I try to apply the K-Map using the button using the Load Transformation Matrix button, and then the LDDMM matrix option, I receive an error message that the load images must be isotropic images. Perhaps I have misunderstood what you mean by fiber file? Thank you, Elizabeth >>> XIN LI 09/17/08 11:13 AM >>> Elizabeth, Please also apply the Kimap to the fiber file to get the updated fiber file. Then load the updated target image into ROIEditor and load the updated fiber file as a raw ROI data file. In that way, you can get what you want. Xin ----- Original Message ----- From: Elizabeth Finger Date: Tuesday, September 16, 2008 3:45 pm Subject: Re: [Mristudio-users] viewing automated tract details from LDMM To: mristudio-users at mristudio.org > Thank you Xin- > > That has seemingly worked so far. Can you tell me after the new > subject image is updated (it shows up as Updated_Target.img in > Landmarker, how I then can visualize the automated tracts which have > been segmented, and how to find the # fibers and FA values for those tracts? > > Elizabeth > > >>> XIN LI 09/16/08 3:21 PM >>> > Elizabeth, > > There are two image files in the LDDMM processing result, "Template" > and "Target". Please load them to Landmarker, "Template" as a template > and "Target" as a subject. Please click the button "Load > Transformation Matrix" in the subject window, select the radio box > "LDDMM Matrix (VTK Format)" and load the file "Kimap.vtk" that is in > the LDDMM processing result. Landmarker will show you a new subject > image updated based on the LDDMM matrix. > > > Xin > > > > ----- Original Message ----- > From: Elizabeth Finger > Date: Tuesday, September 16, 2008 2:48 pm > Subject: [Mristudio-users] viewing automated tract details from LDMM > To: mristudio-users at mristudio.org > > > > Hello- > > > > Are there any step- by step instructions available after > retrieving > > results from the LDMM remote processing? I was able to retrieve my > > > results, but it is not clear to me which templates and files should > be > > loaded next into Landmarker and how I can view the automated white > > > matter tracts and associated stastistics? > > > > Thank you, > > Elizabeth Finger > > -------------------------------------------------------------------------------- > > This information is directed in confidence solely to the person > named > > above and may contain confidential and/or privileged material. This > > > information may not otherwise be distributed, copied or disclosed. > If > > you have received this e-mail in error, please notify the sender > > immediately via a return e-mail and destroy original message. Thank > > > you for your cooperation. > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > > -------------------------------------------------------------------------------- > This information is directed in confidence solely to the person named > above and may contain confidential and/or privileged material. This > information may not otherwise be distributed, copied or disclosed. If > you have received this e-mail in error, please notify the sender > immediately via a return e-mail and destroy original message. Thank > you for your cooperation. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From xli16 at jhmi.edu Wed Sep 17 14:33:16 2008 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 17 Sep 2008 14:33:16 -0400 Subject: [Mristudio-users] viewing automated tract details from LDMM In-Reply-To: <48D0F0AB020000A000005141@lhscgwiao.lhsc.on.ca> References: <48D0F0AB020000A000005141@lhscgwiao.lhsc.on.ca> Message-ID: Elizabeth, If you would like to load the fiber file into Landmarker, you have to save it as binary image or analyze image in DtiStudio. Other file formats don't work in Landmarker. Landmarker only apply LDDMM matrix to isotropic images. But since you already got the updated target image, it means that the subject is an isotropic image. Are the size of the fiber image different from that of the subject image? Xin ----- Original Message ----- From: Elizabeth Finger Date: Wednesday, September 17, 2008 11:58 am Subject: Re: [Mristudio-users] viewing automated tract details from LDMM To: mristudio-users at mristudio.org > Thanks Xin- > > I have completed fiber tracking and saved the file with all fibers in > DTI studio. When I try to load this file into Landmarker, no matter > the image parameters or Image data format I enter, I cannot pull up > the correct image. If I draw an ROI in fiber tracking and save this > in binary format, I can open up the fiber file in Landmarker, however > when I try to apply the K-Map using the button using the Load > Transformation Matrix button, and then the LDDMM matrix option, I > receive an error message that the load images must be isotropic > images. Perhaps I have misunderstood what you mean by fiber file? > > Thank you, > Elizabeth > > >>> XIN LI 09/17/08 11:13 AM >>> > Elizabeth, > > Please also apply the Kimap to the fiber file to get the updated > fiber file. Then load the updated target image into ROIEditor and load > the updated fiber file as a raw ROI data file. In that way, you can > get what you want. > > > Xin > > > > > ----- Original Message ----- > From: Elizabeth Finger > Date: Tuesday, September 16, 2008 3:45 pm > Subject: Re: [Mristudio-users] viewing automated tract details from LDMM > To: mristudio-users at mristudio.org > > > > Thank you Xin- > > > > That has seemingly worked so far. Can you tell me after the new > > subject image is updated (it shows up as Updated_Target.img in > > Landmarker, how I then can visualize the automated tracts which > have > > been segmented, and how to find the # fibers and FA values for > those tracts? > > > > Elizabeth > > > > >>> XIN LI 09/16/08 3:21 PM >>> > > Elizabeth, > > > > There are two image files in the LDDMM processing result, > "Template" > > and "Target". Please load them to Landmarker, "Template" as a > template > > and "Target" as a subject. Please click the button "Load > > Transformation Matrix" in the subject window, select the radio box > > > "LDDMM Matrix (VTK Format)" and load the file "Kimap.vtk" that is > in > > the LDDMM processing result. Landmarker will show you a new subject > > > image updated based on the LDDMM matrix. > > > > > > Xin > > > > > > > > ----- Original Message ----- > > From: Elizabeth Finger > > Date: Tuesday, September 16, 2008 2:48 pm > > Subject: [Mristudio-users] viewing automated tract details from LDMM > > To: mristudio-users at mristudio.org > > > > > > > Hello- > > > > > > Are there any step- by step instructions available after > > retrieving > > > results from the LDMM remote processing? I was able to retrieve > my > > > > > results, but it is not clear to me which templates and files > should > > be > > > loaded next into Landmarker and how I can view the automated > white > > > > > matter tracts and associated stastistics? > > > > > > Thank you, > > > Elizabeth Finger > > > -------------------------------------------------------------------------------- > > > This information is directed in confidence solely to the person > > > named > > > above and may contain confidential and/or privileged material. > This > > > > > information may not otherwise be distributed, copied or > disclosed. > > If > > > you have received this e-mail in error, please notify the sender > > > > immediately via a return e-mail and destroy original message. > Thank > > > > > you for your cooperation. > > > > > > _______________________________________________ > > > Mristudio-users mailing list > > > Mristudio-users at mristudio.org > > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > > > > -------------------------------------------------------------------------------- > > This information is directed in confidence solely to the person > named > > above and may contain confidential and/or privileged material. This > > > information may not otherwise be distributed, copied or disclosed. > If > > you have received this e-mail in error, please notify the sender > > immediately via a return e-mail and destroy original message. Thank > > > you for your cooperation. > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > > -------------------------------------------------------------------------------- > This information is directed in confidence solely to the person named > above and may contain confidential and/or privileged material. This > information may not otherwise be distributed, copied or disclosed. If > you have received this e-mail in error, please notify the sender > immediately via a return e-mail and destroy original message. Thank > you for your cooperation. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From susumu at mri.jhu.edu Thu Sep 18 18:31:04 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 18 Sep 2008 18:31:04 -0400 Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio In-Reply-To: <48C7D5E5020000A000004F76@lhscgwiao.lhsc.on.ca> Message-ID: <73ap56$4b9f7l@ipex1.johnshopkins.edu> Hi Elizabeth, I think your procedure is right, but the BinaryMap file may not be right. 1) Please do some fiber tracking using DtiStudio. Draw some manual ROIs and see if fibers are correctly reconstructed. 2) If you see fibers are reconstructable, then try to save the ROIs you drew using the "BinaryMap" format. Open the text file and study inside. For each ROI file, there should be 3 lines for "Operation", "Fiber color", and "colormode". At the bottom of the text file, there are explanations about these fields. For example, "Operation" field says "0=OR, 1=AND". 3) In your example, you specified Operation: 1 for the both ROIs. If you have two "AND" ROIs, you do not get any fibers. The first one has to be "OR" and the second one "AND" to combine two ROIs. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Elizabeth Finger Sent: Wednesday, September 10, 2008 2:13 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio Hello- I have been following the proior posts on this topic but cannot seem to open up in DTI studio the ROI's saved as a binary map which I created in ROI Editor. I have attached the binary map file that I created in ROI Editor and then edited to include the Operation: 1 to each binary file to signify AND. Then in DTI-Studio- Fibertracking, I load my FA map and eigenvector_0 and complete the fiber tracking. When I then in the fiber tab under ROI Operation click on load, binary map, and select my file, nothing (no ROIs nor fibers) appear on the screen, and no ROI statistics are available. I have tried this with several subjects and with several different ROIs. Perhaps there is a step I have missed? Thank you, Elizabeth Finger ---------------------------------------------------------------------------- ---- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From susumu at mri.jhu.edu Thu Sep 18 18:40:09 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 18 Sep 2008 18:40:09 -0400 Subject: [Mristudio-users] viewing automated tract details from LDMM In-Reply-To: <48D0F0AB020000A000005141@lhscgwiao.lhsc.on.ca> Message-ID: <73ap56$4b9h8l@ipex1.johnshopkins.edu> Hi Elizabeth, Landmarker is a software program to normalize images to a template space. If you are interested in normalizing tractography results, the only way is to convert the tracking results (streamline information for each tract) to a binary "images", in which pixels that contain the streamlines are 1 and all the other pixels are 0. The Landmarker has two image normalization tools. One is AIR that can do linear and low-order non-linear transformation. For a high-order transformation, you need to use LDDMM. Either way, you first have to do AIR-based normalization as initialization. This will not only bring the subject brain shape closer to the atlas, it also makes the matrix and pixel dimensions identical to those of the atlas. For example, if you choose our template (JHU or ICBM), they are 181x217x181 (1x1x1mm). Then the images are ready for LDDMM. If LDDMM sees the dimensions of the atlas and the subject data are different, it won't run. Hope this will help. We are currently working on more detailed documents about how to use LDDMM. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Elizabeth Finger Sent: Wednesday, September 17, 2008 11:58 AM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] viewing automated tract details from LDMM Thanks Xin- I have completed fiber tracking and saved the file with all fibers in DTI studio. When I try to load this file into Landmarker, no matter the image parameters or Image data format I enter, I cannot pull up the correct image. If I draw an ROI in fiber tracking and save this in binary format, I can open up the fiber file in Landmarker, however when I try to apply the K-Map using the button using the Load Transformation Matrix button, and then the LDDMM matrix option, I receive an error message that the load images must be isotropic images. Perhaps I have misunderstood what you mean by fiber file? Thank you, Elizabeth >>> XIN LI 09/17/08 11:13 AM >>> Elizabeth, Please also apply the Kimap to the fiber file to get the updated fiber file. Then load the updated target image into ROIEditor and load the updated fiber file as a raw ROI data file. In that way, you can get what you want. Xin ----- Original Message ----- From: Elizabeth Finger Date: Tuesday, September 16, 2008 3:45 pm Subject: Re: [Mristudio-users] viewing automated tract details from LDMM To: mristudio-users at mristudio.org > Thank you Xin- > > That has seemingly worked so far. Can you tell me after the new > subject image is updated (it shows up as Updated_Target.img in > Landmarker, how I then can visualize the automated tracts which have > been segmented, and how to find the # fibers and FA values for those tracts? > > Elizabeth > > >>> XIN LI 09/16/08 3:21 PM >>> > Elizabeth, > > There are two image files in the LDDMM processing result, "Template" > and "Target". Please load them to Landmarker, "Template" as a template > and "Target" as a subject. Please click the button "Load > Transformation Matrix" in the subject window, select the radio box > "LDDMM Matrix (VTK Format)" and load the file "Kimap.vtk" that is in > the LDDMM processing result. Landmarker will show you a new subject > image updated based on the LDDMM matrix. > > > Xin > > > > ----- Original Message ----- > From: Elizabeth Finger > Date: Tuesday, September 16, 2008 2:48 pm > Subject: [Mristudio-users] viewing automated tract details from LDMM > To: mristudio-users at mristudio.org > > > > Hello- > > > > Are there any step- by step instructions available after > retrieving > > results from the LDMM remote processing? I was able to retrieve my > > > results, but it is not clear to me which templates and files should > be > > loaded next into Landmarker and how I can view the automated white > > > matter tracts and associated stastistics? > > > > Thank you, > > Elizabeth Finger > > ---------------------------------------------------------------------------- ---- > > This information is directed in confidence solely to the person > named > > above and may contain confidential and/or privileged material. This > > > information may not otherwise be distributed, copied or disclosed. > If > > you have received this e-mail in error, please notify the sender > > immediately via a return e-mail and destroy original message. Thank > > > you for your cooperation. > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > > > ---------------------------------------------------------------------------- ---- > This information is directed in confidence solely to the person named > above and may contain confidential and/or privileged material. This > information may not otherwise be distributed, copied or disclosed. If > you have received this e-mail in error, please notify the sender > immediately via a return e-mail and destroy original message. Thank > you for your cooperation. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users ---------------------------------------------------------------------------- ---- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Fri Sep 19 11:34:50 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 19 Sep 2008 11:34:50 -0400 Subject: [Mristudio-users] How to save the image file after coregistration In-Reply-To: <210019.49085.qm@web56404.mail.re3.yahoo.com> Message-ID: <73ap56$4bib32@ipex1.johnshopkins.edu> Hi Basar, There are two "save" buttons in the window; one is at the upper left and the other in the right column of the viewing window. Please use the one in the viewing window. Then an window pops up asking which data you want to save. You have to move the one you want to save from the left to the right box. Here you have to choose "AIR_..." image. This should work. Please let me know if not. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Basar Sarikaya Sent: Thursday, September 11, 2008 11:05 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] How to save the image file after coregistration Hi, my question may seem a little absurd. I've used AIR to coregister two CT angio data sets (which were preconverted to image file with MRIcro) now I can see the file with the name beginning with AIR... But I can not save it. Either "save" or "save as" only saves a filesize of 0 kbyte. I would really appreciate any answer or help to my rather unrelated question. Basar Sarikaya, M. D. Assistant Professor of Radiology Gaziosmanpasa University Medical Faculty, Tokat, Turkey Visiting Research Scholar to Duke University Medical Center, Durham, NC, US -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080919/a85d09bb/attachment-0001.html From susumu at mri.jhu.edu Fri Sep 19 12:58:10 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 19 Sep 2008 12:58:10 -0400 Subject: [Mristudio-users] Directional fiber coloring In-Reply-To: Message-ID: <73ap56$4bjnol@ipex1.johnshopkins.edu> Hi S.C. Do you mean color-coded orientation maps or visualization of fiber tracking results in which the streamlines are colored based on the orientations? If the latter is the case, DtiStudio is not supporting such a color scheme. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Friday, September 12, 2008 4:40 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Directional fiber coloring Dear all, Philips console provides directional fiber coloring and it is nice feature to have for fiber tractography. I wonder if this is possible on DTIstudio. I would appreciate if anyone let me know this. S.C. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080919/0f4edbb6/attachment.html From choisj70 at gmail.com Fri Sep 19 13:15:54 2008 From: choisj70 at gmail.com (Seongjin) Date: Fri, 19 Sep 2008 13:15:54 -0400 Subject: [Mristudio-users] Directional fiber coloring In-Reply-To: <73ap56$4bjnol@ipex1.johnshopkins.edu> References: <73ap56$4bjnol@ipex1.johnshopkins.edu> Message-ID: Thanks for your reply. I am just curious about if DTIstudio developers have a plan to support the colored fiber tracking based on its orientation. I meant the colored fiber tracking as 'visualization of fiber tracking results in which the streamlines are colored based on the orientations'. All the best, S.C. On Fri, Sep 19, 2008 at 12:58 PM, susumu wrote: > Hi S.C. > > > > Do you mean color-coded orientation maps or visualization of fiber tracking > results in which the streamlines are colored based on the orientations? > > > > If the latter is the case, DtiStudio is not supporting such a color scheme. > > > > Susumu > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > *Sent:* Friday, September 12, 2008 4:40 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] Directional fiber coloring > > > > Dear all, > > > > Philips console provides directional fiber coloring and it is nice feature > to have for fiber tractography. > > I wonder if this is possible on DTIstudio. I would appreciate if anyone let > me know this. > > > > S.C. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080919/87001940/attachment.html From hjiang at jhmi.edu Fri Sep 19 16:10:51 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Fri, 19 Sep 2008 16:10:51 -0400 Subject: [Mristudio-users] Directional fiber coloring Message-ID: <48D3CF0B020000630001670D@cis27.hosts.jhmi.edu> hi, no such plan at this moment. a drawback of such method is that it may confuse the users if the user want to display multiple bundles of fibers. regards, hangyi >>> "[Seongjin]" 09/19/08 1:15 PM >>> Thanks for your reply. I am just curious about if DTIstudio developers have a plan to support the colored fiber tracking based on its orientation. I meant the colored fiber tracking as 'visualization of fiber tracking results in which the streamlines are colored based on the orientations'. All the best, S.C. On Fri, Sep 19, 2008 at 12:58 PM, susumu wrote: > Hi S.C. > > > > Do you mean color-coded orientation maps or visualization of fiber tracking > results in which the streamlines are colored based on the orientations? > > > > If the latter is the case, DtiStudio is not supporting such a color scheme. > > > > Susumu > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > *Sent:* Friday, September 12, 2008 4:40 PM > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* [Mristudio-users] Directional fiber coloring > > > > Dear all, > > > > Philips console provides directional fiber coloring and it is nice feature > to have for fiber tractography. > > I wonder if this is possible on DTIstudio. I would appreciate if anyone let > me know this. > > > > S.C. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > From choisj70 at gmail.com Fri Sep 19 16:29:41 2008 From: choisj70 at gmail.com (Seongjin) Date: Fri, 19 Sep 2008 16:29:41 -0400 Subject: [Mristudio-users] Directional fiber coloring In-Reply-To: <48D3CF0B020000630001670D@cis27.hosts.jhmi.edu> References: <48D3CF0B020000630001670D@cis27.hosts.jhmi.edu> Message-ID: Thanks for your reply and comments. S.C. On Fri, Sep 19, 2008 at 4:10 PM, Hangyi Jiang wrote: > hi, > > no such plan at this moment. a drawback of such method is that it may > confuse the users if the user want to display multiple bundles of fibers. > > regards, > > hangyi > > > > > > >>> "[Seongjin]" 09/19/08 1:15 PM >>> > Thanks for your reply. > I am just curious about if DTIstudio developers have a plan to support the > colored fiber tracking based on its orientation. I meant the colored fiber > tracking as 'visualization of fiber tracking results in which the > streamlines are colored based on the orientations'. > > All the best, > > S.C. > > On Fri, Sep 19, 2008 at 12:58 PM, susumu wrote: > > > Hi S.C. > > > > > > > > Do you mean color-coded orientation maps or visualization of fiber > tracking > > results in which the streamlines are colored based on the orientations? > > > > > > > > If the latter is the case, DtiStudio is not supporting such a color > scheme. > > > > > > > > Susumu > > > > > > ------------------------------ > > > > *From:* mristudio-users-bounces at mristudio.org [mailto: > > mristudio-users-bounces at mristudio.org] *On Behalf Of *[Seongjin] > > *Sent:* Friday, September 12, 2008 4:40 PM > > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > > *Subject:* [Mristudio-users] Directional fiber coloring > > > > > > > > Dear all, > > > > > > > > Philips console provides directional fiber coloring and it is nice > feature > > to have for fiber tractography. > > > > I wonder if this is possible on DTIstudio. I would appreciate if anyone > let > > me know this. > > > > > > > > S.C. > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080919/85217a23/attachment-0001.html From susumu at mri.jhu.edu Sun Sep 21 21:06:35 2008 From: susumu at mri.jhu.edu (susumu) Date: Sun, 21 Sep 2008 21:06:35 -0400 Subject: [Mristudio-users] Mac version? In-Reply-To: Message-ID: <73ap56$4c8sgq@ipex1.johnshopkins.edu> Hi S.C. There is no Mac version of our software. Recent Intel-based Mac can run Windows. Then you can run our software. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Monday, September 15, 2008 12:13 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] Mac version? Dear DTI studio users, One of my colleagues want to use DTI studio on her Mac book. I wonder if there is any Mac version of DTI studio? Best, S.C. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080921/14cb5b16/attachment.html From basarsarikayamd at yahoo.com Mon Sep 22 12:36:58 2008 From: basarsarikayamd at yahoo.com (Basar Sarikaya) Date: Mon, 22 Sep 2008 09:36:58 -0700 (PDT) Subject: [Mristudio-users] Gradient table for GE Message-ID: <374558.82945.qm@web56404.mail.re3.yahoo.com> I need a 33-direction gradient table for 1.5 T GE Signa Excite. The scan was done in Dec 2006. I wonder if there's anybody who has that table in the group. Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080922/6de73a32/attachment.html From postmaster at paran.com Wed Sep 10 14:34:05 2008 From: postmaster at paran.com (postmaster at paran.com) Date: Thu, 11 Sep 2008 03:34:05 +0900 Subject: [Mristudio-users] [ERR] ROI uploading and viewing in DTI Studio Message-ID: <1221070422720528.92.nrmail2TR@nrmail2> Transmit Report: To: nsckpark at paran.com, 2008/09/11 03:34:01, 451, Requested action aborted: No failover server -------------- next part -------------- An embedded message was scrubbed... From: Elizabeth Finger Subject: [Mristudio-users] ROI uploading and viewing in DTI Studio Date: Wed, 10 Sep 2008 14:12:53 -0400 Size: 7674 Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080911/ddf8d7cc/attachment-0001.mht From postmaster at paran.com Wed Sep 10 15:31:06 2008 From: postmaster at paran.com (postmaster at paran.com) Date: Thu, 11 Sep 2008 04:31:06 +0900 Subject: [Mristudio-users] [ERR] Re: ROI uploading and viewing in DTI Studio Message-ID: <1221073248344940.20.nrmail2TR@nrmail2> Transmit Report: To: nsckpark at paran.com, 2008/09/11 04:31:02, 451, Requested action aborted: No failover server -------------- next part -------------- An embedded message was scrubbed... From: Elizabeth Finger Subject: Re: [Mristudio-users] ROI uploading and viewing in DTI Studio Date: Wed, 10 Sep 2008 15:00:28 -0400 Size: 7470 Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080911/5e17db87/attachment-0001.mht From postmaster at paran.com Wed Sep 10 15:05:16 2008 From: postmaster at paran.com (postmaster at paran.com) Date: Thu, 11 Sep 2008 04:05:16 +0900 Subject: [Mristudio-users] [ERR] Re: ROI uploading and viewing in DTI Studio Message-ID: <1221072339805589.44.nrmail2TR@nrmail2> Transmit Report: To: nsckpark at paran.com, 2008/09/11 04:05:12, 451, Requested action aborted: No failover server -------------- next part -------------- An embedded message was scrubbed... From: XIN LI Subject: Re: [Mristudio-users] ROI uploading and viewing in DTI Studio Date: Wed, 10 Sep 2008 14:45:12 -0400 Size: 6073 Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080911/b5be5076/attachment-0001.mht From postmaster at paran.com Wed Sep 10 18:01:12 2008 From: postmaster at paran.com (postmaster at paran.com) Date: Thu, 11 Sep 2008 07:01:12 +0900 Subject: [Mristudio-users] [ERR] Re: ROI uploading and viewing in DTI Studio Message-ID: <1221083164793285.0.nrmail7TR@nrmail7> Transmit Report: To: nsckpark at paran.com, 2008/09/11 07:01:09, 451, Requested action aborted: No failover server -------------- next part -------------- An embedded message was scrubbed... From: XIN LI Subject: Re: [Mristudio-users] ROI uploading and viewing in DTI Studio Date: Wed, 10 Sep 2008 17:45:36 -0400 Size: 7486 Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080911/fea4b086/attachment-0001.mht From yj3 at duke.edu Tue Sep 16 14:30:25 2008 From: yj3 at duke.edu (Yi Jiang) Date: Tue, 16 Sep 2008 14:30:25 -0400 Subject: [Mristudio-users] radial diffusivity References: Message-ID: <1C7D5BCC53D6435EB833715232ECFDE2@panpan> Is there a way to calculate radial diffusivity in MRIStudio? -- actually it's very simple, just sqrt(lamda2*lamda3). But I did not find it after I calculate the tensors. Thank you very much! Best, Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080916/96256cbb/attachment-0001.html From susumu at mri.jhu.edu Fri Sep 19 09:37:37 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 19 Sep 2008 09:37:37 -0400 Subject: [Mristudio-users] ROIEditor and LandMarker data format In-Reply-To: <55aa985a0809091402u7e4adb48y75a84448c38a346d@mail.gmail.com> Message-ID: <73ap56$4bg86p@ipex1.johnshopkins.edu> Hi Mark, Please see the attached article. All the measurements in this article was done by RoiEditor and Landmarker. RoiEditor has a very powerful interface to support manual ROI drawing (Manual and Hybrid approaches in Fig. 1A). If you normalize the brain shape by Landmarker, you can use the automated quantification function in RoiEditor (Automated approach I and II in Fig. 1A). We use the "Hybrid Approach" often, while the automated approaches are mostly for just an initial screening. These two programs use data stored by DtiStudio such as FA and Trace maps. They are usually raw data or Analyze format. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of mark gold Sent: Tuesday, September 09, 2008 5:02 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ROIEditor and LandMarker data format Hi, This is my first time to use ROIEditor and LandMarker. Follow the manual I installed these two software. But I don't know what kind of data should import to ROIEditor or LandMarker. The raw data? or FA and b0 image from MRIstudio. Thanks. Best, Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080919/c92ec5c9/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: article.pdf Type: application/pdf Size: 1319142 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080919/c92ec5c9/attachment-0001.pdf From susumu at mri.jhu.edu Mon Sep 22 14:22:51 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 22 Sep 2008 14:22:51 -0400 Subject: [Mristudio-users] Gradient table for GE In-Reply-To: <374558.82945.qm@web56404.mail.re3.yahoo.com> Message-ID: <73ap56$4cgihf@ipex1.johnshopkins.edu> I hope this will work. Some combinations are already converted to the DtiStudio format but you have to do the conversion by yourself for the rest of the combinations. Please let me know if this doesn't work. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Basar Sarikaya Sent: Monday, September 22, 2008 12:37 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Gradient table for GE I need a 33-direction gradient table for 1.5 T GE Signa Excite. The scan was done in Dec 2006. I wonder if there's anybody who has that table in the group. Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080922/a845aaef/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: GEtensor.doc Type: application/msword Size: 857088 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080922/a845aaef/attachment-0001.doc From susumu at mri.jhu.edu Tue Sep 23 19:07:03 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 23 Sep 2008 19:07:03 -0400 Subject: [Mristudio-users] radial diffusivity In-Reply-To: <1C7D5BCC53D6435EB833715232ECFDE2@panpan> Message-ID: <73alti$3o1sol@ipex2.johnshopkins.edu> Please try the Version 3 (beta) posted in www.mristudio.org. It should have it. oh, wait. I thought radial is (l2+l3)/2? Is it sqrt(l2*l3)? Hangyi, is it true? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Yi Jiang Sent: Tuesday, September 16, 2008 2:30 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] radial diffusivity Is there a way to calculate radial diffusivity in MRIStudio? -- actually it's very simple, just sqrt(lamda2*lamda3). But I did not find it after I calculate the tensors. Thank you very much! Best, Yi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080923/9f2f7b0b/attachment.html From nestr007 at umn.edu Tue Sep 23 22:37:55 2008 From: nestr007 at umn.edu (nestr007 at umn.edu) Date: Tue, 23 Sep 2008 21:37:55 -0500 Subject: [Mristudio-users] MS Vista Support In-Reply-To: <73alti$3o1sol@ipex2.johnshopkins.edu> References: <73alti$3o1sol@ipex2.johnshopkins.edu> Message-ID: Hello, I'm trying to run DTI studio on computer with MS Vista as an operation system. I'm experiencing all the time the same problem: when opening images the 3D image does not appear. There are only 2D images and empty window where's normally 3D image. Is there any solution? Thank you. Igor From basarsarikayamd at yahoo.com Wed Sep 24 07:44:41 2008 From: basarsarikayamd at yahoo.com (Basar Sarikaya) Date: Wed, 24 Sep 2008 04:44:41 -0700 (PDT) Subject: [Mristudio-users] 33 Dir Gradient Table problem solved Message-ID: <476407.62397.qm@web56405.mail.re3.yahoo.com> Hi, The search for 33 Dir GE Signa 1.5 T gradient table has ended. I have attached a copy for others who may need it. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080924/39d8a80a/attachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: GE 33-dir.doc Type: application/msword Size: 25600 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080924/39d8a80a/attachment-0001.doc From hjiang at jhmi.edu Wed Sep 24 10:00:05 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Wed, 24 Sep 2008 10:00:05 -0400 Subject: [Mristudio-users] MS Vista Support Message-ID: <48DA0FA50200006300016991@cis27.hosts.jhmi.edu> hi, Igor, as my knowledge, this is one of the vista's problems, missing drivers for some video cards; to verify this, you can run some graphic tools (e.g. Photoshop, or even a game) to see if they work well. actually, Microsoft knows these porblems, they are working on these issues. another possibiblity is that the video drivers were only partially installed when you install the vista. you may try: 1. re-install (or updata) the vista in case that the video drivers were not fully installed, especially the OpenGL part; 1. or, visit MS-vista website to get upgraded drivers for your video card; 2. or: try to contact the manufacturer of the video card, see if they have their own drivers for vista. regards, hangyi >>> 09/23/08 10:37 PM >>> Hello, I'm trying to run DTI studio on computer with MS Vista as an operation system. I'm experiencing all the time the same problem: when opening images the 3D image does not appear. There are only 2D images and empty window where's normally 3D image. Is there any solution? Thank you. Igor _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From CGiza at mednet.ucla.edu Wed Sep 24 11:03:54 2008 From: CGiza at mednet.ucla.edu (Giza, Christopher) Date: Wed, 24 Sep 2008 08:03:54 -0700 Subject: [Mristudio-users] MS Vista Support References: <73alti$3o1sol@ipex2.johnshopkins.edu> Message-ID: <58CE253ED5AD5F4FBC8694B5DF27D63902349012@admedmail4.ad.medctr.ucla.edu> I am running DTI studio in Vista without a problem, except: On my work computer (with 2+ GB RAM) - no problem. Vista Ultimate. On my home computer (with only 1 GB RAM), Vista Home - the 3D image only appears if I resize the viewing box, and then only with certain configurations of the 4 viewing panels. I don't know if your problem is due to RAM or to the version of Vista you are using. Chris -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of nestr007 at umn.edu Sent: Tuesday, September 23, 2008 7:38 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] MS Vista Support Hello, I'm trying to run DTI studio on computer with MS Vista as an operation system. I'm experiencing all the time the same problem: when opening images the 3D image does not appear. There are only 2D images and empty window where's normally 3D image. Is there any solution? Thank you. Igor _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users 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 nestr007 at umn.edu Wed Sep 24 12:51:25 2008 From: nestr007 at umn.edu (nestr007 at umn.edu) Date: Wed, 24 Sep 2008 11:51:25 -0500 Subject: [Mristudio-users] MS Vista Support In-Reply-To: <58CE253ED5AD5F4FBC8694B5DF27D63902349012@admedmail4.ad.medctr.ucla.edu> References: <73alti$3o1sol@ipex2.johnshopkins.edu> <58CE253ED5AD5F4FBC8694B5DF27D63902349012@admedmail4.ad.medctr.ucla.edu> Message-ID: I'm using Vista Home with 1GB RAM. You are right that 3D image only appears after resizing the viewing box.... Thank you for help. Probably I should consider a computer upgrade. Igor On Sep 24 2008, Giza, Christopher wrote: >I am running DTI studio in Vista without a problem, except: > >On my work computer (with 2+ GB RAM) - no problem. Vista Ultimate. >On my home computer (with only 1 GB RAM), Vista Home - the 3D image only >appears if I resize the viewing box, and then only with certain >configurations of the 4 viewing panels. > >I don't know if your problem is due to RAM or to the version of Vista >you are using. > >Chris > >-----Original Message----- >From: mristudio-users-bounces at mristudio.org >[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of >nestr007 at umn.edu >Sent: Tuesday, September 23, 2008 7:38 PM >To: DTI Studio, ROI Editor, Landmarker Questions/Support >Subject: [Mristudio-users] MS Vista Support > >Hello, > >I'm trying to run DTI studio on computer with MS Vista as an operation >system. > >I'm experiencing all the time the same problem: when opening images the >3D image does not appear. There are only 2D images and empty window >where's normally 3D image. > >Is there any solution? Thank you. > >Igor >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > 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. > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users > -- Igor Nestrasil, MD Post-Doctoral Associate Office Address: Department of Neurology UMN Twin Cities 12-125 PWB 420 Delaware St SE Minneapolis, MN 55455 Phone:612-625-7973 Fax: 612-625-7950 E-mail Address: nestr007 at umn.edu From alandarkenergy at gmail.com Thu Sep 25 14:03:15 2008 From: alandarkenergy at gmail.com (Alan Francis) Date: Thu, 25 Sep 2008 14:03:15 -0400 Subject: [Mristudio-users] ROIEditor and LandMarker data format In-Reply-To: <73ap56$4bg86p@ipex1.johnshopkins.edu> References: <55aa985a0809091402u7e4adb48y75a84448c38a346d@mail.gmail.com> <73ap56$4bg86p@ipex1.johnshopkins.edu> Message-ID: Hello Folks: Does DTI studio work on Linux 64 using Red Hat Enterprise 5 or Fedora 8? thanks, Alan Francis Harvard Medical School On Fri, Sep 19, 2008 at 9:37 AM, susumu wrote: > Hi Mark, > > > > Please see the attached article. All the measurements in this article was > done by RoiEditor and Landmarker. RoiEditor has a very powerful interface to > support manual ROI drawing (Manual and Hybrid approaches in Fig. 1A). If you > normalize the brain shape by Landmarker, you can use the automated > quantification function in RoiEditor (Automated approach I and II in Fig. > 1A). We use the "Hybrid Approach" often, while the automated approaches are > mostly for just an initial screening. > > > > These two programs use data stored by DtiStudio such as FA and Trace maps. > They are usually raw data or Analyze format. > > > > Susumu > > > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *mark gold > *Sent:* Tuesday, September 09, 2008 5:02 PM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] ROIEditor and LandMarker data format > > > > Hi, > > > > This is my first time to use ROIEditor and LandMarker. Follow the manual I > installed these two software. But I don't know what kind of data should > import to ROIEditor or LandMarker. The raw data? or FA and b0 image from > MRIstudio. Thanks. > > > > Best, > > > > Mark > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080925/ecb0fa65/attachment.html From susumu at mri.jhu.edu Thu Sep 25 15:33:27 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 25 Sep 2008 15:33:27 -0400 Subject: [Mristudio-users] ROIEditor and LandMarker data format In-Reply-To: Message-ID: <73alti$3om4vj@ipex2.johnshopkins.edu> Unfortunately not. Our quest for seeking for funding to extend our software to other platforms have not been successful. It is Windows only. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Alan Francis Sent: Thursday, September 25, 2008 2:03 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] ROIEditor and LandMarker data format Hello Folks: Does DTI studio work on Linux 64 using Red Hat Enterprise 5 or Fedora 8? thanks, Alan Francis Harvard Medical School On Fri, Sep 19, 2008 at 9:37 AM, susumu wrote: Hi Mark, Please see the attached article. All the measurements in this article was done by RoiEditor and Landmarker. RoiEditor has a very powerful interface to support manual ROI drawing (Manual and Hybrid approaches in Fig. 1A). If you normalize the brain shape by Landmarker, you can use the automated quantification function in RoiEditor (Automated approach I and II in Fig. 1A). We use the "Hybrid Approach" often, while the automated approaches are mostly for just an initial screening. These two programs use data stored by DtiStudio such as FA and Trace maps. They are usually raw data or Analyze format. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of mark gold Sent: Tuesday, September 09, 2008 5:02 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ROIEditor and LandMarker data format Hi, This is my first time to use ROIEditor and LandMarker. Follow the manual I installed these two software. But I don't know what kind of data should import to ROIEditor or LandMarker. The raw data? or FA and b0 image from MRIstudio. Thanks. Best, Mark _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20080925/d059444b/attachment-0001.html From bob_ge at 163.com Sun Oct 5 02:45:51 2008 From: bob_ge at 163.com (bob) Date: Sun, 05 Oct 2008 14:45:51 +0800 Subject: [Mristudio-users] about algorithm of fiber tracking Message-ID: <48E8621C.3465BA.10078@m12-16.163.com> Is it FACT(fiber assignment by continuous tracking)? thank you. ????????bob ????????bob_ge at 163.com ??????????2008-10-05 From hjiang at jhmi.edu Mon Oct 6 09:46:16 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Mon, 06 Oct 2008 09:46:16 -0400 Subject: [Mristudio-users] about algorithm of fiber tracking Message-ID: <48E9DE68020000630001706D@cis27.hosts.jhmi.edu> yes. it is. also, please refer to the paper below for the details. "DtiStudio: resource program for diffusion tensor computation and fiber bundle tracking", Comput. Methods & Programs Biomed. 2006 Feb;81(2):106-16. Epub 2006 Jan 18. regards, hangyi >>> bob 10/05/08 2:45 AM >>> Is it FACT(fiber assignment by continuous tracking)? thank you. ????????bob ????????bob_ge at 163.com ??????????2008-10-05 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From takeshiasami at yahoo.com Fri Oct 10 16:32:34 2008 From: takeshiasami at yahoo.com (Takeshi Asami) Date: Fri, 10 Oct 2008 13:32:34 -0700 (PDT) Subject: [Mristudio-users] (no subject) Message-ID: <131655.84406.qm@web46116.mail.sp1.yahoo.com> Could you please remove me from the list ? Thank You, Takeshi Asami takeshiasami at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081010/29530e49/attachment.html From bob_ge at 163.com Fri Oct 10 23:49:07 2008 From: bob_ge at 163.com (bob) Date: Sat, 11 Oct 2008 11:49:07 +0800 Subject: [Mristudio-users] how to Flip Eigen Vector Message-ID: <48F021B4.38C7F9.04064@m12-14.163.com> I know that "The easiest way to iterate through the trial-and-error is by clicking the ?Flip Eigen vector? check boxes" in order to figure out the relationship between diffusion and imaging gradients, but I don't know to check the results of fiber tracking so as to we decide it is correct. could you explain it for me? thanks. ????????bob ????????bob_ge at 163.com ??????????2008-10-11 From bob_ge at 163.com Sat Oct 11 03:06:41 2008 From: bob_ge at 163.com (bob) Date: Sat, 11 Oct 2008 15:06:41 +0800 Subject: [Mristudio-users] how to Flip Eigen Vector Message-ID: <48F05000.38E05D.04064@m12-14.163.com> I forgot a word "how", it should be "but I don't know how to check the results of fiber tracking so as to we decide if it is correct. could you explain it for me? thanks. " ======= 2008-10-11 11:49:07 ????????======= > I know that "The easiest way to iterate through the trial-and-error is by clicking the ?Flip Eigen vector? check boxes" in order to figure out the relationship between diffusion and imaging gradients, but I don't know to check the results of fiber tracking so as to we decide it is correct. could you explain it for me? thanks. > >????????bob >????????bob_ge at 163.com >??????????2008-10-11 > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users = = = = = = = = = = = = = = = = = = = = ????????? ?? ????????bob ????????bob_ge at 163.com ??????????2008-10-11 From sreading at jhmi.edu Sun Oct 12 23:36:54 2008 From: sreading at jhmi.edu (Sarah A Reading) Date: Sun, 12 Oct 2008 23:36:54 -0400 Subject: [Mristudio-users] ROIeditor - FA data Message-ID: Is there any way to get FA data to more than just two decimal points? For example, when I get the statistics from my ROI a mean FA may be 0.39, is there a way to get the data to something like 0.3946? Thanks, Sarah. From c.bieck at T-Online.de Mon Oct 13 12:06:00 2008 From: c.bieck at T-Online.de (Christian Bieck) Date: Mon, 13 Oct 2008 16:06 +0000 (GMT) Subject: [Mristudio-users] Optic radiation ROIs Message-ID: <1KpPvx-1Pw4ga0@fwd00.aul.t-online.de> Hello, In the course of my diploma thesis I'm analyzing the optic radiation in regard to their FA values. After extracting the optic radiation using anatomical landmarks and the DTIStudio functions AND, OR and NOT, I would now like to examine the posterior parts of the optic radiation ending in the calcarine sulcus. However, I find myself unable to do so using the aforementioned functions as these result in the removal of whole fiber tracts, including the posterior parts. Is there a way to only focus on the posterior parts of the optic radiation and get their FA values, maybe through using ROIEditor? I would very much appreciate any input on this matter. Thank you for your time, Christian Bieck -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081013/5839e797/attachment.html From Elizabeth.Finger at lhsc.on.ca Tue Oct 21 13:22:05 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Tue, 21 Oct 2008 13:22:05 -0400 Subject: [Mristudio-users] imported ROIs are flipped from front to back of brain Message-ID: <48FDD77D020000A000005AD0@lhscgwiao.lhsc.on.ca> Hello- I have created automated ROI's in AFNI, and then used MRIcro to convert them from the Head/Brik format to an Analyze format (.hdr and .img files). By changing the header to match the header file of ROI's created in DTI studio (e.g. DB Name: ROI; Aux File ROI Save As; Extents: 13694; Gmax 255; Reg 114, and extension .roihdr) I am able to load the ROIs into ROI editor using the raw format. The only problem is that they are flipped in the A-P direction (e.g. a frontal lobe ROI shows up in the occipital lobe). The same thing happens if the ROI's are created in SPM (they can only be loaded into DTI studio in raw format, and the location of the ROI is flipped from front to back. If I load the roi.img file into ROI editor as just a regular image (not under the ROI tab) it displays the ROI drawing in the correct A-P orientation. I have not been able to find a way in any of the programs to flip the ROI orientation so that it stays aligned with the anatomical and so that it displays correctly when loaded as an ROI. Any suggestions would be much appreciated. Thanks, Elizabeth Finger -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From choisj70 at gmail.com Tue Oct 21 13:46:57 2008 From: choisj70 at gmail.com (Seongjin) Date: Tue, 21 Oct 2008 13:46:57 -0400 Subject: [Mristudio-users] Q. AIR-generated gradient table Message-ID: Dear DTI studio users, After registration using AIR, a gradient table is generated. What is this gradient for? Is this table should be used for fiber tracking to see the effect of AIR? Thanks in advance. All the best, SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081021/9ac5b886/attachment-0001.html From susumu at mri.jhu.edu Tue Oct 21 15:17:06 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 21 Oct 2008 15:17:06 -0400 Subject: [Mristudio-users] imported ROIs are flipped from front to back of brain In-Reply-To: <48FDD77D020000A000005AD0@lhscgwiao.lhsc.on.ca> Message-ID: <73ap56$4mqlsu@ipex1.johnshopkins.edu> The default setting of Analyze follows the Neurology convention: the image's right is the patient's right. MriStudio follows the Radiology convention: the image's right is the patient's left. If you load an image in the neurology convention to MriStudio programs, the image is inverted. This is, in one sense, a good thing because you never mixed up right and left. If you read Analyze format as "Analyze" in programs in MriStudio family, the programs should automatically flip the Neurology convention to Radiology convention, but if you read *.img as a raw file, the programs don't know that it has to convert the formats. To flip the images or ROI files, you can use the following trick; > Load the image. > Save it as "Analyze" format. The *.img saved in this way is neurology-radiology converted. > Load the *.img as "RAW" format Hope this will help. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Elizabeth Finger Sent: Tuesday, October 21, 2008 1:22 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] imported ROIs are flipped from front to back of brain Hello- I have created automated ROI's in AFNI, and then used MRIcro to convert them from the Head/Brik format to an Analyze format (.hdr and .img files). By changing the header to match the header file of ROI's created in DTI studio (e.g. DB Name: ROI; Aux File ROI Save As; Extents: 13694; Gmax 255; Reg 114, and extension .roihdr) I am able to load the ROIs into ROI editor using the raw format. The only problem is that they are flipped in the A-P direction (e.g. a frontal lobe ROI shows up in the occipital lobe). The same thing happens if the ROI's are created in SPM (they can only be loaded into DTI studio in raw format, and the location of the ROI is flipped from front to back. If I load the roi.img file into ROI editor as just a regular image (not under the ROI tab) it displays the ROI drawing in the correct A-P orientation. I have not been able to find a way in any of the programs to flip the ROI orientation so that it stays aligned with the anatomical and so that it displays correctly when loaded as an ROI. Any suggestions would be much appreciated. Thanks, Elizabeth Finger ---------------------------------------------------------------------------- ---- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From Elizabeth.Finger at lhsc.on.ca Tue Oct 21 15:26:47 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Tue, 21 Oct 2008 15:26:47 -0400 Subject: [Mristudio-users] imported ROIs are flipped from front to backof brain Message-ID: <48FDF4B7020000A000005AF0@lhscgwiao.lhsc.on.ca> Thank you- that worked perfectly! Elizabeth >>> susumu 10/21/08 3:17 PM >>> The default setting of Analyze follows the Neurology convention: the image's right is the patient's right. MriStudio follows the Radiology convention: the image's right is the patient's left. If you load an image in the neurology convention to MriStudio programs, the image is inverted. This is, in one sense, a good thing because you never mixed up right and left. If you read Analyze format as "Analyze" in programs in MriStudio family, the programs should automatically flip the Neurology convention to Radiology convention, but if you read *.img as a raw file, the programs don't know that it has to convert the formats. To flip the images or ROI files, you can use the following trick; > Load the image. > Save it as "Analyze" format. The *.img saved in this way is neurology-radiology converted. > Load the *.img as "RAW" format Hope this will help. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Elizabeth Finger Sent: Tuesday, October 21, 2008 1:22 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] imported ROIs are flipped from front to back of brain Hello- I have created automated ROI's in AFNI, and then used MRIcro to convert them from the Head/Brik format to an Analyze format (.hdr and .img files). By changing the header to match the header file of ROI's created in DTI studio (e.g. DB Name: ROI; Aux File ROI Save As; Extents: 13694; Gmax 255; Reg 114, and extension .roihdr) I am able to load the ROIs into ROI editor using the raw format. The only problem is that they are flipped in the A-P direction (e.g. a frontal lobe ROI shows up in the occipital lobe). The same thing happens if the ROI's are created in SPM (they can only be loaded into DTI studio in raw format, and the location of the ROI is flipped from front to back. If I load the roi.img file into ROI editor as just a regular image (not under the ROI tab) it displays the ROI drawing in the correct A-P orientation. I have not been able to find a way in any of the programs to flip the ROI orientation so that it stays aligned with the anatomical and so that it displays correctly when loaded as an ROI. Any suggestions would be much appreciated. Thanks, Elizabeth Finger ---------------------------------------------------------------------------- ---- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From jsadino at hotmail.com Wed Oct 22 19:44:30 2008 From: jsadino at hotmail.com (Jeff Sadino) Date: Wed, 22 Oct 2008 17:44:30 -0600 Subject: [Mristudio-users] Importing from ROIEditor into DTI Studio Message-ID: Hello, I have saved an ROI binary map in ROIEditor with 3 ROI's. I edited the text file with the necessary "Operation: 0" lines. When I try to load the ROI map file into DTI Studio, I get an error saying: "Unrecognized Image-ROI data file!" I checked the locations of my binary ROIs and tried it in multiple different DTI Studio versions, but all give the same error. When I close ROIEditor and relod the image and ROI map file, it works just fine. Also, when I reload the ROI map file into ROIEditor, my object names all reset to generic "Object 1", "Object 2", etc. Is there any way to preserve the Object names? Thank you very much! Jeff _________________________________________________________________ Store, manage and share up to 5GB with Windows Live SkyDrive. http://skydrive.live.com/welcome.aspx?provision=1?ocid=TXT_TAGLM_WL_skydrive_102008 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081022/f74f781b/attachment.html From vikey.han at 163.com Thu Oct 23 08:56:15 2008 From: vikey.han at 163.com (vikey.han) Date: Thu, 23 Oct 2008 20:56:15 +0800 (CST) Subject: [Mristudio-users] gradient table Message-ID: <26282606.459291224766575369.JavaMail.coremail@bj163app64.163.com> Hello, I have downloaded public data of In vivo human database from http://lbam.med.jhmi.edu/, and now there's no gradient table for it, would you like send it to me? thank you very much. best, bob -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081023/62ae88a0/attachment.html From jmcentee at jhmi.edu Thu Oct 23 09:28:20 2008 From: jmcentee at jhmi.edu (Julie E McEntee) Date: Thu, 23 Oct 2008 09:28:20 -0400 Subject: [Mristudio-users] Importing from ROIEditor into DTI Studio In-Reply-To: References: Message-ID: Jeff, I am assuming that you are trying to open the ROI binary map in DTI Studio to do fiber tracking. If this is the case, then when you start DTI Studio, choose Fiber tracking from the File menu. Enter/load the fa map and vector and make sure that the parameters are correct. When the fa map opens, go to the Fiber tab (bottom right) and choose: fiber display: 2D fiber selection: ROI drawing enabled ROI operation: load, as image Than choose your ROI binary map. I'm sorry, but I don't know how to get it to preserve the object names. 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: Jeff Sadino Date: Wednesday, October 22, 2008 7:44 pm Subject: [Mristudio-users] Importing from ROIEditor into DTI Studio To: mristudio-users at mristudio.org > Hello, > > I have saved an ROI binary map in ROIEditor with 3 ROI's. I edited > the text file with the necessary "Operation: 0" lines. When I try to > load the ROI map file into DTI Studio, I get an error saying: > "Unrecognized Image-ROI data file!" I checked the locations of my > binary ROIs and tried it in multiple different DTI Studio versions, > but all give the same error. When I close ROIEditor and relod the > image and ROI map file, it works just fine. > > Also, when I reload the ROI map file into ROIEditor, my object names > all reset to generic "Object 1", "Object 2", etc. Is there any way to > preserve the Object names? > > Thank you very much! > Jeff > > _________________________________________________________________ > Store, manage and share up to 5GB with Windows Live SkyDrive. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From xli16 at jhmi.edu Thu Oct 23 10:07:32 2008 From: xli16 at jhmi.edu (XIN LI) Date: Thu, 23 Oct 2008 10:07:32 -0400 Subject: [Mristudio-users] Importing from ROIEditor into DTI Studio In-Reply-To: References: Message-ID: Jeff, If you save ROIs in ROIEditor as ROIEditor defined format (a WORD image file and a ROIEditor defined header), the object names can be preserved. Xin ----- Original Message ----- From: Jeff Sadino Date: Wednesday, October 22, 2008 7:44 pm Subject: [Mristudio-users] Importing from ROIEditor into DTI Studio To: mristudio-users at mristudio.org > Hello, > > I have saved an ROI binary map in ROIEditor with 3 ROI's. I edited > the text file with the necessary "Operation: 0" lines. When I try to > load the ROI map file into DTI Studio, I get an error saying: > "Unrecognized Image-ROI data file!" I checked the locations of my > binary ROIs and tried it in multiple different DTI Studio versions, > but all give the same error. When I close ROIEditor and relod the > image and ROI map file, it works just fine. > > Also, when I reload the ROI map file into ROIEditor, my object names > all reset to generic "Object 1", "Object 2", etc. Is there any way to > preserve the Object names? > > Thank you very much! > Jeff > > _________________________________________________________________ > Store, manage and share up to 5GB with Windows Live SkyDrive. > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From c.bieck at T-Online.de Tue Oct 28 13:49:00 2008 From: c.bieck at T-Online.de (Christian Bieck) Date: Tue, 28 Oct 2008 17:49 +0000 (GMT) Subject: [Mristudio-users] Optic radiations Message-ID: <1Kush3-1J6KJs0@fwd08.aul.t-online.de> Hello, Since my last inquiry seemed to have escaped notice, I write you again in the hopes of finding a solution to my problem. As I wrote in my last email, I?m analyzing the FA values of the optic radiations and have, so far, extracted them by using anatomical landmarks and the DTIStudio functions AND, OR and NOT. The focus of my research concerns the posterior parts of the optic radiations ending in the primary visual cortex, but I find myself unable to extract them properly. Using the ROI-Operations in the Fiber Tab during Fiber Tracking oftentimes results in the removal of entire fiber tracts instead of just the anterior parts and any attempts to work with ROI Editor have not been successful so far. I have seen at least one paper in which the anterior/posterior parts and their FA values were examined via DTIStudio, so I know it?s possible, but I?m completely puzzled as how to actually do it. I would appreciate it *very* much if you could point me in the right direction. Thank you for your time. Cheers, Christian Bieck -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081028/2e1bbb9d/attachment-0001.html From tangjinsonghn at yahoo.com.cn Wed Oct 29 05:29:21 2008 From: tangjinsonghn at yahoo.com.cn (jinsong tang) Date: Wed, 29 Oct 2008 17:29:21 +0800 (CST) Subject: [Mristudio-users] how to input ROI img into MRIstudio Message-ID: <261708.6196.qm@web15602.mail.cnb.yahoo.com> Hello, I have created a ROI file from marsbar, which was saved as image file. When I try to load this ROI file into MRIstudio. I found the message" unrecognized file". So I want to ask how to input image ROI file into MRIstudio? Thanks Jinsong --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081029/94a8ed3e/attachment.html From gaolion at gmail.com Wed Oct 29 07:51:19 2008 From: gaolion at gmail.com (lion gao) Date: Wed, 29 Oct 2008 19:51:19 +0800 Subject: [Mristudio-users] how to input ROI img into MRIstudio In-Reply-To: <261708.6196.qm@web15602.mail.cnb.yahoo.com> References: <261708.6196.qm@web15602.mail.cnb.yahoo.com> Message-ID: <99161220810290451h31e7afddu8f816eb3cbbab10e@mail.gmail.com> me too, I'd like to know that as well -- very critical question! Many Thanks! ..Galen 2008/10/29 jinsong tang : > Hello, > > I have created a ROI file from marsbar, which was saved as image file. When > I try to load this ROI file into MRIstudio. I found the message" > unrecognized file". So I want to ask how to input image ROI file into > MRhIstudio? > > Thanks > > Jinsong > > ________________________________ > ???????????? > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > From susumu at mri.jhu.edu Wed Oct 29 14:04:48 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 29 Oct 2008 14:04:48 -0400 Subject: [Mristudio-users] how to input ROI img into MRIstudio In-Reply-To: <261708.6196.qm@web15602.mail.cnb.yahoo.com> References: <261708.6196.qm@web15602.mail.cnb.yahoo.com> Message-ID: <8EC80B9DF08E4BFE8816615732EDB6FF@SusumuThinkPad> Hi Jinsong, If I understand it correctly, ?marsbar? is a function in SPM? If so, 1) Hangyi, could you find out the format of the ROI of this software? Ken may know it. 2) Jinsong, we?ll look into the file format. Meanwhile, if you just need a program to create ROIs, our RoiEditor has a very strong functions and interfaces to create ROIs in DTI data. You may want to try it. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jinsong tang Sent: Wednesday, October 29, 2008 5:29 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] how to input ROI img into MRIstudio Hello, I have created a ROI file from marsbar, which was saved as image file. When I try to load this ROI file into MRIstudio. I found the message" unrecognized file". So I want to ask how to input image ROI file into MRIstudio? Thanks Jinsong _____ ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081029/a012a125/attachment.html From tangjinsonghn at yahoo.com.cn Thu Oct 30 05:43:20 2008 From: tangjinsonghn at yahoo.com.cn (jinsong tang) Date: Thu, 30 Oct 2008 17:43:20 +0800 (CST) Subject: [Mristudio-users] =?gb2312?b?IFJFo7ogUmU6ICBob3cgdG8gaW5wdXQgUk9J?= =?gb2312?b?IGltZyBpbnRvIE1SSXN0dWRpbw==?= In-Reply-To: <8EC80B9DF08E4BFE8816615732EDB6FF@SusumuThinkPad> Message-ID: <719103.53147.qm@web15601.mail.cnb.yahoo.com> Hello Susumu, Yes marsbar is a tool in SPM. The ROI file was created from SPM T test result. Does RoiEditor also can create ROI base on statistical result? I heared RoiEditor is poderful tool to create ROI file, I will try it. Thanks, Jinsong susumu ??? v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);} Hi Jinsong, If I understand it correctly, ?marsbar? is a function in SPM? If so, 1) Hangyi, could you find out the format of the ROI of this software? Ken may know it. 2) Jinsong, we?ll look into the file format. Meanwhile, if you just need a program to create ROIs, our RoiEditor has a very strong functions and interfaces to create ROIs in DTI data. You may want to try it. Susumu --------------------------------- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of jinsong tang Sent: Wednesday, October 29, 2008 5:29 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] how to input ROI img into MRIstudio Hello, I have created a ROI file from marsbar, which was saved as image file. When I try to load this ROI file into MRIstudio. I found the message" unrecognized file". So I want to ask how to input image ROI file into MRIstudio? Thanks Jinsong --------------------------------- ???????????? _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users --------------------------------- ???????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081030/0851cff9/attachment-0001.html From junyiwang2002 at yahoo.com Thu Oct 30 10:18:58 2008 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Thu, 30 Oct 2008 07:18:58 -0700 (PDT) Subject: [Mristudio-users] Fw: Optic radiations Message-ID: <147981.69565.qm@web50509.mail.re2.yahoo.com> Hi Christian, I tried to reply but the email was not delivered?for some reasons. Jun Yi ----- Forwarded Message ---- From: Jun Yi Wang To: mristudio-users at mristudio.org Sent: Tuesday, October 28, 2008 1:30:03 PM Subject: Re: [Mristudio-users] Optic radiations Hi Christian, The other papers might have used the CUT operation.? You can use the CUT operation placing at the two ends of the?part of the fibers that you want to extract, e.g., one is placed near the LGN and?another is placed in the middle of the fiber pathway.? But the result may contain fibers from other fiber tracts, such as the corpus callosum.? The CUT operation cannot be combined with other operations, so it will be difficult to delete fibers from other tracts if I understand these operations right. Good luck, Jun Yi Wang ________________________________ From: Christian Bieck To: mristudio-users at mristudio.org Sent: Tuesday, October 28, 2008 12:49:00 PM Subject: [Mristudio-users] Optic radiations Hello, Since my last inquiry seemed to have escaped notice, I write you again in the hopes of finding a solution to my problem. As I wrote in my last email, I?m analyzing the FA values of the optic radiations and have, so far, extracted them by using anatomical landmarks and the DTIStudio functions AND, OR and NOT. The focus of my research concerns the posterior parts of the optic radiations ending in the primary visual cortex, but I find myself unable to extract them properly. Using the ROI-Operations in the Fiber Tab during Fiber Tracking oftentimes results in the removal of entire fiber tracts instead of just the anterior parts and any attempts to work with ROI Editor have not been successful so far. I have seen at least one paper in which the anterior/posterior parts and their FA values were examined via DTIStudio, so I know it?s possible, but I?m completely puzzled as how to actually do it. I would appreciate it *very* much if you could point me in the right direction. Thank you for your time. Cheers, Christian Bieck -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081030/f4def27f/attachment.html From jarnety at gmail.com Mon Oct 20 19:49:38 2008 From: jarnety at gmail.com (Jarnet Han) Date: Mon, 20 Oct 2008 16:49:38 -0700 Subject: [Mristudio-users] ACPC alignment Message-ID: <9f1c9c480810201649x323b0a00w32238867de45a0f2@mail.gmail.com> Hi everyone, I was just wondering about the easiest way to do ACPC alignment before loading up the files into DTI studio (or does DTI studio have a built-in way to do this?). Currently, we are using the protocol from Mori's paper which appears to be based on ACPC aligned brains. Thanks in advance. Best, JH -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081020/376bb8d1/attachment.html From sumita.rachapudi at duke.edu Tue Oct 21 14:05:47 2008 From: sumita.rachapudi at duke.edu (Sumita P Rachapudi) Date: Tue, 21 Oct 2008 14:05:47 -0400 Subject: [Mristudio-users] Q. AIR-generated gradient table In-Reply-To: Message-ID: Please remove me from your mailing list. "[Seongjin]" Sent by: mristudio-users-bounces at mristudio.org 10/21/2008 01:47 PM Please respond to "DTI Studio, ROI Editor, Landmarker Questions/Support" To "DTI Studio, ROI Editor, Landmarker Questions/Support" cc Subject [Mristudio-users] Q. AIR-generated gradient table Dear DTI studio users, After registration using AIR, a gradient table is generated. What is this gradient for? Is this table should be used for fiber tracking to see the effect of AIR? Thanks in advance. All the best, SC_______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081021/c4010555/attachment.html From jasper at jhu.edu Thu Oct 30 07:33:55 2008 From: jasper at jhu.edu (Jasper Chen) Date: Thu, 30 Oct 2008 07:33:55 -0400 Subject: [Mristudio-users] exporting ROI from ROIEditor Message-ID: Hi everyone, Does anyone have any experience with exporting ROI data from ROIEditor? I saved the ROI data as Analyze, but when I attempted to open the ROI data using another imaging program such as ImageJ, the image would not come up. Is there some way to extract this information from the ROI file? Thanks, Jasper From lucas_lessa at yahoo.com.br Thu Oct 30 11:22:05 2008 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Thu, 30 Oct 2008 08:22:05 -0700 (PDT) Subject: [Mristudio-users] MTR In-Reply-To: <719103.53147.qm@web15601.mail.cnb.yahoo.com> Message-ID: <471357.6975.qm@web110213.mail.gq1.yahoo.com> Hello everyone, I need to process magnetic transfer imaging and FA along the cortico-spinal tract. I'd like to do in DTI to make sure that both mesurements will be done in the same place, but I don't know if is possible to do MTI in DTI, is it? If no can anyone suggest me a (free) sofware that I can use with DTI to do so? Thank you. Lucas Lessa S?o Paulo/Brazil. Novos endere?os, o Yahoo! que voc? conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses From xli16 at jhmi.edu Thu Oct 30 12:09:31 2008 From: xli16 at jhmi.edu (XIN LI) Date: Thu, 30 Oct 2008 12:09:31 -0400 Subject: [Mristudio-users] exporting ROI from ROIEditor In-Reply-To: References: Message-ID: Jasper, I found a bug that causes this problem. Sorry for that. You may save your ROI data as ROIEditor format. You will get a WORD ROI image and a ROIEditor defined header file. You may load this WORD ROI image to other programs as a raw image file. If you have to load your ROI data as analyze images, you may try the beta version of ROIEditor. I have attached it to this email. Regards, Xin ----- Original Message ----- From: Jasper Chen Date: Thursday, October 30, 2008 10:56 am Subject: [Mristudio-users] exporting ROI from ROIEditor To: mristudio-users at mristudio.org > Hi everyone, > > Does anyone have any experience with exporting ROI data from > ROIEditor? I saved the ROI data as Analyze, but when I attempted to > open the ROI data using another imaging program such as ImageJ, the > image would not come up. Is there some way to extract this information > from the ROI file? > > Thanks, > > Jasper > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > -------------- next part -------------- A non-text attachment was scrubbed... Name: ROIEditor.zip Type: application/x-zip-compressed Size: 783327 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081030/bc0c6eaf/attachment-0001.bin From jabbim at mail.nih.gov Wed Oct 29 12:20:14 2008 From: jabbim at mail.nih.gov (Jabbi, Mbemba (NIH/NIMH) [F]) Date: Wed, 29 Oct 2008 12:20:14 -0400 Subject: [Mristudio-users] how to save a statistics and image file Message-ID: <694AFC9BAB001E49A6307A803D33749602069C8E@nihcesmlbx2.nih.gov> Dear all, I am new to DTI_studio and we are presently doing fiber tracking with preexisting binary ROIs. However, I am not able to figure out how to save the resulting statistics and images from my predetermined ROIs after fiber tracking in DTI_studio. Thanks a lot for your help in advance! Best, Mbemba ------------------------------------ Mbemba Jabbi Ph.D. Section on Integrative Neuroimaging Cognitive Brain Disorders Branch National Institutes of Mental Health 9000 Rockville Pike, B10, R4C108 Bethesda, MD 20892-1365 email: jabbim at mail.nih.gov phone: 301/594-4840; fax: 301/496-7437 ------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081029/b8841ad5/attachment.html From support at mristudio.org Thu Oct 30 13:40:39 2008 From: support at mristudio.org (support at mristudio.org) Date: Thu, 30 Oct 2008 13:40:39 -0400 (EDT) Subject: [Mristudio-users] how to save a statistics and image file In-Reply-To: <694AFC9BAB001E49A6307A803D33749602069C8E@nihcesmlbx2.nih.gov> References: <694AFC9BAB001E49A6307A803D33749602069C8E@nihcesmlbx2.nih.gov> Message-ID: <2112.162.129.28.138.1225388439.squirrel@webmail.mristudio.org> copy and paste (selecting -> right clicking -> copy ->...;) > Dear all, > > I am new to DTI_studio and we are presently doing fiber tracking with > preexisting binary ROIs. However, I am not able to figure out how to > save the resulting statistics and images from my predetermined ROIs > after fiber tracking in DTI_studio. Thanks a lot for your help in > advance! > > Best, > > Mbemba > > > > ------------------------------------ > > Mbemba Jabbi Ph.D. > > Section on Integrative Neuroimaging > > Cognitive Brain Disorders Branch > > National Institutes of Mental Health > > 9000 Rockville Pike, B10, R4C108 > > Bethesda, MD 20892-1365 > > email: jabbim at mail.nih.gov > > phone: 301/594-4840; fax: 301/496-7437 > > ------------------------------------ > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From susumu at mri.jhu.edu Tue Oct 28 14:19:38 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 28 Oct 2008 14:19:38 -0400 Subject: [Mristudio-users] Optic radiations In-Reply-To: <1Kush3-1J6KJs0@fwd08.aul.t-online.de> References: <1Kush3-1J6KJs0@fwd08.aul.t-online.de> Message-ID: <8745A419B99C479CB957A87097BCA951@SusumuThinkPad> Hi Christian The optic radiation is a difficult tract to reconstruct. Maybe you can get a good result in one subject but you may find a poor result in the other. That's why we didn't include it in our protocol paper in Neuroimage 30, 630, 2007. The reasons are following; 1) It has quite a sharp turn where it exits the LGN and merges into the sagittal stratum (a huge sheet-like bundle running sagittally, which includes the inferior fronto-occipital fasciculu, inferior longitudinal fasciculus, projections from the splenium of the corpus callosum, and posterior thalamic radiation). With 2-2.5 mm resolution, the turn is quite sharp. 2) The way it exits the thalamus is oblique with respect to the coronal, sagittal, and axial slices and it is difficult to get the cross-section within one plane in a very selective manner. 3) As also pointed in #1, it merges to the sagittal stratum and therefore it is difficult to extract it selectively. To solve the #2 issue, you may need to define the LGN or the posterior thalamus three-dimensionally as one of the ROIs. Sorry if this is not really a solution. It is one of the limitations of the DTI-based tractography. You are interested in connection between A - B and between A and B there is a non-specific large bundle (A - large bundle - B). In this kind of situation, depending on how the A and B branches come out from the large bundle, you may get only a portion of the fiber you want. The size of the reconstruction may also be influenced by status of unrelated fibers in the large bundle. In general, there are several approached you may take; 1) If there is an existing knowledge that the A-B connection is the majority of the large bundle, you may just have to measure the size of the large bundle using the ROI delineation or the tractography of the bundle itself (not using ROIs in A and B, because there is no guarantee that it actually increases the specificity in this situation). In your case, this means measurement of the sagittal stratum or the posterior thalamic radiation. 2) Identify regions where the tract is more pure before merging to the large bundle (e.g. A - large bundle or large bundle - B regions). For example, if you are interested in the corticospinal tract, the lower pons region is anatomically known to be more pure CST. For the optic radiation, it is where the OR comes out from the LGN or exits to the CF, although I'm not sure if you can see a nicely defined tract in such regions. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Christian Bieck Sent: Tuesday, October 28, 2008 1:49 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Optic radiations Hello, Since my last inquiry seemed to have escaped notice, I write you again in the hopes of finding a solution to my problem. As I wrote in my last email, I'm analyzing the FA values of the optic radiations and have, so far, extracted them by using anatomical landmarks and the DTIStudio functions AND, OR and NOT. The focus of my research concerns the posterior parts of the optic radiations ending in the primary visual cortex, but I find myself unable to extract them properly. Using the ROI-Operations in the Fiber Tab during Fiber Tracking oftentimes results in the removal of entire fiber tracts instead of just the anterior parts and any attempts to work with ROI Editor have not been successful so far. I have seen at least one paper in which the anterior/posterior parts and their FA values were examined via DTIStudio, so I know it's possible, but I'm completely puzzled as how to actually do it. I would appreciate it *very* much if you could point me in the right direction. Thank you for your time. Cheers, Christian Bieck -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081028/48fbaddf/attachment-0001.html From junyiwang2002 at yahoo.com Tue Oct 28 14:30:03 2008 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Tue, 28 Oct 2008 11:30:03 -0700 (PDT) Subject: [Mristudio-users] Optic radiations Message-ID: <822106.12103.qm@web50502.mail.re2.yahoo.com> Hi Christian, The other papers might have used the CUT operation.? You can use the CUT operation placing at the two ends of the?part of the fibers that you want to extract, e.g., one is placed near the LGN and?another is placed in the middle of the fiber pathway.? But the result may contain fibers from other fiber tracts, such as the corpus callosum.? The CUT operation cannot be combined with other operations, so it will be difficult to delete fibers from other tracts if I understand these operations right. Good luck, Jun Yi Wang ________________________________ From: Christian Bieck To: mristudio-users at mristudio.org Sent: Tuesday, October 28, 2008 12:49:00 PM Subject: [Mristudio-users] Optic radiations Hello, Since my last inquiry seemed to have escaped notice, I write you again in the hopes of finding a solution to my problem. As I wrote in my last email, I?m analyzing the FA values of the optic radiations and have, so far, extracted them by using anatomical landmarks and the DTIStudio functions AND, OR and NOT. The focus of my research concerns the posterior parts of the optic radiations ending in the primary visual cortex, but I find myself unable to extract them properly. Using the ROI-Operations in the Fiber Tab during Fiber Tracking oftentimes results in the removal of entire fiber tracts instead of just the anterior parts and any attempts to work with ROI Editor have not been successful so far. I have seen at least one paper in which the anterior/posterior parts and their FA values were examined via DTIStudio, so I know it?s possible, but I?m completely puzzled as how to actually do it. I would appreciate it *very* much if you could point me in the right direction. Thank you for your time. Cheers, Christian Bieck -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081028/92f2a5ed/attachment.html From Srinivasan at kennedykrieger.org Wed Oct 29 17:09:39 2008 From: Srinivasan at kennedykrieger.org (Priti Srinivasan) Date: Wed, 29 Oct 2008 17:09:39 -0400 Subject: [Mristudio-users] how to input ROI img into MRIstudio Message-ID: <490898E0.E224.0081.0@kennedykrieger.org> Hi Jinsong, I've been trying to do the same thing. Actually I wrote the activation cluster from the fMRI model to an image file. There is an option to export the activated cluster (ROIs) in ANALYZE format. Once it is in this format it can be read by ROIeditor/DTIstudio. Susumu: I am able to import these ROIs from an fMRI activation map onto DTIstudio...but..I am having problems understanding if the orientations are correct. As per SPM (which follows neurological format) we had an activated cluster only in the left side of the brain. I saved this cluster out in ANALYZE format to be read out by DTIstudio. (My understanding is that DTIstudio follows radiological convention by default and hence it automatically does the R/L flip for display but does not make any changes to the header file.) Since my cluster is on the left and the format is in ANALYZE....I expected DTIstudio to make a flip and give me the cluster on the right side of the brain (which is the left side in neurological convention)...but it still pops up on the left. Hence I am not sure if there is a problem while saving out the files as ANALYZE in SPM or while reading it in DTIstudio. It would be great if you could help me solve this issue. Many thanks, Priti Please consider the environment when printing this E-Mail. 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/20081029/a0b7f590/attachment.html From Sumei.Wang at uphs.upenn.edu Tue Oct 28 16:40:32 2008 From: Sumei.Wang at uphs.upenn.edu (Wang, Sumei) Date: Tue, 28 Oct 2008 16:40:32 -0400 Subject: [Mristudio-users] Normalization Message-ID: <4BFD060857263F43AEA4C10586DDE44603C803C0@uphsmbx8.UPHS.PENNHEALTH.PRV> Hi Dear all, I am trying to do tract-specific analyses in brain tumor patients. First I generated the fibers, then I normalized the FA, ADC maps as well as the fibers to the template usind landmarker. I applied linear normalization. I found the internal structure such as white matter was not well aligned. Should I do non-linear registration? How to do it? Can anybody help? Thank you very much. Sumei 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 Ihssan.Abdulkareem at liverpool.ac.uk Fri Oct 31 07:06:06 2008 From: Ihssan.Abdulkareem at liverpool.ac.uk (Abdul-Kareem, Ihssan) Date: Fri, 31 Oct 2008 11:06:06 +0000 Subject: [Mristudio-users] (no subject) Message-ID: <058E257E30A22D4698E8593ED7498ED6A21646@EVSSTAFF1.livad.liv.ac.uk> Dear all I constructed the corticospinal tract using multiple regions of interests, I want to register the fiber image with the structural image, does anybody know how to save the fiber image and then coregister it with the structural one regards -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081031/8e1fca08/attachment.html From Ihssan.Abdulkareem at liverpool.ac.uk Fri Oct 31 07:07:01 2008 From: Ihssan.Abdulkareem at liverpool.ac.uk (Abdul-Kareem, Ihssan) Date: Fri, 31 Oct 2008 11:07:01 +0000 Subject: [Mristudio-users] AIR Message-ID: <058E257E30A22D4698E8593ED7498ED6A21647@EVSSTAFF1.livad.liv.ac.uk> Hi all anybody knows how to do Automatic image registration in DTI studio. I dont have this tab in my 2.02 version regards -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081031/49ce40d9/attachment.html From lucas_lessa at yahoo.com.br Fri Oct 31 12:11:21 2008 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Fri, 31 Oct 2008 09:11:21 -0700 (PDT) Subject: [Mristudio-users] MTR Message-ID: <575746.41433.qm@web110201.mail.gq1.yahoo.com> Hello everyone, I need to process magnetic transfer imaging and FA along the cortico-spinal tract. I'd like to do in DTI to make sure that both mesurements will be done in the same place, but I don't know if is possible to do MTI in DTI, is it? If no can anyone suggest me a (free) sofware that I can use with DTI to do so? Thank you. Lucas Lessa S?o Paulo/Brazil. Novos endere?os, o Yahoo! que voc? conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses From aimanba1 at jhu.edu Fri Oct 31 12:23:41 2008 From: aimanba1 at jhu.edu (Anuar Imanbayev) Date: Fri, 31 Oct 2008 12:23:41 -0400 Subject: [Mristudio-users] AIR In-Reply-To: <058E257E30A22D4698E8593ED7498ED6A21647@EVSSTAFF1.livad.liv.ac.uk> References: <058E257E30A22D4698E8593ED7498ED6A21647@EVSSTAFF1.livad.liv.ac.uk> Message-ID: Hi Ihssan, There is a 32 Aug 2008 version available that does have Automatic Image Registration enabled. I'm sure Susumu and Kazi can set you up with this newest version! If Susumu ok's this and it's not illegal or anything, I can send you the program via e-mail. Is DTI Studio freeware or for-profit? I got it for free thru my laboratory, but then I don't know anything about its rules on sharing with others. Personally, I don't see a problem as long as work gets credited, academically and financially. Best, Anuar ----- Original Message ----- From: "Abdul-Kareem, Ihssan" Date: Friday, October 31, 2008 7:18 am Subject: [Mristudio-users] AIR To: mristudio-users at mristudio.org > Hi all > anybody knows how to do Automatic image registration in DTI studio. I > dont have > this tab in my 2.02 version > regards > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From support at mristudio.org Fri Oct 31 12:27:37 2008 From: support at mristudio.org (support at mristudio.org) Date: Fri, 31 Oct 2008 12:27:37 -0400 (EDT) Subject: [Mristudio-users] AIR In-Reply-To: <058E257E30A22D4698E8593ED7498ED6A21647@EVSSTAFF1.livad.liv.ac.uk> References: <058E257E30A22D4698E8593ED7498ED6A21647@EVSSTAFF1.livad.liv.ac.uk> Message-ID: <3637.162.129.28.138.1225470457.squirrel@webmail.mristudio.org> the latest version is downloadable in https://www.mristudio.org the image registration command is located in the lower part of the "image" tab, a button labeled as "Automatic Image Registration" regards, > Hi all > anybody knows how to do Automatic image registration in DTI studio. I dont have > this tab in my 2.02 version > regards > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From susumu at mri.jhu.edu Fri Oct 31 15:12:32 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 31 Oct 2008 15:12:32 -0400 Subject: [Mristudio-users] AIR In-Reply-To: References: <058E257E30A22D4698E8593ED7498ED6A21647@EVSSTAFF1.livad.liv.ac.uk> Message-ID: <057E0921181644B0B66C73E2CDB566E1@SusumuThinkPad> DtiStudio can be freely copied and distributed. Registration is recommended (not required) just for important notice such as bug reports and tutorial. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Anuar Imanbayev Sent: Friday, October 31, 2008 12:24 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] AIR Hi Ihssan, There is a 32 Aug 2008 version available that does have Automatic Image Registration enabled. I'm sure Susumu and Kazi can set you up with this newest version! If Susumu ok's this and it's not illegal or anything, I can send you the program via e-mail. Is DTI Studio freeware or for-profit? I got it for free thru my laboratory, but then I don't know anything about its rules on sharing with others. Personally, I don't see a problem as long as work gets credited, academically and financially. Best, Anuar ----- Original Message ----- From: "Abdul-Kareem, Ihssan" Date: Friday, October 31, 2008 7:18 am Subject: [Mristudio-users] AIR To: mristudio-users at mristudio.org > Hi all > anybody knows how to do Automatic image registration in DTI studio. I > dont have > this tab in my 2.02 version > regards > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From SCopeland at mednet.ucla.edu Fri Oct 31 15:34:58 2008 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Fri, 31 Oct 2008 12:34:58 -0700 Subject: [Mristudio-users] More AIR Message-ID: Hello all ? I would like to be able to register my anatomic scan to the mean b0 of my DTIs so that I can draw ROIs on the anatomic scan. However, when I push the ?AIR? button, it allows me to enter mean of b0s as the one to register to, but it does not recognize the analyze format or raw format anatomic images in the same folder. The only files that show up in the list are the raw data files, or the files created when doing the tensor calculations (FA, etc). I am working in DTI studio (not landmarker or ROI editor). I don?t want to normalize, just coregister anatomic and DTI scans from the same subject. Is there a way to do this? Thanks very much, Sarah Copeland 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 SCopeland at mednet.ucla.edu Fri Oct 31 15:35:05 2008 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Fri, 31 Oct 2008 12:35:05 -0700 Subject: [Mristudio-users] More AIR Message-ID: Hello all ? I would like to be able to register my anatomic scan to the mean b0 of my DTIs so that I can draw ROIs on the anatomic scan. However, when I push the ?AIR? button, it allows me to enter mean of b0s as the one to register to, but it does not recognize the analyze format or raw format anatomic images in the same folder. The only files that show up in the list are the raw data files, or the files created when doing the tensor calculations (FA, etc). I am working in DTI studio (not landmarker or ROI editor). I don?t want to normalize, just coregister anatomic and DTI scans from the same subject. Is there a way to do this? Thanks very much, Sarah Copeland 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 SCopeland at mednet.ucla.edu Fri Oct 31 15:35:14 2008 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Fri, 31 Oct 2008 12:35:14 -0700 Subject: [Mristudio-users] More AIR Message-ID: Hello all ? I would like to be able to register my anatomic scan to the mean b0 of my DTIs so that I can draw ROIs on the anatomic scan. However, when I push the ?AIR? button, it allows me to enter mean of b0s as the one to register to, but it does not recognize the analyze format or raw format anatomic images in the same folder. The only files that show up in the list are the raw data files, or the files created when doing the tensor calculations (FA, etc). I am working in DTI studio (not landmarker or ROI editor). I don?t want to normalize, just coregister anatomic and DTI scans from the same subject. Is there a way to do this? Thanks very much, Sarah Copeland 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 junyiwang2002 at yahoo.com Fri Oct 31 16:08:36 2008 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Fri, 31 Oct 2008 13:08:36 -0700 (PDT) Subject: [Mristudio-users] More AIR References: Message-ID: <55617.56182.qm@web50501.mail.re2.yahoo.com> Hi Sarah, The AIR in DTI studio is used for coregistering different volumes in the same DTI scan.? These volumes have the same image resolutions.? You need to use SPM or FSL for coregister images with different image resolutions and FOVs. Jun Yi Wang ________________________________ From: "Copeland, Sarah A." To: "mristudio-users at mristudio.org" Sent: Friday, October 31, 2008 2:34:58 PM Subject: [Mristudio-users] More AIR Hello all ? I would like to be able to register my anatomic scan to the mean b0 of my DTIs so? that I can draw ROIs on the anatomic scan. However, when I push the ?AIR? button, it allows me to enter mean of b0s as the one to register to, but it does not recognize the analyze format or raw format anatomic images in the same folder. The only files that show up in the list are the raw data files, or the files created when doing the tensor calculations (FA, etc). I am working in DTI studio (not landmarker or ROI editor). I don?t want to normalize, just coregister anatomic and DTI scans from the same subject. Is there a way to do this? Thanks very much, Sarah Copeland 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. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081031/182d2b62/attachment.html From Ihssan.Abdulkareem at liverpool.ac.uk Fri Oct 31 17:59:08 2008 From: Ihssan.Abdulkareem at liverpool.ac.uk (Abdul-Kareem, Ihssan) Date: Fri, 31 Oct 2008 21:59:08 +0000 Subject: [Mristudio-users] =?windows-1256?b?0c86ICBBSVI=?= References: <058E257E30A22D4698E8593ED7498ED6A21647@EVSSTAFF1.livad.liv.ac.uk> <3637.162.129.28.138.1225470457.squirrel@webmail.mristudio.org> Message-ID: <058E257E30A22D4698E8593ED7498ED6A21648@EVSSTAFF1.livad.liv.ac.uk> Hi Many thanks for your kind help Regards ________________________________ ??: mristudio-users-bounces at mristudio.org ???????? ?? support at mristudio.org ????? ???????: ?????? 31/10/2008 04:27 ? ???: DTI Studio, ROI Editor,Landmarker Questions/Support ???????: Re: [Mristudio-users] AIR the latest version is downloadable in https://www.mristudio.org the image registration command is located in the lower part of the "image" tab, a button labeled as "Automatic Image Registration" regards, > Hi all > anybody knows how to do Automatic image registration in DTI studio. I dont have > this tab in my 2.02 version > regards > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081031/f6833101/attachment-0001.html From SCopeland at mednet.ucla.edu Sat Nov 1 16:27:58 2008 From: SCopeland at mednet.ucla.edu (Copeland, Sarah A.) Date: Sat, 01 Nov 2008 13:27:58 -0700 Subject: [Mristudio-users] More AIR In-Reply-To: <55617.56182.qm@web50501.mail.re2.yahoo.com> References: <55617.56182.qm@web50501.mail.re2.yahoo.com> Message-ID: Hi - Thanks for the quick response! I saw this posting from Susumu on 5/16/08: You can use functions available in Landmarker to do this type of resampling. Also, make sure that the center and angles of the images are the same. Otherwise, even if the matrix dimensions are all adjusted, brain locations are not the same. You can read the center and orientation information from DICOM files and type in these numbers to Landmarker "translation" and "rotation" operation. Otherwise, you can use "AIR" to do rigid alignment between MPRAGE and DTI (you can use b0 or DWI). AIR can adjust matrix dimensions and brain locations all at once. So, this could be an easier way. Which made it sound as though this kind of registration is possible. Is this no longer true? Or is this still a possibility? Thanks again - Sarah Copeland ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang [junyiwang2002 at yahoo.com] Sent: Friday, October 31, 2008 1:08 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] More AIR Hi Sarah, The AIR in DTI studio is used for coregistering different volumes in the same DTI scan. These volumes have the same image resolutions. You need to use SPM or FSL for coregister images with different image resolutions and FOVs. Jun Yi Wang ________________________________ From: "Copeland, Sarah A." To: "mristudio-users at mristudio.org" Sent: Friday, October 31, 2008 2:34:58 PM Subject: [Mristudio-users] More AIR Hello all ? I would like to be able to register my anatomic scan to the mean b0 of my DTIs so that I can draw ROIs on the anatomic scan. However, when I push the ?AIR? button, it allows me to enter mean of b0s as the one to register to, but it does not recognize the analyze format or raw format anatomic images in the same folder. The only files that show up in the list are the raw data files, or the files created when doing the tensor calculations (FA, etc). I am working in DTI studio (not landmarker or ROI editor). I don?t want to normalize, just coregister anatomic and DTI scans from the same subject. Is there a way to do this? Thanks very much, Sarah Copeland 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. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users 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 dearfreud at gmail.com Sun Nov 2 11:24:46 2008 From: dearfreud at gmail.com (Takahiko Kawashima) Date: Mon, 03 Nov 2008 01:24:46 +0900 Subject: [Mristudio-users] Alternative way Message-ID: Dear users, Hi, I'm trying to calculate FA of tracts not running along only one axis, such as uncinate fasciculus (UF). At first I planned to combine CUT with other operations to calculate FA only between the CUT ROIs (in the case of UF, one one coronal and one on axial slice). But recently I've found it was a fundamental misunderstanding. (by reading Dr If possible, I'd like to get a mean FA of summed "each fiber" FA in depicted fibers within a defined region. Could anybody tell me some alternative ways to do this, please? Or, if I want to calculate FA within a defined region, can't I do anything but to consider a mean FA of "all the voxels" on which the fibers run? Because I am totally a beginner and poor in English, this question might look quite embarrassing and illegible. I hope your kind answer, and I'll really appreciate it. Best Regards, Takahiko Kawashima @ Kyoto university -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081103/ad43afea/attachment.html From support at mristudio.org Sun Nov 2 13:51:21 2008 From: support at mristudio.org (support at mristudio.org) Date: Sun, 2 Nov 2008 13:51:21 -0500 (EST) Subject: [Mristudio-users] More AIR In-Reply-To: References: <55617.56182.qm@web50501.mail.re2.yahoo.com> Message-ID: <2476.71.166.94.202.1225651881.squirrel@webmail.mristudio.org> hi,Sarah, the AIR in DTI Studio have no problem to do registration on images with diffferent dimensions, orientations and/or pixel size; just try it. regards, > Hi - > > Thanks for the quick response! I saw this posting from Susumu on 5/16/08: > > You can use functions available in Landmarker to do this type of resampling. > Also, make sure that the center and angles of the images are the same. > Otherwise, even if the matrix dimensions are all adjusted, brain locations > are not the same. You can read the center and orientation information from > DICOM files and type in these numbers to Landmarker "translation" and > "rotation" operation. Otherwise, you can use "AIR" to do rigid alignment > between MPRAGE and DTI (you can use b0 or DWI). AIR can adjust matrix > dimensions and brain locations all at once. So, this could be an easier way. > > Which made it sound as though this kind of registration is possible. Is this no > longer true? Or is this still a possibility? > > Thanks again - > > Sarah Copeland > ________________________________________ > From: mristudio-users-bounces at mristudio.org > [mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang > [junyiwang2002 at yahoo.com] > Sent: Friday, October 31, 2008 1:08 PM > To: DTI Studio, ROI Editor, Landmarker Questions/Support > Subject: Re: [Mristudio-users] More AIR > > Hi Sarah, > > The AIR in DTI studio is used for coregistering different volumes in the same > DTI scan. These volumes have the same image resolutions. You need to use SPM > or FSL for coregister images with different image resolutions and FOVs. > > Jun Yi Wang > > ________________________________ > From: "Copeland, Sarah A." > To: "mristudio-users at mristudio.org" > Sent: Friday, October 31, 2008 2:34:58 PM > Subject: [Mristudio-users] More AIR > > Hello all ? > > I would like to be able to register my anatomic scan to the mean b0 of my DTIs > so that I can draw ROIs on the anatomic scan. However, when I push the ?AIR? > button, it allows me to enter mean of b0s as the one to register to, but it does > not recognize the analyze format or raw format anatomic images in the same > folder. The only files that show up in the list are the raw data files, or the > files created when doing the tensor calculations (FA, etc). I am working in DTI > studio (not landmarker or ROI editor). I don?t want to normalize, just > coregister anatomic and DTI scans from the same subject. Is there a way to do > this? > > Thanks very much, > > Sarah Copeland > > 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. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > 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. > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From susumu at mri.jhu.edu Sun Nov 2 15:42:50 2008 From: susumu at mri.jhu.edu (susumu) Date: Sun, 02 Nov 2008 15:42:50 -0500 Subject: [Mristudio-users] More AIR In-Reply-To: References: <55617.56182.qm@web50501.mail.re2.yahoo.com> Message-ID: Hi Sarah, You can register DTI images and anatomical images using Landmarker->AIR function. In Landmarker, the first image you open is always the template and the second image you open will be registered to the first one. Landmarker can read Analyze or Raw. When you are using raw, please choose "all files" in the "files of types". You should be able to see all files including raw and analyze in this way. Once you find the file you want to open, then click open. You'll get a dialog box, in which you can specify the format (raw or analyze). If you choose raw, you have to input file size and other parameters. These fields are inactivated when you choose analyze because they are retrieved from the analyze header file. Please let us know if you still can't open the files. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Copeland, Sarah A. Sent: Saturday, November 01, 2008 4:28 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] More AIR Hi - Thanks for the quick response! I saw this posting from Susumu on 5/16/08: You can use functions available in Landmarker to do this type of resampling. Also, make sure that the center and angles of the images are the same. Otherwise, even if the matrix dimensions are all adjusted, brain locations are not the same. You can read the center and orientation information from DICOM files and type in these numbers to Landmarker "translation" and "rotation" operation. Otherwise, you can use "AIR" to do rigid alignment between MPRAGE and DTI (you can use b0 or DWI). AIR can adjust matrix dimensions and brain locations all at once. So, this could be an easier way. Which made it sound as though this kind of registration is possible. Is this no longer true? Or is this still a possibility? Thanks again - Sarah Copeland ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang [junyiwang2002 at yahoo.com] Sent: Friday, October 31, 2008 1:08 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] More AIR Hi Sarah, The AIR in DTI studio is used for coregistering different volumes in the same DTI scan. These volumes have the same image resolutions. You need to use SPM or FSL for coregister images with different image resolutions and FOVs. Jun Yi Wang ________________________________ From: "Copeland, Sarah A." To: "mristudio-users at mristudio.org" Sent: Friday, October 31, 2008 2:34:58 PM Subject: [Mristudio-users] More AIR Hello all - I would like to be able to register my anatomic scan to the mean b0 of my DTIs so that I can draw ROIs on the anatomic scan. However, when I push the "AIR" button, it allows me to enter mean of b0s as the one to register to, but it does not recognize the analyze format or raw format anatomic images in the same folder. The only files that show up in the list are the raw data files, or the files created when doing the tensor calculations (FA, etc). I am working in DTI studio (not landmarker or ROI editor). I don't want to normalize, just coregister anatomic and DTI scans from the same subject. Is there a way to do this? Thanks very much, Sarah Copeland 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. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users 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. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Sun Nov 2 15:58:04 2008 From: susumu at mri.jhu.edu (susumu) Date: Sun, 02 Nov 2008 15:58:04 -0500 Subject: [Mristudio-users] Alternative way In-Reply-To: References: Message-ID: <257AA7577B524E6AA0BCFA2D2472221C@SusumuThinkPad> Dear Takahiro, There are two options, as you already know. One is to report the average FA of the entire reconstructed fiber. After reconstruction, you get only one FA number. If you use CUT, that is the averaged FA of all pixels in between the two ROIs. The second option is to report FA of pixels at each axial, sagittal, or coronal slice. This is a good method for something like the corticospinal tract, which is rather linear. Unfortunately, for something like the UF and corpus callosum, with U-shape trajectory, this approach is not optimum. At this point, there is not a good solution for that. There may be some time consuming way to separate the U-shape trajectory to two I-shape trajectories. For example, you can save the tracking results as a 1/0 binary image and read it by RoiEditor. Using the threshold tool, you can re-define the pixels within the UF in RoiEditor. With a bit of trick like manually introduce a gap within the trajectory, you can separate the one U-shape trajectory to two regions like upper UF and lower UF. Then RoiEditor can report FA values along coronal planes. Well, maybe this is too complicated. Alternatively, you can use Landmarker to normalize the binarized UF images and create a pixel-by-pixel population-averaged map, although, you introduce a new nuisance factor (= registration quality). Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Takahiko Kawashima Sent: Sunday, November 02, 2008 11:25 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Alternative way Dear users, Hi, I'm trying to calculate FA of tracts not running along only one axis, such as uncinate fasciculus (UF). At first I planned to combine CUT with other operations to calculate FA only between the CUT ROIs (in the case of UF, one one coronal and one on axial slice). But recently I've found it was a fundamental misunderstanding. (by reading Dr If possible, I'd like to get a mean FA of summed "each fiber" FA in depicted fibers within a defined region. Could anybody tell me some alternative ways to do this, please? Or, if I want to calculate FA within a defined region, can't I do anything but to consider a mean FA of "all the voxels" on which the fibers run? Because I am totally a beginner and poor in English, this question might look quite embarrassing and illegible. I hope your kind answer, and I'll really appreciate it. Best Regards, Takahiko Kawashima @ Kyoto university -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081102/744b2e73/attachment-0001.html From dearfreud at gmail.com Mon Nov 3 07:09:17 2008 From: dearfreud at gmail.com (Kawashima Takahiko) Date: Mon, 03 Nov 2008 21:09:17 +0900 Subject: [Mristudio-users] Alternative way In-Reply-To: <257AA7577B524E6AA0BCFA2D2472221C@SusumuThinkPad> References: <257AA7577B524E6AA0BCFA2D2472221C@SusumuThinkPad> Message-ID: <0C63101D-60D9-465B-9D6C-18BB03B83D04@gmail.com> Dear Dr Mori, Thank you very much for your kind, detailed explanation. I'd like to go through each method you've shown and choose one. Sincerely, Takahiko Kawashima > Dear Takahiro, > > > > There are two options, as you already know. One is to report the > average FA of the entire reconstructed fiber. After reconstruction, > you get only one FA number. If you use CUT, that is the averaged FA > of all pixels in between the two ROIs. > > > > The second option is to report FA of pixels at each axial, > sagittal, or coronal slice. This is a good method for something > like the corticospinal tract, which is rather linear. > Unfortunately, for something like the UF and corpus callosum, with > U-shape trajectory, this approach is not optimum. > > > > At this point, there is not a good solution for that. There may be > some time consuming way to separate the U-shape trajectory to two I- > shape trajectories. For example, you can save the tracking results > as a 1/0 binary image and read it by RoiEditor. Using the threshold > tool, you can re-define the pixels within the UF in RoiEditor. With > a bit of trick like manually introduce a gap within the trajectory, > you can separate the one U-shape trajectory to two regions like > upper UF and lower UF. Then RoiEditor can report FA values along > coronal planes. > > > > Well, maybe this is too complicated. Alternatively, you can use > Landmarker to normalize the binarized UF images and create a pixel- > by-pixel population-averaged map, although, you introduce a new > nuisance factor (= registration quality). > > > > Susumu > > > > From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users- > bounces at mristudio.org] On Behalf Of Takahiko Kawashima > Sent: Sunday, November 02, 2008 11:25 AM > To: mristudio-users at mristudio.org > Subject: [Mristudio-users] Alternative way > > > > Dear users, > > > > Hi, > > > > I'm trying to calculate FA of tracts not running along only one > axis, such as uncinate fasciculus (UF). > > > > At first I planned to combine CUT with other operations to > calculate FA only between the CUT ROIs (in the case of UF, one one > coronal and one on axial slice). > > But recently I've found it was a fundamental misunderstanding. (by > reading Dr > > > > If possible, I'd like to get a mean FA of summed "each fiber" FA in > depicted fibers within a defined region. > > Could anybody tell me some alternative ways to do this, please? > > Or, if I want to calculate FA within a defined region, can't I do > anything but to consider a mean FA of "all the voxels" on which the > fibers run? > > > > Because I am totally a beginner and poor in English, this question > might look quite embarrassing and illegible. > > I hope your kind answer, and I'll really appreciate it. > > > > > > Best Regards, > > > > Takahiko Kawashima @ Kyoto university > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users From loumuscarella at hotmail.com Mon Nov 3 16:29:05 2008 From: loumuscarella at hotmail.com (Lou muscarella) Date: Mon, 03 Nov 2008 16:29:05 -0500 Subject: [Mristudio-users] Alternative way In-Reply-To: <0C63101D-60D9-465B-9D6C-18BB03B83D04@gmail.com> References: <257AA7577B524E6AA0BCFA2D2472221C@SusumuThinkPad> <0C63101D-60D9-465B-9D6C-18BB03B83D04@gmail.com> Message-ID: How do I get off this list serve? Please take me off> Date: Mon, 3 Nov 2008 21:09:17 +0900> From: dearfreud at gmail.com> To: mristudio-users at mristudio.org> Subject: Re: [Mristudio-users] Alternative way> > Dear Dr Mori,> > > Thank you very much for your kind, detailed explanation.> > I'd like to go through each method you've shown and choose one.> > > Sincerely,> > Takahiko Kawashima> > Dear Takahiro,> >> >> >> > There are two options, as you already know. One is to report the > > average FA of the entire reconstructed fiber. After reconstruction, > > you get only one FA number. If you use CUT, that is the averaged FA > > of all pixels in between the two ROIs.> >> >> >> > The second option is to report FA of pixels at each axial, > > sagittal, or coronal slice. This is a good method for something > > like the corticospinal tract, which is rather linear. > > Unfortunately, for something like the UF and corpus callosum, with > > U-shape trajectory, this approach is not optimum.> >> >> >> > At this point, there is not a good solution for that. There may be > > some time consuming way to separate the U-shape trajectory to two I- > > shape trajectories. For example, you can save the tracking results > > as a 1/0 binary image and read it by RoiEditor. Using the threshold > > tool, you can re-define the pixels within the UF in RoiEditor. With > > a bit of trick like manually introduce a gap within the trajectory, > > you can separate the one U-shape trajectory to two regions like > > upper UF and lower UF. Then RoiEditor can report FA values along > > coronal planes.> >> >> >> > Well, maybe this is too complicated. Alternatively, you can use > > Landmarker to normalize the binarized UF images and create a pixel- > > by-pixel population-averaged map, although, you introduce a new > > nuisance factor (= registration quality).> >> >> >> > Susumu> >> >> >> > From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users- > > bounces at mristudio.org] On Behalf Of Takahiko Kawashima> > Sent: Sunday, November 02, 2008 11:25 AM> > To: mristudio-users at mristudio.org> > Subject: [Mristudio-users] Alternative way> >> >> >> > Dear users,> >> >> >> > Hi,> >> >> >> > I'm trying to calculate FA of tracts not running along only one > > axis, such as uncinate fasciculus (UF).> >> >> >> > At first I planned to combine CUT with other operations to > > calculate FA only between the CUT ROIs (in the case of UF, one one > > coronal and one on axial slice).> >> > But recently I've found it was a fundamental misunderstanding. (by > > reading Dr> >> >> >> > If possible, I'd like to get a mean FA of summed "each fiber" FA in > > depicted fibers within a defined region.> >> > Could anybody tell me some alternative ways to do this, please?> >> > Or, if I want to calculate FA within a defined region, can't I do > > anything but to consider a mean FA of "all the voxels" on which the > > fibers run?> >> >> >> > Because I am totally a beginner and poor in English, this question > > might look quite embarrassing and illegible.> >> > I hope your kind answer, and I'll really appreciate it.> >> >> >> >> >> > Best Regards,> >> >> >> > Takahiko Kawashima @ Kyoto university> >> > _______________________________________________> > Mristudio-users mailing list> > Mristudio-users at mristudio.org> > http://lists.mristudio.org/mailman/listinfo/mristudio-users> _______________________________________________> Mristudio-users mailing list> Mristudio-users at mristudio.org> http://lists.mristudio.org/mailman/listinfo/mristudio-users _________________________________________________________________ When your life is on the go?take your life with you. http://clk.atdmt.com/MRT/go/115298558/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081103/387de37d/attachment.html From susumu at mri.jhu.edu Mon Nov 3 16:37:28 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 03 Nov 2008 16:37:28 -0500 Subject: [Mristudio-users] Alternative way In-Reply-To: References: <257AA7577B524E6AA0BCFA2D2472221C@SusumuThinkPad> <0C63101D-60D9-465B-9D6C-18BB03B83D04@gmail.com> Message-ID: Hi all, If you want to unsubscribe the email list, please go to http://lists.mristudio.org/mailman/listinfo/mristudio-users and change the option of your account. If you can't figure out how to do it, please send us an email. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Lou muscarella Sent: Monday, November 03, 2008 4:29 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Alternative way How do I get off this list serve? Please take me off > Date: Mon, 3 Nov 2008 21:09:17 +0900 > From: dearfreud at gmail.com > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] Alternative way > > Dear Dr Mori, > > > Thank you very much for your kind, detailed explanation. > > I'd like to go through each method you've shown and choose one. > > > Sincerely, > > Takahiko Kawashima > > Dear Takahiro, > > > > > > > > There are two options, as you already know. One is to report the > > average FA of the entire reconstructed fiber. After reconstruction, > > you get only one FA number. If you use CUT, that is the averaged FA > > of all pixels in between the two ROIs. > > > > > > > > The second option is to report FA of pixels at each axial, > > sagittal, or coronal slice. This is a good method for something > > like the corticospinal tract, which is rather linear. > > Unfortunately, for something like the UF and corpus callosum, with > > U-shape trajectory, this approach is not optimum. > > > > > > > > At this point, there is not a good solution for that. There may be > > some time consuming way to separate the U-shape trajectory to two I- > > shape trajectories. For example, you can save the tracking results > > as a 1/0 binary image and read it by RoiEditor. Using the threshold > > tool, you can re-define the pixels within the UF in RoiEditor. With > > a bit of trick like manually introduce a gap within the trajectory, > > you can separate the one U-shape trajectory to two regions like > > upper UF and lower UF. Then RoiEditor can report FA values along > > coronal planes. > > > > > > > > Well, maybe this is too complicated. Alternatively, you can use > > Landmarker to normalize the binarized UF images and create a pixel- > > by-pixel population-averaged map, although, you introduce a new > > nuisance factor (= registration quality). > > > > > > > > Susumu > > > > > > > > From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users- > > bounces at mristudio.org] On Behalf Of Takahiko Kawashima > > Sent: Sunday, November 02, 2008 11:25 AM > > To: mristudio-users at mristudio.org > > Subject: [Mristudio-users] Alternative way > > > > > > > > Dear users, > > > > > > > > Hi, > > > > > > > > I'm trying to calculate FA of tracts not running along only one > > axis, such as uncinate fasciculus (UF). > > > > > > > > At first I planned to combine CUT with other operations to > > calculate FA only between the CUT ROIs (in the case of UF, one one > > coronal and one on axial slice). > > > > But recently I've found it was a fundamental misunderstanding. (by > > reading Dr > > > > > > > > If possible, I'd like to get a mean FA of summed "each fiber" FA in > > depicted fibers within a defined region. > > > > Could anybody tell me some alternative ways to do this, please? > > > > Or, if I want to calculate FA within a defined region, can't I do > > anything but to consider a mean FA of "all the voxels" on which the > > fibers run? > > > > > > > > Because I am totally a beginner and poor in English, this question > > might look quite embarrassing and illegible. > > > > I hope your kind answer, and I'll really appreciate it. > > > > > > > > > > > > Best Regards, > > > > > > > > Takahiko Kawashima @ Kyoto university > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/mristudio-users > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users _____ When your life is on the go-take your life with you. Try Windows MobileR today -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081103/3eaef5de/attachment-0001.html From Sumei.Wang at uphs.upenn.edu Tue Nov 4 20:21:22 2008 From: Sumei.Wang at uphs.upenn.edu (Wang, Sumei) Date: Tue, 04 Nov 2008 20:21:22 -0500 Subject: [Mristudio-users] More AIR In-Reply-To: Message-ID: <4BFD060857263F43AEA4C10586DDE44603C803DC@uphsmbx8.UPHS.PENNHEALTH.PRV> Hi Dear all, I have some questions about the normalization of fiber tracts. First I generated the fibers using DTIstudio. Then I normalized b0, FA and ADC maps to the template using Landmarker. I saved the transformation matrix and applied it to the generated fibers. However the normalized fibers I got is very thin. It is quite different from the original one. Is this correct? Can anybody help? Thanks Sumei -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org]On Behalf Of Copeland, Sarah A. Sent: Saturday, November 01, 2008 4:28 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] More AIR Hi - Thanks for the quick response! I saw this posting from Susumu on 5/16/08: You can use functions available in Landmarker to do this type of resampling. Also, make sure that the center and angles of the images are the same. Otherwise, even if the matrix dimensions are all adjusted, brain locations are not the same. You can read the center and orientation information from DICOM files and type in these numbers to Landmarker "translation" and "rotation" operation. Otherwise, you can use "AIR" to do rigid alignment between MPRAGE and DTI (you can use b0 or DWI). AIR can adjust matrix dimensions and brain locations all at once. So, this could be an easier way. Which made it sound as though this kind of registration is possible. Is this no longer true? Or is this still a possibility? Thanks again - Sarah Copeland ________________________________________ From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang [junyiwang2002 at yahoo.com] Sent: Friday, October 31, 2008 1:08 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] More AIR Hi Sarah, The AIR in DTI studio is used for coregistering different volumes in the same DTI scan. These volumes have the same image resolutions. You need to use SPM or FSL for coregister images with different image resolutions and FOVs. Jun Yi Wang ________________________________ From: "Copeland, Sarah A." To: "mristudio-users at mristudio.org" Sent: Friday, October 31, 2008 2:34:58 PM Subject: [Mristudio-users] More AIR Hello all ? I would like to be able to register my anatomic scan to the mean b0 of my DTIs so that I can draw ROIs on the anatomic scan. However, when I push the ?AIR? button, it allows me to enter mean of b0s as the one to register to, but it does not recognize the analyze format or raw format anatomic images in the same folder. The only files that show up in the list are the raw data files, or the files created when doing the tensor calculations (FA, etc). I am working in DTI studio (not landmarker or ROI editor). I don?t want to normalize, just coregister anatomic and DTI scans from the same subject. Is there a way to do this? Thanks very much, Sarah Copeland 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. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users 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. _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users 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 c.bieck at T-Online.de Thu Nov 6 04:13:00 2008 From: c.bieck at T-Online.de (Christian Bieck) Date: Thu, 06 Nov 2008 09:13 +0000 (GMT) Subject: [Mristudio-users] Optic radiations Message-ID: <1Ky0w3-294IMq0@fwd01.aul.t-online.de> This message seems to have bounced due to the attached picture exceeding the size limit, so I uploaded the picture instead. Hello, Thank you very much for the very fast replies. I tried using the CUT operations in the Fiber Tab after fiber tracking, but could not achieve any satisfactory results as the CUT operation ended in adding fibers that were not previously there. This may be due to, as Jun Yi Wang wrote, the CUT operation not being able to be combined with other operations (AND, OR, NOT) of which I made heavy use during extracting the optic radiation. Basing the application of the AND, OR and NOT operations on the anatomy of the optic radiation as detailed in neuroanatomic publications, I ended up with something along the lines of what you see in the attached picture (http://i202.photobucket.com/albums/aa215/Senalsun/Opticradiationscut.jpg). While there is still *a lot* of fine-tuning to be done, I would like to know if there is a way of getting rid of the part circled in red so that I may only get the FA statistics of the optic radiation circled in green, without any of these posterior fibers getting cut out in the process. As an alternative way, is it possible to extract the saved Fiber ROIs and FA values as a spreadsheet so I could copy it into Excel or SPSS? My supervisor told me it would be a good idea, if all else fails, to put the Fiber ROI data into a spreadsheet, then only look at the coordinates beyond a certain x, y or z value signifying the fiber tracts in the visual cortex and then look these positions up in the FA values map. Again, thank you very much for your time and help. Sincerely, Christian Bieck -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081106/851a697e/attachment.html From junyiwang2002 at yahoo.com Thu Nov 6 09:39:30 2008 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Thu, 06 Nov 2008 06:39:30 -0800 (PST) Subject: [Mristudio-users] Optic radiations References: <1Ky0w3-294IMq0@fwd01.aul.t-online.de> Message-ID: <142967.89338.qm@web50509.mail.re2.yahoo.com> Hi Christian, After you click on the Statistics button, you can select a parameter and click on the Statistics Profile button to open up the list of values at each slice.? For you case, you can look at the coronal section and select the range of slices you desire.? You can copy/paste your selection into a spreadsheet. Jun Yi ________________________________ From: Christian Bieck To: mristudio-users at mristudio.org Sent: Thursday, November 6, 2008 3:13:00 AM Subject: [Mristudio-users] Optic radiations This message seems to have bounced due to the attached picture exceeding the size limit, so I uploaded the picture instead. Hello, Thank you very much for the very fast replies. I tried using the CUT operations in the Fiber Tab after fiber tracking, but could not achieve any satisfactory results as the CUT operation ended in adding fibers that were not previously there. This may be due to, as Jun Yi Wang wrote, the CUT operation not being able to be combined with other operations (AND, OR, NOT) of which I made heavy use during extracting the optic radiation. Basing the application of the AND, OR and NOT operations on the anatomy of the optic radiation as detailed in neuroanatomic publications, I ended up with something along the lines of what you see in the attached picture (http://i202.photobucket.com/albums/aa215/Senalsun/Opticradiationscut.jpg). While there is still *a lot* of fine-tuning to be done, I would like to know if there is a way of getting rid of the part circled in red so that I may only get the FA statistics of the optic radiation circled in green, without any of these posterior fibers getting cut out in the process. As an alternative way, is it possible to extract the saved Fiber ROIs and FA values as a spreadsheet so I could copy it into Excel or SPSS? My supervisor told me it would be a good idea, if all else fails, to put the Fiber ROI data into a spreadsheet, then only look at the coordinates beyond a certain x, y or z value signifying the fiber tracts in the visual cortex and then look these positions up in the FA values map. Again, thank you very much for your time and help. Sincerely, Christian Bieck -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081106/59cf3da5/attachment.html From raj.jaswal at gmail.com Thu Nov 6 17:01:48 2008 From: raj.jaswal at gmail.com (Raj Jaswal) Date: Thu, 06 Nov 2008 14:01:48 -0800 Subject: [Mristudio-users] Beginning DTIStudio In-Reply-To: <32a27f2a0810201534v4813aa2di935bec4d4cd32bb8@mail.gmail.com> References: <32a27f2a0810201534v4813aa2di935bec4d4cd32bb8@mail.gmail.com> Message-ID: <32a27f2a0811061401g4769fe67k64c0e63e838b9035@mail.gmail.com> ---------- Forwarded message ---------- From: Raj Jaswal Date: Mon, Oct 20, 2008 at 2:34 PM Subject: Beginning DTIStudio To: "DTI Studio, ROI Editor, Landmarker Questions/Support" < mristudio-users at mristudio.org>, "support at mristudio.org" < support at mristudio.org> Hi all, I am relatively new to the realm of DTI and imaging in general. Any help from anyone would be greatly appreciated! I'm having some difficulty in taking my raw images (from a 3T Siemens) and doing the DTI Mapping and Fiber Tracking through DTIStudio. The first thing I do is use DicomWorks software to convert the raw data from the Siemens machine into a structured DICOM format. I have two sets of DTI data from the machine: * Set 1 is 32 slices with a 5mm thickness using 12 gradient directions (416 total files) * Set 2 is 50 slices with a 3mm thickness using 12 gradient directions (650 total files) I am trying to analyze Set 1 first. The process I go through is the following (Please correct me if I am wrong anywhere!): 1. File --> DTI Mapping (I select "Siemens, GE, or Philips DICOM" and click Continue) 2. I use the gradient table provided by mristudio.org and select the first 12 gradients under Siemens DICOM (Lines 0-11). 3. b-Value is 700. And I add the folder of Set 1 to the "DICOM Image-File Folders" section and click OK. 4. All 416 files are processed and just to check, I get 13 files in the drop down box in the Image tab (12 gradients + 1 b0) 5. I click on the "DtiMap" tab and click on the "Original - ADC - Mean - STD" button to view the images. (12 images due to gradients) 6. Next, I click on the "Tensor, Color Map etc." button in order to perform the tensor calculation. I leave the noise level at 10 and leave "Consider B-Value" checked. The other options I do not change. Click OK. At the Automatic Outlier Rejection window I click "No". (32 slices are being processed). 7. I go back to the "Image" tab and save the following files: 7a. Anisotropy-FA --> test.FA 7b. color map 0 --> test.color 7c. eigenvector 0 --> test.vec 7d. tensor images (all 6) --> test.d 7e. dwi file --> test.dwi 7f. b0 file --> test.b0 7g. eigenvalue 0 file --> test.ev0 8. File --> Fiber Tracking. I load the test.FA and test.vec files with image dimensions of 128x128 and Voxel size of 64x64 with a 5mm thickness. The rest options are default for now. 9. I click on the "Color Map" button select both the .fa and .vec files and click OK. 10. I then click on the "Fiber" tab and check off ""show items in 2D image", "roi drawing enable", and "user defined". 11. I proceed to draw an arbitrary ROI in the image in the top-right quadrant. 12. The area selected has 16 fibers (according to statistics button). I click on the save icon next to the "FACT" button. 13. I click on the save icon under the "ROI - Operation" section as well. I save it as the Graphic Compatible (Default) option. 14. From here, I open ROI Editor and load the "test.FA" file and set the image dimension to 128x128 (32 slices) and the voxel size to 64x64 with a slice thickness of 5mm. The image data format is selected as type Float. I can attach screenshots of what I get after steps 8, 9, and 14. If possible, can anyone let me know if I'm on the right track or if there is anything wrong with what I am doing? Also, is there an instruction set or tutorial for using ROIEditor and LandMarker? Thank you very much for your time. - RJ -- - RJ -- - RJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081106/cf6737df/attachment-0001.html From maggie.ouyang at gmail.com Fri Nov 7 11:39:14 2008 From: maggie.ouyang at gmail.com (Ouyang, Luo) Date: Fri, 07 Nov 2008 10:39:14 -0600 Subject: [Mristudio-users] ROI operation&AIR Message-ID: <2af85f760811070839w2c4b76ddqd9c68c6b32a4266c@mail.gmail.com> Dear all, I wanted to use DTI-studio for fiber-tracking. All the Rois were generated from Roi-editor or MRIcro. However, when I loaded the multiple rois in DTI-studio, it seemed that only the latest loaded ROI had been used for tracking and no roi operation could be used. Could anyone tell me if there is a way to load two or more ROIs simultaneously and to do the "and" operation on the ROIs? Another question. I have downloaded the .c files of AIR from their website. However, it failed to be compiled using VC. Could anyone show me which compiler should I use? Or if anyone want to share his/her .exe files, I'd be grateful. Thanks a lot! Maggie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081107/8a2dd9a1/attachment.html From xli16 at jhmi.edu Fri Nov 7 11:53:29 2008 From: xli16 at jhmi.edu (XIN LI) Date: Fri, 07 Nov 2008 11:53:29 -0500 Subject: [Mristudio-users] ROI operation&AIR In-Reply-To: <2af85f760811070839w2c4b76ddqd9c68c6b32a4266c@mail.gmail.com> References: <2af85f760811070839w2c4b76ddqd9c68c6b32a4266c@mail.gmail.com> Message-ID: Maggie, Please take a look at this post. http://lists.mristudio.org/pipermail/mristudio-users/2008/000073.html Hope it will help. Xin ----- Original Message ----- From: "Ouyang, Luo" Date: Friday, November 7, 2008 11:40 am Subject: [Mristudio-users] ROI operation&AIR To: mristudio-users at mristudio.org > Dear all, > > I wanted to use DTI-studio for fiber-tracking. All the Rois were generated > from Roi-editor or MRIcro. However, when I loaded the multiple rois in > DTI-studio, it seemed that only the latest loaded ROI had been used for > tracking and no roi operation could be used. Could anyone tell me if > there > is a way to load two or more ROIs simultaneously and to do the "and" > operation on the ROIs? > > Another question. I have downloaded the .c files of AIR from their website. > However, it failed to be compiled using VC. Could anyone show me which > compiler should I use? Or if anyone want to share his/her .exe files, > I'd be > grateful. > > Thanks a lot! > > Maggie > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From susumu at mri.jhu.edu Sun Nov 9 01:00:14 2008 From: susumu at mri.jhu.edu (susumu) Date: Sun, 09 Nov 2008 01:00:14 -0500 Subject: [Mristudio-users] ROI operation&AIR In-Reply-To: <2af85f760811070839w2c4b76ddqd9c68c6b32a4266c@mail.gmail.com> References: <2af85f760811070839w2c4b76ddqd9c68c6b32a4266c@mail.gmail.com> Message-ID: Hi Maggie, Please try the ?Binary Map? option. The best way to learn this format is to save ROIs by DtiStudio and study the saved files. Please do the following; 1) Using DtiStudio, draw one ROI as ?OR?, second ROI as ?AND?, and third ROI as ?NOT?. 2) Save the ROI. In the ROI section, there is the ?save? icon. After clicking it, a new dialog window appears. Here, choose the ?binary map? format. 3) Assign a file name and save it. 4) Go to the directory where you saved the ROI files. You should find 4 new files. Three large files to save the ROI locations by 1/0 binary information. This file has the same 3D dimension as the images. The fourth file is a text file, which you can open and read inside. 5) At the bottom of the text file (the fourth file), there is a description about the syntax. The file is self-explanatory. Once you understand the content, it is very easy to modify this file to load ROI files you created by RoiEditor and other software. Please let us know if you have any problem with this approach. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Ouyang, Luo Sent: Friday, November 07, 2008 11:39 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ROI operation&AIR Dear all, I wanted to use DTI-studio for fiber-tracking. All the Rois were generated from Roi-editor or MRIcro. However, when I loaded the multiple rois in DTI-studio, it seemed that only the latest loaded ROI had been used for tracking and no roi operation could be used. Could anyone tell me if there is a way to load two or more ROIs simultaneously and to do the "and" operation on the ROIs? Another question. I have downloaded the .c files of AIR from their website. However, it failed to be compiled using VC. Could anyone show me which compiler should I use? Or if anyone want to share his/her .exe files, I'd be grateful. Thanks a lot! Maggie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081109/e281e4ee/attachment.html From susumu at mri.jhu.edu Sun Nov 9 16:17:17 2008 From: susumu at mri.jhu.edu (susumu) Date: Sun, 09 Nov 2008 16:17:17 -0500 Subject: [Mristudio-users] Beginning DTIStudio In-Reply-To: <32a27f2a0811061401g4769fe67k64c0e63e838b9035@mail.gmail.com> References: <32a27f2a0810201534v4813aa2di935bec4d4cd32bb8@mail.gmail.com> <32a27f2a0811061401g4769fe67k64c0e63e838b9035@mail.gmail.com> Message-ID: Hi RJ, The procedure you described seems fine. You can send me some screen shots to me at susumu at mri.jhu.edu. I'm happy to take a look at the result to make sure that your results are correct. Please draw an ROI on genu, body, or splenium of the corpus callosum. Also another one at the cerebral peduncle. susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Raj Jaswal Sent: Thursday, November 06, 2008 5:02 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Beginning DTIStudio ---------- Forwarded message ---------- From: Raj Jaswal Date: Mon, Oct 20, 2008 at 2:34 PM Subject: Beginning DTIStudio To: "DTI Studio, ROI Editor, Landmarker Questions/Support" , "support at mristudio.org" Hi all, I am relatively new to the realm of DTI and imaging in general. Any help from anyone would be greatly appreciated! I'm having some difficulty in taking my raw images (from a 3T Siemens) and doing the DTI Mapping and Fiber Tracking through DTIStudio. The first thing I do is use DicomWorks software to convert the raw data from the Siemens machine into a structured DICOM format. I have two sets of DTI data from the machine: * Set 1 is 32 slices with a 5mm thickness using 12 gradient directions (416 total files) * Set 2 is 50 slices with a 3mm thickness using 12 gradient directions (650 total files) I am trying to analyze Set 1 first. The process I go through is the following (Please correct me if I am wrong anywhere!): 1. File --> DTI Mapping (I select "Siemens, GE, or Philips DICOM" and click Continue) 2. I use the gradient table provided by mristudio.org and select the first 12 gradients under Siemens DICOM (Lines 0-11). 3. b-Value is 700. And I add the folder of Set 1 to the "DICOM Image-File Folders" section and click OK. 4. All 416 files are processed and just to check, I get 13 files in the drop down box in the Image tab (12 gradients + 1 b0) 5. I click on the "DtiMap" tab and click on the "Original - ADC - Mean - STD" button to view the images. (12 images due to gradients) 6. Next, I click on the "Tensor, Color Map etc." button in order to perform the tensor calculation. I leave the noise level at 10 and leave "Consider B-Value" checked. The other options I do not change. Click OK. At the Automatic Outlier Rejection window I click "No". (32 slices are being processed). 7. I go back to the "Image" tab and save the following files: 7a. Anisotropy-FA --> test.FA 7b. color map 0 --> test.color 7c. eigenvector 0 --> test.vec 7d. tensor images (all 6) --> test.d 7e. dwi file --> test.dwi 7f. b0 file --> test.b0 7g. eigenvalue 0 file --> test.ev0 8. File --> Fiber Tracking. I load the test.FA and test.vec files with image dimensions of 128x128 and Voxel size of 64x64 with a 5mm thickness. The rest options are default for now. 9. I click on the "Color Map" button select both the .fa and .vec files and click OK. 10. I then click on the "Fiber" tab and check off ""show items in 2D image", "roi drawing enable", and "user defined". 11. I proceed to draw an arbitrary ROI in the image in the top-right quadrant. 12. The area selected has 16 fibers (according to statistics button). I click on the save icon next to the "FACT" button. 13. I click on the save icon under the "ROI - Operation" section as well. I save it as the Graphic Compatible (Default) option. 14. From here, I open ROI Editor and load the "test.FA" file and set the image dimension to 128x128 (32 slices) and the voxel size to 64x64 with a slice thickness of 5mm. The image data format is selected as type Float. I can attach screenshots of what I get after steps 8, 9, and 14. If possible, can anyone let me know if I'm on the right track or if there is anything wrong with what I am doing? Also, is there an instruction set or tutorial for using ROIEditor and LandMarker? Thank you very much for your time. - RJ -- - RJ -- - RJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081109/74aad58f/attachment-0001.html From susumu at mri.jhu.edu Sun Nov 9 16:43:01 2008 From: susumu at mri.jhu.edu (susumu) Date: Sun, 09 Nov 2008 16:43:01 -0500 Subject: [Mristudio-users] Optic radiations In-Reply-To: <142967.89338.qm@web50509.mail.re2.yahoo.com> References: <1Ky0w3-294IMq0@fwd01.aul.t-online.de> <142967.89338.qm@web50509.mail.re2.yahoo.com> Message-ID: <8C18A4501AD446B78D9E9D91157A2796@SusumuThinkPad> Hi Christian, As Jun Yi said, you can get statistics at each coronal section using the "profile" button. This may be a good approach to study the optic radiation in the occipital lobe, although it should include not only the OR but also other fibers such as IFO and ILF as you can see from your reconstruction results. By adding more ROI in the LGN, the specificity to the OR may increase but you may loose a lot of the OR (sensitivity) as an expense of unknown increase in the specificity. The tracts in the green area is a mixture of many tracts anyway and extract of the pure OR may be impossible by DTI. The CUT operation is always a two-ROI method, which can't be combined with third ROI. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang Sent: Thursday, November 06, 2008 9:40 AM To: c.bieck at t-online.de; mristudio-users at mristudio.org Subject: Re: [Mristudio-users] Optic radiations Hi Christian, After you click on the Statistics button, you can select a parameter and click on the Statistics Profile button to open up the list of values at each slice. For you case, you can look at the coronal section and select the range of slices you desire. You can copy/paste your selection into a spreadsheet. Jun Yi _____ From: Christian Bieck To: mristudio-users at mristudio.org Sent: Thursday, November 6, 2008 3:13:00 AM Subject: [Mristudio-users] Optic radiations This message seems to have bounced due to the attached picture exceeding the size limit, so I uploaded the picture instead. Hello, Thank you very much for the very fast replies. I tried using the CUT operations in the Fiber Tab after fiber tracking, but could not achieve any satisfactory results as the CUT operation ended in adding fibers that were not previously there. This may be due to, as Jun Yi Wang wrote, the CUT operation not being able to be combined with other operations (AND, OR, NOT) of which I made heavy use during extracting the optic radiation. Basing the application of the AND, OR and NOT operations on the anatomy of the optic radiation as detailed in neuroanatomic publications, I ended up with something along the lines of what you see in the attached picture (http://i202.photobucket.com/albums/aa215/Senalsun/Opticradiationscut.jpg). While there is still *a lot* of fine-tuning to be done, I would like to know if there is a way of getting rid of the part circled in red so that I may only get the FA statistics of the optic radiation circled in green, without any of these posterior fibers getting cut out in the process. As an alternative way, is it possible to extract the saved Fiber ROIs and FA values as a spreadsheet so I could copy it into Excel or SPSS? My supervisor told me it would be a good idea, if all else fails, to put the Fiber ROI data into a spreadsheet, then only look at the coordinates beyond a certain x, y or z value signifying the fiber tracts in the visual cortex and then look these positions up in the FA values map. Again, thank you very much for your time and help. Sincerely, Christian Bieck -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081109/861eb9ff/attachment.html From Sumei.Wang at uphs.upenn.edu Mon Nov 10 09:18:19 2008 From: Sumei.Wang at uphs.upenn.edu (Wang, Sumei) Date: Mon, 10 Nov 2008 09:18:19 -0500 Subject: [Mristudio-users] Normalized Fibers In-Reply-To: Message-ID: <4BFD060857263F43AEA4C10586DDE44603C803ED@uphsmbx8.UPHS.PENNHEALTH.PRV> Dear all, I am working on the brain tumor project. I applied linear and non-linear normalization process using the template provided by landmarker. The result looks good. The brain was well aligned. I saved the transformation matrix and used it to the generated fibers (corticospinal tract). However, the fiber become very thin and the location was a little bit shifted after the normalization process. Does anybody have such kind of problem? Thank you very much for the help. Best wishes Sumei 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081110/308082c6/attachment.html From susumu at mri.jhu.edu Mon Nov 10 10:50:16 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 10 Nov 2008 10:50:16 -0500 Subject: [Mristudio-users] Normalized Fibers In-Reply-To: <4BFD060857263F43AEA4C10586DDE44603C803ED@uphsmbx8.UPHS.PENNHEALTH.PRV> Message-ID: <73ap56$4to67h@ipex1.johnshopkins.edu> did you use AIR-based or LDDMM-based normlization? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Wang, Sumei Sent: Monday, November 10, 2008 9:18 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: [Mristudio-users] Normalized Fibers Dear all, I am working on the brain tumor project. I applied linear and non-linear normalization process using the template provided by landmarker. The result looks good. The brain was well aligned. I saved the transformation matrix and used it to the generated fibers (corticospinal tract). However, the fiber become very thin and the location was a little bit shifted after the normalization process. Does anybody have such kind of problem? Thank you very much for the help. Best wishes Sumei 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081110/2c5cc2d1/attachment-0001.html From Sumei.Wang at uphs.upenn.edu Mon Nov 10 10:53:11 2008 From: Sumei.Wang at uphs.upenn.edu (Wang, Sumei) Date: Mon, 10 Nov 2008 10:53:11 -0500 Subject: [Mristudio-users] Normalized Fibers In-Reply-To: <73ap56$4to67h@ipex1.johnshopkins.edu> Message-ID: <4BFD060857263F43AEA4C10586DDE44603C803EE@uphsmbx8.UPHS.PENNHEALTH.PRV> I applied Air-based normalization. Thanks. Sumei -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org]On Behalf Of susumu Sent: Monday, November 10, 2008 10:50 AM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] Normalized Fibers did you use AIR-based or LDDMM-based normlization? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Wang, Sumei Sent: Monday, November 10, 2008 9:18 AM To: DTI Studio, ROI Editor,Landmarker Questions/Support Subject: [Mristudio-users] Normalized Fibers Dear all, I am working on the brain tumor project. I applied linear and non-linear normalization process using the template provided by landmarker. The result looks good. The brain was well aligned. I saved the transformation matrix and used it to the generated fibers (corticospinal tract). However, the fiber become very thin and the location was a little bit shifted after the normalization process. Does anybody have such kind of problem? Thank you very much for the help. Best wishes Sumei 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. 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081110/143afefe/attachment.html From Elizabeth.Finger at lhsc.on.ca Wed Nov 12 16:08:16 2008 From: Elizabeth.Finger at lhsc.on.ca (Elizabeth Finger) Date: Wed, 12 Nov 2008 16:08:16 -0500 Subject: [Mristudio-users] question on calculating and generating probabilistic maps for groups Message-ID: <491AFF70020000A0000060D4@lhscgwiao.lhsc.on.ca> Hello- I have a question on developing Probabilistic maps of fiber tracts. I have a patient group and a control group in my study. In addition to reporting mean FA values along my tracts of interest (uncinate fasiculus and other tracts defined using ROIs in the amygdala), I am very interested in examining the probablities of the presence of these tracts spatially in the brain, as was done in Mori et al. Magnetic Resonance in Medicine 2002. I have looked at the ROI editor functions but am not sure if the technique used in Mori et al. 2002 to calculate and generate these probability maps for groups of subjects has been automated now in the DTI studio programs? Thank you, Elizabeth Finger -------------------------------------------------------------------------------- This information is directed in confidence solely to the person named above and may contain confidential and/or privileged material. This information may not otherwise be distributed, copied or disclosed. If you have received this e-mail in error, please notify the sender immediately via a return e-mail and destroy original message. Thank you for your cooperation. From susumu at mri.jhu.edu Thu Nov 13 14:50:39 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 13 Nov 2008 14:50:39 -0500 Subject: [Mristudio-users] MTR In-Reply-To: <471357.6975.qm@web110213.mail.gq1.yahoo.com> Message-ID: <73ap56$4up5bs@ipex1.johnshopkins.edu> Hi Lucas, sorry for my slow reply. MTI and DTI are two different types of data acquisition. Do you mean how to co-register these two images? Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Lucas Lessa Sent: Thursday, October 30, 2008 11:22 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] MTR Hello everyone, I need to process magnetic transfer imaging and FA along the cortico-spinal tract. I'd like to do in DTI to make sure that both mesurements will be done in the same place, but I don't know if is possible to do MTI in DTI, is it? If no can anyone suggest me a (free) sofware that I can use with DTI to do so? Thank you. Lucas Lessa S?o Paulo/Brazil. Novos endere?os, o Yahoo! que voc? conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Thu Nov 13 15:24:29 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 13 Nov 2008 15:24:29 -0500 Subject: [Mristudio-users] ACPC alignment In-Reply-To: <9f1c9c480810201649x323b0a00w32238867de45a0f2@mail.gmail.com> Message-ID: <73ap56$4upde9@ipex1.johnshopkins.edu> Hi JH, You have to be careful if you want to move your DTI data. There are two options to do post-processing ACPC alignment; reorient raw DWIs or reorient after tensor calculation. The latter approach (reorient after tensor calculation) also has two options; reorient tensor (or vector) or reorient a rotation-invariant scalar images such as ADC, FA, and eivenvalues. Let's go over the image analysis process; Raw DWI - tensor map (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) - scalar map (FA, ADC, eigenvalues) You can't simply reorient the first two images (raw DWI and tensor) because they are "rotationally variant". For example, if you want to rotate the raw DWIs by 10 degree to get the ACPC alignment, you have to also rotate your b-table. If your first gradient orientation is [0, 1, 0] (y gradient) and rotate the brain about x axis, your gradient orientation now becomes something like [0, 0.9, 0.03]. If you rotate the tensor map by 10 degree, you have to make sure that all tensor elements in each pixel also have to be rotated. In the third step (scalar map), you can do any rotation you wants without worrying any reorientation. Another question is how you define the rotation angles to achieve ACPC. If the brain orientation is not correct both in sagittal and axial images, you get a complex situation to get the brain straight. For reorientation, what we can offer is the following; 1) Do tensor calculation and obtain the tensor map without worrying the brain orientation. 2) use one of our atlases as a target of the brain orientation. All our atlases are ACPC aligned (more precisely the orientation of ICBM-152). 3) use Landmarker -> rigid rotation option to reorient your data to the orientation of the atlas. Here you want to reorient the tensor map you obtained in the step #1. Landmarker knows how to reorient tensor data. 4) reload the re-oriented tensor map to DtiStudio and recalculate all the images such as FA/ADC/eigenvalues/eigenvectors You can skip #4 if you reorient FA/ADC/eigenvalues (not tensor) in step #3. But in this approach, you can't get reoriented eigenvector maps and therefore you can't do tractography after rotation. If you do manual ROI-based analysis, it is important that your brain data are all oriented in the same way so that the axial slices of interest (or coronal or sagittal) are oriented in a comparable manner among subjects. If you use affine transformation (instead of rigid) in step #3, you can also make the size of the brain the same. In this way, your manual ROI drawing becomes even more reproducible because you can write a protocol like, "extract axial slice #60 in the atlas coordinate and draw ROI on the internal capsule". This is not really related to your question, but hope it'll help. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jarnet Han Sent: Monday, October 20, 2008 7:50 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ACPC alignment Hi everyone, I was just wondering about the easiest way to do ACPC alignment before loading up the files into DTI studio (or does DTI studio have a built-in way to do this?). Currently, we are using the protocol from Mori's paper which appears to be based on ACPC aligned brains. Thanks in advance. Best, JH -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081113/502566f4/attachment-0001.html From miaomiaolong at 126.com Sat Nov 15 10:05:31 2008 From: miaomiaolong at 126.com (=?gbk?B?wfrtte21?=) Date: Sat, 15 Nov 2008 23:05:31 +0800 (CST) Subject: [Mristudio-users] MTR In-Reply-To: <73ap56$4up5bs@ipex1.johnshopkins.edu> References: <73ap56$4up5bs@ipex1.johnshopkins.edu> Message-ID: <9980108.256811226761531919.JavaMail.coremail@bj126app42.126.com> Hi, i think both MTR and DTI images can be processed with SPM package. with the preprocess panel ,the coregisteration is relatively simple. ?2008-11-14?susumu ??? >Hi Lucas, > >sorry for my slow reply. MTI and DTI are two different types of data >acquisition. Do you mean how to co-register these two images? > >Susumu > >-----Original Message----- >From: mristudio-users-bounces at mristudio.org >[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Lucas Lessa >Sent: Thursday, October 30, 2008 11:22 AM >To: DTI Studio, ROI Editor, Landmarker Questions/Support >Subject: [Mristudio-users] MTR > >Hello everyone, > >I need to process magnetic transfer imaging and FA along the cortico-spinal >tract. >I'd like to do in DTI to make sure that both mesurements will be done in the >same place, but I don't know if is possible to do MTI in DTI, is it? >If no can anyone suggest me a (free) sofware that I can use with DTI to do >so? > >Thank you. > >Lucas Lessa >S?o Paulo/Brazil. > > > > Novos endere?os, o Yahoo! que voc? conhece. Crie um email novo com a >sua cara @ymail.com ou @rocketmail.com. >http://br.new.mail.yahoo.com/addresses > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users > >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081115/4236a449/attachment.html From grojasy at puc.cl Mon Nov 17 09:40:03 2008 From: grojasy at puc.cl (Gonzalo Rojas) Date: Mon, 17 Nov 2008 11:40:03 -0300 Subject: [Mristudio-users] Fiber-tracking window... Message-ID: <49218243.90904@puc.cl> Hi: In the Fiber-Tracking window "Images parameters (for Fiber-Tracking)": which are the "FA-Map" file and the "Principal Vector" ?... Sincerely, Gonzalo Rojas Costa From susumu at mri.jhu.edu Mon Nov 17 10:13:16 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 17 Nov 2008 10:13:16 -0500 Subject: [Mristudio-users] Fiber-tracking window... In-Reply-To: <49218243.90904@puc.cl> References: <49218243.90904@puc.cl> Message-ID: <8D3D930BE4A84F04A6081118791B5189@SusumuThinkPad> Hi Gonzalo, The upper section specifies the file paths for the FA and vector maps. The other sections, such as "Image Dimension" and "voxel size" should be identical for these two files. The FA and vector maps need to be first generated by "DtiMapping". Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Gonzalo Rojas Sent: Monday, November 17, 2008 9:40 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Fiber-tracking window... Hi: In the Fiber-Tracking window "Images parameters (for Fiber-Tracking)": which are the "FA-Map" file and the "Principal Vector" ?... Sincerely, Gonzalo Rojas Costa _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From rajagov2 at ccf.org Wed Nov 19 14:09:14 2008 From: rajagov2 at ccf.org (Rajagopalan, Venkateswaran) Date: Wed, 19 Nov 2008 14:09:14 -0500 Subject: [Mristudio-users] multiplication of two image sets Message-ID: <77A88E90A851594AAEF830450587C39D01EDA934@CCHSCLEXMB56.cc.ad.cchs.net> Hi All, I want to multiply two image data sets (or stacks), can anyone please tell me how i can do this in in DTI studio. Thanks ain advance. Venkaetswaran 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 (2008). 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/20081119/b2e0651c/attachment.html From megjim1 at gmail.com Wed Nov 19 14:32:40 2008 From: megjim1 at gmail.com (Jim Li) Date: Wed, 19 Nov 2008 13:32:40 -0600 Subject: [Mristudio-users] about md5sum mismatch In-Reply-To: <575b44a30811191040y49b11a56ib591a26ec534fe94@mail.gmail.com> References: <575b44a30811191040y49b11a56ib591a26ec534fe94@mail.gmail.com> Message-ID: <575b44a30811191132q4f2d50a5q7bfa822e7a971b91@mail.gmail.com> Hello, I tried several different ways to download the "Landmarker-latest-x86.zip" file from MRIstudio. But my md5sum result is always 17dc03ddc049cd583972828eee3830cd, which is quite different from what's listed in the MRI studio website. Same thing happened to my "ROIEditor-latest-x86.rar" whose md5sum didn't match the listed "2476773da50af97072589243d1bdbf89 ROIEditor-latest-x86.zip" (Shouldn't it be ".rar" instead of ".zip"?). However, my md5sum agrees with the listed value on the website for "vcredist_x86.exe" and "DtiStudio-latest-x86.exe". I guess that means a corrupted download for the first two files, but not for the last two, which seems weird. Anyway, could anybody suggest a reliable way to correctly download the first two files? Thanks, Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081119/f12ba22f/attachment.html From xli16 at jhmi.edu Wed Nov 19 15:15:29 2008 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 19 Nov 2008 15:15:29 -0500 Subject: [Mristudio-users] about md5sum mismatch In-Reply-To: <575b44a30811191132q4f2d50a5q7bfa822e7a971b91@mail.gmail.com> References: <575b44a30811191040y49b11a56ib591a26ec534fe94@mail.gmail.com> <575b44a30811191132q4f2d50a5q7bfa822e7a971b91@mail.gmail.com> Message-ID: Jim, The ROIEditor package was compressed as a rar file not a zip file. Xin ----- Original Message ----- From: Jim Li Date: Wednesday, November 19, 2008 2:32 pm Subject: [Mristudio-users] about md5sum mismatch To: mristudio-users at mristudio.org > Hello, > > I tried several different ways to download the > "Landmarker-latest-x86.zip<>" > file from MRIstudio. But my md5sum result is always > 17dc03ddc049cd583972828eee3830cd, which is quite different from what's > listed in the MRI studio website. > > Same thing happened to my > "ROIEditor-latest-x86.rar<>" > whose md5sum didn't match the listed "2476773da50af97072589243d1bdbf89 > ROIEditor-latest-x86.zip" (Shouldn't it be ".rar" instead of ".zip"?). > However, my md5sum agrees with the listed value on the website for > "vcredist_x86.exe" and "DtiStudio-latest-x86.exe". > > I guess that means a corrupted download for the first two files, but > not for > the last two, which seems weird. Anyway, could anybody suggest a reliable > way to correctly download the first two files? > Thanks, > > Jim > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From xli16 at jhmi.edu Wed Nov 19 15:22:16 2008 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 19 Nov 2008 15:22:16 -0500 Subject: [Mristudio-users] multiplication of two image sets In-Reply-To: <77A88E90A851594AAEF830450587C39D01EDA934@CCHSCLEXMB56.cc.ad.cchs.net> References: <77A88E90A851594AAEF830450587C39D01EDA934@CCHSCLEXMB56.cc.ad.cchs.net> Message-ID: Venkaetswaran, ROIEditor has this feature. By clicking the button "operation", you can add, subtract, multiply or divide two image data. Regards, Xin ----- Original Message ----- From: "Rajagopalan, Venkateswaran" Date: Wednesday, November 19, 2008 2:09 pm Subject: [Mristudio-users] multiplication of two image sets To: mristudio-users at mristudio.org > Hi All, > > I want to multiply two image data sets (or stacks), can anyone please > tell me how i can do this in in DTI studio. > > Thanks ain advance. > > Venkaetswaran > > > 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 (2008). > 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 > From xli16 at jhmi.edu Wed Nov 19 15:29:55 2008 From: xli16 at jhmi.edu (XIN LI) Date: Wed, 19 Nov 2008 15:29:55 -0500 Subject: [Mristudio-users] about md5sum mismatch In-Reply-To: <575b44a30811191132q4f2d50a5q7bfa822e7a971b91@mail.gmail.com> References: <575b44a30811191040y49b11a56ib591a26ec534fe94@mail.gmail.com> <575b44a30811191132q4f2d50a5q7bfa822e7a971b91@mail.gmail.com> Message-ID: Jim, Sorry, I misunderstood you. Yes, it should be ".rar" not ".zip" on the MD5SUM webpage. I have sent your message to Anthony. He will give you some help. Regards, Xin ----- Original Message ----- From: Jim Li Date: Wednesday, November 19, 2008 2:32 pm Subject: [Mristudio-users] about md5sum mismatch To: mristudio-users at mristudio.org > Hello, > > I tried several different ways to download the > "Landmarker-latest-x86.zip<>" > file from MRIstudio. But my md5sum result is always > 17dc03ddc049cd583972828eee3830cd, which is quite different from what's > listed in the MRI studio website. > > Same thing happened to my > "ROIEditor-latest-x86.rar<>" > whose md5sum didn't match the listed "2476773da50af97072589243d1bdbf89 > ROIEditor-latest-x86.zip" (Shouldn't it be ".rar" instead of ".zip"?). > However, my md5sum agrees with the listed value on the website for > "vcredist_x86.exe" and "DtiStudio-latest-x86.exe". > > I guess that means a corrupted download for the first two files, but > not for > the last two, which seems weird. Anyway, could anybody suggest a reliable > way to correctly download the first two files? > Thanks, > > Jim > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > From leechrist at cc.nih.gov Tue Nov 4 15:23:15 2008 From: leechrist at cc.nih.gov (Lee, Christabel (NIH/CC/DRD) [C]) Date: Tue, 04 Nov 2008 20:23:15 -0000 Subject: [Mristudio-users] Alternative way References: <257AA7577B524E6AA0BCFA2D2472221C@SusumuThinkPad> <0C63101D-60D9-465B-9D6C-18BB03B83D04@gmail.com> Message-ID: Yes, please kindly take me off too. Thank you, ________________________________ From: Lou muscarella [mailto:loumuscarella at hotmail.com] Sent: Mon 11/3/2008 4:29 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Alternative way How do I get off this list serve? Please take me off > Date: Mon, 3 Nov 2008 21:09:17 +0900 > From: dearfreud at gmail.com > To: mristudio-users at mristudio.org > Subject: Re: [Mristudio-users] Alternative way > > Dear Dr Mori, > > > Thank you very much for your kind, detailed explanation. > > I'd like to go through each method you've shown and choose one. > > > Sincerely, > > Takahiko Kawashima > > Dear Takahiro, > > > > > > > > There are two options, as you already know. One is to report the > > average FA of the entire reconstructed fiber. After reconstruction, > > you get only one FA number. If you use CUT, that is the averaged FA > > of all pixels in between the two ROIs. > > > > > > > > The second option is to report FA of pixels at each axial, > > sagittal, or coronal slice. This is a good method for something > > like the corticospinal tract, which is rather linear. > > Unfortunately, for something like the UF and corpus callosum, with > > U-shape trajectory, this approach is not optimum. > > > > > > > > At this point, there is not a good solution for that. There may be > > some time consuming way to separate the U-shape trajectory to two I- > > shape trajectories. For example, you can save the tracking results > > as a 1/0 binary image and read it by RoiEditor. Using the threshold > > tool, you can re-define the pixels within the UF in RoiEditor. With > > a bit of trick like manually introduce a gap within the trajectory, > > you can separate the one U-shape trajectory to two regions like > > upper UF and lower UF. Then RoiEditor can report FA values along > > coronal planes. > > > > > > > > Well, maybe this is too complicated. Alternatively, you can use > > Landmarker to normalize the binarized UF images and create a pixel- > > by-pixel population-averaged map, although, you introduce a new > > nuisance factor (= registration quality). > > > > > > > > Susumu > > > > > > > > From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users- > > bounces at mristudio.org] On Behalf Of Takahiko Kawashima > > Sent: Sunday, November 02, 2008 11:25 AM > > To: mristudio-users at mristudio.org > > Subject: [Mristudio-users] Alternative way > > > > > > > > Dear users, > > > > > > > > Hi, > > > > > > > > I'm trying to calculate FA of tracts not running along only one > > axis, such as uncinate fasciculus (UF). > > > > > > > > At first I planned to combine CUT with other operations to > > calculate FA only between the CUT ROIs (in the case of UF, one one > > coronal and one on axial slice). > > > > But recently I've found it was a fundamental misunderstanding. (by > > reading Dr > > > > > > > > If possible, I'd like to get a mean FA of summed "each fiber" FA in > > depicted fibers within a defined region. > > > > Could anybody tell me some alternative ways to do this, please? > > > > Or, if I want to calculate FA within a defined region, can't I do > > anything but to consider a mean FA of "all the voxels" on which the > > fibers run? > > > > > > > > Because I am totally a beginner and poor in English, this question > > might look quite embarrassing and illegible. > > > > I hope your kind answer, and I'll really appreciate it. > > > > > > > > > > > > Best Regards, > > > > > > > > Takahiko Kawashima @ Kyoto university > > > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/mristudio-users > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users ________________________________ When your life is on the go-take your life with you. Try Windows Mobile? today -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 7906 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081104/309af548/attachment.bin From akolasny at jhu.edu Wed Nov 19 17:20:55 2008 From: akolasny at jhu.edu (akolasny at jhu.edu) Date: Wed, 19 Nov 2008 17:20:55 -0500 (EST) Subject: [Mristudio-users] about md5sum mismatch In-Reply-To: References: <575b44a30811191040y49b11a56ib591a26ec534fe94@mail.gmail.com> <575b44a30811191132q4f2d50a5q7bfa822e7a971b91@mail.gmail.com> Message-ID: <43428.69.243.84.253.1227133255.squirrel@webmail.cis.jhu.edu> Thanks for pointing this out. I reran 'md5sum' on all the binaries. When the new beta software was included, we forgot to update the MD5SUM file. The 'latest' binaries are symbolically linked to the latest version. So, 'latest' binaries will change when new binaries are made available. Sorry, Anthony > Jim, > > Sorry, I misunderstood you. Yes, it should be ".rar" not ".zip" on the > MD5SUM webpage. > > I have sent your message to Anthony. He will give you some help. > > > Regards, > > Xin > > > ----- Original Message ----- > From: Jim Li > Date: Wednesday, November 19, 2008 2:32 pm > Subject: [Mristudio-users] about md5sum mismatch > To: mristudio-users at mristudio.org > > >> Hello, >> >> I tried several different ways to download the >> "Landmarker-latest-x86.zip<>" >> file from MRIstudio. But my md5sum result is always >> 17dc03ddc049cd583972828eee3830cd, which is quite different from what's >> listed in the MRI studio website. >> >> Same thing happened to my >> "ROIEditor-latest-x86.rar<>" >> whose md5sum didn't match the listed "2476773da50af97072589243d1bdbf89 >> ROIEditor-latest-x86.zip" (Shouldn't it be ".rar" instead of ".zip"?). >> However, my md5sum agrees with the listed value on the website for >> "vcredist_x86.exe" and "DtiStudio-latest-x86.exe". >> >> I guess that means a corrupted download for the first two files, but >> not for >> the last two, which seems weird. Anyway, could anybody suggest a >> reliable >> way to correctly download the first two files? >> Thanks, >> >> Jim >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > From megjim1 at gmail.com Wed Nov 19 13:40:41 2008 From: megjim1 at gmail.com (Jim Li) Date: Wed, 19 Nov 2008 12:40:41 -0600 Subject: [Mristudio-users] about md5sum mismatch Message-ID: <575b44a30811191040y49b11a56ib591a26ec534fe94@mail.gmail.com> Hello, I tried several different ways to download the "Landmarker-latest-x86.zip" file from MRIstudio. But my md5sum result is always 17dc03ddc049cd583972828eee3830cd, which is quite different from what's listed in the MRI studio website. Same thing happened to my "ROIEditor-latest-x86.rar" whose md5sum didn't match the listed "2476773da50af97072589243d1bdbf89 ROIEditor-latest-x86.zip" (Shouldn't it be ".rar" instead of ".zip"?). However, my md5sum agrees with the listed value on the website for "vcredist_x86.exe" and "DtiStudio-latest-x86.exe". I guess that means a corrupted download for the first two files, but not for the last two, which seems weird. Anyway, could anybody suggest a reliable way to correctly download the first two files? Thanks, Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081119/fcd51b9b/attachment-0001.html From choisj70 at gmail.com Thu Nov 20 12:41:47 2008 From: choisj70 at gmail.com (Seongjin) Date: Thu, 20 Nov 2008 12:41:47 -0500 Subject: [Mristudio-users] Q. Multi b-values Message-ID: Dear all, I am working with multi-b-value DTI data now. I did not input any number in the b-value input field in the "Others (Optional)" box (left-bottom of the DW-Image Parameters window). Then it ask me to type in a number. However, my table already have multi-b-values in the gradient table. What should I do in this case? Thanks in advance. -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081120/6844d0dc/attachment.html From megjim1 at gmail.com Thu Nov 20 15:13:18 2008 From: megjim1 at gmail.com (Jim Li) Date: Thu, 20 Nov 2008 14:13:18 -0600 Subject: [Mristudio-users] about md5sum mismatch In-Reply-To: <43428.69.243.84.253.1227133255.squirrel@webmail.cis.jhu.edu> References: <575b44a30811191040y49b11a56ib591a26ec534fe94@mail.gmail.com> <575b44a30811191132q4f2d50a5q7bfa822e7a971b91@mail.gmail.com> <43428.69.243.84.253.1227133255.squirrel@webmail.cis.jhu.edu> Message-ID: <575b44a30811201213k68902347pe50ea5480b2cb165@mail.gmail.com> Thanks a lot, Anthony and Xin. Now all my md5sum numbers match with your updated list, :) Cheers, Jim On Wed, Nov 19, 2008 at 4:20 PM, wrote: > Thanks for pointing this out. > > I reran 'md5sum' on all the binaries. When the new beta > software was included, we forgot to update the MD5SUM file. > > The 'latest' binaries are symbolically linked to the latest version. > So, 'latest' binaries will change when new binaries are made available. > > Sorry, > Anthony > > > Jim, > > > > Sorry, I misunderstood you. Yes, it should be ".rar" not ".zip" on the > > MD5SUM webpage. > > > > I have sent your message to Anthony. He will give you some help. > > > > > > Regards, > > > > Xin > > > > > > ----- Original Message ----- > > From: Jim Li > > Date: Wednesday, November 19, 2008 2:32 pm > > Subject: [Mristudio-users] about md5sum mismatch > > To: mristudio-users at mristudio.org > > > > > >> Hello, > >> > >> I tried several different ways to download the > >> "Landmarker-latest-x86.zip<>" > >> file from MRIstudio. But my md5sum result is always > >> 17dc03ddc049cd583972828eee3830cd, which is quite different from what's > >> listed in the MRI studio website. > >> > >> Same thing happened to my > >> "ROIEditor-latest-x86.rar<>" > >> whose md5sum didn't match the listed "2476773da50af97072589243d1bdbf89 > >> ROIEditor-latest-x86.zip" (Shouldn't it be ".rar" instead of ".zip"?). > >> However, my md5sum agrees with the listed value on the website for > >> "vcredist_x86.exe" and "DtiStudio-latest-x86.exe". > >> > >> I guess that means a corrupted download for the first two files, but > >> not for > >> the last two, which seems weird. Anyway, could anybody suggest a > >> reliable > >> way to correctly download the first two files? > >> Thanks, > >> > >> Jim > >> _______________________________________________ > >> Mristudio-users mailing list > >> Mristudio-users at mristudio.org > >> > > _______________________________________________ > > Mristudio-users mailing list > > Mristudio-users at mristudio.org > > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081120/767246ea/attachment.html From choisj70 at gmail.com Fri Nov 21 09:25:27 2008 From: choisj70 at gmail.com (Seongjin) Date: Fri, 21 Nov 2008 09:25:27 -0500 Subject: [Mristudio-users] NRRD format Message-ID: Dear DTI studio users, I am trying to break former multi-b-value DTI data into each data set of a single b-value. I saved with analyze format but it is not allowed in the DTI calculation on DTI studio. So I tried RAW format but it gave out a message "Number of files in this fold is less than expected: (Img_Slices*Img_Blocks) I retried with NRRD fromat but it did work neigther with an error message "NRRD-DWMRI header error: not a valid NRRD-DWMRI file". Is there any instruction on this matters? Is there anyone who has suggestion on this case? All the best, -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081121/02e2730c/attachment.html From susumu at mri.jhu.edu Fri Nov 21 11:04:15 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 21 Nov 2008 11:04:15 -0500 Subject: [Mristudio-users] NRRD format In-Reply-To: Message-ID: <73ap56$50h2o5@ipex1.johnshopkins.edu> Hi SC, Raw format should work for multi-b. Please make sure that your raw data are integer (word). The error message is due to the mismatch between the b-table and image size. There could be some mistakes in b-table format. Please close the application once after the error message and restart -> DtiMapping. In the b-table section of the data input window, the software remembers the previous b-table you input. If there is any mistakes in the syntax, you can see how the software interpreted it. This is the easiest way to catch errors. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of [Seongjin] Sent: Friday, November 21, 2008 9:25 AM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] NRRD format Dear DTI studio users, I am trying to break former multi-b-value DTI data into each data set of a single b-value. I saved with analyze format but it is not allowed in the DTI calculation on DTI studio. So I tried RAW format but it gave out a message "Number of files in this fold is less than expected: (Img_Slices*Img_Blocks) I retried with NRRD fromat but it did work neigther with an error message "NRRD-DWMRI header error: not a valid NRRD-DWMRI file". Is there any instruction on this matters? Is there anyone who has suggestion on this case? All the best, -SC -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081121/10f04a08/attachment.html From hjiang at jhmi.edu Fri Nov 21 12:46:49 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Fri, 21 Nov 2008 12:46:49 -0500 Subject: [Mristudio-users] NRRD format Message-ID: <4926ADB90200006300019209@cis27.hosts.jhmi.edu> hi, first of all, DTI Studio does accept multiple b-values dataset. to do this, you can define the gradients in the gradient table by this format: #: x, y, z, b-value e.g.: 0: 1, 0, 0, 600 1: 0, 1, 0, 600 ... 8: 1, 0, 0, 800 9: 0, 1, 0, 800 ... "DTI Mapping" does not accept Analyze DWIs, for NRRD, the header should follow the NRRD-DWMRI format, not the NRRD format, they are not same. for RAW format, it is supposed that each file contains only one image volume, so that you need to put all image files into one folder. my suggestion is that you'd better to put all image volumes into one single file (Philps REC format). before you do this, as Susumu said, please make sure that your raw data type is in 16-bit unsigned integer (word). you can put all multiple b-value dataset into one file, or seperate them into multiple single_b-value dataset. and then process the dataset as Philips REC files or pre-edit a ".dpf" file and let program to get the image parameters from the ".dpf" file.... regards, hangyi >>> "[Seongjin]" 11/21/08 9:25 AM >>> Dear DTI studio users, I am trying to break former multi-b-value DTI data into each data set of a single b-value. I saved with analyze format but it is not allowed in the DTI calculation on DTI studio. So I tried RAW format but it gave out a message "Number of files in this fold is less than expected: (Img_Slices*Img_Blocks) I retried with NRRD fromat but it did work neigther with an error message "NRRD-DWMRI header error: not a valid NRRD-DWMRI file". Is there any instruction on this matters? Is there anyone who has suggestion on this case? All the best, -SC From bob_ge at 163.com Sun Nov 23 21:50:48 2008 From: bob_ge at 163.com (bob) Date: Mon, 24 Nov 2008 10:50:48 +0800 Subject: [Mristudio-users] the structure of .dat file Message-ID: <492A167B.086EF0.13117@m12-11.163.com> Hi, The tracking results can be also saved as a .dat file. I'd like to know the structure of this format, can you tell me about it so that I can use it? thanks. ???????? bob ??????? 2008-11-24 From hjiang at jhmi.edu Mon Nov 24 09:52:27 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Mon, 24 Nov 2008 09:52:27 -0500 Subject: [Mristudio-users] the structure of .dat file Message-ID: <492A795B0200006300019335@cis27.hosts.jhmi.edu> please goto www.mristudio.org -> FAQ to get the information. hangyi >>> bob 11/23/08 9:50 PM >>> Hi, The tracking results can be also saved as a .dat file. I'd like to know the structure of this format, can you tell me about it so that I can use it? thanks. ???????? bob ??????? 2008-11-24 _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From hjyu at ic.sunysb.edu Mon Nov 24 11:56:47 2008 From: hjyu at ic.sunysb.edu (hjyu) Date: Mon, 24 Nov 2008 11:56:47 -0500 Subject: [Mristudio-users] ImgVal Calculation Message-ID: <492adccf.1d4.5dd0.11366@ic.sunysb.edu> I have a question regarding the ImgVal calculation under statistical profile for fiber tracking. I got very different mean FA values (differences ranging from 0.04 to 0.1) when I tried these two methods (keeping all parameters consistent and same version of DTI): 1. Load previously saved fiber track (binary) into DTI studio, click on fiber statistics and I have for Mean of ImgVal and Std. of ImgVal 2. Using MATLAB, apply the same binary fiber track onto FA image (analyze format), calculate mean/std values for all the pixels/voxels belonging to this fiber track How are these mean ImgVal calculated? I assume it is just a mean values for all the pixels/voxels that are contained in the fiber track of interest. Thanks in advance for your help. HJ From kreisel.stefan at web.de Wed Nov 26 04:42:14 2008 From: kreisel.stefan at web.de (Stefan Kreisel) Date: Wed, 26 Nov 2008 10:42:14 +0100 Subject: [Mristudio-users] Linux / Command line Message-ID: <1987905395@web.de> Hi there. First of all I would like to thank the developers for providing the program. Its easy to use and does provide options not available in other packages (especially when acquiring unaveraged multiple runs and creating error corrected averages). One comment, one question: Here the comment: Just in case anybody has tried to get dtistudio running under linux: It works well emulated by wine (if you get the right driver for your graphic card that is). There are just a few icons missing in the task bar. Results are identical to those under windows (would not have been a surprise if things would have been different). However, things become unstable when working with larger datasets (i.e. more diffusion directions) as wine emulates only the 32bit version. Here the question: It would be supperb if one could integrate dtistudio (especially the error correction/averaging bit :)) in pipelines (e.g. LONI). As these usually run under linux and need some sort of command line interface, I was wondering if dtistudio can be accessed through (undocumented?) command line options? Otherwise a workaround could be things like GUI-scripts. Thanks. Stefan Kreisel From alfred86514-2007 at 163.com Wed Nov 26 08:51:35 2008 From: alfred86514-2007 at 163.com (alfred86514-2007) Date: Wed, 26 Nov 2008 21:51:35 +0800 (CST) Subject: [Mristudio-users] Linux / Command line In-Reply-To: <1987905395@web.de> References: <1987905395@web.de> Message-ID: <21676170.1150581227707495697.JavaMail.coremail@bj163app14.163.com> Dear Stefan Kreisel I am glad to receive your letter.But actually,I didn't know the DTIstudio very clearly.I will introduce my friend who has used it for you,if you wanted. Alfred ?2008-11-26?"Stefan Kreisel" ??? >Hi there. >First of all I would like to thank the developers for providing the program. Its easy to use and does provide options not available in other packages (especially when acquiring unaveraged multiple runs and creating error corrected averages). >One comment, one question: >Here the comment: Just in case anybody has tried to get dtistudio running under linux: It works well emulated by wine (if you get the right driver for your graphic card that is). There are just a few icons missing in the task bar. Results are identical to those under windows (would not have been a surprise if things would have been different). However, things become unstable when working with larger datasets (i.e. more diffusion directions) as wine emulates only the 32bit version. >Here the question: It would be supperb if one could integrate dtistudio (especially the error correction/averaging bit :)) in pipelines (e.g. LONI). As these usually run under linux and need some sort of command line interface, I was wondering if dtistudio can be accessed through (undocumented?) command line options? Otherwise a workaround could be things like GUI-scripts. >Thanks. >Stefan Kreisel >_______________________________________________ >Mristudio-users mailing list >Mristudio-users at mristudio.org >http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081126/fb437a0f/attachment.html From nbulak at gata.edu.tr Thu Nov 27 00:25:15 2008 From: nbulak at gata.edu.tr (=?iso-8859-9?Q?Nail_Bulakba=FE=FD?=) Date: Thu, 27 Nov 2008 07:25:15 +0200 Subject: [Mristudio-users] Vista Message-ID: <6D516B4B9E363E4DAFB7DB856A55F3EA01F97F56@gatamailsrv.gatadomain.com.tr> Hi, I have just begun to use Vista but it does not allow to open Philips Dicom files on MRI Studio. Is there any opinion? Thanks Nail -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081127/2a38d4be/attachment.html From susumu at mri.jhu.edu Thu Nov 27 08:57:01 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 27 Nov 2008 08:57:01 -0500 Subject: [Mristudio-users] Vista In-Reply-To: <6D516B4B9E363E4DAFB7DB856A55F3EA01F97F56@gatamailsrv.gatadomain.com.tr> References: <6D516B4B9E363E4DAFB7DB856A55F3EA01F97F56@gatamailsrv.gatadomain.com.tr> Message-ID: Hi Nail, I should be able to run on Vista without a problem. Which version of DtiStudio and Philips operating system are you using? We are happy to look into the issue. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Nail Bulakbasi Sent: Thursday, November 27, 2008 12:25 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Vista Hi, I have just begun to use Vista but it does not allow to open Philips Dicom files on MRI Studio. Is there any opinion? Thanks Nail -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081127/0bc0354c/attachment-0001.html From nbulak at gata.edu.tr Fri Nov 28 03:20:24 2008 From: nbulak at gata.edu.tr (=?iso-8859-9?Q?Nail_Bulakba=FE=FD?=) Date: Fri, 28 Nov 2008 10:20:24 +0200 Subject: [Mristudio-users] Vista Message-ID: <6D516B4B9E363E4DAFB7DB856A55F3EA01F97FE9@gatamailsrv.gatadomain.com.tr> Hi Susumu, I use DtiStudio Version 2.4.01 (Oct 2007) and Philips 3T Achieva with Release 2.1.5.2. 2007-09-01. Thanks Nail ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Thursday, November 27, 2008 3:57 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] Vista Hi Nail, I should be able to run on Vista without a problem. Which version of DtiStudio and Philips operating system are you using? We are happy to look into the issue. Susumu ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Nail Bulakbasi Sent: Thursday, November 27, 2008 12:25 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Vista Hi, I have just begun to use Vista but it does not allow to open Philips Dicom files on MRI Studio. Is there any opinion? Thanks Nail -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081128/3771a47b/attachment.html From nbulak at gata.edu.tr Fri Nov 28 04:30:37 2008 From: nbulak at gata.edu.tr (=?iso-8859-9?Q?Nail_Bulakba=FE=FD?=) Date: Fri, 28 Nov 2008 11:30:37 +0200 Subject: [Mristudio-users] Vista Message-ID: <6D516B4B9E363E4DAFB7DB856A55F3EA01F97FEF@gatamailsrv.gatadomain.com.tr> Hi Susumu I also need gradient table for Philips 3T Achieva. Thanks Nail ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Thursday, November 27, 2008 3:57 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] Vista Hi Nail, I should be able to run on Vista without a problem. Which version of DtiStudio and Philips operating system are you using? We are happy to look into the issue. Susumu ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Nail Bulakbasi Sent: Thursday, November 27, 2008 12:25 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Vista Hi, I have just begun to use Vista but it does not allow to open Philips Dicom files on MRI Studio. Is there any opinion? Thanks Nail -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081128/28232d64/attachment.html From grojasy at puc.cl Fri Nov 28 08:41:23 2008 From: grojasy at puc.cl (Gonzalo Rojas) Date: Fri, 28 Nov 2008 10:41:23 -0300 Subject: [Mristudio-users] Vista In-Reply-To: <6D516B4B9E363E4DAFB7DB856A55F3EA01F97FEF@gatamailsrv.gatadomain.com.tr> References: <6D516B4B9E363E4DAFB7DB856A55F3EA01F97FEF@gatamailsrv.gatadomain.com.tr> Message-ID: <492FF503.6010504@puc.cl> Hi: Here you can find the 32 directions gradient table for Philips 3T Achieva... Sincerely, Gonzalo Rojas Costa Nail Bulakba?? escribi?: > Hi Susumu > > > > I also need gradient table for Philips 3T Achieva. Thanks > > > > Nail > > > > ------------------------------------------------------------------------ > > *From:* mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] *On Behalf Of *susumu > *Sent:* Thursday, November 27, 2008 3:57 PM > *To:* 'DTI Studio, ROI Editor, Landmarker Questions/Support' > *Subject:* Re: [Mristudio-users] Vista > > > > Hi Nail, > > > > I should be able to run on Vista without a problem. Which version of > DtiStudio and Philips operating system are you using? We are happy to > look into the issue. > > > > Susumu > > > > ------------------------------------------------------------------------ > > *From:* mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] *On Behalf Of *Nail Bulakbasi > *Sent:* Thursday, November 27, 2008 12:25 AM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] Vista > > > > Hi, > > > > I have just begun to use Vista but it does not allow to open Philips > Dicom files on MRI Studio. Is there any opinion? > > Thanks > > > > Nail > > > ------------------------------------------------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Philips_3T_High_Gradient_Table.txt Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081128/543cb7a0/attachment.txt From grojasy at puc.cl Fri Nov 28 08:49:20 2008 From: grojasy at puc.cl (Gonzalo Rojas) Date: Fri, 28 Nov 2008 10:49:20 -0300 Subject: [Mristudio-users] Vista In-Reply-To: <6D516B4B9E363E4DAFB7DB856A55F3EA01F97FEF@gatamailsrv.gatadomain.com.tr> References: <6D516B4B9E363E4DAFB7DB856A55F3EA01F97FEF@gatamailsrv.gatadomain.com.tr> Message-ID: <492FF6E0.6040905@puc.cl> Hi: And the gradient table for 16 directions, Achieva 3T... Sincerely, Gonzalo Rojas Costa Nail Bulakba?? escribi?: > Hi Susumu > > > > I also need gradient table for Philips 3T Achieva. Thanks > > > > Nail > > > > ------------------------------------------------------------------------ > > *From:* mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] *On Behalf Of *susumu > *Sent:* Thursday, November 27, 2008 3:57 PM > *To:* 'DTI Studio, ROI Editor, Landmarker Questions/Support' > *Subject:* Re: [Mristudio-users] Vista > > > > Hi Nail, > > > > I should be able to run on Vista without a problem. Which version of > DtiStudio and Philips operating system are you using? We are happy to > look into the issue. > > > > Susumu > > > > ------------------------------------------------------------------------ > > *From:* mristudio-users-bounces at mristudio.org > [mailto:mristudio-users-bounces at mristudio.org] *On Behalf Of *Nail Bulakbasi > *Sent:* Thursday, November 27, 2008 12:25 AM > *To:* mristudio-users at mristudio.org > *Subject:* [Mristudio-users] Vista > > > > Hi, > > > > I have just begun to use Vista but it does not allow to open Philips > Dicom files on MRI Studio. Is there any opinion? > > Thanks > > > > Nail > > > ------------------------------------------------------------------------ > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: dir.txt Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081128/360090f3/attachment-0001.txt From lucas_lessa at yahoo.com.br Fri Nov 28 11:13:00 2008 From: lucas_lessa at yahoo.com.br (Lucas Lessa) Date: Fri, 28 Nov 2008 08:13:00 -0800 (PST) Subject: [Mristudio-users] Problem reading DICOM imagens Message-ID: <466093.7003.qm@web110208.mail.gq1.yahoo.com> Hello everyone, I'm having problem to read DICOM images from Philips Achieva Scanner. I imported the DTI data using DICOM imagens istead of RECPAR file, but when?I tried to read then in DTI Studio the system crashes. Trying to reconvert then to RECPAR file I discovered that this DICOM file uses a different header tha can't be readed by normal dicom converters. Does someone know how to convert this dicom data set to a file(s) that I can use in DTI. Thank you. Lucas Lessa. Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com From arun.bokde at tcd.ie Fri Nov 28 12:42:12 2008 From: arun.bokde at tcd.ie (Arun Bokde, PhD) Date: Fri, 28 Nov 2008 18:42:12 +0100 Subject: [Mristudio-users] problem with REC/PAR Message-ID: <5D55FC0A54F25C45B8757BE038B01D91433459120B@EXMB21.cortado.com> Hello, I am having problems reading a PAR/REC file from a Philips 3T Achieva. There are 17 volumes in the file (for the different directions + no diffusion) yet DTI studio reads it as a single volume of 1020 slices. The image sequence is in Slices. On the image parameters window it states : # of Image-Blocks: 1. It is incorrect but I cannot figure out how to correct it or to change the parameters after reading the file. Any suggestions? I am using DTI Studio (v 2.4.01) on Win XP system. Regards, Arun From susumu at mri.jhu.edu Fri Nov 28 13:02:46 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 28 Nov 2008 13:02:46 -0500 Subject: [Mristudio-users] problem with REC/PAR In-Reply-To: <5D55FC0A54F25C45B8757BE038B01D91433459120B@EXMB21.cortado.com> Message-ID: <73ap56$5220db@ipex1.johnshopkins.edu> Hi Arun, The REC file has all 17 images in one file. If you read it as "raw" image, you'd get one big 3D volume is 1020 slices. You need to specify the "REC" format and set the number of slices = 60. Then, at the bottom of the data input window, you should get the correct number of the volume, which is 17. Please try. -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Arun Bokde, PhD Sent: Friday, November 28, 2008 12:42 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] problem with REC/PAR Hello, I am having problems reading a PAR/REC file from a Philips 3T Achieva. There are 17 volumes in the file (for the different directions + no diffusion) yet DTI studio reads it as a single volume of 1020 slices. The image sequence is in Slices. On the image parameters window it states : # of Image-Blocks: 1. It is incorrect but I cannot figure out how to correct it or to change the parameters after reading the file. Any suggestions? I am using DTI Studio (v 2.4.01) on Win XP system. Regards, Arun _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Fri Nov 28 15:55:23 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 28 Nov 2008 15:55:23 -0500 Subject: [Mristudio-users] Linux / Command line In-Reply-To: <1987905395@web.de> Message-ID: <73ap56$522jv8@ipex1.johnshopkins.edu> Hi Stefan, I don't have much experience with the emulation mode, but even with the native Windows, DtiStudio gets unstable once the data size exceeds some point, if you are using the 32-bit system. With the 64-bit operating system, most of the memory-related issues should be solved. If you are using a 32-bit system, you can try "partial" slice processing. With this function, you can divide the processing in separate batches (e.g. slice 0-29 for the first batch and 30-59 for the second batch). Later you can combine the two files. As for the command-line mode, there is such a version. If you are interested in, please contact Hangyi. It is one of our future goals to strengthen the command-mode approach. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Stefan Kreisel Sent: Wednesday, November 26, 2008 4:42 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Linux / Command line Hi there. First of all I would like to thank the developers for providing the program. Its easy to use and does provide options not available in other packages (especially when acquiring unaveraged multiple runs and creating error corrected averages). One comment, one question: Here the comment: Just in case anybody has tried to get dtistudio running under linux: It works well emulated by wine (if you get the right driver for your graphic card that is). There are just a few icons missing in the task bar. Results are identical to those under windows (would not have been a surprise if things would have been different). However, things become unstable when working with larger datasets (i.e. more diffusion directions) as wine emulates only the 32bit version. Here the question: It would be supperb if one could integrate dtistudio (especially the error correction/averaging bit :)) in pipelines (e.g. LONI). As these usually run under linux and need some sort of command line interface, I was wondering if dtistudio can be accessed through (undocumented?) command line options? Otherwise a workaround could be things like GUI-scripts. Thanks. Stefan Kreisel _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From james.neeley at duke.edu Tue Dec 2 14:55:57 2008 From: james.neeley at duke.edu (Jim Neeley) Date: Tue, 02 Dec 2008 14:55:57 -0500 Subject: [Mristudio-users] DTIstudio on Vista potential problem Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081202/07feee84/attachment.html From Markus.Gschwind at unige.ch Wed Dec 3 04:19:50 2008 From: Markus.Gschwind at unige.ch (Markus Gschwind) Date: Wed, 03 Dec 2008 10:19:50 +0100 Subject: [Mristudio-users] how to make a "fiber-movie" Message-ID: Dear MRIStudioUsers, I wonder if there is a way of making a movie of the fibers in 3D view. So far, I have managed to take a movie screenshot (with Camstudio), however it is quite difficult to make it look nice. Is there another way? Thanks in advance! Markus -- Dr. med. Markus Gschwind, M.D. Laboratory for Neurology and Imaging of Cognition Dept of Neurosciences University Medical Center (CMU) 1 Michel-Servet - 1211 GENEVA - CH Tel 0041 (0) 22 379 5324 Fax 0041 (0) 22 379 5402 email: markus.gschwind at unige.ch http://labnic.unige.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081203/2b9335aa/attachment.html From hui.jing.yu at gmail.com Fri Nov 21 13:56:14 2008 From: hui.jing.yu at gmail.com (Hui Jing Yu) Date: Fri, 21 Nov 2008 13:56:14 -0500 Subject: [Mristudio-users] ImgVal Calculation Message-ID: <49270455.07025a0a.76e5.6d7d@mx.google.com> Dear DTI Studio users, I have a question regarding the ImgVal calculation under statistical profile for fiber tracking. I got very different mean FA values (differences ranging from 0.04 to 0.1) when I tried these two methods (keeping all parameters consistent and same version of DTI): 1. Load previously saved fiber track (binary) into DTI studio, click on fiber statistics and I have for Mean of ImgVal and Std. of ImgVal 2. Using MATLAB, apply the same binary fiber track onto FA image (analyze format), calculate mean/std values for all the pixels/voxels belonging to this fiber track How are these mean ImgVal calculated? I assume it is just a mean values for all the pixels/voxels that are contained in the fiber track of interest. Thanks in advance for your help. HJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081121/83b89f72/attachment-0001.html From jmckinst at nsi.edu Mon Nov 24 13:59:29 2008 From: jmckinst at nsi.edu (Jeff McKinstry) Date: Mon, 24 Nov 2008 10:59:29 -0800 (PST) Subject: [Mristudio-users] the structure of .dat file In-Reply-To: <492A795B0200006300019335@cis27.hosts.jhmi.edu> References: <492A795B0200006300019335@cis27.hosts.jhmi.edu> Message-ID: <2869.199.106.86.2.1227553169.squirrel@mercury.nsi.edu> I would like to use mristudio on dti data from a rodent brain. Will this work, or are there strong assumptions about segmentation and allignment of human brains that will prevent it from working? Do you think it will work? Thanks, Jeff From qianglf at sina.com Tue Dec 2 23:10:29 2008 From: qianglf at sina.com (qianglf at sina.com) Date: Wed, 03 Dec 2008 12:10:29 +0800 Subject: [Mristudio-users] help Message-ID: <20081203041029.7D757108804@mail3-62.sinamail.sina.com.cn>  I hope that you can give me a gradient table for 3.0T siemens MR thank you! ------------------------------------------------------------------- ???????????????????(http://space.sina.com.cn/ ) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081203/3be324a4/attachment.html From hjiang at jhmi.edu Wed Dec 3 10:16:26 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Wed, 03 Dec 2008 10:16:26 -0500 Subject: [Mristudio-users] the structure of .dat file Message-ID: <49365C7A0200006300019937@cis27.hosts.jhmi.edu> it works well, just try it. hangyi >>> Jeff McKinstry 11/24/08 1:59 PM >>> I would like to use mristudio on dti data from a rodent brain. Will this work, or are there strong assumptions about segmentation and allignment of human brains that will prevent it from working? Do you think it will work? Thanks, Jeff _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From james.neeley at duke.edu Wed Dec 3 12:25:46 2008 From: james.neeley at duke.edu (Jim Neeley) Date: Wed, 03 Dec 2008 12:25:46 -0500 Subject: [Mristudio-users] the structure of .dat file {rodent brain} In-Reply-To: <2869.199.106.86.2.1227553169.squirrel@mercury.nsi.edu> References: <492A795B0200006300019335@cis27.hosts.jhmi.edu> <2869.199.106.86.2.1227553169.squirrel@mercury.nsi.edu> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081203/39060f46/attachment.html From susumu at mri.jhu.edu Wed Dec 3 16:04:18 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 03 Dec 2008 16:04:18 -0500 Subject: [Mristudio-users] help In-Reply-To: <20081203041029.7D757108804@mail3-62.sinamail.sina.com.cn> Message-ID: <73ap56$536674@ipex1.johnshopkins.edu> Please try this (the first one). Send me the color coded map if you have any doubt about the table. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of qianglf at sina.com Sent: Tuesday, December 02, 2008 11:10 PM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] help I hope that you can give me a gradient table for 3.0T siemens MR thank you! _____ ??????????????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081203/4b606230/attachment.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: NewSiemens12.txt Url: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081203/4b606230/attachment.txt From susumu at mri.jhu.edu Wed Dec 3 16:33:57 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 03 Dec 2008 16:33:57 -0500 Subject: [Mristudio-users] the structure of .dat file In-Reply-To: <2869.199.106.86.2.1227553169.squirrel@mercury.nsi.edu> Message-ID: <73ap56$536ag7@ipex1.johnshopkins.edu> As Hangyi said, it should work. We are using DtiStudio for mouse/rat data from Bruker scanners. This is for DTI calculation. You also mentioned about segmentation and alignment. Could you elaborate more about the segmentation and alignment you want to do? Do you want to do atlas based segmentation? -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jeff McKinstry Sent: Monday, November 24, 2008 1:59 PM To: mristudio-users at mristudio.org Subject: Re: [Mristudio-users] the structure of .dat file I would like to use mristudio on dti data from a rodent brain. Will this work, or are there strong assumptions about segmentation and allignment of human brains that will prevent it from working? Do you think it will work? Thanks, Jeff _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From susumu at mri.jhu.edu Wed Dec 3 16:36:46 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 03 Dec 2008 16:36:46 -0500 Subject: [Mristudio-users] ImgVal Calculation In-Reply-To: <49270455.07025a0a.76e5.6d7d@mx.google.com> Message-ID: <73ap56$536ao0@ipex1.johnshopkins.edu> This is an interesting observation. It should be a simple binary masking. The pixel with fibers are 1 and other pixels are 0. We multiply this masking to loaded images and calculate average and STD. Do you think our values are off? If so, this is definitely something we should look into. Could you send us (not by MailingList) one fiber file and a co-registered FA map? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hui Jing Yu Sent: Friday, November 21, 2008 1:56 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ImgVal Calculation Dear DTI Studio users, I have a question regarding the ImgVal calculation under statistical profile for fiber tracking. I got very different mean FA values (differences ranging from 0.04 to 0.1) when I tried these two methods (keeping all parameters consistent and same version of DTI): 1. Load previously saved fiber track (binary) into DTI studio, click on fiber statistics and I have for Mean of ImgVal and Std. of ImgVal 2. Using MATLAB, apply the same binary fiber track onto FA image (analyze format), calculate mean/std values for all the pixels/voxels belonging to this fiber track How are these mean ImgVal calculated? I assume it is just a mean values for all the pixels/voxels that are contained in the fiber track of interest. Thanks in advance for your help. HJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081203/54944628/attachment-0001.html From junyiwang2002 at yahoo.com Wed Dec 3 17:01:13 2008 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Wed, 03 Dec 2008 14:01:13 -0800 (PST) Subject: [Mristudio-users] ImgVal Calculation References: <73ap56$536ao0@ipex1.johnshopkins.edu> Message-ID: <606492.50770.qm@web50512.mail.re2.yahoo.com> Hi Dr. Mori, I have a question to your response.? The fiber density (fiber count/voxel) is usually more than 1, so many line propagations or fibers will go through the same voxels.? When DTI Studio calculates mean FA for a reconstructed fiber tract, does it calculate based on all voxels in the fiber tract with each voxel?appear once or based on fibers so that voxels belong to multiple fibers?will be appear multiple times? Thanks, Jun Yi ________________________________ From: susumu To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wednesday, December 3, 2008 3:36:46 PM Subject: Re: [Mristudio-users] ImgVal Calculation This is an interesting observation. It should be a simple binary masking. The pixel with fibers are 1 and other pixels are 0. We multiply this masking to loaded images and calculate average and STD. Do you think our values are off? If so, this is definitely something we should look into. Could you send us (not by MailingList) one fiber file and a co-registered FA map? ? ________________________________ From:mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hui Jing Yu Sent: Friday, November 21, 2008 1:56 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ImgVal Calculation ? Dear DTI Studio users, ? I have a question regarding the ImgVal calculation under statistical profile for fiber tracking.? I got very different mean FA values (differences ranging from 0.04 to 0.1)? when I tried these two methods (keeping all parameters consistent and same version of DTI): 1.?????? Load previously saved fiber track (binary) into DTI studio, click on fiber statistics and I have ?for Mean of ImgVal and Std. of ImgVal 2.?????? Using MATLAB, apply the same binary fiber track onto FA image (analyze format), calculate mean/std values for all the pixels/voxels belonging to this fiber track How are these mean ImgVal calculated?? I assume it is just a mean values for all the pixels/voxels that are contained in the fiber track of interest. ? Thanks in advance for your help. ? HJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081203/df736ed0/attachment.html From susumu at mri.jhu.edu Wed Dec 3 17:06:45 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 03 Dec 2008 17:06:45 -0500 Subject: [Mristudio-users] ImgVal Calculation In-Reply-To: <606492.50770.qm@web50512.mail.re2.yahoo.com> Message-ID: <73ap56$536c14@ipex1.johnshopkins.edu> Good question. No matter how many reconstructed streamlines go through a pixel (1 or 10), the pixel is "1". It is a binary operation. It would be interesting to try normalized-line-number-weighted map, but DtiStudio doesn't do it. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang Sent: Wednesday, December 03, 2008 5:01 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] ImgVal Calculation Hi Dr. Mori, I have a question to your response. The fiber density (fiber count/voxel) is usually more than 1, so many line propagations or fibers will go through the same voxels. When DTI Studio calculates mean FA for a reconstructed fiber tract, does it calculate based on all voxels in the fiber tract with each voxel appear once or based on fibers so that voxels belong to multiple fibers will be appear multiple times? Thanks, Jun Yi _____ From: susumu To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wednesday, December 3, 2008 3:36:46 PM Subject: Re: [Mristudio-users] ImgVal Calculation This is an interesting observation. It should be a simple binary masking. The pixel with fibers are 1 and other pixels are 0. We multiply this masking to loaded images and calculate average and STD. Do you think our values are off? If so, this is definitely something we should look into. Could you send us (not by MailingList) one fiber file and a co-registered FA map? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hui Jing Yu Sent: Friday, November 21, 2008 1:56 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ImgVal Calculation Dear DTI Studio users, I have a question regarding the ImgVal calculation under statistical profile for fiber tracking. I got very different mean FA values (differences ranging from 0.04 to 0.1) when I tried these two methods (keeping all parameters consistent and same version of DTI): 1. Load previously saved fiber track (binary) into DTI studio, click on fiber statistics and I have for Mean of ImgVal and Std. of ImgVal 2. Using MATLAB, apply the same binary fiber track onto FA image (analyze format), calculate mean/std values for all the pixels/voxels belonging to this fiber track How are these mean ImgVal calculated? I assume it is just a mean values for all the pixels/voxels that are contained in the fiber track of interest. Thanks in advance for your help. HJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081203/87ac9890/attachment.html From hui.jing.yu at gmail.com Wed Dec 3 17:10:03 2008 From: hui.jing.yu at gmail.com (Hui Jing Yu) Date: Wed, 03 Dec 2008 17:10:03 -0500 Subject: [Mristudio-users] ImgVal Calculation In-Reply-To: <73ap56$536c14@ipex1.johnshopkins.edu> References: <606492.50770.qm@web50512.mail.re2.yahoo.com> <73ap56$536c14@ipex1.johnshopkins.edu> Message-ID: <004001c95593$e5259a10$af70ce30$@sunysb.edu> Hi, I received the following response from Hangyi before (I believe he agrees with Jun Yi) that the statistical calculation is normalized or weighted by fiber count. -----Original Message----- From: Hangyi Jiang [mailto:hjiang at jhmi.edu] Sent: Monday, November 24, 2008 1:20 PM To: hjyu at ic.sunysb.edu Subject: Re: [Mristudio-users] ImgVal Calculation hi, this kind of statistics in DTI Studio is based the fibers, not the pixels. for example, if there are three fibers passing through a voxel, the image intensity of this voxel will be counted three times when we calcualte the average image intensity along the fibers. that is why we named them as "Statistics ALONG THE FIBERS", not "..along the VOXELS that have fibers". regards, Hangyi From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Wednesday, December 03, 2008 5:07 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] ImgVal Calculation Good question. No matter how many reconstructed streamlines go through a pixel (1 or 10), the pixel is "1". It is a binary operation. It would be interesting to try normalized-line-number-weighted map, but DtiStudio doesn't do it. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang Sent: Wednesday, December 03, 2008 5:01 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] ImgVal Calculation Hi Dr. Mori, I have a question to your response. The fiber density (fiber count/voxel) is usually more than 1, so many line propagations or fibers will go through the same voxels. When DTI Studio calculates mean FA for a reconstructed fiber tract, does it calculate based on all voxels in the fiber tract with each voxel appear once or based on fibers so that voxels belong to multiple fibers will be appear multiple times? Thanks, Jun Yi _____ From: susumu To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wednesday, December 3, 2008 3:36:46 PM Subject: Re: [Mristudio-users] ImgVal Calculation This is an interesting observation. It should be a simple binary masking. The pixel with fibers are 1 and other pixels are 0. We multiply this masking to loaded images and calculate average and STD. Do you think our values are off? If so, this is definitely something we should look into. Could you send us (not by MailingList) one fiber file and a co-registered FA map? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hui Jing Yu Sent: Friday, November 21, 2008 1:56 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ImgVal Calculation Dear DTI Studio users, I have a question regarding the ImgVal calculation under statistical profile for fiber tracking. I got very different mean FA values (differences ranging from 0.04 to 0.1) when I tried these two methods (keeping all parameters consistent and same version of DTI): 1. Load previously saved fiber track (binary) into DTI studio, click on fiber statistics and I have for Mean of ImgVal and Std. of ImgVal 2. Using MATLAB, apply the same binary fiber track onto FA image (analyze format), calculate mean/std values for all the pixels/voxels belonging to this fiber track How are these mean ImgVal calculated? I assume it is just a mean values for all the pixels/voxels that are contained in the fiber track of interest. Thanks in advance for your help. HJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081203/6e3d0e12/attachment-0001.html From susumu at mri.jhu.edu Wed Dec 3 17:16:12 2008 From: susumu at mri.jhu.edu (susumu) Date: Wed, 03 Dec 2008 17:16:12 -0500 Subject: [Mristudio-users] ImgVal Calculation In-Reply-To: <004001c95593$e5259a10$af70ce30$@sunysb.edu> Message-ID: <73ap56$536c3j@ipex1.johnshopkins.edu> oooops, I'll talk with Hangyi tomorrow and clarify the issue. Maybe we should provide both methods. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hui Jing Yu Sent: Wednesday, December 03, 2008 5:10 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] ImgVal Calculation Hi, I received the following response from Hangyi before (I believe he agrees with Jun Yi) that the statistical calculation is normalized or weighted by fiber count. -----Original Message----- From: Hangyi Jiang [mailto:hjiang at jhmi.edu] Sent: Monday, November 24, 2008 1:20 PM To: hjyu at ic.sunysb.edu Subject: Re: [Mristudio-users] ImgVal Calculation hi, this kind of statistics in DTI Studio is based the fibers, not the pixels. for example, if there are three fibers passing through a voxel, the image intensity of this voxel will be counted three times when we calcualte the average image intensity along the fibers. that is why we named them as "Statistics ALONG THE FIBERS", not "..along the VOXELS that have fibers". regards, Hangyi From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Wednesday, December 03, 2008 5:07 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] ImgVal Calculation Good question. No matter how many reconstructed streamlines go through a pixel (1 or 10), the pixel is "1". It is a binary operation. It would be interesting to try normalized-line-number-weighted map, but DtiStudio doesn't do it. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang Sent: Wednesday, December 03, 2008 5:01 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] ImgVal Calculation Hi Dr. Mori, I have a question to your response. The fiber density (fiber count/voxel) is usually more than 1, so many line propagations or fibers will go through the same voxels. When DTI Studio calculates mean FA for a reconstructed fiber tract, does it calculate based on all voxels in the fiber tract with each voxel appear once or based on fibers so that voxels belong to multiple fibers will be appear multiple times? Thanks, Jun Yi _____ From: susumu To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wednesday, December 3, 2008 3:36:46 PM Subject: Re: [Mristudio-users] ImgVal Calculation This is an interesting observation. It should be a simple binary masking. The pixel with fibers are 1 and other pixels are 0. We multiply this masking to loaded images and calculate average and STD. Do you think our values are off? If so, this is definitely something we should look into. Could you send us (not by MailingList) one fiber file and a co-registered FA map? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hui Jing Yu Sent: Friday, November 21, 2008 1:56 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ImgVal Calculation Dear DTI Studio users, I have a question regarding the ImgVal calculation under statistical profile for fiber tracking. I got very different mean FA values (differences ranging from 0.04 to 0.1) when I tried these two methods (keeping all parameters consistent and same version of DTI): 1. Load previously saved fiber track (binary) into DTI studio, click on fiber statistics and I have for Mean of ImgVal and Std. of ImgVal 2. Using MATLAB, apply the same binary fiber track onto FA image (analyze format), calculate mean/std values for all the pixels/voxels belonging to this fiber track How are these mean ImgVal calculated? I assume it is just a mean values for all the pixels/voxels that are contained in the fiber track of interest. Thanks in advance for your help. HJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081203/4eeaea57/attachment.html From susumu at mri.jhu.edu Thu Dec 4 11:33:47 2008 From: susumu at mri.jhu.edu (susumu) Date: Thu, 04 Dec 2008 11:33:47 -0500 Subject: [Mristudio-users] ImgVal Calculation In-Reply-To: <004001c95593$e5259a10$af70ce30$@sunysb.edu> Message-ID: <73ap56$538hc4@ipex1.johnshopkins.edu> Ok, I confirmed that I was wrong. DtiStudio does quantification for each streamline. As a result, a pixel that contains 10 streamlines is 10 times more weighted than another pixel that contains only one streamline. Sorry for the confusion and I think this explains the HJ's question about the discrepancy. If you want the 1/0 binarized approach without weighting, you can save the fiber coordinates as a "binary" data, load it to RoiEditor, together with an FA map. This will give you the tract-specific FA reports (all pixels, projection to axial, sagittal, and coronal). We will incorporate the choice in DtiStudio. Please let me know if you have further questions. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hui Jing Yu Sent: Wednesday, December 03, 2008 5:10 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] ImgVal Calculation Hi, I received the following response from Hangyi before (I believe he agrees with Jun Yi) that the statistical calculation is normalized or weighted by fiber count. -----Original Message----- From: Hangyi Jiang [mailto:hjiang at jhmi.edu] Sent: Monday, November 24, 2008 1:20 PM To: hjyu at ic.sunysb.edu Subject: Re: [Mristudio-users] ImgVal Calculation hi, this kind of statistics in DTI Studio is based the fibers, not the pixels. for example, if there are three fibers passing through a voxel, the image intensity of this voxel will be counted three times when we calcualte the average image intensity along the fibers. that is why we named them as "Statistics ALONG THE FIBERS", not "..along the VOXELS that have fibers". regards, Hangyi From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu Sent: Wednesday, December 03, 2008 5:07 PM To: 'DTI Studio, ROI Editor, Landmarker Questions/Support' Subject: Re: [Mristudio-users] ImgVal Calculation Good question. No matter how many reconstructed streamlines go through a pixel (1 or 10), the pixel is "1". It is a binary operation. It would be interesting to try normalized-line-number-weighted map, but DtiStudio doesn't do it. _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jun Yi Wang Sent: Wednesday, December 03, 2008 5:01 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] ImgVal Calculation Hi Dr. Mori, I have a question to your response. The fiber density (fiber count/voxel) is usually more than 1, so many line propagations or fibers will go through the same voxels. When DTI Studio calculates mean FA for a reconstructed fiber tract, does it calculate based on all voxels in the fiber tract with each voxel appear once or based on fibers so that voxels belong to multiple fibers will be appear multiple times? Thanks, Jun Yi _____ From: susumu To: "DTI Studio, ROI Editor, Landmarker Questions/Support" Sent: Wednesday, December 3, 2008 3:36:46 PM Subject: Re: [Mristudio-users] ImgVal Calculation This is an interesting observation. It should be a simple binary masking. The pixel with fibers are 1 and other pixels are 0. We multiply this masking to loaded images and calculate average and STD. Do you think our values are off? If so, this is definitely something we should look into. Could you send us (not by MailingList) one fiber file and a co-registered FA map? _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Hui Jing Yu Sent: Friday, November 21, 2008 1:56 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] ImgVal Calculation Dear DTI Studio users, I have a question regarding the ImgVal calculation under statistical profile for fiber tracking. I got very different mean FA values (differences ranging from 0.04 to 0.1) when I tried these two methods (keeping all parameters consistent and same version of DTI): 1. Load previously saved fiber track (binary) into DTI studio, click on fiber statistics and I have for Mean of ImgVal and Std. of ImgVal 2. Using MATLAB, apply the same binary fiber track onto FA image (analyze format), calculate mean/std values for all the pixels/voxels belonging to this fiber track How are these mean ImgVal calculated? I assume it is just a mean values for all the pixels/voxels that are contained in the fiber track of interest. Thanks in advance for your help. HJ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081204/19db0952/attachment-0001.html From chenqin8124 at gmail.com Thu Dec 4 22:12:18 2008 From: chenqin8124 at gmail.com (June.Chen) Date: Fri, 05 Dec 2008 11:12:18 +0800 Subject: [Mristudio-users] how to build makeaheader Message-ID: Hi, all Maybe I ask a simple question. I want to normalize one subject to the FA template in Landmarker 1.4 version. But when I press the linear of Automatic Image registration, it alerts me to download AIR and build a makeaheader.exe. I have no idea how to do this. Could anyone kindly send me the file to tell me how to build this? Thanks very much. June -- June Chen M.D. Department of Neurology West China Hospital Sichuan University Wai Nan Guo Xue Lane 37# Chengdu,P.R.China,610041 Tel: +86 8542 3960 (Lab) Fax: +86 8542 2549 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081205/b52a6e87/attachment.html From Markus.Gschwind at unige.ch Fri Dec 5 02:46:55 2008 From: Markus.Gschwind at unige.ch (Markus Gschwind) Date: Fri, 05 Dec 2008 08:46:55 +0100 Subject: [Mristudio-users] how to make a "fiber-movie" In-Reply-To: References: Message-ID: Dear MRIStudioUsers, I wonder if there is a way of making a movie of the fibers in 3D view. So far, I have managed to take a movie screenshot (with Camstudio), however it is quite difficult to make it look nice. Is there another way? Thanks in advance! Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081205/772e2995/attachment.html From susumu at mri.jhu.edu Fri Dec 5 09:11:54 2008 From: susumu at mri.jhu.edu (susumu) Date: Fri, 05 Dec 2008 09:11:54 -0500 Subject: [Mristudio-users] how to make a "fiber-movie" In-Reply-To: Message-ID: <73ap56$53ghj2@ipex1.johnshopkins.edu> DtiStudio itself doesn't have a function to create a movie. I think the screenshot you described could be the only way. Sorry Markus. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Markus Gschwind Sent: Friday, December 05, 2008 2:47 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] how to make a "fiber-movie" Dear MRIStudioUsers, I wonder if there is a way of making a movie of the fibers in 3D view. So far, I have managed to take a movie screenshot (with Camstudio), however it is quite difficult to make it look nice. Is there another way? Thanks in advance! Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081205/cf3da61e/attachment.html From megjim1 at gmail.com Fri Dec 5 17:57:35 2008 From: megjim1 at gmail.com (Jim Li) Date: Fri, 05 Dec 2008 16:57:35 -0600 Subject: [Mristudio-users] about effect of masking Message-ID: <575b44a30812051457n67e9f82dq66bb41a7bc092ce3@mail.gmail.com> Hi all, Can anybody give me a hint? In the DTIstudio software I clicked the "Tensor, Color map, etc" button in the "Calculation" section of the "DtiMap" tab. Then, from the pop-out window called "DTI-Map Options", I saw a choice called "Select a mask-image". Under what situation should we use that choice? Should it be a default choice when the brain has some lesions, given that the lesional area can be at about the same level as the background noise level and thus can be easily wiped out even if we choose a low background noise level from which to create a mask-image? Thanks a lot, Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081205/778b8800/attachment.html From susumu at mri.jhu.edu Fri Dec 5 19:57:29 2008 From: susumu at mri.jhu.edu (susumu at mri.jhu.edu) Date: Sat, 06 Dec 2008 00:57:29 +0000 Subject: [Mristudio-users] about effect of masking Message-ID: <2097558458-1228525049-cardhu_decombobulator_blackberry.rim.net-1593300881-@bxe032.bisx.prod.on.blackberry> Hi Jim, When you do tensor calculation, you want to mask out the areas outside the brain. The easiest way is to use the threshold value to mask out the noise floor. This approach however leaves a lot of extra-brain tissues. RoiEditor (and many other programs) offers much more tools to define the brain as a binary map and remove other tissues using tools such as region growing and skull-strip tools. If you have any binary masking generated by another program you can load such a file through this function. Susumu ------Original Message------ From: Jim Li Sender: mristudio-users-bounces at mristudio.org To: DTI Studio, ROI Editor, Landmarker Questions/Support ReplyTo: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] about effect of masking Sent: Dec 5, 2008 17:57 Hi all, ? Can anybody give me a hint? ? In the ?DTIstudio software I clicked the "Tensor, Color map, etc" button in the "Calculation" section of the "DtiMap" tab. Then, from the?pop-out window called "DTI-Map Options", I saw a choice called "Select a mask-image". Under what situation should we use that choice? Should it be a default choice when the brain has some lesions, given that?the lesional area?can be at about the same level as the background?noise level and thus can be easily wiped out even if we choose a low background noise level from which?to create a mask-image? ? ? Thanks a lot, ? Jim _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users Sent via BlackBerry by AT&T From megjim1 at gmail.com Mon Dec 8 13:53:10 2008 From: megjim1 at gmail.com (Jim Li) Date: Mon, 08 Dec 2008 12:53:10 -0600 Subject: [Mristudio-users] about effect of masking Message-ID: <575b44a30812081053l8ccd153q6c62e54c72f1eca7@mail.gmail.com> Hi Susumu, Thanks a lot for your information. I tried the skull-stripping of ROIEditor using the default setting. The result is not bad, but I hope to add/remove some areas manually on top of the outcoming mask file to define a better mask. Also I hope to better understand the default parameters in the skull-stripping algorithm so I can tailor them to my need. I wish there's an instruction manual for ROIEditor that can tell me all of these... Cheers, Jim ----------------------------------------- Hi Jim, When you do tensor calculation, you want to mask out the areas outside the brain. The easiest way is to use the threshold value to mask out the noise floor. This approach however leaves a lot of extra-brain tissues. RoiEditor (and many other programs) offers much more tools to define the brain as a binary map and remove other tissues using tools such as region growing and skull-strip tools. If you have any binary masking generated by another program you can load such a file through this function. Susumu ------Original Message------ From: Jim Li Sender: mristudio-users-bounces at mristudio.org To: DTI Studio, ROI Editor, Landmarker Questions/Support ReplyTo: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] about effect of masking Sent: Dec 5, 2008 17:57 Hi all, Can anybody give me a hint? In the DTIstudio software I clicked the "Tensor, Color map, etc" button in the "Calculation" section of the "DtiMap" tab. Then, from the pop-out window called "DTI-Map Options", I saw a choice called "Select a mask-image". Under what situation should we use that choice? Should it be a default choice when the brain has some lesions, given that the lesional area can be at about the same level as the background noise level and thus can be easily wiped out even if we choose a low background noise level from which to create a mask-image? Thanks a lot, Jim _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users Sent via BlackBerry by AT&T -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081208/622f011c/attachment-0001.html From susumu at mri.jhu.edu Mon Dec 8 18:24:48 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 08 Dec 2008 18:24:48 -0500 Subject: [Mristudio-users] DTIstudio on Vista potential problem In-Reply-To: Message-ID: <73ap56$5476d3@ipex1.johnshopkins.edu> Hi Jim, ? Can I expect problems on any listed vendor for any specific MRI version on a XP laptop? vista laptop? > DtiStudio should be able to process all these data. Vista laptop should be fine. The only issue could be memory. If you are using a 32-bit XP or Vista and/or only 1GB memory, it happens frequently. I have a vista laptop which I could use but not yet loaded, for any specific MRI version? > No, XP and Vista use the same version of DtiStudio. There are 32 and 64-bit versions. ? Can anyone send me Philips gradient files (should be 6 direction) or are they in the rec files? No the gradient orientation is not specified in the Philips REC/PAR file. Jon Farrell has a nice web-based software to make a gradient table for Philips scanner based on imaging parameters and the version of the operating system. Jon, could you send us the URL of your software? I am attempting to run without success an Indiana site study 0008,0020 Study Date: 20040625 0008,0070 Manufacturer: GE MEDICAL SYSTEMS 0008,103E Series Description: dti scheme9 0018,1020 Software Versions(s): 09 without imbedded gradient vectors and using Bessar normalized gradients. It loads but I get no FA map. on a 3 yr old laptop and 2 2 yr old PCs installed in an MRI research room. You need to get a correct gradient table because it is not always available through data headers. memory is OK, Any graphics card requirements? No, DtiStudio is not graphics-heavy, but depending on the size of your data, you need a decent amount of RAM. Susumu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081208/e8b4176d/attachment.html From james.neeley at duke.edu Tue Dec 9 16:40:42 2008 From: james.neeley at duke.edu (Jim Neeley) Date: Tue, 09 Dec 2008 16:40:42 -0500 Subject: [Mristudio-users] DTIstudio on Vista potential problem In-Reply-To: <73ap56$5476d3@ipex1.johnshopkins.edu> References: <73ap56$5476d3@ipex1.johnshopkins.edu> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081209/95632413/attachment.html From james.neeley at duke.edu Tue Dec 9 17:23:36 2008 From: james.neeley at duke.edu (Jim Neeley) Date: Tue, 09 Dec 2008 17:23:36 -0500 Subject: [Mristudio-users] DTIstudio on Vista potential problem In-Reply-To: <73ap56$5476d3@ipex1.johnshopkins.edu> References: <73ap56$5476d3@ipex1.johnshopkins.edu> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081209/0c57787c/attachment.html From susumu at mri.jhu.edu Tue Dec 9 18:14:50 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 09 Dec 2008 18:14:50 -0500 Subject: [Mristudio-users] about effect of masking In-Reply-To: <575b44a30812081053l8ccd153q6c62e54c72f1eca7@mail.gmail.com> Message-ID: <73ap56$54g878@ipex1.johnshopkins.edu> There are three ways for skull stripping in RoiEditor. 1) Simple thresholding: This produce the same results as the DtiStudio's masking function. 2) Region growing: if you use this function together with b0 or average(all DWIs), you should be able to achieve very decent skull stripping. We use this routinely. We use average(DWIs) often. 3) Skull-stripping button: The region growing may leak out to some tissues outside the brain if high-intensity areas of the brain and outside tissues are connected. This skull-stripping function poses some restrictions in the shape of the object. Namely, the brain surface should be smooth without anything budding out in an extreme manner. If the region growing function consistently leaks out and defines tissues outside the brain, you can try this function. This function also allows you to load "second image", such as an anatomical T2. The brain contour defined by b0 or average(DWIs) will be superimposed on the second image (please note, the brain contour will not align perfectly because of subject motion and DTI (EPI)-related brain distortion). This b0-defined contour then will be used as an initial guess of the brain contour of the second image and do the skull strip. We use this function for skull-strip of co-registered T2 (and T1). It works decently, but not perfect (I've never seen any perfect automated skull-strip that works for all images anyway). susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jim Li Sent: Monday, December 08, 2008 1:53 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] about effect of masking Hi Susumu, Thanks a lot for your information. I tried the skull-stripping of ROIEditor using the default setting. The result is not bad, but I hope to add/remove some areas manually on top of the outcoming mask file to define a better mask. Also I hope to better understand the default parameters in the skull-stripping algorithm so I can tailor them to my need. I wish there's an instruction manual for ROIEditor that can tell me all of these... Cheers, Jim ----------------------------------------- Hi Jim, When you do tensor calculation, you want to mask out the areas outside the brain. The easiest way is to use the threshold value to mask out the noise floor. This approach however leaves a lot of extra-brain tissues. RoiEditor (and many other programs) offers much more tools to define the brain as a binary map and remove other tissues using tools such as region growing and skull-strip tools. If you have any binary masking generated by another program you can load such a file through this function. Susumu ------Original Message------ From: Jim Li Sender: mristudio-users-bounces at mristudio.org To: DTI Studio, ROI Editor, Landmarker Questions/Support ReplyTo: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] about effect of masking Sent: Dec 5, 2008 17:57 Hi all, Can anybody give me a hint? In the DTIstudio software I clicked the "Tensor, Color map, etc" button in the "Calculation" section of the "DtiMap" tab. Then, from the pop-out window called "DTI-Map Options", I saw a choice called "Select a mask-image". Under what situation should we use that choice? Should it be a default choice when the brain has some lesions, given that the lesional area can be at about the same level as the background noise level and thus can be easily wiped out even if we choose a low background noise level from which to create a mask-image? Thanks a lot, Jim _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users Sent via BlackBerry by AT&T -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081209/52677cc3/attachment-0001.html From zhou1 at jhmi.edu Tue Dec 9 19:34:53 2008 From: zhou1 at jhmi.edu (Zhipeng Hou) Date: Tue, 09 Dec 2008 19:34:53 -0500 Subject: [Mristudio-users] DTIstudio on Vista potential problem In-Reply-To: References: <73ap56$5476d3@ipex1.johnshopkins.edu> Message-ID: <568cc7760812091634s16bc2887j240e8512436759b0@mail.gmail.com> Use x86 for win32 system: https://www.mristudio.org/download/binaries/DtiStudio-latest-x86.exe On Tue, Dec 9, 2008 at 5:23 PM, Jim Neeley wrote: > Tried 64 bit version, PC will not load it - says: > "DtiStudio-latest-x64.exe is not a valid Win32 application" > > > > Thanks Jim Neeley, > Neuroradiology research assistant, Cell: 919-696-6105 FAX: 919 684-7153 > Office: 684-7434, MRI: 684-7405 Snail: DUMC 3808 > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081209/793a8b00/attachment.html From ksea03 at gmail.com Tue Dec 9 23:07:19 2008 From: ksea03 at gmail.com (eunkyung kim) Date: Wed, 10 Dec 2008 13:07:19 +0900 Subject: [Mristudio-users] how can I make vector map? Message-ID: Dear all Hello! I'm trying to find a proper way to operate DTI studio. I have GE dicom data format. However, I don't know how can I make vector and anisotropy maps. When I read DTI manual, "Image processing" says that to generate color-code maps I must load vector and anisotropy maps. But I can't find these maps. Please let me know how to save vector maps or anisotropy maps. Thanks a lot. >From Eun kyung Kim -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081210/ae5053ae/attachment.html From hjiang at jhmi.edu Wed Dec 10 10:18:14 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Wed, 10 Dec 2008 10:18:14 -0500 Subject: [Mristudio-users] how can I make vector map? Message-ID: <493F97660200006300019E21@cis27.hosts.jhmi.edu> hi, eigen vector and anisotropy maps are consequences of tensor calculation. please goto "File->DTI Mapping" load the images in, and then goto "DTI" tab, clicking "Tensor, color map etc.." button to get them. you can also refer to the user manual to get some ideals. hope it helps, >>> eunkyung kim 12/09/08 11:07 PM >>> Dear all Hello! I'm trying to find a proper way to operate DTI studio. I have GE dicom data format. However, I don't know how can I make vector and anisotropy maps. When I read DTI manual, "Image processing" says that to generate color-code maps I must load vector and anisotropy maps. But I can't find these maps. Please let me know how to save vector maps or anisotropy maps. Thanks a lot. >From Eun kyung Kim From james.neeley at duke.edu Wed Dec 10 11:24:35 2008 From: james.neeley at duke.edu (Jim Neeley) Date: Wed, 10 Dec 2008 11:24:35 -0500 Subject: [Mristudio-users] DTIstudio on Vista potential problem In-Reply-To: <568cc7760812091634s16bc2887j240e8512436759b0@mail.gmail.com> References: <73ap56$5476d3@ipex1.johnshopkins.edu> <568cc7760812091634s16bc2887j240e8512436759b0@mail.gmail.com> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081210/c3665967/attachment.html From ksea03 at gmail.com Thu Dec 11 02:38:01 2008 From: ksea03 at gmail.com (eunkyung kim) Date: Thu, 11 Dec 2008 16:38:01 +0900 Subject: [Mristudio-users] how can I make vector map? In-Reply-To: <493F97660200006300019E21@cis27.hosts.jhmi.edu> References: <493F97660200006300019E21@cis27.hosts.jhmi.edu> Message-ID: thank you for you commnets. It helped a lot! 2008/12/11 Hangyi Jiang > hi, > > eigen vector and anisotropy maps are consequences of tensor calculation. > please goto "File->DTI Mapping" load the images in, and then goto "DTI" tab, > clicking "Tensor, color map etc.." button to get them. you can also refer > to the user manual to get some ideals. > > hope it helps, > > > > > > >>> eunkyung kim 12/09/08 11:07 PM >>> > Dear all > > Hello! I'm trying to find a proper way to operate DTI studio. > I have GE dicom data format. > However, I don't know how can I make vector and anisotropy maps. > When I read DTI manual, "Image processing" says that to generate color-code > maps I must load vector and anisotropy maps. > But I can't find these maps. Please let me know how to save vector maps or > anisotropy maps. > > Thanks a lot. > > >From Eun kyung Kim > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081211/7ffa9c04/attachment.html From ksea03 at gmail.com Thu Dec 11 05:19:39 2008 From: ksea03 at gmail.com (eunkyung kim) Date: Thu, 11 Dec 2008 19:19:39 +0900 Subject: [Mristudio-users] The difference of ROI tracking and Fiber tracking Message-ID: Dear all Hi. I have tried to Fiber tracking(FACT), but I wonder the difference between two things. When I use ROI-shape button, I can see some ROI tracts drawing. But as you know, DTI-Studio has Fiber Tracking(FACT) button, too. I can't see the difference between two things. what can I do to solve the problems? The processes I used 1. Loading FA and vector map and generate color map 2. In Fiber tab, draw ROI tracts. (selected, show fibers on 2D images, ROI-Drawing Enable, Multiple-View of ROI) 3. save maps in two ways. 1)ROI-Operation save (Binary maps) 2)using save button next to the Fiber tracking(FACT) 4. Fiber tracking(FACT) button 5. load Binary map using load buttion in the ROI-Operation Then I should find some thing changes on screen, but I don't. Please let me know.. Eun kyung Kim -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081211/dfc10102/attachment.html From hjiang at jhmi.edu Thu Dec 11 10:52:59 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Thu, 11 Dec 2008 10:52:59 -0500 Subject: [Mristudio-users] The difference of ROI tracking and Fiber tracking Message-ID: <4940F10B0200006300019F1F@cis27.hosts.jhmi.edu> hi, if I'm right, your first step is by using "File->Fiber Tracking" command. if so, using this command or button "Fiber tracking(FACT)" will start a same routine for fiber tracking. "File->Fiber Tracking" command is designed when you do fiber tracking in the first begining, while "FACT" is used when you want to do it again with different parameters. hangyi >>> eunkyung kim 12/11/08 5:19 AM >>> Dear all Hi. I have tried to Fiber tracking(FACT), but I wonder the difference between two things. When I use ROI-shape button, I can see some ROI tracts drawing. But as you know, DTI-Studio has Fiber Tracking(FACT) button, too. I can't see the difference between two things. what can I do to solve the problems? The processes I used 1. Loading FA and vector map and generate color map 2. In Fiber tab, draw ROI tracts. (selected, show fibers on 2D images, ROI-Drawing Enable, Multiple-View of ROI) 3. save maps in two ways. 1)ROI-Operation save (Binary maps) 2)using save button next to the Fiber tracking(FACT) 4. Fiber tracking(FACT) button 5. load Binary map using load buttion in the ROI-Operation Then I should find some thing changes on screen, but I don't. Please let me know.. Eun kyung Kim From megjim1 at gmail.com Thu Dec 11 18:28:21 2008 From: megjim1 at gmail.com (Jim Li) Date: Thu, 11 Dec 2008 17:28:21 -0600 Subject: [Mristudio-users] about effect of masking Message-ID: <575b44a30812111528n66843989qd76dcad3747986ad@mail.gmail.com> Hi Susumu, Thanks a lot for your detailed instruction. I'll try them. Jim ----------------------------- There are three ways for skull stripping in RoiEditor. 1) Simple thresholding: This produce the same results as the DtiStudio's masking function. 2) Region growing: if you use this function together with b0 or average(all DWIs), you should be able to achieve very decent skull stripping. We use this routinely. We use average(DWIs) often. 3) Skull-stripping button: The region growing may leak out to some tissues outside the brain if high-intensity areas of the brain and outside tissues are connected. This skull-stripping function poses some restrictions in the shape of the object. Namely, the brain surface should be smooth without anything budding out in an extreme manner. If the region growing function consistently leaks out and defines tissues outside the brain, you can try this function. This function also allows you to load "second image", such as an anatomical T2. The brain contour defined by b0 or average(DWIs) will be superimposed on the second image (please note, the brain contour will not align perfectly because of subject motion and DTI (EPI)-related brain distortion). This b0-defined contour then will be used as an initial guess of the brain contour of the second image and do the skull strip. We use this function for skull-strip of co-registered T2 (and T1). It works decently, but not perfect (I've never seen any perfect automated skull-strip that works for all images anyway). susumu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081211/03e50463/attachment.html From ksea03 at gmail.com Thu Dec 11 20:21:57 2008 From: ksea03 at gmail.com (eunkyung kim) Date: Fri, 12 Dec 2008 10:21:57 +0900 Subject: [Mristudio-users] The difference of ROI tracking and Fiber tracking In-Reply-To: <4940F10B0200006300019F1F@cis27.hosts.jhmi.edu> References: <4940F10B0200006300019F1F@cis27.hosts.jhmi.edu> Message-ID: Thank you! 2008/12/12 Hangyi Jiang > hi, > > if I'm right, your first step is by using "File->Fiber Tracking" command. > > if so, using this command or button "Fiber tracking(FACT)" will start a > same routine for fiber tracking. > > "File->Fiber Tracking" command is designed when you do fiber tracking in > the first begining, while "FACT" is used when you want to do it again with > different parameters. > > hangyi > > > > > > >>> eunkyung kim 12/11/08 5:19 AM >>> > Dear all > > Hi. I have tried to Fiber tracking(FACT), but I wonder the difference > between two things. > When I use ROI-shape button, I can see some ROI tracts drawing. > But as you know, DTI-Studio has Fiber Tracking(FACT) button, too. > I can't see the difference between two things. what can I do to solve the > problems? > > The processes I used > 1. Loading FA and vector map and generate color map > 2. In Fiber tab, draw ROI tracts. (selected, show fibers on 2D images, > ROI-Drawing Enable, Multiple-View of ROI) > 3. save maps in two ways. 1)ROI-Operation save (Binary maps) > 2)using save button next to the Fiber > tracking(FACT) > 4. Fiber tracking(FACT) button > 5. load Binary map using load buttion in the ROI-Operation > Then I should find some thing changes on screen, but I don't. > Please let me know.. > > > Eun kyung Kim > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081212/40d982da/attachment.html From james.neeley at duke.edu Sun Dec 14 23:51:23 2008 From: james.neeley at duke.edu (Jim Neeley) Date: Sun, 14 Dec 2008 23:51:23 -0500 Subject: [Mristudio-users] XP laptop and vista usage In-Reply-To: <73ap56$522jv8@ipex1.johnshopkins.edu> References: <73ap56$522jv8@ipex1.johnshopkins.edu> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081214/0f263d08/attachment.html From albertleemon at gmail.com Mon Dec 15 09:32:33 2008 From: albertleemon at gmail.com (=?BIG5?B?p/Wycg==?=) Date: Mon, 15 Dec 2008 22:32:33 +0800 Subject: [Mristudio-users] Is there any method to load NIfTi data in DTI Mapping module? Message-ID: <80363be10812150632y5c8e4181l143ebb23bf42869b@mail.gmail.com> Dear all Hi. If I use the AIR module to do eddy correction, It always crashes! So I turn to FlAIR module in FSL. If It means I can't use DTIStudio anymore in the follow-up produces?Is there any method to load NIfTi data in DTI Mapping module? Which software can convert the NIfTi data into Raw or NRRD format?Please let me know.. Thanks a lot! -- albert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/5b9c5682/attachment.html From junyiwang2002 at yahoo.com Mon Dec 15 10:40:36 2008 From: junyiwang2002 at yahoo.com (Jun Yi Wang) Date: Mon, 15 Dec 2008 07:40:36 -0800 (PST) Subject: [Mristudio-users] Is there any method to load NIfTi data in DTI Mapping module? References: <80363be10812150632y5c8e4181l143ebb23bf42869b@mail.gmail.com> Message-ID: <836116.88772.qm@web50504.mail.re2.yahoo.com> Hi Albert, I just use FSL to convert?nifti-gz to?analyze and use DTI Studio to convert analyze to raw format. Jun Yi ________________________________ From: ?? To: mristudio-users at mristudio.org Sent: Monday, December 15, 2008 8:32:33 AM Subject: [Mristudio-users] Is there any method to load NIfTi data in DTI Mapping module? Dear all? ? Hi. If I use the AIR module to do eddy correction, It always crashes! So I turn to FlAIR module in FSL. If It means I can't use DTIStudio anymore in the follow-up produces?Is there any method to load NIfTi data in DTI Mapping module?? Which software can convert the ?NIfTi data into ?Raw or NRRD format?Please let me know.. Thanks a lot! -- albert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/90dc99cf/attachment.html From susumu at mri.jhu.edu Mon Dec 15 11:00:21 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 15 Dec 2008 11:00:21 -0500 Subject: [Mristudio-users] Is there any method to load NIfTi data in DTIMapping module? In-Reply-To: <80363be10812150632y5c8e4181l143ebb23bf42869b@mail.gmail.com> Message-ID: <73ap56$5600gi@ipex1.johnshopkins.edu> Hi Albert, there could be three reasons; 1) memory issue: To check if this is the reason, please specify a small amount of slices to be processed in the "Slices to be processed" box in the initial data import window. If the AIR works in this way, you have memory shortage. 2) error in your gradient table or image dimensions. After you load all the data, please check if you have the correct number of images. For example, if you have Siemens 12-orientation data, you should have 13 3D data. Small mistakes (such as ";" instead of ":" and missing ",") are difficult to catch. After reading all the data, you can close the window and reopen the initial data import window. The program still remembers that exact gradient table you input. If you have any error in the previous table, you can see how DtiStudio interpreted the table. For example, if you type "3: 0, 1 0" instead of "3: 0, 1, 0" (missing ","), you see "3: 0, 0, 0" in the re-opened window. 3) you may not have the AIR executable file. Please make sure you have it. AIR is not included in DtiStudio. DtiStudio calls the AIR executable file. If none of these work, please let us know. We have happy to take a look at your data. We also have a beta version that can read Nifty data, although it is not for raw DTI data, which are usually DICOM. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of ?? Sent: Monday, December 15, 2008 9:33 AM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Is there any method to load NIfTi data in DTIMapping module? Dear all Hi. If I use the AIR module to do eddy correction, It always crashes! So I turn to FlAIR module in FSL. If It means I can't use DTIStudio anymore in the follow-up produces?Is there any method to load NIfTi data in DTI Mapping module? Which software can convert the NIfTi data into Raw or NRRD format?Please let me know.. Thanks a lot! -- albert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/b2468aba/attachment-0001.html From GKlein2 at NSHS.edu Mon Dec 15 11:15:19 2008 From: GKlein2 at NSHS.edu (Klein, Gad) Date: Mon, 15 Dec 2008 11:15:19 -0500 Subject: [Mristudio-users] Unsubscribe References: <73ap56$5600gi@ipex1.johnshopkins.edu> Message-ID: Please unsubscribe me from this mailing list. Thank you. Gad Klein Neuropsychology Research Fellow Comprehensive Epilepsy Center Long Island Jewish Medical Center 270-05 76th Avenue New Hyde Park, New York 11040 Phone: (718) 470-5005 ext. 60846 --------------------------------------------------------------------------------- The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or 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 communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3612 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/f64facae/attachment.bin From susumu at mri.jhu.edu Mon Dec 15 11:22:03 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 15 Dec 2008 11:22:03 -0500 Subject: [Mristudio-users] XP laptop and vista usage In-Reply-To: Message-ID: <73ap56$560891@ipex1.johnshopkins.edu> Hi Jim, When memory shortage happens, usually DtiStudio clashes. It doesn't give wrong FA maps, I believe. Do you mean the same dataset can be processed in one computer but not in the other? To check the memory issue, as I mentioned in the previous email I sent this morning, you can use "Slices to be processed" window to specify only few slices to be processed. If this gives you correct FA maps, but not when the entire slices are processed, then it is definitely the memory issue. The most common mistake that would give strange FA maps is typos and syntax errors in the gradient table. Again please refer to the email I sent out today. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Jim Neeley Sent: Sunday, December 14, 2008 11:51 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] XP laptop and vista usage My problem with DiStudio appears to be main memory related. I get bad data on the FA map with all values of FA 0 or .7 and higher on one machine the problemgoes away when I remove other memory users. I would like to know if there is a way to flag memory shortage other than obvoiusly bad data. I had a memory limit warning using ImageJ with a link for help. But with DtiStudio, I just got snowy or blizzard covered images. Will try more. I have an idea for using the 16x16 array for finding the best contiguous area which fits a required ROI size. Thanks Jim Neeley, Neuroradiology research assistant, Cell: 919-696-6105 FAX: 919 684-7153 Office: 684-7434, MRI: 684-7405 Snail: DUMC 3808 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/9a114187/attachment.html From hjiang at jhmi.edu Mon Dec 15 11:24:33 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Mon, 15 Dec 2008 11:24:33 -0500 Subject: [Mristudio-users] XP laptop and vista usage Message-ID: <49463E71020000630001A157@cis27.hosts.jhmi.edu> if IT IS the memory problem, you can process partial of image-slices when you do tensor calculation, and then combine them together later. hangyi >>> Jim Neeley 12/14/08 11:51 PM >>> From hjiang at jhmi.edu Mon Dec 15 11:27:06 2008 From: hjiang at jhmi.edu (Hangyi Jiang) Date: Mon, 15 Dec 2008 11:27:06 -0500 Subject: [Mristudio-users] Is there any method to load NIfTi data in DTI Mapping module? Message-ID: <49463F0A020000630001A15B@cis27.hosts.jhmi.edu> save the Nifti as the dual files (.hdr/.img), and then load them into DTI Studio as Analyze format. >>> ?? 12/15/08 9:32 AM >>> Dear all Hi. If I use the AIR module to do eddy correction, It always crashes! So I turn to FlAIR module in FSL. If It means I can't use DTIStudio anymore in the follow-up produces?Is there any method to load NIfTi data in DTI Mapping module? Which software can convert the NIfTi data into Raw or NRRD format?Please let me know.. Thanks a lot! -- albert From Michele.Wessa at zi-mannheim.de Mon Dec 15 11:36:18 2008 From: Michele.Wessa at zi-mannheim.de (Wessa, Michele) Date: Mon, 15 Dec 2008 17:36:18 +0100 Subject: [Mristudio-users] Unsubscribe References: <73ap56$5600gi@ipex1.johnshopkins.edu> Message-ID: Please unsubscribe me from this mailing list. Thank you. ------------------------------------------- Dr. Mich?le Wessa Institut f?r Neuropsychologie und Klinische Psychologie Ruprecht-Karls Universit?t Heidelberg Zentralinstitut f?r Seelische Gesundheit J5 68159 Mannheim -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3784 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/92543d35/attachment-0001.bin From Mark.Boyett at manchester.ac.uk Mon Dec 15 11:31:31 2008 From: Mark.Boyett at manchester.ac.uk (MARK BOYETT) Date: Mon, 15 Dec 2008 16:31:31 +0000 Subject: [Mristudio-users] Unsubscribe In-Reply-To: References: <73ap56$5600gi@ipex1.johnshopkins.edu> Message-ID: <20081215163131906.00000004012@universi-3022c3> In addition, please unsubscribe me from the mailing list. Thank you Mark Boyett ________________________________ From: Klein, Gad [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Klein, Gad Sent: 15 December 2008 16:15 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Unsubscribe Please unsubscribe me from this mailing list. Thank you. Gad Klein Neuropsychology Research Fellow Comprehensive Epilepsy Center Long Island Jewish Medical Center 270-05 76th Avenue New Hyde Park, New York 11040 Phone: (718) 470-5005 ext. 60846 --------------------------------------------------------------------------------- The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or 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 communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/86c0dcaa/attachment.html From susumu at mri.jhu.edu Mon Dec 15 11:41:30 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 15 Dec 2008 11:41:30 -0500 Subject: [Mristudio-users] The difference of ROI tracking and Fiber tracking In-Reply-To: Message-ID: <73ap56$560ep2@ipex1.johnshopkins.edu> Hi Eun, In DtiStudio, all fiber tracking from all pixels (with FA values above the threshold you set) is complete in the beginning. While you are drawing ROIs, it is just a procedure to visualize fibers that penetrate the ROIs. The "Fiber tracking" button is to redo the initial fiber tracking. If tracking is going well in the first run, you don't have to touch this button anymore because it will just redo the entire tracking again. You use this tracking button only when you want to change the setting of the tracking such as changing the FA threshold. Once you extract fiber you want to see using ROIs, you can save the ROIs and tracking results. When you want to save the tracking results, you have choices to save all tracking results or only the one you extracted by the ROIs. You also have choices for the file formats. If you want to load the fibers and edit them in the future by adding more ROIs, you have to save them using the DtiStudio format. Once you convert the data to a binary format (1/0 for each pixel), the streamline information is lost and you can't edit the fibers anymore. Hope this helps. Susumu _____ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of eunkyung kim Sent: Thursday, December 11, 2008 5:20 AM To: Mristudio-users at mristudio.org Subject: [Mristudio-users] The difference of ROI tracking and Fiber tracking Dear all Hi. I have tried to Fiber tracking(FACT), but I wonder the difference between two things. When I use ROI-shape button, I can see some ROI tracts drawing. But as you know, DTI-Studio has Fiber Tracking(FACT) button, too. I can't see the difference between two things. what can I do to solve the problems? The processes I used 1. Loading FA and vector map and generate color map 2. In Fiber tab, draw ROI tracts. (selected, show fibers on 2D images, ROI-Drawing Enable, Multiple-View of ROI) 3. save maps in two ways. 1)ROI-Operation save (Binary maps) 2)using save button next to the Fiber tracking(FACT) 4. Fiber tracking(FACT) button 5. load Binary map using load buttion in the ROI-Operation Then I should find some thing changes on screen, but I don't. Please let me know.. Eun kyung Kim -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/d234ab5d/attachment.html From Penny.Hubbard at manchester.ac.uk Mon Dec 15 11:44:19 2008 From: Penny.Hubbard at manchester.ac.uk (Penny Hubbard) Date: Mon, 15 Dec 2008 16:44:19 +0000 Subject: [Mristudio-users] Unsubscribe In-Reply-To: <20081215163131906.00000004012@universi-3022c3> References: <73ap56$5600gi@ipex1.johnshopkins.edu> <20081215163131906.00000004012@universi-3022c3> Message-ID: Can you unsubscribe me too! Many thanks, Penny penny.hubbard at manchester.ac.uk ________________________________ From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of MARK BOYETT Sent: 15 December 2008 16:32 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Re: [Mristudio-users] Unsubscribe In addition, please unsubscribe me from the mailing list. Thank you Mark Boyett ________________________________ From: Klein, Gad [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Klein, Gad Sent: 15 December 2008 16:15 To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: Unsubscribe Please unsubscribe me from this mailing list. Thank you. Gad Klein Neuropsychology Research Fellow Comprehensive Epilepsy Center Long Island Jewish Medical Center 270-05 76th Avenue New Hyde Park, New York 11040 Phone: (718) 470-5005 ext. 60846 ------------------------------------------------------------------------ --------- The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or 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 communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/7e5e2f2c/attachment-0001.html From drniks at gmail.com Mon Dec 15 11:54:37 2008 From: drniks at gmail.com (Nikhil Gohokar) Date: Mon, 15 Dec 2008 11:54:37 -0500 Subject: [Mristudio-users] Unsubscribe In-Reply-To: References: <73ap56$5600gi@ipex1.johnshopkins.edu> <20081215163131906.00000004012@universi-3022c3> Message-ID: Unsubscribe me as well. Thanks a lot. Nikhil Gohokar On Mon, Dec 15, 2008 at 11:44 AM, Penny Hubbard < Penny.Hubbard at manchester.ac.uk> wrote: > > > Can you unsubscribe me too! > > > > Many thanks, > > > > Penny > > penny.hubbard at manchester.ac.uk > ------------------------------ > > *From:* mristudio-users-bounces at mristudio.org [mailto: > mristudio-users-bounces at mristudio.org] *On Behalf Of *MARK BOYETT > *Sent:* 15 December 2008 16:32 > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Re: [Mristudio-users] Unsubscribe > > > > In addition, please unsubscribe me from the mailing list. Thank you > > > > Mark Boyett > > > ------------------------------ > > *From:* Klein, Gad [mailto:mristudio-users-bounces at mristudio.org] *On > Behalf Of *Klein, Gad > *Sent:* 15 December 2008 16:15 > *To:* DTI Studio, ROI Editor, Landmarker Questions/Support > *Subject:* Unsubscribe > > > > Please unsubscribe me from this mailing list. Thank you. > > > > > > Gad Klein > > Neuropsychology Research Fellow > > Comprehensive Epilepsy Center > > Long Island Jewish Medical Center > 270-05 76th Avenue > > New Hyde Park, New York 11040 > > Phone: (718) 470-5005 ext. 60846 > > > > > > --------------------------------------------------------------------------------- > The information contained in this electronic e-mail transmission > and any attachments are intended only for the use of the individual > or entity to whom or 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 communication > is not the intended recipient, or the employee or agent responsible > for delivering this communication to the intended recipient, you > are hereby notified that any dissemination, distribution, copying > or disclosure of this communication and any attachment is strictly > prohibited. If you have received this transmission in error, please > notify the sender immediately by telephone and electronic mail, > and delete the original communication and any attachment from any > computer, server or other electronic recording or storage device > or medium. Receipt by anyone other than the intended recipient is > not a waiver of any attorney-client, physician-patient or other > privilege. Thank you. > > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Nikhil Gohokar Research Assistant Henry Ford Hospital, Detroit. Future belongs to those who believe in the beauty of their dreams .... -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/dc35b98a/attachment.html From susumu at mri.jhu.edu Mon Dec 15 12:02:10 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 15 Dec 2008 12:02:10 -0500 Subject: [Mristudio-users] Unsubscribe In-Reply-To: <20081215163131906.00000004012@universi-3022c3> Message-ID: <73ap56$560luo@ipex1.johnshopkins.edu> Hi all, If you want unsubscribe the MriStudio mailing list, please do so at http://lists.mristudio.org/mailman/listinfo/mristudio-users. You can also send an email directly to xli16 at jhmi.edu or susumu at mri.jhu.edu. We are also thinking about moving to a forum-type communication rather than the mailing list. We would appreciate any suggestions or opinions. Please send suggestions to xli16 at jhmi.edu or susumu at mri.jhu.edu, but not to the mailing list. Thanks, Susumu ---------------------------------------------------------------------------- ----- The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or 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 communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/3ada8f82/attachment.html From nellienajafian at yahoo.com Mon Dec 15 15:04:24 2008 From: nellienajafian at yahoo.com (nilofar najafian) Date: Mon, 15 Dec 2008 12:04:24 -0800 (PST) Subject: [Mristudio-users] take off mail list Message-ID: <762004.99456.qm@web82607.mail.mud.yahoo.com> Hi, would you please take me off the mailing list. Thanks nellienajafian at yahoo.com From Teresa.Fuchs at med.uni-muenchen.de Mon Dec 15 15:19:13 2008 From: Teresa.Fuchs at med.uni-muenchen.de (Fuchs, Teresa) Date: Mon, 15 Dec 2008 21:19:13 +0100 Subject: [Mristudio-users] take off mail list Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/6be43dc2/attachment.html From mallik.kasam at gmail.com Mon Dec 15 15:21:14 2008 From: mallik.kasam at gmail.com (Mallikarjuna Kasam) Date: Mon, 15 Dec 2008 14:21:14 -0600 Subject: [Mristudio-users] please unsubscribe me.. Message-ID: From dengjs at ustc.edu.cn Mon Dec 15 18:49:58 2008 From: dengjs at ustc.edu.cn (JianSong Deng) Date: Tue, 16 Dec 2008 07:49:58 +0800 Subject: [Mristudio-users] Unsubscribe Message-ID: <429384998.31667@ustc.edu.cn> Please unsubscribe me from this mailing list. Thank you. -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 3612 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081216/215fb180/attachment.bin From albertleemon at gmail.com Mon Dec 15 21:21:43 2008 From: albertleemon at gmail.com (=?BIG5?B?p/Wycg==?=) Date: Tue, 16 Dec 2008 10:21:43 +0800 Subject: [Mristudio-users] Is there any method to load NIfTi data in DTI Mapping module? In-Reply-To: <49463F0A020000630001A15B@cis27.hosts.jhmi.edu> References: <49463F0A020000630001A15B@cis27.hosts.jhmi.edu> Message-ID: <80363be10812151821h6e348dd6n3cceacde35110476@mail.gmail.com> Dear all: I am grateful for all your help. I try the following: First?I use mricro to save GE DICOMs to the FSL(4D Nifti nii).After eddy correction, I use mricro to save the *.nifti-gz as the dual files (.hdr/.img), and then load them into DTI Studio as Analyze format.It works in the MRI view3D module. Then, in the MRI view3D module, I convert analyze to raw format. So I select all(B0+15 directions) files in the "Image you have " window to "raw data" format. Then click "DTI Mapping", check "Raw files", the error bar hints "Numbers of files in this fold is less than expected:(Img_Slices*Img_Blocks)... " I wonder whether we should save only one volume every time?Or I make any other mistake? On Tue, Dec 16, 2008 at 12:27 AM, Hangyi Jiang wrote: > save the Nifti as the dual files (.hdr/.img), and then load them into > DTI Studio as Analyze format. > > > > > >>> ?? 12/15/08 9:32 AM >>> > Dear all > > > Hi. > > If I use the AIR module to do eddy correction, It always crashes! So I > turn > to FlAIR module in FSL. If It means I can't use DTIStudio anymore in the > follow-up produces?Is there any method to load NIfTi data in DTI Mapping > module? > > Which software can convert the NIfTi data into Raw or NRRD > format?Please > let me know.. > > Thanks a lot! > > > -- > albert > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > -- albert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081216/4da2a64c/attachment.html From elkaavimiller at gmail.com Mon Dec 15 21:39:29 2008 From: elkaavimiller at gmail.com (Elka Miller) Date: Mon, 15 Dec 2008 18:39:29 -0800 Subject: [Mristudio-users] take off mail list In-Reply-To: References: Message-ID: <8bccbbf10812151839t7e0e33c9x62c00e5059fee92e@mail.gmail.com> Hi, would you please take me off the mailing list. Thanks elkaavimiller at gmail.com On Mon, Dec 15, 2008 at 12:19 PM, Fuchs, Teresa < Teresa.Fuchs at med.uni-muenchen.de> wrote: > > Hi, > would you please take me off the mailing list. > Thanks > teresa.fuchs at med.uni-muenchen.de > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users > > -- Elka -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081215/5fdb58f6/attachment.html From albertleemon at gmail.com Mon Dec 15 21:57:55 2008 From: albertleemon at gmail.com (=?BIG5?B?p/Wycg==?=) Date: Tue, 16 Dec 2008 10:57:55 +0800 Subject: [Mristudio-users] what's the function of "Open .d" in Image Processing Message-ID: <80363be10812151857y50052e9ar1e70e885a1529563@mail.gmail.com> Hi,all. I can't find detailed description about "Open .d" button in manual. What does it work? Thanks in advance! -- albert -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081216/97214064/attachment.html From albertleemon at gmail.com Mon Dec 15 22:29:54 2008 From: albertleemon at gmail.com (=?BIG5?B?p/Wycg==?=) Date: Tue, 16 Dec 2008 11:29:54 +0800 Subject: [Mristudio-users] Is there any method to load NIfTi data in DTI Mapping module? In-Reply-To: <80363be10812151821h6e348dd6n3cceacde35110476@mail.gmail.com> References: <49463F0A020000630001A15B@cis27.hosts.jhmi.edu> <80363be10812151821h6e348dd6n3cceacde35110476@mail.gmail.com> Message-ID: <80363be10812151929s7009724hcd6a9dea009f77b0@mail.gmail.com> I find Hangyi said that "DTI Mapping" does not accept Analyze DWIs, for NRRD, the header should follow the NRRD-DWMRI format, not the NRRD format, they are not same. for RAW format, it is supposed that each file contains only one image volume, so that you need to put all image files into one folder in [Mristudio-users] NRRD format.So I save the analyze file again. Each file contains only one image volume ,that is, b0+15 direction means 16 raw data files in the same directory. Then I click "DTI Mapping", check "Raw files", the error bar hints "File size is less than expected:ImgWidth*ImgHeigth*2bytes+header... " Is there anything wrong? On Tue, Dec 16, 2008 at 10:21 AM, ?? wrote: > Dear all: > > I am grateful for all your help. > I try the following: > First?I use mricro to save GE DICOMs to the FSL(4D Nifti nii).After eddy > correction, I use mricro to save the *.nifti-gz as the dual files > (.hdr/.img), and then load them into DTI Studio as Analyze format.It works > in the MRI view3D module. > > Then, in the MRI view3D module, I convert analyze to raw format. So I > select all(B0+15 directions) files in the "Image you have " window to "raw > data" format. Then click "DTI Mapping", check "Raw files", the error bar > hints "Numbers of files in this fold is less than > expected:(Img_Slices*Img_Blocks)... " > > I wonder whether we should save only one volume every time?Or I make any > other mistake? > > > > On Tue, Dec 16, 2008 at 12:27 AM, Hangyi Jiang wrote: > >> save the Nifti as the dual files (.hdr/.img), and then load them into >> DTI Studio as Analyze format. >> >> >> >> >> >>> ?? 12/15/08 9:32 AM >>> >> Dear all >> >> >> Hi. >> >> If I use the AIR module to do eddy correction, It always crashes! So I >> turn >> to FlAIR module in FSL. If It means I can't use DTIStudio anymore in the >> follow-up produces?Is there any method to load NIfTi data in DTI Mapping >> module? >> >> Which software can convert the NIfTi data into Raw or NRRD >> format?Please >> let me know.. >> >> Thanks a lot! >> >> >> -- >> albert >> _______________________________________________ >> Mristudio-users mailing list >> Mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/mristudio-users >> > > > > -- > albert > > > -- ?? Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081216/fb189001/attachment-0001.html From CGlobas at web.de Tue Dec 16 01:37:20 2008 From: CGlobas at web.de (Christoph Globas) Date: Tue, 16 Dec 2008 07:37:20 +0100 Subject: [Mristudio-users] unsuscribe Message-ID: <1198592656@web.de> Please unsuscribe me from this mailing list. thank you! -- Dr. med. Christoph Globas Forschungskolleg Geriatrie der Robert- Bosch- Stiftung Klinik f?r Geriatrische Rehabilitation Robert- Bosch- Krankenhaus Auerbachstr. 110 70376 Stuttgart Tel.: 0711/8101-5605 Email: cglobas at web.de From jonfarrell at jhu.edu Mon Dec 8 22:09:47 2008 From: jonfarrell at jhu.edu (Jonathan Farrell) Date: Mon, 08 Dec 2008 22:09:47 -0500 Subject: [Mristudio-users] DTIstudio on Vista potential problem In-Reply-To: <73ap56$5476d3@ipex1.johnshopkins.edu> References: <73ap56$5476d3@ipex1.johnshopkins.edu> Message-ID: <493DE17B.9060703@jhu.edu> Hi Susumu Researchers who perform DTI on the Philips MRI system can use my software to compute the correct gradient table for fiber tracking. The tables are fully compatible with DTIstudio and CATNAP. Also, I have heard of users adapting them for FSL. A description of the software, together with Matlab files and the Java applet can be found on my website. As you know, the relationship between the examination parameters (such as fat shift, foldover, overplus, scanner software release...etc) and the directions in the gradient table are not straightforward. For single cases, the JAVA applet is quite useful. For more efficient processing, I would recommend the matlab files. If you use the matlab code, then my program requires the .par file and a few parameters that are specified by the user at the command line. http://godzilla.kennedykrieger.org/~jfarrell/software_web.htm#DTI_gradient_table_creator http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html I hope this helps. Sincerely - Jon ========================================================= Jonathan Farrell Ph.D. Candidate, Biophysics and Biophysical Chemistry The Johns Hopkins University School of Medicine F.M. Kirby Research Center for Functional Brain Imaging Kennedy Krieger Institute Baltimore, MD 21218 (443) 923-9513 ========================================================= susumu wrote: > > Hi Jim, > > > > ? Can I expect problems > > on any listed vendor for any specific MRI version > > on a XP laptop? vista laptop? > > > > > DtiStudio should be able to process all these data. Vista laptop > should be fine. The only issue could be memory. If you are using a > 32-bit XP or Vista and/or only 1GB memory, it happens frequently. > > > > I have a vista laptop which I could use but not yet loaded, > > for any specific MRI version? > > > > > No, XP and Vista use the same version of DtiStudio. There are 32 and > 64-bit versions. > > > > ? Can anyone send me Philips gradient files > > (should be 6 direction) or are they in the rec files? > > > > No the gradient orientation is not specified in the Philips REC/PAR > file. Jon Farrell has a nice web-based software to make a gradient > table for Philips scanner based on imaging parameters and the version > of the operating system. Jon, could you send us the URL of your software? > > > > I am attempting to run without success an Indiana site study > > **0008,0020 Study Date: 20040625** > > **0008,0070 Manufacturer: GE MEDICAL SYSTEMS** > > **0008,103E Series Description: dti scheme9 ** > > **0018,1020 Software Versions(s): 09 ** > > **without imbedded gradient vectors and using Bessar normalized > gradients.** > > It loads but I get no FA map. > > on a 3 yr old laptop and 2 2 yr old PCs installed in an MRI research > room. > > > > You need to get a correct gradient table because it is not always > available through data headers. > > > > memory is OK, > > Any graphics card requirements? > > > > No, DtiStudio is not graphics-heavy, but depending on the size of your > data, you need a decent amount of RAM. > > > > > > > Susumu > From mustela at mce.hggm.es Tue Dec 16 12:21:28 2008 From: mustela at mce.hggm.es (Santiago Reig) Date: Tue, 16 Dec 2008 18:21:28 +0100 Subject: [Mristudio-users] Fiber tracking protocols In-Reply-To: References: Message-ID: <20081216171829.7B2302C4004@dns.hggm.es> Hi, I wonder where can I find standardized protocols for fiber tracking segmentations of specific tracts. Something like segmentation protocols for manual tracing of brain structures, and would allow estimation of repeatability, measurement error, etc... Thanks in advance Santiago ><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?> `?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.?? Santiago Reig, PhD. Gregorio Maranon Hospital, Universidad Complutense de Madrid Experimental Surgery and Medicine Lab Dr. Esquerdo 46, 28007 Madrid, SPAIN Fax# 34 91 426 5108, Ph# 34 91 426 5067 mustela at mce.hggm.es http://www.hggm.es/image From susumu at mri.jhu.edu Tue Dec 16 12:57:59 2008 From: susumu at mri.jhu.edu (susumu) Date: Tue, 16 Dec 2008 12:57:59 -0500 Subject: [Mristudio-users] Fiber tracking protocols In-Reply-To: <20081216171829.7B2302C4004@dns.hggm.es> Message-ID: <73alti$4g2jp8@ipex2.johnshopkins.edu> Hi Santiago, We have this paper: Wakana S, Caprihan A., Panzenboeck MM, Fallon JH, Perry M, Gollub RL, Hua K, Zhang J, Dubey P, Blitz A, van Zijl PCM, Mori S. "Reproducibility of quantitative tractography methods applied to cerebral white matter", NeuroImage, 36, 630-644 (2007) Which could be a good place to start. Susumu **************************************************************************** To unsubscribe from Mristudio-users, get a password reminder, or change your subscription options go to: http://lists.mristudio.org/mailman/listinfo/mristudio-users **************************************************************************** -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Santiago Reig Sent: Tuesday, December 16, 2008 12:21 PM To: mristudio-users at mristudio.org Subject: [Mristudio-users] Fiber tracking protocols Hi, I wonder where can I find standardized protocols for fiber tracking segmentations of specific tracts. Something like segmentation protocols for manual tracing of brain structures, and would allow estimation of repeatability, measurement error, etc... Thanks in advance Santiago ><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?> `?.??.???`?.?.???`?...?><((((?>`?.??.???`?.?.???`?...?><((((?>`?.??.?? Santiago Reig, PhD. Gregorio Maranon Hospital, Universidad Complutense de Madrid Experimental Surgery and Medicine Lab Dr. Esquerdo 46, 28007 Madrid, SPAIN Fax# 34 91 426 5108, Ph# 34 91 426 5067 mustela at mce.hggm.es http://www.hggm.es/image _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users From vpna at yahoo.com Tue Dec 16 13:14:34 2008 From: vpna at yahoo.com (Vo Phuoc Nhu An) Date: Tue, 16 Dec 2008 10:14:34 -0800 (PST) Subject: [Mristudio-users] unsuscribe Message-ID: <202670.75541.qm@web51103.mail.re2.yahoo.com> Please unsuscribe me from this mailing list. thank you! Dr. An Vo University of Texas at Arlington, > Dr. med. Christoph Globas > Forschungskolleg Geriatrie der Robert- Bosch- Stiftung > Klinik f?r Geriatrische Rehabilitation > Robert- Bosch- Krankenhaus > Auerbachstr. 110 > 70376 Stuttgart > Tel.: 0711/8101-5605 > Email: cglobas at web.de > > _______________________________________________ > Mristudio-users mailing list > Mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/mristudio-users From npchoo10 at snu.ac.kr Tue Dec 16 19:03:31 2008 From: npchoo10 at snu.ac.kr (IL Han Choo (Choo IH), MD, PhD) Date: Wed, 17 Dec 2008 09:03:31 +0900 (KST) Subject: [Mristudio-users] unsuscribe Message-ID: <2744603.1229472211271.JavaMail.root@auk2.snu.ac.kr> Please unsuscribe me from your mailing list. Cordially, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081217/bfac3c6d/attachment.html From cxie at mcw.edu Tue Dec 16 23:00:59 2008 From: cxie at mcw.edu (Xie, Chunming) Date: Tue, 16 Dec 2008 22:00:59 -0600 Subject: [Mristudio-users] =?gb2312?b?tPC4tDogIHVuc3VzY3JpYmU=?= References: <2744603.1229472211271.JavaMail.root@auk2.snu.ac.kr> Message-ID: <22BC8E7C89E0D14ABA4C08C7FB5B509E0C62B392@MCWPOST.mcwcorp.net> Please unsuscribe me from your mailing list. Best? ________________________________ From: mristudio-users-bounces at mristudio.org ?? IL Han Choo (Choo IH), MD, PhD Sent: 2008-12-16 (???) 18:03 To: mristudio-users at mristudio.org Subject: [Mristudio-users] unsuscribe Please unsuscribe me from your mailing list. Cordially, -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3619 bytes Desc: not available Url : http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081216/416af421/attachment-0001.bin From vikey.han at 163.com Thu Dec 18 08:55:16 2008 From: vikey.han at 163.com (vikey.han) Date: Thu, 18 Dec 2008 21:55:16 +0800 (CST) Subject: [Mristudio-users] file header Message-ID: <22222205.1229051229608516127.JavaMail.coremail@bj163app131.163.com> Hello, I want to read the "Fiber.dat' file and edit it, and don't know what are the meanings of the variables "nReserved ", "fReserved " and "cReserved" in the file header and each fiber struct? thanks. vikey -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081218/3e706605/attachment.html From guhuid at tsinghua.org.cn Fri Dec 19 07:21:19 2008 From: guhuid at tsinghua.org.cn (guhuid at tsinghua.org.cn) Date: Fri, 19 Dec 2008 20:21:19 +0800 (CST) Subject: [Mristudio-users] unsuscribe In-Reply-To: <22BC8E7C89E0D14ABA4C08C7FB5B509E0C62B392@MCWPOST.mcwcorp.net> References: <22BC8E7C89E0D14ABA4C08C7FB5B509E0C62B392@MCWPOST.mcwcorp.net> <2744603.1229472211271.JavaMail.root@auk2.snu.ac.kr> Message-ID: <6836504.109801229689279617.JavaMail.coremail@mailserver3> Please unsuscribe me from your mailing list. Best? From drlin2000 at hotmail.com Mon Dec 22 09:52:37 2008 From: drlin2000 at hotmail.com (weixin) Date: Mon, 22 Dec 2008 22:52:37 +0800 Subject: [Mristudio-users] =?utf-8?q?unsuscribe=E2=80=8F?= Message-ID: Please unsuscribe me from your mailing list. Best? _________________________________________________________________ ???????????????????????? http://www.microsoft.com/windows/windowslive/events.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081222/4133b16a/attachment.html From yj3 at duke.edu Tue Dec 23 13:28:59 2008 From: yj3 at duke.edu (Yi Jiang) Date: Tue, 23 Dec 2008 13:28:59 -0500 Subject: [Mristudio-users] bug in DTIstudio 3.0 (beta) tensor calculation? References: <73alti$4g2jp8@ipex2.johnshopkins.edu> Message-ID: Dear All, I have a DTI dataset with 1 b0 and 6 DWIs, matrix size 512x256x256 each. I tried both the 64bit version 2.4.01 (Oct 2007) and 64 bits version 3.0.0 (Sep 2008) DTIstudio to do DTI tensor calculation. For the version 2.4.01, no matter I used automatic outlier rejection or not, with all default settings (such as the background threshold is 10), I was able to obtain reasonable diffusion tensor images such as FA or colormaps. For the version 3.0.0 Sep 2008, if I used the standard linear fitting method, the resulted images were all reasonable. If I used automatic outlier pixel rejection, the resulted images (FA, colormap, eigenvalue etc.) were all zero. If I used the automatic outlier image rejection when its error > 3% (default), the resulted images (FA, colormap, eigenvalue etc.) were all zero. If I used the automatic outlier image rejection when its error > 99%, the resulted images (FA, colormap, eigenvalue etc.) were all zero. The weird thing is I have use the default settings in the version 3.0.0 (with automatic outlier image rejection when its error > 3%) to calculate diffusion tensors for some other datassets (1 b0 and 12 DWIs, matrix size 512x256x256 each), the resulted images were all reasonable. Only for this 1 b0 and 6 DWIs one (similar or better SNR than the other 12 direction DTI datasets), the results are not consistent. Can anyone help? Thanks a lot! Best, Yi From james.neeley at duke.edu Tue Dec 23 14:21:22 2008 From: james.neeley at duke.edu (Jim Neeley) Date: Tue, 23 Dec 2008 14:21:22 -0500 Subject: [Mristudio-users] bug in DTIstudio 3.0 (beta) tensor calculation? In-Reply-To: References: <73alti$4g2jp8@ipex2.johnshopkins.edu> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081223/70976b8e/attachment.html From yj3 at duke.edu Tue Dec 23 14:46:56 2008 From: yj3 at duke.edu (Yi Jiang) Date: Tue, 23 Dec 2008 14:46:56 -0500 Subject: [Mristudio-users] bug in DTIstudio 3.0 (beta) tensor calculation? References: <73alti$4g2jp8@ipex2.johnshopkins.edu> Message-ID: <2496335DC3A54FB9B4882CE7E73659AC@panpan> Thank you very much for your help. However, I always work on the same computer, where I can get good results for a 1 b0+12 DWI dataset, but not the 1 b0 + 6 DWI dataset, using the 3.0 version. It seems to me the former should take more memory? Best, Yi ----- Original Message ----- From: Jim Neeley To: Yi Jiang ; DTI Studio, ROI Editor, Landmarker Questions/Support Sent: Tuesday, December 23, 2008 2:21 PM Subject: Re: [Mristudio-users] bug in DTIstudio 3.0 (beta) tensor calculation? You and I may share a memory problem. Using the same dti series b0+6 dir images from several MRIs I have bad FA maps but pixel value distribution is 0.72 to 1.0 on my laptop with limited paging maemory, apx 1.2 GB. It works on another laptop (newer vista ) The problem for me is on one laptop and one office PC in a research room. But not on the 2nd laptop or another PC in the same research room which is the same as the other desktop except for the wide screen and graphics card. It would seem that there is a paging issue or paging space because you may get around it if you clean up files in the paging area desk top items - pictures or music files which use us virtual memory. Thanks Jim Neeley, Neuroradiology research assistant, Cell: 919-696-6105 FAX: 919 684-7153 Office: 684-7434, MRI: 684-7405 Snail: DUMC 3808 ------------------------------------------------------------------------------ _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081223/57944527/attachment.html From james.neeley at duke.edu Tue Dec 23 15:03:18 2008 From: james.neeley at duke.edu (Jim Neeley) Date: Tue, 23 Dec 2008 15:03:18 -0500 Subject: [Mristudio-users] bug in DTIstudio 3.0 (beta) tensor calculation? In-Reply-To: References: <73alti$4g2jp8@ipex2.johnshopkins.edu> Message-ID: An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081223/219c997c/attachment-0001.html From yj3 at duke.edu Tue Dec 23 15:20:41 2008 From: yj3 at duke.edu (Yi Jiang) Date: Tue, 23 Dec 2008 15:20:41 -0500 Subject: [Mristudio-users] bug in DTIstudio 3.0 (beta) tensor calculation? References: <73alti$4g2jp8@ipex2.johnshopkins.edu> Message-ID: No different MRI vendor involved. All DWI and b0 images are read in properly. If used the standard linear fitting method, I was able to get diffusion tensors calcualted fine. Yi ----- Original Message ----- From: Jim Neeley To: Yi Jiang ; DTI Studio, ROI Editor, Landmarker Questions/Support Sent: Tuesday, December 23, 2008 3:03 PM Subject: Re: [Mristudio-users] bug in DTIstudio 3.0 (beta) tensor calculation? The only other question for me - are the gradients the same? My problems are in getting to high FA values not zeros. All zeros seems to be a calculation problem where the numbers are all discarded. How about scale of the values, different MRI vendor involved? Compare the tail of the DICOM header where scale is defined. Thanks Jim Neeley, Neuroradiology research assistant, Cell: 919-696-6105 FAX: 919 684-7153 Office: 684-7434, MRI: 684-7405 Snail: DUMC 3808 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20081223/77b918e0/attachment.html From susumu at mri.jhu.edu Mon Dec 29 16:18:20 2008 From: susumu at mri.jhu.edu (susumu) Date: Mon, 29 Dec 2008 16:18:20 -0500 Subject: [Mristudio-users] bug in DTIstudio 3.0 (beta) tensor calculation? In-Reply-To: Message-ID: <73ap56$59cjrv@ipex1.johnshopkins.edu> Hi Yi, The outlier-rejection requires diffusion-weighted images more than 6. I think the behavior of the Version 3 is related to this. Let me use an analogy of a simple linear fitting. When there are only two data points and you need to find a best-matching line, you have only one answer, which is connecting the two points. In this case, you are SOLVING the equation. If you have more than 2 points, you do FITTING, not SOLVING. When you do the fitting, you can use the outlier detection and rejection. For example, if you have 10 points and one of them is completely off, you can set some criteria for rejection and remove such a bad data point. If you have only two points and one of them is corrupted, you can't do anything. You just have to use the data as is. For DTI, the 6-orientation is the required number of images and you SOLVE the tensor equation if you have only 6 DWIs. When you have, say, 12 orientations, you can use the outlier detection and can reject up to (theoretically) 6 images. In addition, we are going to release a better version of the outlier rejection soon. So, at this point, I would suggest you not to use the outlier rejection for your data. Susumu -----Original Message----- From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Yi Jiang Sent: Tuesday, December 23, 2008 1:29 PM To: DTI Studio, ROI Editor, Landmarker Questions/Support Subject: [Mristudio-users] bug in DTIstudio 3.0 (beta) tensor calculation? Dear All, I have a DTI dataset with 1 b0 and 6 DWIs, matrix size 512x256x256 each. I tried both the 64bit version 2.4.01 (Oct 2007) and 64 bits version 3.0.0 (Sep 2008) DTIstudio to do DTI tensor calculation. For the version 2.4.01, no matter I used automatic outlier rejection or not, with all default settings (such as the background threshold is 10), I was able to obtain reasonable diffusion tensor images such as FA or colormaps. For the version 3.0.0 Sep 2008, if I used the standard linear fitting method, the resulted images were all reasonable. If I used automatic outlier pixel rejection, the resulted images (FA, colormap, eigenvalue etc.) were all zero. If I used the automatic outlier image rejection when its error > 3% (default), the resulted images (FA, colormap, eigenvalue etc.) were all zero. If I used the automatic outlier image rejection when its error > 99%, the resulted images (FA, colormap, eigenvalue etc.) were all zero. The weird thing is I have use the default settings in the version 3.0.0 (with automatic outlier image rejection when its error > 3%) to calculate diffusion tensors for some other datassets (1 b0 and 12 DWIs, matrix size 512x256x256 each), the resulted images were all reasonable. Only for this 1 b0 and 6 DWIs one (similar or better SNR than the other 12 direction DTI datasets), the results are not consistent. Can anyone help? Thanks a lot! Best, Yi _______________________________________________ Mristudio-users mailing list Mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/mristudio-users