[Freesurfer] incomplete forceps
Dear Freesurfer experts, we have a problem with the forceps. After the first trac-all we had a forcpes minor with a really unusually structure so we tried to fix it with an rerun of the trac-all. The result was a forceps minor with a third thigh in the sagittal axis. We did a second rerun and now the forceps minor normalized. Our problem is that we don´t know if we should do more trac-all reruns by other patients with difficult tracula or how we should interpret this result. Do you have any ideas to solve this? The second problem is that we have many many tracula results with incomplete forcepes minor or major. We know that the forcepes are the most difficult tracts because of the curvature but do you have some ideas to fix that problem? Kind regards Benjamin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Probably activation due to vessels
Thanks for your help. It works fine if one uses preproc-sess -per-run -fwhm 5 -fsd bold -s sess01 ... . On Fri, 19 Oct 2012 12:49:00 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to run preproc like: preproc-sess -per-session -fwhm 5 -fsd bold -s sess01 In this case, you are just specifiying -per-session and not specifying -mni305 or -surface When you run mkanalysis-sess, specify -native instead of -mni305 or -surface, like: mkanalysis-sess -native -fwhm 5 ... doug On 10/19/2012 03:59 AM, Jörg Pfannmöller wrote: Hi Doug, the preprocessing is fine the quaility factor for the registration between functional and anatomical is ~0.3. Have I to use feat to do the volume analysis? Cheers pfannmoe On Thu, 18 Oct 2012 11:50:38 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: It is too hard to tell what is going on here from just this image. I would not immediately conclude that it is a vessel. Does the activation otherwise look ok? What about other contrasts? Is the registration accurate? When trying to debug these things, it often makes sense to analyze the data in the volume. doug On 10/17/2012 12:31 PM, Jörg Pfannmöller wrote: It is attached to this mail. On Tue, 16 Oct 2012 16:16:54 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: can you send a pic? On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote: Hi Doug, the analysis is done on the cortex surface. The following commands are used for the analysis of the functional activation in the right hemisphere cortex: preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -nosmooth plot-twf-sess -s sessionID -fsd bold -mc tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl ./label_01.tcl. Left hemisphere and sub-cortical analysis are also carried out. Results are depicted on the flatted cortex surface in the primary somatosensory cortex. This label is a combination of the freesurfer areas BA1, BA2, BA3a and BA3b. The activation is masked to this label. An example of the line like pattern is uploaded on your ftp server using my email (pfannmoelj ... uni-greifswald.de, the at sign is replaced by dots) as the password. There is a snaking line in the middle of the image which is a candidate for a vessel. In other images the straight line like patterns or line like patterns with gaps are found. Is there a way to analyze the data in a volume based stream without differentiation between cortex and sub-cortical brain in which the distance of the line like pattern relative to the gray substance is visible? This could be used in order to classify between true activation and vessel activation. We have epi data with spatial resolution of 2x2x4mm^3 (used to generate attached image) and 1.5x1.5x2mm^3 which both show line like patterns. Structural data are taken using the single echo freesurfer protocol for the flash sequence, recommended for cortex. I hope those information are of help. Sincerely yours pfannmoe On Mon, 15 Oct 2012 17:52:04 -0400 Douglas N Grevegr...@nmr.mgh.harvard.eduwrote: Hi Jorg, can you tell us a little more? A picture would be good. Also, describe how you have done your analysis (eg, on the surface or in the volume, how much smoothing). doug On 10/15/2012 11:01 AM, wrote: Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like a volume based mode which does not sxclude the cortex. In this mode the vessels couls be identified and removed. Any help is highly apprexiated. Respectfully yours pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___
Re: [Freesurfer] Probably activation due to vessels
Sorry, I have to cancel my last contribution. Another Problem crossed my way. If I have more than one run, only the first one is preprocessed if i use -per-session. What can I do about it? If I use -per-run all runs are preprocessed, but selxavg3-sess tells me that it can not determine the file format of the fmc files. Actually those files are called fmcpr, if I use -per-run. How can do I have to proceed if there is more than one run? On Mon, 6 May 2013 10:54:54 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Thanks for your help. It works fine if one uses preproc-sess -per-run -fwhm 5 -fsd bold -s sess01 ... . On Fri, 19 Oct 2012 12:49:00 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to run preproc like: preproc-sess -per-session -fwhm 5 -fsd bold -s sess01 In this case, you are just specifiying -per-session and not specifying -mni305 or -surface When you run mkanalysis-sess, specify -native instead of -mni305 or -surface, like: mkanalysis-sess -native -fwhm 5 ... doug On 10/19/2012 03:59 AM, Jörg Pfannmöller wrote: Hi Doug, the preprocessing is fine the quaility factor for the registration between functional and anatomical is ~0.3. Have I to use feat to do the volume analysis? Cheers pfannmoe On Thu, 18 Oct 2012 11:50:38 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: It is too hard to tell what is going on here from just this image. I would not immediately conclude that it is a vessel. Does the activation otherwise look ok? What about other contrasts? Is the registration accurate? When trying to debug these things, it often makes sense to analyze the data in the volume. doug On 10/17/2012 12:31 PM, Jörg Pfannmöller wrote: It is attached to this mail. On Tue, 16 Oct 2012 16:16:54 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: can you send a pic? On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote: Hi Doug, the analysis is done on the cortex surface. The following commands are used for the analysis of the functional activation in the right hemisphere cortex: preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -nosmooth plot-twf-sess -s sessionID -fsd bold -mc tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl ./label_01.tcl. Left hemisphere and sub-cortical analysis are also carried out. Results are depicted on the flatted cortex surface in the primary somatosensory cortex. This label is a combination of the freesurfer areas BA1, BA2, BA3a and BA3b. The activation is masked to this label. An example of the line like pattern is uploaded on your ftp server using my email (pfannmoelj ... uni-greifswald.de, the at sign is replaced by dots) as the password. There is a snaking line in the middle of the image which is a candidate for a vessel. In other images the straight line like patterns or line like patterns with gaps are found. Is there a way to analyze the data in a volume based stream without differentiation between cortex and sub-cortical brain in which the distance of the line like pattern relative to the gray substance is visible? This could be used in order to classify between true activation and vessel activation. We have epi data with spatial resolution of 2x2x4mm^3 (used to generate attached image) and 1.5x1.5x2mm^3 which both show line like patterns. Structural data are taken using the single echo freesurfer protocol for the flash sequence, recommended for cortex. I hope those information are of help. Sincerely yours pfannmoe On Mon, 15 Oct 2012 17:52:04 -0400 Douglas N Grevegr...@nmr.mgh.harvard.eduwrote: Hi Jorg, can you tell us a little more? A picture would be good. Also, describe how you have done your analysis (eg, on the surface or in the volume, how much smoothing). doug On 10/15/2012 11:01 AM, wrote: Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like a
Re: [Freesurfer] Loading V5.2 on Virtualbox
Hello Will, Clicking the Terminal icon on the desktop will load Freesurfer. From that point on its just a matter of typing the appropriate commands. -Zeke On 05/04/2013 09:27 AM, will brown wrote: I am endeavouring to install FreeSurfer on a windows 8 PC. Virtualbox is installed along with the relevant FreeSurfer download, I have followed the installation instructions on the freesurfer wiki but when the virtualbox is running I do not see the XTerm shortcut that is shown on the last pane of the installation instructions https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage, all I see is the attached screenshot. I have also downloaded the fast tutorial files (admittedly they were downloaded to the host machine other than virtualbox and I'm not sure how to move them to virtualbox if I need to do so). So, I believe I've got everything relevant downloaded, how do I now get FreeSurfer running? Any help would be greatly appreciated. Thanks, Will. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Gradient unwarp software / Siemens Verio scanner
Hi, I'm currently exploring gradient unwarping of data on a Siemens Trio scanner (sonata coils) and a Siemens Verio scanner. I have got lists with coil coefficients for both scanners. According to the FS mail archives, you provide a binary for gradient unwarping, but not any scanner tables (due to licensing), or the conversion scripts mentioned here:https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping. With some googling, I have found this version:https://code.google.com/p/gradunwarp/ https://code.google.com/p/gradunwarp/https://code.google.com/p/gradunwarp/ which seems to be the latest available version of the software (originally written by Czanner). This package also provides the table conversion scripts. The development appears to be stalled, however. I have used this version for (what seems to be) successful gradient unwarping of Siemens Trio data. A couple of questions: 1) Can you enlighten me as to the latest and 'most proper' version of the software to use for gradient unwarping (bug fixes, scanner support)? Is the binary in FS further developed than the google docs version, and if so, have I somehow missed the table conversion scripts? 2) At DRCMR (see below), we have a Siemens Verio scanner, as well as a list with the associated gradient coil coefficients. As of now, it seems like the correction software (public FS + google doc version) does not support this scanner type. Is this something that could possibly be included? Or is a newer (possibly non-public) version available that supports it already? We're aware that the scanner can perform correction by itself, but as far as I know this is only in 3D, and also requires you to do it immediately after the sequence. Best Regards, Christian Thode Larsen PhD Student Technical University of Denmark (DTU) / Danish Research Centre for Magnetic Resonance (DRCMR) Supervisor: Koen Van Leemput ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tip and tricks with patient with one big ventricle...
Gonzalo, Freeview will have a few small usability features to make it behave more like tkmedit and tksurfer, but that update doesnt affect recon-all. Nick Hi Nick: Ok... Tomorrow Sunday I will download and begin to test it... And which other new features has version 5.3.0 over 5.2.0 ?... Sincerely, Gonzalo Rojas Costa On Fri, May 3, 2013 at 5:46 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: this link is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/ the centos6_x86_64 build is there now. the others will appear as they finish their builds, which can take quite a bit of time... so check back every day or so n. -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] The Asymmetry of surface area or thickness
Follow the steps here: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi On 05/06/2013 01:41 AM, xiangbo_2010 wrote: Dear experts I want to analysis the asymmetry of surface area or thickness, what I do next? thanks! Bo Xiang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Probably activation due to vessels
If you use -per-session, all of them should be processed. Why do you think they are not? Also, just saying something is not working is not very informative. Send command lines and terminal output of the error. thanks! doug On 05/06/2013 05:46 AM, Jörg Pfannmöller wrote: Sorry, I have to cancel my last contribution. Another Problem crossed my way. If I have more than one run, only the first one is preprocessed if i use -per-session. What can I do about it? If I use -per-run all runs are preprocessed, but selxavg3-sess tells me that it can not determine the file format of the fmc files. Actually those files are called fmcpr, if I use -per-run. How can do I have to proceed if there is more than one run? On Mon, 6 May 2013 10:54:54 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Thanks for your help. It works fine if one uses preproc-sess -per-run -fwhm 5 -fsd bold -s sess01 ... . On Fri, 19 Oct 2012 12:49:00 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to run preproc like: preproc-sess -per-session -fwhm 5 -fsd bold -s sess01 In this case, you are just specifiying -per-session and not specifying -mni305 or -surface When you run mkanalysis-sess, specify -native instead of -mni305 or -surface, like: mkanalysis-sess -native -fwhm 5 ... doug On 10/19/2012 03:59 AM, Jörg Pfannmöller wrote: Hi Doug, the preprocessing is fine the quaility factor for the registration between functional and anatomical is ~0.3. Have I to use feat to do the volume analysis? Cheers pfannmoe On Thu, 18 Oct 2012 11:50:38 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: It is too hard to tell what is going on here from just this image. I would not immediately conclude that it is a vessel. Does the activation otherwise look ok? What about other contrasts? Is the registration accurate? When trying to debug these things, it often makes sense to analyze the data in the volume. doug On 10/17/2012 12:31 PM, Jörg Pfannmöller wrote: It is attached to this mail. On Tue, 16 Oct 2012 16:16:54 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: can you send a pic? On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote: Hi Doug, the analysis is done on the cortex surface. The following commands are used for the analysis of the functional activation in the right hemisphere cortex: preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -nosmooth plot-twf-sess -s sessionID -fsd bold -mc tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl ./label_01.tcl. Left hemisphere and sub-cortical analysis are also carried out. Results are depicted on the flatted cortex surface in the primary somatosensory cortex. This label is a combination of the freesurfer areas BA1, BA2, BA3a and BA3b. The activation is masked to this label. An example of the line like pattern is uploaded on your ftp server using my email (pfannmoelj ... uni-greifswald.de, the at sign is replaced by dots) as the password. There is a snaking line in the middle of the image which is a candidate for a vessel. In other images the straight line like patterns or line like patterns with gaps are found. Is there a way to analyze the data in a volume based stream without differentiation between cortex and sub-cortical brain in which the distance of the line like pattern relative to the gray substance is visible? This could be used in order to classify between true activation and vessel activation. We have epi data with spatial resolution of 2x2x4mm^3 (used to generate attached image) and 1.5x1.5x2mm^3 which both show line like patterns. Structural data are taken using the single echo freesurfer protocol for the flash sequence, recommended for cortex. I hope those information are of help. Sincerely yours pfannmoe On Mon, 15 Oct 2012 17:52:04 -0400 Douglas N Grevegr...@nmr.mgh.harvard.eduwrote: Hi Jorg, can you tell us a little more? A picture would be good. Also, describe how you have done your analysis (eg, on the surface or in the volume, how much smoothing). doug On 10/15/2012 11:01 AM, wrote: Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them.
Re: [Freesurfer] question about glm setup
Hello Dr. Greve, Thank you for your reply. I have set up the qdec. I have gender as the discrete factor and age and clinical score as continuous factors. In order to look at the relationship between clinical score and whole brain cortical thickness while accounting for age and gender effects, do I select score as the continuous factor and age as the nuisance factor or should it be the other way round ? Thanking you in anticipation, Subha - Original Message - From: Douglas Greve Sent: 05/05/13 11:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] question about glm setup Hi Subha, yes, you can. You will need to create a table in the format with QDEC expects. Have you looked at the tutorial? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis doug On 5/4/13 11:31 AM, Subhabrata Chaudhury wrote: Hi, I am new to freesurfer. I have run reconall on 50 AD subjects. I have also run recon-all -qcache. So I have the following - 1) Whole brain thickness map for each AD subject 2) age of each subject 3) gender of each subject 4) clinical score of each subject I DO NOT have control subjects. I want to run a glm to investigate whether if there is a relation between the clinical score for each subject and their cortical thickness while accounting for age, gender and whole brain average thickness. Can I use qdec for this ? This is my first time doing this sort of analysis, so I will be grateful if I can get some step-by-step help. Thank you very much Subha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] R: Re: version 5.3 coming out soon
Hi Bruce, thank for new 5.3. I'm finishing tracula analyis with 5.2 (I only have a subject that give me some problem). Do you advice me to cancel my analysis and re-run it by new version 5.3? Is the results obtained with version 5.2 reliable? Thank you very much, Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 4-mag-2013 14.55 A: lukas.sch...@ukb.uni-bonn.de Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] version 5.3 coming out soon Hi Luke Nick will post a command line you can run that should take about 2 hours/dataset. Rerunning shouldn't be necessary. Sorry for the trouble, I really, really wish we had more engineering resources. Bruce On Sat, 4 May 2013, lukas.sch...@ukb.uni-bonn.de wrote: Hi Bruce, Thanks a lot for the info. Would it mean we have to completely reprocess the data processed with 5.2? Or at which point of the preprocessing pipeline we should step in to fix the problems of 5.2...? I just have finished to process about 200 data sets with 5.2... Best wishes, Luke Am 03.05.2013 um 02:58 schrieb Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi All, We have recently uncovered problems with version 5.2. Based on these problems, we are recommending that people stop using 5.2, mainly in regards to usage of the surface data. A new version, 5.3, will be released within two weeks, and a beta version for each platform will be available within a couple days. There were two main problems that were uncovered. First, a change was made that was only meant to affect the white surface placement in high-resolution data sets, but unfortunately is being applied to all data sets. This causes the white surface to contract a small amount. This causes the surface area to be smaller and cortex to be measured as thicker relative to version 5.1. Visually, the surfaces do not necessarily look less accurate, but we feel that the systematic differences with previous versions are ill-advised without a clear reason for the change. Second, a change made to the placement of the pial surface in order to improve the positioning based on T2/FLAIR that caused it to extend too far in some data sets during the T1-based pial surface deformation. This unfortunately became the default behavior, which was not intended. None of the dozens of test data sets we ran displayed this problem. The behavior was reported by other users which led us to the bug. In general, we rigorously test each version. However, our systematic comparison of a new version with previous versions which would have caught these problems was conducted prior to these changes. We are now tightening and regimenting our testing procedures to ensure this doesnt happen again. Note that there are no problems with the volumetric segmentation (aseg) in version 5.2. We realize that this will cause a substantial inconvenience for users. We have isolated and fixed the problems and have run two rounds of alpha testing and have one more to go, after which we will release a beta version in a couple of days to anyone that wants it. sorry for the problems. Bruce ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Open Brain Mapping at the 1st HBM Hackathon
Sent on behalf of Thomas Grabowski, OHBM 2013, LOC Chair: Open Brain Mapping at the 1st HBM Hackathon: Open Brain Mapping in the Cloud ** OHBM 2013 is only six weeks away, bringing the brain mapping community to Seattle, a city at the forefront of open neuroscience and information technology. The Local Organizing Committee, the Allen Institute for Brain Science, and Amazon Web Services are excited for the opportunity to highlight these aspects of our field in the HBM Hackathonhttp://humanbrainmapping.org/hackathon, a meeting-long event integrated with and running parallel to the activity in the poster and exhibition space. Our goals are to accelerate the development of a critical mass of cloud-based data, analytic, and computational resources for human brain mapping, and to provide OHBM attendees with access to and knowledge about them. The event is being supported by a broad spectrum of partners from the open neuroimaging community, making it possible to allow an unprecedented degree of access to key resources in the field, including the Allen Human Brain Atlas, the first data release of the Human Connectome Project, the NITRC Computational Environment, and more. Experts from the Allen Institute, Amazon Web Services, Human Connectome Project, NITRC, INCF, LONI, NDAR, BIRN, and others will bring their expertise on-venue. Register for the HBM Hackathon http://humanbrainmapping.org/hackathon to participate in a contest organized around three challenges, to tinker less formally, or just to be open to open neuroscience. You’ll also receive $100 in free AWS credits to make use of cloud computing technologies. The contest is organized around three Challenges: ** Challenge 1. Best imaging and gene expression relationship discovered via integration of imaging data with the Allen Human Brain Atlas. ** Challenge 2. Best cortical neural systems relationship or visualization based on integration of resting state fMRI data with other HBM Hackathon accessible datasets. ** Challenge 3. To be announced the week of the meeting and pursued completely on site. *See the list of datasets http://ohbm-seattle.github.io/datasets* ** Winning entries in each category receive: * - An invitation to submit project to Frontiers in Brain Imaging Methods with Open Access Publication Fees waived (must undergo standard peer review) - Amazon Kindle Fire and/or Paperwhite (limit 3 per team) - AWS hosts AMI and/or data resulting from the hackathon free of charge - Free GitHub Membership with private repositories (Challenge 1: one year silver, Challenge 2: 1 year bronze, Challenge 3: six months bronze) * ** To learn more, visit the HBM Hackathon Blog http://ohbm-seattle.github.io/or join the discussion group http://www.linkedin.com/groups/HBM-Hackathon-4957800. And be sure to register at: humanbrainmapping.org/hackathon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Pial surface errors
Hi Valeria what version are you running? It's hard to tell from a single slice, but what is the white-matter appearing stuff that is outside the white matter surface? I think that is what's messing stuff up. If you want to upload the data subject one of us will take a look (that is, upload the entire subject directory) cheers Bruce On Mon, 6 May 2013, Contarino Valeria wrote: Dear Freesurfers, I usually get very satisfying results but in my last analysis I noticed some errors in a few subjects' pial surface (see attached example image). I really don't get how it failed in that way. What I know I can surely do is to manually modify the WM and run again the autorecon command. Could someone kindly advice me on how to avoid/solve the problem in a less time-consuming way? Thank you. Regards, Valeria Elisa Contarino, MEng Neuroradiology Department IRCCS Foundation Neurological Institute C.Besta Via Celoria 11, 20133 Milano, Italy ph: +39 02 23942472 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] DTI metrics along the whole tract?
Hi Tracula team I am using tracula to study the corticospinal tract in a patient population. I am wondering if there would be a way to have the different DTI metrics from the whole tract at different depth/portion of the tracts. Something like the information given by the pathstats.byvoxel.txt file, but for the whole width of the tract? If not, do you see a way to sample the value of the diffusion metrics on a certain tract starting from the cortex (like with projfrac or projdist with the WM surface)? Thanks very much for your help Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] BBregister issue during autorecon3 with T2pial option (5.2.0 with updated beta binaries)
Hi, all. I'm trying to refine my pial surfaces with a T2 (or, in this case, t2*) image and I'm running into an error inside bbregister/fslregister. I'm running the command: recon-all -s gf04 -3T -autorecon3 -T2pial -T2 /mindhive/gablab/fluid/Analysis/Nipype/flash/gf04/tissue_parameters/T2star.mgz and the recon process makes it to the point of #@# Refine Pial Surfs w/ T2/FLAIR when it runs: bbregister --s gf04 --mov /mindhive/gablab/fluid/Data/gf04/mri/orig/T2raw.mgz --lta /mindhive/gablab/fluid/Data/gf04/mri/transforms/T2raw.lta --init-fsl --T2 bbregister does some initial processing, then calls fslregister, like so: fslregister --s gf04 --mov /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/template.nii --reg /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/fslregister --dof 6 --fsvol brainmask which immediately crashes with: /mindhive/gablab/fluid/Data/gf04 mri_convert ERROR: could not determine file for /mindhive/gablab/fluid/Data/gf04/mri/ERROR: /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/fslregister/refvol.fslregister.nii And so on. running the fslregister command manually and changing brainmask to brainmask.mgz seems to fix the problem (after manually creating/filling the appropriate tmp directory, of course). Any thoughts? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] BBregister issue during autorecon3 with T2pial option (5.2.0 with updated beta binaries)
Newer version of linux changed the way cshell behaves which causes bbregister to crash in some instances. Get a new version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister doug On 5/6/13 8:10 PM, Todd Thompson wrote: Hi, all. I'm trying to refine my pial surfaces with a T2 (or, in this case, t2*) image and I'm running into an error inside bbregister/fslregister. I'm running the command: recon-all -s gf04 -3T -autorecon3 -T2pial -T2 /mindhive/gablab/fluid/Analysis/Nipype/flash/gf04/tissue_parameters/T2star.mgz and the recon process makes it to the point of #@# Refine Pial Surfs w/ T2/FLAIR when it runs: bbregister --s gf04 --mov /mindhive/gablab/fluid/Data/gf04/mri/orig/T2raw.mgz --lta /mindhive/gablab/fluid/Data/gf04/mri/transforms/T2raw.lta --init-fsl --T2 bbregister does some initial processing, then calls fslregister, like so: fslregister --s gf04 --mov /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/template.nii --reg /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/fslregister --dof 6 --fsvol brainmask which immediately crashes with: /mindhive/gablab/fluid/Data/gf04 mri_convert ERROR: could not determine file for /mindhive/gablab/fluid/Data/gf04/mri/ERROR: /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/fslregister/refvol.fslregister.nii And so on. running the fslregister command manually and changing brainmask to brainmask.mgz seems to fix the problem (after manually creating/filling the appropriate tmp directory, of course). Any thoughts? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
