Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Error in segmentSubjectT1_autoEstimateAlveusML
by Pascale Patenaude 14 Mar '20

14 Mar '20

External Email - Use Caution Hello FreeSurfer developers, When trying to run segmentHA_T1.sh with the dev version of FreeSurfer to accomplish hippocampal subfield and amygdala subnuclei segmentation (see FreeSurfer module https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) I get this error: Open file failed because file '/tmp/MCR_3413898417/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m' has invalid content. Details: 'file is closed.failbit is set.' Attempt to execute SCRIPT kvlWriteImage as a function: /tmp/MCR_3413898417/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m Error in segmentSubjectT1_autoEstimateAlveusML (line 1547) This tmp/MCR_3413898417/.mcrCache8.4/segmen0/autofs directory does not exist. I also have the matlab runtime required for this FreeSurfer module installed. Does anyone have any suggestions on how this can be fixed? Thank you in advance, Pascale

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dmri_pathstats segment
by Wang, Lily 13 Mar '20

13 Mar '20

Hi, I am trying to get voxel by voxel stats for fmajor on a threshold that's not the 0.2 default because when I looked at merged nii, fmajor is constructed correctly but on a different threshold. This is the command I used: dmri_pathstats --intrk fmajor_PP_avg33_mni_bbr/path.pd.trk --dtbase ../dmri/dtifit --outvox new_fmajor --pthr 0.4 And I am getting in the terminal: INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction INFO: Rejected 940 streamlines as length outliers INFO: Have 1460 total streamlines (min/mean/max length: 75/101/117) INFO: Have 1460 non-truncated streamlines (min/mean/max length: 75/101/117) Segmentation fault (core dumped) Am I running the command incorrectly? Thank you, Lily

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Re: [Freesurfer] Freesurfer Set-Up Help
by fsbuild 13 Mar '20

13 Mar '20

External Email - Use Caution Hello Liam, Have you tried following the “Setup Instructions” under, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall. ? For the 6.0.0 release: If you are on the Mac, running the .pkg installer should give you the distribution under /Applications/freesurferThen you would set FREESURFER_HOME to /Applications/freesurfer If you are on Linux, you need to choose a location to install it.  It is typically put under /usr/local, and if you expand the archive there, you will get /usr/local/freesurfer, e.g, assuming the archive is in your downloads folder$ cd /usr/local$ sudo tar zxpf ~/Downloads/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gzThen you would set FREESURFER_HOME to /usr/local/freesurfer - or follow what is under the section “Setup & Configuration” - R. On Mar 13, 2020, at 21:24, Liam Sullivan <maillts28(a)gmail.com> wrote:        External Email - Use Caution        Hi there,I have been trying to learn and set-up Freesurfer for a research project I am working on, but I am having trouble with the set-up/installation process.Once Freesurfer is set-up, I will be using it to measure hippocampal volumes post-ablation.I have followed the instructions online to the best of my ability but can't seem to figure this out. Any assistance would be very much appreciated. And if possible, if someone is able to chat with me via phone, that would be even better.Thank you.Best,Liam_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer Set-Up Help
by Liam Sullivan 13 Mar '20

13 Mar '20

External Email - Use Caution Hi there, I have been trying to learn and set-up Freesurfer for a research project I am working on, but I am having trouble with the set-up/installation process. Once Freesurfer is set-up, I will be using it to measure hippocampal volumes post-ablation. I have followed the instructions online to the best of my ability but can't seem to figure this out. Any assistance would be very much appreciated. And if possible, if someone is able to chat with me via phone, that would be even better. Thank you. Best, Liam

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FreeSurfer Cortical Parcellation using isoDWI image only?
by Yixin Ma 13 Mar '20

13 Mar '20

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask if it's possible to run FreeSurfer Cortical Parcellation by just using the isoDWI image. If it's possible, it will reduce the scan time and avoid misregistration between T1 and DWI. I started from just input the masked isoDWI (mask generated from MRtrix3) for -reconall command, and attached is a screenshot of the image of NU.mgz, which shows a clear delineation of WM/GM matter. So I think it's promising, although the recon-all stopped because of the wrong contrast. My ideas on tackling this problem are: 1) generate a corresponding "fake" T1-weighted image by either adjusting the value directly or using a brain Atlas and deformable registration to create one. 2) Tweak some parameters in FreeSurfer. Any suggestions or comments on my ideas are appreciated. Thank you very much and all the best, Yixin Ma [image: Screen Shot 2020-03-12 at 3.06.22 PM.png]

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Functional connectivity analysis ERROR: cannot find.../dof
by Renew Andrade 13 Mar '20

13 Mar '20

External Email - Use Caution Dear FreeSurfer experts: I cannot fix the problem that I mention in the subject. I put the output of the terminal below. I was doing functional connectivity analysis walkthrough tutorial and I followed until group analysis when applying "isxconcat-sess”. I cannot proceed because the “.dof” files are in "/sessx/rest/*” where x is a number from 0 to 9 and * indicates location. So I don’t know why this files are here and not in the analysis subdirectory i.e. “fc.lpccseed.lh”. What is the problem? How should I fix it? Thank you for all the help!! Sincerely, Andrade.

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error when running recon-all
by ZhangBo 13 Mar '20

13 Mar '20

External Email - Use Caution Hi team, I encountered an error when running the test "Candal" dataset. For some patients' files, I found the error information in the log file. So, after "recon-all" finished, I re-run recall for these files with errors. However, error still happened? What's wrong? Thanks. log file for a patient is in the attachment. Best wishes. Bo

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freeview error
by Ortug, Alpen 12 Mar '20

12 Mar '20

Hello FreeSurfer Experts, I'm attempting to install Freesurfer. I am trying to test my installation. $>recon-all -i sample-001.nii.gz -s bert -all ............ $>recon-all -s bert finished without error at Wed Mar 11 19:09:43 EDT 2020 done However, after this I am getting an error message when I try to open in Freeview. It is attached. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform:Ubuntu 19.10 3) uname -a: Linux antalya 5.3.0-40-generic #32-Ubuntu SMP Fri Jan 31 20:24:34 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 4) error file: see attached Many thanks Best Alpen ORTUG, PhD Post-doctoral Research Fellow Division of Newborn Medicine Boston Children's Hospital Harvard Medical School 401 Park Dr. Boston, MA 02215, USA

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Re: [Freesurfer] Freeview error: GLXBadContext
by fsbuild 12 Mar '20

12 Mar '20

External Email - Use Caution Hello Alek, When you say you are running Ubuntu 14 via a Windows 10 PC, do you mean you are running the add-on windows subsystem for linux (known as WSL) that allows you run an Ubuntu shell on Windows 10?    And then when you say you are remotely viewing things, does that mean you are remotely logging into that Windows machine? If you are in fact using WSL, then for X Window based GUI application like Freeview to run in WSL, you need to have an X server installed and running on the windows side, e.g., Xming.  Then WSL can send X windows based graphics from the Linux shell back to Xming on the Windows side for rendering..  But  Windows OS has to be able to handle rendering the graphics thru Xming using the drivers for whatever the graphics card/hardware is (which could include a GPU). If you look at this thread for the same error you posted, but on a pure linux desktop, https://stackoverflow.com/questions/9769613/x-error-badalloc-…, it reads to me like this may have been solved by updating the *mesa* libraries in linux which support displaying graphics (directly on the linux OS driving the graphics card).  Translating this to the Windows WSL environment however - it would seem the same error could be from the graphics received by the X-server on the Windows side not being compatible/supported by the graphics drivers/hardware there.  It might also have something to do with how the X-server is configured. I don’t have much experience with WSL, but I would think that in the Ubuntu linux shell you’d want to set display for the console,  $ export DISPLAY=:0 Then it sounds like that /usr/bin/xeyes or other *simple* X programs already get displayed correctly,  $ /usr/bin/xeyes Do you get the same error if you run a simple freeview command to open a single volume, e..g. $ freeview $FREESURFER_HOME/subjects/bert/mri/brain.mgz I would try the above directly on the windows machine (not remotely logged in). - R. On Mar 11, 2020, at 10:46, Duvnjak, Aleksandar <aleksandar.duvnjak16(a)imperial.ac.uk> wrote:        External Email - Use Caution        Dear FreeSurfer experts,Version: Freesurfer version 6.0Platform: Ubuntu 14.04 (Via a Windows 10 PC) Upon completion of our first FreeSurfer job, in which we ran an array on ~50 subjects, we have tried to view the basic outputs (e.g. T1.mgz) using both freeview -v and FSLview. Upon running freeview -v, the app opens but shows no discernible image (see screengrab below). Upon exiting the viewing platform the command line reads: X Error: GLXBadContext 150  Extension:    143 (Uknown extension)  Minor opcode: 5 (Unknown request)  Resource id:  0x8000c8I have found reference to this error in the archives at: https://www.mail-archive..com/freesurfer@nmr.mgh.harvard.edu/msg30… much like with this original query, we are running freeview remotely via a high-performace-computing system, and when we type glxgears at the command line spinning gears do popup. Furthermore, (and although this does not relate directly to Freesurfer, it may provide additional useful information) upon trying to view the same T1.mgz file with FSLview rather than freeview we receive the message "missing header/image file" within the viewer but no error in the command line. We appreciate this may be a simple solution, however as it is our first time running FreeSurfer, it is difficult to know how to proceed. I have attached the recon-all report log for the subject attempting to be viewed in the screengrab below.<pastedImagebase640.png>Kind regards,Aleks Duvnjak<recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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within-subject contrast between runs
by Milde, Christopher 11 Mar '20

11 Mar '20

External Email - Use Caution Dear Freesurfer Experts, I have a very basic questions about creating subject-wise contrasts between runs Background Study with two runs per subject where each run corresponds two a different condition (i.e. Stimulation A (on - off) and Stimulation B (on - off). I performed the preprocessing and 1st levels stats in the native subjects space Questions * How can I obtain a within-subjects contrast between two runs (the Stimulation A vs. Stimulation B ) obtained in two runs within one session? * Can I obtain this within-subject contrast by staying in the native subject space? * Do I have to concatenate both runs and create a new parradigm file? Thanks for your support Sincerely Chris

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