Freesurfer July 2021

freesurfer@nmr.mgh.harvard.edu

91 participants
121 discussions

18 Jul '21

External Email - Use Caution Hi, I am looking at various brain volumes in the aprarc and aseg stats generated by recon-all and SAMSEG> stats. Some of the subjects were scanned on Philip and some on GE, and some on GE at time point 1 and PH on time point 2. Q1: Is there a measure in the aparc, aseg, and SAMSEG stats files that is fairly resistant to scanner variability? I clearly see eTIV for the same subject have 15% or more discrepancy between GE and PH. Interestingly, cortical thickness relative difference between PH and GE is 1.23% in controls. Q2: Is there a way to harmonize between GE and PH values? Many thanks, AJ

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Re: [Freesurfer] FreeView issue!
by fsbuild 18 Jul '21

18 Jul '21

External Email - Use Caution There are some reports of running Qt 5.12 on MacOS BigSur (your version is 11.4),  that setting the environment variable below in your (e.g.., bash) shell can help the main application window start.  No need to send another crash report if freeview window still does not come up. - R. $ export QT_MAC_WANTS_LAYER=1 On Jul 17, 2021, at 21:49, Sahil Bajaj <sahil.brain(a)gmail.com> wrote:        External Email - Use Caution        Hi,Both the commands you sent work fine - one displays no output and the other displays clock. Please find below the full crash report I get after I run following FreeView command:BT136080:~ bajsah$ freeview /Applications/freesurfer/7.1.1/bin/freeview: line 2: 45349 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"On Sat, Jul 17, 2021 at 12:18 AM fsbuild <fsbuild(a)contbay.com> wrote:Something is probably not right trying to launch the window since it works to run the binary and produce the help output.You can check the following command produces no output,$ otool -L /Applications/freesurfer/7.1.1/Freeview.app/Contents/MacOS/freeview | grep notIf Xquartz is installed, then you should be able to run the following and see a clock,$ /opt/X11/bin/xclockIf the above work, then reproduce the segfault and the system should display a window with the crash report.  You should be able to select all the crash report text and paste it into an email to send along.- R.Sahil Bajaj (sahil.brain(a)gmail.com)  July 16, 2021 at 20:35Yes, actually I have the environment already set up, please see below:When I open the terminal I get:Last login: Fri Jul 16 16:46:38 on ttys000-------- freesurfer-darwin-macOS-7.1..1-20200811-8b40551 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.1.1FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjectsMNI_DIR           /Applications/freesurfer/7.1.1/mniFSL_DIR           /usr/local/fslThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`..For more details, please visit MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1AqPFzKRhx6oyH5_KyxUJoilycl76z9lWCYpgu… I type freeview, I get:BT136080:~ bajsah$ freeview /Applications/freesurfer/7.1.1/bin/freeview: line 2:  8086 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"When I type which freeview and --help, I get:BT136080:~ bajsah$ which freeview/Applications/freesurfer/7.1.1/bin/freeviewBT136080:~ bajsah$ freeview --helpUsage: freeview [OPTION <ARGUMENT:SUB-OPTION>]...Volume and surface viewer and editor for freesurfer.-v, --volume <FILE>...       Load one or multiple volume files. Available sub-options are: ......Screenshot for the above stuff is attached below:fsbuild (fsbuild(a)contbay.com)  July 16, 2021 at 19:49        External Email - Use Caution        Just wondering if you already tried using bash to setup the environment. - R.%] bashbash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.shSetting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.1.1FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjectsbash-3.2$ which freeview/Applications/freesurfer/7.1.1/bin/freeviewbash-3.2$ freeview --help. . . output deleted . . ... . . if that succeeds then see if freeview will open an empty window . .. .bash-3.2$ freeview_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon -all and mri_convert errors
by Podell, Jamie 17 Jul '21

17 Jul '21

External Email - Use Caution Hi, I am trying to run recon -all on a T1 .nii file and keep running into errors. It says both "No such file or directory" and "bad number of dimensions." Since it seemed to me to be a problem with the .nii file, I tried running mri_convert separately but got the same errors. The file definitely exists in the location I designated (I can open it in freeview, etc.)... Do I need to manually change something about the .nii file to get it to run? Appreciate any help and am hoping there is a simple fix! Here is what the log says: /Users/jamiepodell/Desktop/PSH_MRI/008 \n mri_convert /Users/jamiepodell/Desktop/PSH_MRI/s008_T1.nii /Users/jamiepodell/Desktop/PSH_MRI/008/mri/orig/001.mgz \n mri_convert /Users/jamiepodell/Desktop/PSH_MRI/s008_T1.nii /Users/jamiepodell/Desktop/PSH_MRI/008/mri/orig/001.mgz reading from /Users/jamiepodell/Desktop/PSH_MRI/s008_T1.nii... error: No such file or directory error: niiRead(): bad number of dimensions (10703) in /Users/jamiepodell/Desktop/PSH_MRI/s008_T1.nii Darwin Jamies-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64 Thanks, Jamie Jamie E. Podell, MD Assistant Professor Division of Neurocritical Care and Emergency Neurology Department of Neurology Program in Trauma University of Maryland School of Medicine

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dwi_orig_las issue trac-all -prep
by AmirHussein Abdolalizadeh 17 Jul '21

17 Jul '21

External Email - Use Caution Dear FreeSufer users/experts, I am trying to do TRACULA (FS 7.1.1) on a subject with b = 0,1000 in 60 directions. The preprocessing steps of denoising, bias-field, eddy/motion correction were done using MRtrix (in .mif format) and their outputs are converted into .nii, .bvec, and .bval. I changed the dmrirc.example into the attached file to omit the associated preprocessing steps. Running the trac-all -prep -c dmrirc.pilot results in an error right at the beginning: reading info from /<a long path!>/AnalyzeDWI/pilot/dmri/dwi_orig_las.1.nii.gz... error: niiRead(): error opening file /<path>/AnalyzeDWI/pilot/dmri/dwi_orig_las.1.nii.gz It is not present in the output folder. Interestingly, this file is generated a few lines above and then renamed into dwi_orig_las and then into dwi.nii.gz: mv -f /<path>/AnalyzeDWI/pilot/dmri/dwi_orig_las.1.nii.gz /<path>/AnalyzeDWI/pilot/dmri/dwi_orig_las.nii.gz A few lines later: mv -f /<path>/AnalyzeDWI/pilot/dmri/dwi_orig_las.nii.gz /<path>/AnalyzeDWI/pilot/dmri/dwi.nii.gz Thus, my guess is due to this renames it cannot find it. Any help is appreciated. Bests, Amir p.s. the MRtrix-preprocessed file is itself LAS: orientLAS /<path>/AnalyzeDWI/pilot/dmri/dwi_orig.1.nii.gz /<path>/AnalyzeDWI/pilot/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -8

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Re: [Freesurfer] FreeView issue!
by fsbuild 16 Jul '21

16 Jul '21

External Email - Use Caution Just wondering if you already tried using bash to setup the environment.  - R. %] bashbash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.1.1FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjects bash-3.2$ which freeview/Applications/freesurfer/7.1.1/bin/freeviewbash-3.2$ freeview --help. . . output deleted . . .. . . if that succeeds then see if freeview will open an empty window . . .bash-3.2$ freeview On Jul 16, 2021, at 17:33, Sahil Bajaj <sahil.brain(a)gmail.com> wrote:        External Email - Use Caution        Hi RuopengThanks for your quick response.If I use that I still get the similar error: BT136080:~ bajsah$ $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeviewSegmentation fault: 11Segmentation fault: 11SahilOn Fri, Jul 16, 2021 at 1:23 PM Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:What if you run:$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview -f fsaverage/surf/lh.inflated> On Jul 16, 2021, at 1:07 PM, Sahil Bajaj <sahil.brain(a)gmail.com> wrote:> >         External Email - Use Caution        > > > Hi everyone,> > I am having following error while opening freeview in terminal:> > BT136080:01_Project_FreeSurfer bajsah$ freeview -f fsaverage/surf/lh.inflated> /Applications/freesurfer/7.1.1/bin/freeview: line 2: 27046 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"> > Somehow, this was working fine a few weeks ago, but I can't open freeview now. I double checked the folder: /Applications/freesurfer/7.1.1/bin/freeview and everything seems to be at place.> > Any suggestions/tips to resolve this, please?> > Thanks a lot !> Sahil> _______________________________________________> Freesurfer mailing list> Freesurfer(a)nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1sckFV0ZDHm6jVeKBFeCWBRK8w52ulKng6EPlPn…;. 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.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeView issue!
by Sahil Bajaj 16 Jul '21

16 Jul '21

External Email - Use Caution Hi everyone, I am having following error while opening freeview in terminal: BT136080:01_Project_FreeSurfer bajsah$ freeview -f fsaverage/surf/lh.inflated /Applications/freesurfer/7.1.1/bin/freeview: line 2: 27046 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Somehow, this was working fine a few weeks ago, but I can't open freeview now. I double checked the folder: /Applications/freesurfer/7.1.1/bin/freeview and everything seems to be at place. Any suggestions/tips to resolve this, please? Thanks a lot ! Sahil

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Yeo atlas for children!
by Martin Juneja 16 Jul '21

16 Jul '21

External Email - Use Caution Dear experts, I used Yeo's 17-network parcellation to study the association between network-wise cortical volume and a clinical variable in adolescents. I received the following two questions from the reviewers regarding the use of Yeo's atlas. I would really appreciate if someone could help us in addressing these questions: *1) Could the author justify their choice to use a functional parcellation on structural data? How is using this parcellation helpful in understanding the brain? All in all, the authors need to justify the superiority of using Yeo's 17-area parcellations on structural data over other methods of parcellation/analysis. * *2) One issue with Yeo's parcellation also stems from the fact that this parcellation was derived from adult connectomes. Could the authors also address this issue and provide examples that justify their approach.* Thanks.

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Mac OS problem with .pial files
by TILSLEY Penelope 16 Jul '21

16 Jul '21

External Email - Use Caution Hello, I have recently changed from Linux to Mac OS (Big Sur) and have problems with loading lh.pial and rh.pial files on the Mac system. The files were created using the recon-all command on the Linux system, this finished without error. But I wonder if there is some problem going from Linux to Mac regarding these surface files. For example, I can load these files on the Linux, but when trying to load the surfaces on the Mac in Freeview either manually or via the command line the following error is repeatedly printed in the terminal: error: freadFloat: fread failed error: Invalid argument Further, commands such as mris_convert lh.pial lh.pial.asc work on the Linux system but crash and give the same error as above on the Mac. Both systems are running Freesurfer 7.1.1 (freesurfer-darwin-macOS-7.1.1-20200811-8b40551 / Freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) Thanks in advance for your help, Penny

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Thalamic segmentation error Big Sur
by Daniela Vecchio 16 Jul '21

16 Jul '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to segment thalamic nuclei, as described by the tutorial page (https://secure-web.cisco.com/1F9Cs4OMcQ2PV75K6Q0sKfyHoo5UBJNkIWoWVANuievmgb…) but I got an Matlab routine error. I’t happened after the upgrade to MacOS Big Sur and I guess it is a compatibility issue. I tried also to re-install the routine (by fs_install_mcr R2014b ) and to run the process by docker container but the process ended with the same error. (Obviously, I got the same error also trying the hippocampus&amygdala module). ERROR: MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_SegmentThalamicNuclei.sh: line 33: 3322 Killed: 9 /Applications/freesurfer/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei subjHC001/ /Applications/freesurfer/subjects 0.5 /Applications/freesurfer/average/ThalamicNuclei/atlas/AtlasMesh.gz /Applications/freesurfer/average/ThalamicNuclei/atlas/AtlasDump.mgz /Applications/freesurfer/average/ThalamicNuclei/atlas/compressionLookupTable.txt 0.05 L-BFGS v12 '/Applications/freesurfer/bin/fs_run_from_mcr /Applications/freesurfer/bin/' 1 0 Darwin iMac-di-Daniela.local 20.5.0 Darwin Kernel Version 20.5.0: Sat May 8 05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64 I've searched the list and I didn’t found a way to fix it. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the thalamic-nuclei-mainFreeSurferT1.log in case it's of any use. Thanks in advance Best regards, Daniela

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/usr/pubsw reference in 7.1.1
by Drucker, Daniel 16 Jul '21

16 Jul '21

When running tksurfer in 7.1.1 (from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-lin… ) , I get: Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary" Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories: ./library ./tix8.1 ./library ./tix8.1 /usr/pubsw/packages/tcltktixblt/current/lib/tix8.1 This probably means that Tix wasn't installed properly. What should I do about this? It works under 6.0.1. -- Daniel M. Drucker, Ph.D. Director of IT McLean Hospital Imaging Center Harvard Medical School

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Freesurfer July 2021