Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Re: [Freesurfer] $FREESURFER_HOME/bin not being added to PATH (tcsh)
by fsbuild 10 Oct '23

10 Oct '23

External Email - Use Caution If you add these 2 commands to setup the freesurfer environment, e.g., for csh/tcsh as your default shell, $ setenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1$ source $FREESURFER_HOME/SetUpFreeSurfer.csh - to your shell initialization file, $HOME/.cshrc, then FREESURFER_HOME, SUBJECTS_DIR, PATH, etc., should automatically set/modified by source'ing SetUpFreeSurfer.csh when you open a new terminal window.   There is no need to subsequently set SUBJECTS_DIR or other freesurfer environment variables in your shell init file (or in the current terminal window session) unless the settings should be different than the defaults.  Most people add those 2 commands to be the last 2 lines in their shell init file. I would check the defaults set in the current shell environment using only those 2 commands above in your shell init file after opening a new terminal window, $ env | sort … and check FREESURFER_HOME, SUBJECTS_DIR, PATH are set … The freeview command should already be found in your path, i.e., you should see … $ which freeview/usr/local/freesurfer/7.4.1-1/bin/freeview - R. On Oct 9, 2023, at 14:56, Edward Zuniga <eazuniga(a)vcu.edu> wrote:        External Email - Use Caution        Hello,I am attempting to install FreeSurfer on a Centos 7 workstation using the tcsh shell. Below are the contents of my .cshrc file. Should $FREESURFER_HOME/bin be automatically added to the PATH? I tried rebooting, and it still is not adding it to the PATH. My environment variables appear to be set correctly  because I see this when opening a new terminal. I also tried modifying the .cshrc file to add the directory to the PATH manually, but it still will not stick after rebooting.-------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.4.1-1FSFAST_HOME       /usr/local/freesurfer/7.4.1-1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7..4.1-1/subjectsMNI_DIR           /usr/local/freesurfer/7.4.1-1/mniFSL_DIR           /usr/local/FSL/fsl_6_0_7_4[cogdmd@cari6 ~]$ Thanks,Eddie#############################################################umask 002setenv PATH /usr/local/cuda-9.1/bin:$PATHsetenv LD_LIBRARY_PATH /usr/local/cuda-9.1/lib64# auto-inserted by @update.afni.binaries :set path = ( $path  /home/cogdmd/abin  ) setenv R_LIBS ~/R#FSL Setupsetenv FSLDIR /usr/local/FSL/fsl_6_0_7_4setenv PATH ${FSLDIR}/share/fsl/bin:${PATH}source ${FSLDIR}/etc/fslconf/fsl.csh#Freesurfer Setupsetenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1setenv SUBJECTS_DIR $FREESURFER_HOME/subjectssource $FREESURFER_HOME/SetUpFreeSurfer.cshalias spm12 'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; spm fMRI"'alias conn 'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; addpath /usr/local/SPM/conn; conn"'setenv PATH /home/cogdmd/anaconda3/bin:$PATHsetenv ANTSPATH /home/cogdmd/ants-2.4.1/binsetenv PATH ${ANTSPATH}:${PATH}setenv PATH /home/cogdmd/.lcmodel:$PATH############################################################-- Edward A. ZunigaSenior Research AnalystVirginia Commonwealth UniversityC. Kenneth and Dianne Wright Center for Clinical and Translational ResearchInstitute for Drug and Alcohol StudiesCollaborative Advanced Research Imaging (CARI) Facility203 East Cary Street, Suite 202Richmond, Virginia 23219Phone: (804) 828-4184Fax: (804) 827-2565eazuniga@vcu.edu_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Job at University of Chicago, neuroimaging for aging/Alzheimer
by Adam Martersteck 10 Oct '23

10 Oct '23

External Email - Use Caution *Apologies for cross-posting listservs* The University of Chicago’s Neurology Department is seeking a data scientist focused on neuroimaging in aging and Alzheimer’s disease. See the full job posting here. <https://secure-web.cisco.com/1yaxNMxhk779aUROY3cicfsnJIUzCUvaeqRL_tkMqoQ7VB…> University of Chicago’s new Healthy Aging & Alzheimer’s Research Care Center is focused on SuperAging, a phenotype of successful aging, and atypical Alzheimer’s disease and related dementia syndromes. Prior experience with Alzheimer’s disease or aging is *not* a requirement. The primary responsibilities of the positions are to use analytical, statistical, and programming skills to help collect, curate, analyze, and interpret biomedical data, including neuroimaging and biomarker derivatives. The candidate will work alongside investigators and clinicians to develop data-driven solutions and answer scientific questions. See the full list of responsibilities in the job posting for more information. Candidates should have some prior experience with neuroimaging software libraries, and Python and/or R. Experience with high-performance cluster shell scripting and schedulers, and machine learning libraries are desirable. Apply through the portal, but feel free to reach out with questions ( martersteck(a)uchicago.edu) *Adam Martersteck, PhD * *(he/him)**Assistant Professor of Neurology* | The University of Chicago, Healthy Aging & Alzheimer's Research Care (HAARC) Center *Address *| 850 East 58th Street | Chicago, IL 60637 *Phone *| 773-795-1683 *Email *| martersteck(a)uchicago.edu

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Re: [Freesurfer] Hippocampus Segmentation Troubleshoot - Matlab crash
by fsbuild 09 Oct '23

09 Oct '23

External Email - Use Caution Please try using the Matlab runtime environment which can be installed directly into the freesurfer tree via a script we provide.  The runtime environment is free and requires no paid for Matlab license (since it does not include the Matlab compiler). For your existing install of freesurfer 7..1.1, the tested version of the Matlab runtime environment to install is R2014b (listed below as the version to use in the bash/zsh commands).  However, if you were to update to the current freesurfer 7.4.1 release, https://secure-web.cisco.com/1EbuUGpusH65Vnhqyq32iw8lhOzpyphG…, then you could use the more recent R2019b Matlab runtime. $ export FREESURFER_HOME=<your install path> $ cd $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2014b    <— change to R2019b if you end up using freesurfer 7.4.1 … answer y to any installer questions … The output from running that script will list what DYLD_LIBRARY_PATH should be set to.   Please make sure you have otherwise removed any references to your previous matlab environment from DYLD_LIBRARY_PATH, PATH, etc.  It might also work to add $FREESURFER_HOME/MCRv97/bin/glnxa64 to DYLD_LIBRARY_PATH but I would first try what the script prints out as the local paths on your machine. - R. On Oct 9, 2023, at 20:21, Mirsol Choi <mirsol(a)ualberta.ca> wrote:        External Email - Use Caution        Hi there,I am a Master's student who is looking to segment the hippocampus and analyze diffusion data of the segments. I am trying to utilize the segmentation function with this command:segmentHA_T1.sh subj01But I am met with this error saying that Matlab has crashed. The crash log is attached to this email. I have freesurfer version 7.1.1, running on MacOs 11.7.10.I have followed your website instructions to download Matlab R2014b.Following the installation process of Matlab, I was met with this message: Installing Product: MATLAB Compiler Runtime - Core 8.4(Oct 08, 2023 11:29:15) Installing Product: MATLAB Compiler Runtime - GPU 8.4(Oct 08, 2023 11:29:21) Notes: On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/bin/maci64:(Oct 08, 2023 11:29:21) Exiting with status 0(Oct 08, 2023 11:29:21) End - Successful.FinishedR2014b installed successfully in /Applications/freesurfer/7.1.1/MCRv84And so I have appended the path using this code into my bashrc profile: export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/bin/maci64I am wondering if I can get some help with running the hippocampus segmentation protocol .Thank you so much for your time, I greatly appreciate your support. <matlab_crash_dump.28607-2>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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$FREESURFER_HOME/bin not being added to PATH (tcsh)
by Edward Zuniga 09 Oct '23

09 Oct '23

External Email - Use Caution Hello, I am attempting to install FreeSurfer on a Centos 7 workstation using the tcsh shell. Below are the contents of my .cshrc file. Should $FREESURFER_HOME/bin be automatically added to the PATH? I tried rebooting, and it still is not adding it to the PATH. My environment variables appear to be set correctly because I see this when opening a new terminal. I also tried modifying the .cshrc file to add the directory to the PATH manually, but it still will not stick after rebooting. -------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1-1 FSFAST_HOME /usr/local/freesurfer/7.4.1-1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1-1/subjects MNI_DIR /usr/local/freesurfer/7.4.1-1/mni FSL_DIR /usr/local/FSL/fsl_6_0_7_4 [cogdmd@cari6 ~]$ Thanks, Eddie ############################################################# umask 002 setenv PATH /usr/local/cuda-9.1/bin:$PATH setenv LD_LIBRARY_PATH /usr/local/cuda-9.1/lib64 # auto-inserted by @update.afni.binaries : set path = ( $path /home/cogdmd/abin ) setenv R_LIBS ~/R #FSL Setup setenv FSLDIR /usr/local/FSL/fsl_6_0_7_4 setenv PATH ${FSLDIR}/share/fsl/bin:${PATH} source ${FSLDIR}/etc/fslconf/fsl.csh #Freesurfer Setup setenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1 setenv SUBJECTS_DIR $FREESURFER_HOME/subjects source $FREESURFER_HOME/SetUpFreeSurfer.csh alias spm12 'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; spm fMRI"' alias conn 'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; addpath /usr/local/SPM/conn; conn"' setenv PATH /home/cogdmd/anaconda3/bin:$PATH setenv ANTSPATH /home/cogdmd/ants-2.4.1/bin setenv PATH ${ANTSPATH}:${PATH} setenv PATH /home/cogdmd/.lcmodel:$PATH ############################################################ -- Edward A. Zuniga Senior Research Analyst Virginia Commonwealth University C. Kenneth and Dianne Wright Center for Clinical and Translational Research Institute for Drug and Alcohol Studies Collaborative Advanced Research Imaging (CARI) Facility 203 East Cary Street, Suite 202 Richmond, Virginia 23219 Phone: (804) 828-4184 Fax: (804) 827-2565 eazuniga(a)vcu.edu

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RECON ALL Error
by Massimo Valerio 08 Oct '23

08 Oct '23

External Email - Use Caution Dott. Massimo VALERIO Neuropsichiatra Infantile SSD Neurologia Pediatrica Dipartimento di Patologia e Cura del Bambino Regina Margherita A.O.U Citta della Salute e della Scienza della Citta di Torino Presidio Ospedale Infantile Regina Margherita Piazza Polonia 94, 10126 Torino Tel: 011 3135248 Fax: 011 3135439 Email: massimo.valerio(a)unito.it Il giorno dom 8 ott 2023 alle ore 16:22 Massimo Valerio < massimo.valerio(a)unito.it> ha scritto: > Hello FreeSurfer Developers, > > I'm attempting to compute the recon-all of T1 3D of my patient. > ERROR: > > \n mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta > /Applications/freesurfer/subjects/PZDALENE/mri/transforms/cc_up.lta > PZDALENE \n > > will read input aseg from aseg.auto_noCCseg.mgz > > writing aseg with cc labels to aseg.auto.mgz > > will write lta as > /Applications/freesurfer/subjects/PZDALENE/mri/transforms/cc_up.lta > > reading aseg from > /Applications/freesurfer/subjects/PZDALENE/mri/aseg.auto_noCCseg.mgz > > reading norm from /Applications/freesurfer/subjects/PZDALENE/mri/norm.mgz > > 39269 voxels in left wm, 29817 in right wm, xrange [112, 141] > > searching rotation angles z=[-7 7], y=[ 9 23] > > searching scale 1 Z rot 5.0 global minimum found at slice 127.0, > rotations (14.74, -1.72) > > final transformation (x=127.0, yr=14.745, zr=-1.723): > > 0.96663 0.03006 0.25439 -31.60547; > > -0.02907 0.99955 -0.00765 15.74752; > > -0.25451 0.00000 0.96707 33.63651; > > 0.00000 0.00000 0.00000 1.00000; > > mri_cc: no WM voxels found with norm > 40 -- check skull stripping > > > No such file or directory > > Darwin MBPdiNeirurgia4.fritz.box 21.6.0 Darwin Kernel Version 21.6.0: Fri > Sep 15 16:17:23 PDT 2023; root:xnu-8020.240.18.703.5~1/RELEASE_X86_64 x86_64 > > > recon-all -s PZDALENE exited with ERRORS at Sun Oct 8 02:34:07 CEST 2023 > > > > I've searched the list and no similar errors have been reported. > Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive > attached the recon-all.log in case it's of any use. > > 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > 2) Platform: MacOs Monterey 12.7 > 3) uname -a: Darwin MBPdiNeirurgia4.fritz.box 21.6.0 Darwin Kernel > Version 21.6.0: Fri Sep 15 16:17:23 PDT 2023; root:xnu-8020.240.18.703.5~1/RELEASE_X86_64 > x86_64 > 4) recon-all.log: see attached > > > > Dott. Massimo VALERIO > > Neuropsichiatra Infantile > SSD Neurologia Pediatrica > Dipartimento di Patologia e Cura del Bambino Regina Margherita > A.O.U Citta della Salute e della Scienza della Citta di Torino > Presidio Ospedale Infantile Regina Margherita > Piazza Polonia 94, 10126 Torino > Tel: 011 3135248 > Fax: 011 3135439 > Email: massimo.valerio(a)unito.it > > > <https://secure-web.cisco.com/1NNui4wxv6m_TmgOnzlJg9RYl5qaN4AkQ33H4VEWmLcrOo…> Privo > di virus.http://secure-web.cisco.com/1sOwZmGRpeVGH_FSbs-TgSzvLT2A8yzMOa_UqlXrz… > <https://secure-web.cisco.com/1NNui4wxv6m_TmgOnzlJg9RYl5qaN4AkQ33H4VEWmLcrOo…> > <#m_-8264439549155417804_m_3222428717412999766_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >

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fRe: SAMSEG lesion mask pattern on Mac with M2 processor and GPU
by fsbuild 07 Oct '23

07 Oct '23

External Email - Use Caution  Python code  (including 3rd party python packages) in the Intel Mac build cannot be guaranteed to run on Mac M1, M2 arm processors.  Package developers may still build their code using Intel processor specific instructions which cannot be emulated by the Rosetta environment on arm64 Macs.  Rosetta translates Intel processor instructions to arm64 processor instructions; when there is no equivalent arm processor instruction, you get the error “illegal instruction”.  The remedy for this is to re-write and/or re-build the code (to be more portable). There is an arm64 freesurfer development build including an arm64 python with Apple’s tensorflow.   However, the freesurfer python code is not yet entirely compatible with arm64 python and all its packages.  The mri_synthsr script currently does not work with arm64 tensorflow; I don’t know about mri_samseg.   You can try the arm64 development build via the link,  https://secure-web.cisco.com/17oMRv7D8FpOpyCTDI2b6q3ZFH9-liuuaw55Fk0qAsqgBnL3cDmnkVAujZjuxE5eX79DEYS-N-28sS2kPCHZELA_TD9KfXA1gTpkIIQlltrdLjmUYAErTEyV7pXp61dNngBidguhX9Ro7dWKp68cyGlPyIUMglyRLC5Ic8KxVhEd1h6taIbJUs2RF62qX_akkZQzboTafybXKGqtqZO75VJ_VYmF1FbMwq5IEVXbxaM1fZtZ1ZQn6V7EGFGVpOnhJcYCh6SCvDAdGOF8jbC_XE4GUihNWJa4hRA4860MsPxHxc4Or__ON8TElFES-SLctaTntlZ16qO5C18SyRBuAGw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg%26nbsp; Please keep in mind this it not a release build and please report any errors. Fixes for these kinds of issues will become available in the development builds via the link above once they are added into the freesurfer development stream.   We can also notify the list. - R. On Oct 7, 2023, at 03:23, Bianka Forgó <fbia021(a)gmail.com> wrote:        External Email - Use Caution        Dear Freesurfer Developers,I am attempting to use Freesurfer on MacOS Ventura (version 13.5.2) with an M2 Pro silicone chip and GPU. I have successfully installed Freesurfer version 7.4.1.I am trying to use samseg for cross-sectional MS lesion volume analysis by running the following command:run_samseg --input Freesurfer_subjects/T1.nii Freesurfer_subjects/FAMUS/T2FLAIR_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output Freesurfer_subjects/FAMUS/samsegI get the error message:zsh: illegal hardware instruction  run_samseg --input Freesurfer_subjects/FAMUS/T1.nii   --lesion  0 1 As described in the samseg manual, one may be prompted to use Tensorflow when using this module for the first time. I was not prompted to do so but I did install it (and python3 as well) using the instructions here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tE2yZiNK2sSgfXl2g2jsBKvz4UwOnAafBZo84… this, I still get the above error message.I can also see that there is no support for running Tensorflow on Mac with GPU.Does this mean that there's no way for me to run this command or is there anything else I can try to solve this?Of note, the basic samseg command (run_samseg --input <file> [<file> ...] --output <dir> [--threads <threads>] [--pallidum-separate]) is running without any issues.Thank you,Bianka_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Use of infantFS and FS in the interval 2 - 4.5 years of age
by michefabb 07 Oct '23

07 Oct '23

External Email - Use Caution Dear FS experts, I see it is recommended to use infantFS below 2 years of age, whereas FS has been used for 4.5 years and above. I was wondering what could be used in the interval 2 - 4.5 years of age: which are benefits and drawbacks of both? Thanks, appreciated, Mic

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SAMSEG lesion mask pattern on Mac with M2 processor and GPU
by Bianka Forgó 07 Oct '23

07 Oct '23

External Email - Use Caution Dear Freesurfer Developers, I am attempting to use Freesurfer on MacOS Ventura (version 13.5.2) with an M2 Pro silicone chip and GPU. I have successfully installed Freesurfer version 7.4.1. I am trying to use samseg for cross-sectional MS lesion volume analysis by running the following command: run_samseg --input Freesurfer_subjects/T1.nii Freesurfer_subjects/FAMUS/T2FLAIR_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output Freesurfer_subjects/FAMUS/samseg I get the error message: zsh: illegal hardware instruction run_samseg --input Freesurfer_subjects/FAMUS/T1.nii --lesion 0 1 As described in the samseg manual, one may be prompted to use Tensorflow when using this module for the first time. I was not prompted to do so but I did install it (and python3 as well) using the instructions here: https://secure-web.cisco.com/13jV9GWC39Eu7ptAevMhql74Ty0xCnVcRkXqXbKh6yiJZq… After this, I still get the above error message. I can also see that there is no support for running Tensorflow on Mac with GPU. Does this mean that there's no way for me to run this command or is there anything else I can try to solve this? Of note, the basic samseg command (run_samseg --input <file> [<file> ...] --output <dir> [--threads <threads>] [--pallidum-separate]) is running without any issues. Thank you, Bianka

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Re: [Freesurfer] Free surfer quits unexpectedly
by fsbuild 06 Oct '23

06 Oct '23

External Email - Use Caution  Please try the following, … open a new terminal and run the bash shell … I am cd’d to /tmp though it should not matter ... $ cd /tmp$ bashThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1B3JRrCA1-GeI0tKc8qR9oVMx4vfk7xlYLxiqqBDOBuaes… … check the version of Quartz by starting an xterm.  When the xterm window opens check the version from the upper left hand corner XQuartz application pull down menu and check what “About X11” reports.  Check you have Quartz 2.8.2 or later and then quit the xterm window. Mac:/tmp> which xterm/opt/X11/bin/xtermMac:/tmp> xterm & … copy your license.txt file into your home directory.  For example if you downloaded the license by default into your Downloads folder, then copy it from there into $HOME … Mac:/tmp> cd $HOMEMac:~> cp -p -f ./Downloads/license.txt . … set the environment variable FS_LICENSE to point to the license file … later you can put this in your shell init file to be the default when you launch a new terminal window with your default shell …  Mac:~> export FS_LICENSE=$HOME/license.txtMac:~> head -1 $FS_LICENSEyou(a)somedomain.com                   <— email you used to register for the license … setup the freesurfer environment … Mac:~> export FREESURFER_HOME=/Applications/freesurfer/7.4.1Mac:~> source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.4.1FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjectsMNI_DIR           /Applications/freesurfer/7.4.1/mni … first check freeview with no arguments opens an empty window … Mac:~>  which freeview/Applications/freesurfer/7.4.1/bin/freeviewMac:~> freeview … close the freeview window and try to open a knoen to be good volume file ... … check the volume file exists … Mac:~> ls -l $SUBJECTS_DIR/bert/mri/T1.mgz-rwxr-xr-x  1 root  wheel  4502402 Jul 13  2021 /Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz* … try opening the volume file …Mac:~> freeview $SUBJECTS_DIR/bert/mri/T1.mgz If the above works try opening one of your own volume or surface files. BTW - you should update MacOS on your machine from 12.6.7 to 12.7 as there are important security fixes in 12.7. - R. On Oct 4, 2023, at 00:53, Clara Massaneda Tuneu <c.massaneda_tuneu(a)blackdog.org.au> wrote:        External Email - Use Caution        Hi, I'm attempting to install and run FreeSurfer, but every time I try to load data, the program unexpectedly quits. I downloaded the license from the email sent by FreeSurfer and followed the instructions of the video tutorial. I've also downloaded and installed the latest version of XQuartz before installing and executing FreeSurfer. When I tried to open FreeView in my terminal and load the image, there was no message in my terminal explaining why the program crashes. The version of FreeSurfer that I'm using is freesurfer-macOS-darwin_x86_64-7.4.1. My device is a MacBook Pro (2016) running version 12.6.7, with a 2 GHz Dual-Core Intel Core i5 processor and 8GB of memory. I've searched the list, and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this issue? Thanks for your help.  Clara MT_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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SynthSeg volume labels
by Weerasekera, Akila,PHD 05 Oct '23

05 Oct '23

External Email - Use Caution Hi, Using SynthSeg (Freesurfer dev) with --vol, the .csv does not contain all volume labels, do I need to include anything else in the command? [cid:878677f0-6b6f-4a4d-9c3a-54e1808b22ac] Thank you, Akila Akila Weerasekera, PhD | Postdoctoral Research Fellow Maria Mody lab for Developmental Language and Reading Research Laboratory | Eva Ratai Lab for Clinical Spectroscopy | Garry Nolan Lab (Stanford University) | Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 |Charlestown, MA 02129, USA Mobile: (781) 820 4501 aweerasekera(a)mgh.harvard.edu <mailto:aweerasekera@mgh.harvard.edu> http://secure-web.cisco.com/1pRNH3jpPVm0xhHznjcAnuOO_FSI27YNJi0tVFuibJuCEyI…<http://secure-web.cisco.com/1pRNH3jpPVm0xhHznjcAnuOO_FSI27YNJi0tVFuibJuCEyI…> https://secure-web.cisco.com/158m2Mk7xVvNTOqu1Onlo3GW-mrGUVQUQR1Nxh5mCc2yTr…

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