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You don’t need to manually set MINC_BIN_DIR or the MINC_LIB_DIR variables as those should get set when you source the freesurfer setup script. Try manually running the bash shell, set FREESURFER_HOME, and check you can see that directory, $ bash$ export FREESURFER_HOME=/home/ericlyn/local/easybuild/software/2020/Core/freesurfer/7.2.0$ ls $FREESURFER_HOME< … output deleted but you should see the top of the tree including the SetUpFreeSurfer.sh script you are going to source … > Then source the setup script, $ source $FREESURFER_HOME/SetUpFreeSurfer.sh< … output deleted … > Then try running the command in debug mode and see if you get the help output. If you see the help output, then the command ran. $ bash -x `which aparcstats2table` --help + '[' '!' -e /home/ericlyn/local/easybuild/software/2020/Core/freesurfer/7.2.0']'+ exec /homes/1/rd521/freesurfer/dev/bin/fspython /homes/1/rd521/freesurfer/dev/python/scripts/aparcstats2table —help< … help output deleted ... > - R. On Nov 15, 2022, at 22:07, fsbuild <fsbu...@contbay.com> wrote: External Email - Use Caution Difficult to enlarge your screenshots and read the text, but it looks like even though the output from the setup script displays the path to FREESSURFER_HOME, the script wrapper for the shell cannot verify that path actually exists. And it looks like you are using a “dot” directory named “.local” in your path for FREESURFER_HOME which is usually reserved for hidden subdirs in the shell. I would not name any subdirectory to begin with a "dot" for normal use with the shell, so try$ mv .local local… reset FREESURFER_HOME, source the setup script again, and see if running the command works.- R.On Nov 15, 2022, at 19:59, Eric Yin <eric....@mail.utoronto.ca> wrote: External Email - Use Caution Hello! I’m trying to run the aparcstats2table function on a single participant and I cannot seem to get rid of the following segmentation fault error. I checked the forums and did not find anyone with the same problem. <9ECE8F5D2E7645A5962B55E842687C47.png> I have tried a few different options. First, I read that aparcstats2table requires PATH to lead to python2, but this call would throw the error that freesurfer has not been sourced properly even though I sourced it manually. Please find my Freesurfer version in the screenshot as well. I’m running on CentOS Linux v7 (Core). <4E289904EB384B21861CA9E16B7DD234.png> Then I thought that it might be because freesurfer/7.2.0 requires a newer version of python, but it also did not work for python3 or python3.6. <64B17BE84D1E4AFBBF7FFCE28ED15CD7.png> Please let me know if I’m doing something wrong, or if anyone has run into a similar issue. Thank you for your time._______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1FgpEnfiQUT43jn39cU5NylGOXNr2K7trxyVjQCsbuV1y922zM0DyVahr3T580T1fLTgkOboC2T4SIJvoTfE7APBc-ex4Dx--CKm6jX16tN6T3o-T80uKJkn3HWUsm3dTJuRHXSqwLIOxNu5FyBBObxPzqE8JGlCiadH2zWFCzaRxFQryx2RpDxvisyAEU1QQEYJRcuYSGyNaIxJ4HPg15kL6TSiJZdn2elg1IiOegm633g1mGI9dZaLwbxfZWTFrC4CD6D2zYzMJGlx__By64WPq3LtlF-jNdvO9dLDEKMUA2cvne4u6n8PtQPDqfjhXm7HPukEQjlxDVFuJEYezHg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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