Hi Lauri,
This is fixed in v7.2, but if you want to patch your current freesurfer distribution, you can try these commands:
cd $FREESURFER_HOME/bin sudo mv fsvglrun fsvglrun.backup sudo curl -O https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fsvglrun sudo chmod +x fsvglrun
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lauri Tuominen ljtuom@utu.fi Date: Wednesday, August 18, 2021 at 10:42 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Issue with tksurfer-sess External Email - Use Caution
Dear Surfers, I ran into a problem with tksurfer-sess. See below. I have a mac big sur.
I wonder if there is a bug. Any help would be appreciated. Thank you Lauri Tuominen
tksurfer-sess -s subj1 -d ../subjects -analysis ftap.sm05.rh -c ftap -freeview Surface fsaverage rh Map Surface fsaverage rh FreeSurferEnv.csh 7.1.1 Darwin Lauris-MacBook-Pro.local 20.6.0 Darwin Kernel Version 20.6.0: Wed Jun 23 00:26:31 PDT 2021; root:xnu-7195.141.2~5/RELEASE_X86_64 x86_64 Wed 18 Aug 2021 10:35:41 EDT tksurfer: Command not found.
list ftap con/map ftap /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/ftap/sig.nii.gz maplist /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/ftap/sig.nii.gz mri_concat /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/ftap/sig.nii.gz --o /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/tksconcat.nii ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/tksconcat.nii cd /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/mkanalysis setenv SUBJECTS_DIR /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/SUBJECTS_DIR tksurferfv fsaverage rh inflated -overlay /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/tksconcat.nii -annot aparc -surf white -surf pial -fminmax 2 4
Contrasts 0 ftap
/Applications/7.1.1/freesurfer/bin/fsvglrun: line 20: conditional binary operator expected /Applications/7.1.1/freesurfer/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/7.1.1/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then'
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