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 best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <l...@email.gwu.edu> Date: Tuesday, August 17, 2021 at 2:43 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] LGI - output issue External Email - Use Caution Good afternoon FreeSurfer experts, Hope that everyone is well and staying safe! I tried opening LGI freeview (or tksurferfv) output, and I have been running into the following issues (see code and error message outputs below). Any ideas how I could fix this? Please let me know if additional details are needed. Bolded code is what I inserted. Outputs are not bolded. tksurfer HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi zsh: command not found: tksurfer tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi ERROR: cannot find lh.pial_lgi cd $SUBJECTS_DIR/HAR30303_srs2_2/surf tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi freeview -f /Applications/ace_complete/HAR30303_srs2_2/surf/lh.inflated:curvature=/Applications/ace_complete/HAR30303_srs2_2/surf/lh.curv:overlay=lh.pial_lgi:overlay_threshold=2,2,5 -viewport 3d /Applications/freesurfer/bin/fsvglrun: line 20: conditional binary operator expected /Applications/freesurfer/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then' Also within the surf folder, I tried something like: freesurfer -v lh.pial_lgi Output in freeview was just a dark screen - tried changing the color map but nothing improved this issue. Thank you so much!
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