Loading FreeSurfer Images for QA on HiPerGator - tannerjared/MRI_Guide GitHub Wiki

After starting a FreeView session , go to Applications --> Terminal Emulator. You can also start a Console session instead.

The code below is specific to one user and subject so it needs to be edited.

module load freesurfer/7.1.1

cd /blue/clp7934/share/jjtanner/subjects

export SUBJECTS_DIR=$PWD

freeview -v 002_S_5178/mri/T1.mgz 002_S_5178/mri/brainmask.mgz -f 002_S_5178/surf/lh.white:edgecolor=yellow 002_S_5178/surf/lh.pial:edgecolor=red 002_S_5178/surf/rh.white:edgecolor=yellow 002_S_5178/surf/rh.pial:edgecolor=red