Dear Freesurfers, Forgive me for asking about what appears to be a very simple issue but I am stumped. I have defined my SUBJECTS_DIR as evidenced by this output. ----- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni
But upon trying to execute the following: mri_segstats --seg /Applications/freesurfer/subjects/bert/mri/aseg.mgz --sum /Applications/freesurfer/subjects/bert/stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg
I get the error that "SUBJECTS_DIR not defined in environment." My code has been edited to not even use this variable and yet the issue stills stands. Please advise on how to circumvent this error.
Ever thankful, Matthew Goldfinger