Hi Matthew

what shell are you using? If you type

printenv SUBJECTS_DIR

right before calling mri_segstats, what does it return? And when do you get that output? Are you sourcing the FreeSurferEnv.csh file? Don't execute it as otherwise it pushes a new shell, sets all that stuff, then pops out of it erasing all the stuff it set

cheers Bruce

On Mon, 30 Jul 2012, Matthew Goldfinger wrote:

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