Ok the main email is CC'd. Below is what I did and the output I received. The goal is to get a brain volume, Subdural space and/or a CSF volume to estimate how much room for displacement/deformation the brain has. Thanks in advance for your help.

Matthews-MacBook-Pro-2:~] matthew% printenv SUBJECTS_DIR /Applications/freesurfer/subjects [Matthews-MacBook-Pro-2:~] matthew% sudo 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

$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline 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 /Applications/freesurfer/FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg sysname Darwin hostname Matthews-MacBook-Pro-2.local machine x86_64 user root ERROR: SUBJECTS_DIR not defined in environment

On Mon, Jul 30, 2012 at 10:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

Hi Matthew Could you cc the list so others can answer? Can you also send us the screen output showing exactly what you did? Thanks Bruce

On Jul 30, 2012, at 8:19 PM, Matthew Goldfinger mattgoldfinger@gmail.com wrote:

Bruce, When I execute printenv it gives me the correct path name (/Applications/freesurfer/subjects). Upon original set up I automatically sourced to freesurfersetup.csh as was described in the setup instructions. How should I source to have Freesurfer commands available without running into this problem?

Matthew S. Goldfinger

On Mon, Jul 30, 2012 at 8:02 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

...

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

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