Dear Freesurfers,<br>       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. <br><span style="color:rgb(153,153,153)">----- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 --------</span><br style="color:rgb(153,153,153)">

<span style="color:rgb(153,153,153)">Setting up environment for FreeSurfer/FS-FAST (and FSL)</span><br style="color:rgb(153,153,153)"><span style="color:rgb(153,153,153)">FREESURFER_HOME   /Applications/freesurfer</span><br style="color:rgb(153,153,153)">

<span style="color:rgb(153,153,153)">FSFAST_HOME       /Applications/freesurfer/fsfast</span><br style="color:rgb(153,153,153)"><span style="color:rgb(153,153,153)">FSF_OUTPUT_FORMAT nii.gz</span><br style="color:rgb(153,153,153)">

<span style="color:rgb(153,153,153)">SUBJECTS_DIR      /Applications/freesurfer/subjects</span><br style="color:rgb(153,153,153)"><span style="color:rgb(153,153,153)">MNI_DIR           /Applications/freesurfer/mni<br><br>

<font color="#000000">But upon trying to execute the following: <br>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<br>

<br>I get the error that &quot;SUBJECTS_DIR not defined in environment.&quot; 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.<br><br>Ever thankful,<br>

              Matthew Goldfinger<br></font></span>