Carl, Looks like you only use relative path. You need to put in absolute path. Something like setenv FREESURFER_HOME /home/carl/Desktop/freesurfer
Gen On 8/17/10 9:14 AM, "Carl Dambkowski" <cld2...@columbia.edu> wrote: Hi, again (I've emailed once before), I am trying to test my freesurfer installation and everything goes fine (tksurfer, qdec, etc). However, once I get to: recon-all -s bert -autoreco1 i get: FREESURFER_HOME: Undefined variable. However, I believe I've set it up properly with: setenv FREESURFER_HOME Desktop/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh And I get back: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME Desktop/freesurfer FSFAST_HOME Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR Desktop/freesurfer/subjects MNI_DIR Desktop/local/freesurfer/mni With no errors. When I give the command: echo $FREESURFER_HOME I also get back: Desktop/freesurfer Any suggestions? Thanks, Carl ________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator
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