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" cld2121@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

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