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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