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

--
Carl Dambkowski
Research Assistant
Cerebral Localization Laboratory
Columbia University Medical Center
(212) 342-3668