The sudo is causing it to run under a different user (root) which means
that it opens a new shell that does not have the proper environment set.
Why are you running it as root? If you set SUBJECTS_DIR to something
other than
/Applications/freesurfer/subjects you won't have to run as root
doug
On 1/30/15 1:43 PM, Tyler Good wrote:
Hi all,
I've seen very similar questions posted, but I haven't seen one with a
response.
I just installed freesurfer onto a mac os x. I did the following steps:
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
and got this output:
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /Users/Tyler/fsl
after working through the installation testing commands with no issue (qdec,
recon-all --help, tkmedit, tksurfer), I tried to perform the following command:
sudo recon-all -s bert -autorecon1
and got this output:
FREESURFER_HOME: Undefined variable.
I did echo $FREESURFER_HOME to check the export/source worked and it returned
/Applications/freesurfer which is correct!
I'm not sure what is going wrong! Thanks for any help!
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