Do you have write perms to this file and the folder it is in?
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env to
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env.bak
On 1/30/15 3:09 PM, Tyler Good wrote:
Thanks so much for the fast reply Doug!
I changed the directory for freesurfer home...so now if I source, it
returns:
source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Users/Tyler/Documents/freesurfer
FSFAST_HOME /Users/Tyler/Documents/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Users/Tyler/Documents/freesurfer/subjects
MNI_DIR /Users/Tyler/Documents/freesurfer/mni
FSL_DIR /Users/Tyler/fsl
if I run a recon-all:
tyler's-macbook-pro:~ Tyler$ recon-all -s bert -autorecon1
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Users/Tyler/Documents/freesurfer/subjects
Actual FREESURFER_HOME /Users/Tyler/Documents/freesurfer
rm:
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.cmd:
Permission denied
mv: rename
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env
to
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env.bak:
Permission denied
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env:
Permission denied.
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env:
Permission denied.
I had free surfer on a virtual linux box on this machine previously.
I changed the permissions to the bert folder so I would have write
access and be able to avoid using sudo, before getting this message.
Any help would be greatly appreciated!
On Fri, Jan 30, 2015 at 1:50 PM, Douglas Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
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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