you probably want to specify the SUBJECTS_DIR as being somewhere else that you have write permission to. You can do this with the -sd <path> on the recon-all command line, or in the environment.

cheers
Bruce
On Thu, 14 Mar 2013, Varghese Chikku wrote:

Dear FS team,I dowloaded the latest ML  version of  FS and tried to run a
 subject.But this  error is coming up.Any  suggestions?

 chikkuvarghese$ recon-all -i
/Users/chikkuvarghese/Desktop/BL/raw/image00001 -autorecon-all -s BL1
mkdir: /Applications/freesurfer/subjects/BL1: Permission denied
mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied
mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied
cp: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such
file or directory
cat: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such
file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp: 
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
/Applications/freesurfer/subjects/BL1: No such file or directory.
chikkus-MacBook-Pro:~ chikkuvarghese$ 


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