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$