Hi Subin

it looks more likely that you just don't have write access to your SUBJECTS_DIR. Can you check that with ls -l? Or maybe you just haven't set it and it still points to the one we distribute? Typically you want to set the SUBJECTS_DIR env variable to some other directory where you will store all the subjects in a study.

cheers Bruce

On Thu, 21 Jul 2016, Lee Subin Kristine wrote:

Hi FreeSurfer Team,

After I have downloaded the FreeSurfer dev version, I get the following error whenever I use the recon-all comand:

mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6 /usr/local/freesurfer/subjects/NYS/scripts/patchdir.txt: No such file or directory.

recon-all used to work fine when I used the stable 5.3 version. I think it may have something to do with the fact that I previously ran recon-all in v.5.3, and so the current subject directory's stamp is still 5.3 (or blank..) and it does not match the current stamp of the dev version? I am not sure.. Could anyone tell me how I can fix this problem?

Thanks in advance, Subin