Sure. You can either change it in the environment, or pass it to recon-all with -sd <subjects_dir>
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mostafa Fakhri Sent: Saturday, June 25, 2022 9:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] change the $SUBJECTS_DIR
External Email - Use Caution Hello to all, I am new to FreeSurfer. By executing recon-all I get the permission error. Is there a way to change the $SUBJECTS_DIR, such as /share/users/my user/subject name ?
$ recon-all -subject 102109 -i T1w.nii.gz -all
mkdir: cannot create directory `/share/Application/FreeSurfer/Install/freesurfer/subjects/102109': Permission denied mkdir: cannot create directory `/share/Application/FreeSurfer/Install/freesurfer/subjects/102109': Permission denied mkdir: cannot create directory `/share/Application/FreeSurfer/Install/freesurfer/subjects/102109': Permission denied cp: cannot create regular file `/share/Application/FreeSurfer/Install/freesurfer/subjects/102109/scripts/build-stamp.txt': No such file or directory cat: /share/Application/FreeSurfer/Install/freesurfer/subjects/102109/scripts/build-stamp.txt: No such file or directory /share/Application/FreeSurfer/Install/freesurfer/subjects/102109/scripts/patchdir.txt: No such file or directory.
Thanks for the help!
Mostafa