Sure. You can either change it in the environment, or pass it to recon-all with
-sd <subjects_dir>
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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