From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Heese, E. van (Eva) <e.vanheese@amsterdamumc.nl>
Date: Friday, December 22, 2023 at 9:24 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Brouwer, I. (Iman) <i.brouwer2@amsterdamumc.nl>, Gool, J.K. (Jari) <j.gool@amsterdamumc.nl>
Subject: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

Dear FreeSurfer support team,

I am running into some issues regarding the mandatory SUBJECTS_DIR writing permissions when running the hippocampal and amygdala subfields segmentation functionality (segmentHA_T1.sh).

I am using FreeSurfer 7.3.2 on a slurm server. We have a shared FreeSurfer installation which is the FREESURFER_HOME location for many users, hence the absence of writing permissions. When running the subfield segmentations, I get this error:

mv: replace 'imageDump.mgz', overriding mode 0444 (r--r--r--)?

Even when overriding this (by typing y), the error results into issues with the segmentations because it cannot access the imageDump.mgz file and thus cannot use it as the starting template for the segmentation. This has been suggested and confirmed by Philipp Saemann and Juan Eugenio Iglesias in separate correspondence.

The short-term solution offered by our server admin was to make a local copy of the FreeSurfer installation (to be able to get writing permissions) and set the FREESURFER_HOME variable to this local copy. This seems a bit devious, considering many FreeSurfer users might face a similar issue on shared clusters without writing permissions. Is there another workaround possible?

Thanks for your help.

Best wishes,

Eva van Heese