Hi Asa,

I’m wondering if your SUBJECTS_DIR is /tmp/HCP?

It looks like surfreg checks if target is ‘fsaverage_sym’. Can you try passing just ‘fsaverage_sym’?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Asa Borzabadi Farahani
Sent: Wednesday, February 8, 2023 10:38 AM
To: freesurfer@nmr.mgh.harvard.edu <Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Directory

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Hi there experts!

I’m hoping to use the surfreg function on some data in which I can’t make any modifications to the subject directory (I’m using a cluster and the data is for public use thus prohibits any changes to it).

I want to use the fsaverage_sym as my target file, though the function seems to only be looking for this folder within the subjects directory. Thus when running the following command:

surfreg --s 126426 --t /project/60019995/coopapap/data/HCP/fsaverage_sym --lh

I get the following error:

ERROR: cannot find /project/60019995/coopapap/data/HCP/fsaverage_sym in /tmp/HCP

I’m wondering if there is a workaround to using this command even when I can’t make any modifications to the subjects directory. To summarize, I’d like all outputs to go to a personal folder, and I’d like to use a template file that is in my personal folder.

Thank you kindly.

Asa Farahani