I think you can try to use mris_register directly. https://surfer.nmr.mgh.harvard.edu/fswiki/mris_register
From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing Sent: Wednesday, February 8, 2023 11:05 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Directory 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Asa Borzabadi Farahani Sent: Wednesday, February 8, 2023 10:38 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Directory External Email - Use Caution 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
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