Hi Asa,
Give a try of mris_register -
https://surfer.nmr.mgh.harvard.edu/fswiki/mris_register
Here is the syntax:
mris_register [options] <input surface> <input target template or surface> <output surface>
All three parameters should take full path to your files. Combining the information I got from surfreg script, <input target template or surface> is ?h.reg.template.tif from 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 4:12 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Directory
External Email - Use Caution
Hi Yujing, thanks for your response
Yes my subject directory is /tmp/HCP. But I cannot modify it, so I’d like to reference and use the fsaverage_sym template which is located outside of the subjects directory. Is this possible?
If not then I’ll have to find a way to transfer the data from the unmodifiable subjects folder to one that I can play around with directly.
Thanks again and hoping this can be clarified!
Sent from
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From: Huang, Yujing
Sent: February 8, 2023 11:41 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Directory
I think you can try to use mris_register directly.
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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-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
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