I think you can try to use mris_register directly.

https://surfer.nmr.mgh.harvard.edu/fswiki/mris_register

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu <Freesurfer@nmr.mgh.harvard.edumailto: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

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!

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From: Huang, Yujingmailto:YHUANG43@mgh.harvard.edu Sent: February 8, 2023 11:41 AM To: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Directory

I think you can try to use mris_register directly.

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From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu <Freesurfer@nmr.mgh.harvard.edumailto: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