Re: [Freesurfer] mris_register external atlas

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Hi Bruce,

Thanks for your response. I was able to get the smoothwm surface, to make a registration file (lh.sphere.reg).

When I then try to use mri_surf2surf, it says that the dimensions are not aligned (atlas surf files - 163 842 vertices; subject surf files - 127 845 vertices). The lh.sphere.reg file has 127 845 vertices. Is there a way to fix this so that I can proceed?

Thanks, Stefanie ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Sent: Monday, March 31, 2025 4:41 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Subject: Re: [Freesurfer] mris_register external atlas

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Hi Stefanie

The registration is based on the curvature of the smoothwm surface (among other things) so not easily. Lilla might know more about that atlas.

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Stefanie Bradley Sent: Monday, March 31, 2025 4:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_register external atlas

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Hi there,

I am trying to register my Freesurfer subject's cortical surface into a common space to use the parcellations from a pediatric atlas (UNC 4D cortical surface atlas).

With Freesurfer version 8.0.0 in a Linus OS, I am using mris_register as: mris_register -1 individual_subject/lh.sphere 4D_atlas/lh.sphere individual_subject /lh.sphere.FS.reg.

I am getting an error where it says it requires a smoothwm file from the atlas files, though I only have curvature and sphere files from the atlas. Is there a way to register the atlas files to my subjects and then put the parcellations onto my subject's cortical surface?

Thanks,

Stefanie