Hi Stef
I would do it at the end on whichever annot you want to convert into labels
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Stefanie Bradley
Sent: Wednesday, April 2, 2025 3:29 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Zollei,
Lilla,Ph.D. <lzol...@mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_register external atlas
External Email - Use Caution
Hi Bruce,
Thanks. Should I be doing this step before or after mri_surf2surf? (on the
external atlas .annot or the newly registered .annot)?
Thanks,
Stef
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on behalf of Fischl, Bruce R.,PHD
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Subject: Re: [Freesurfer] mris_register external atlas
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You should be able to use mri_annotation2label to extract all the labels in the
annot as separate label files
Cheers
Bruce
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 Stefanie Bradley
Sent: Wednesday, April 2, 2025 3:15 PM
To: Zollei, Lilla,Ph.D.
<lzol...@mgh.harvard.edu<mailto:lzol...@mgh.harvard.edu>>; Freesurfer support
list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_register external atlas
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Thank you, that worked!
To recap, I've been trying to align the annotation files from the UNC cortical
surface atlas to my subjects. I'm using Freesurfer version 8.0.0 with Linux.
Following mri_surf2surf with my registration file, I got a new annotation file,
but when I try to run mri_annotation2label, it stalls out instead of finishing
the command output, trailing off with this: "calling annotation2labelV2()..."
Is there any way to fix this so that I can get the label files from my .annot
file?
Thanks,
Stefanie
________________________________
From: Zollei, Lilla,Ph.D.
<lzol...@mgh.harvard.edu<mailto:lzol...@mgh.harvard.edu>>
Sent: Wednesday, April 2, 2025 10:59 AM
To: Stefanie Bradley
<stefanie.brad...@mail.utoronto.ca<mailto:stefanie.brad...@mail.utoronto.ca>>;
Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: mris_register external atlas
Hi Stephanie,
I believe you want to compute your registration the other way, if you want to
infer atlas parcellation labels to the subj space.
Lilla
________________________________
From: Stefanie Bradley
<stefanie.brad...@mail.utoronto.ca<mailto:stefanie.brad...@mail.utoronto.ca>>
Sent: Wednesday, April 2, 2025 10:49 AM
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Cc: Zollei, Lilla,Ph.D.
<lzol...@mgh.harvard.edu<mailto:lzol...@mgh.harvard.edu>>
Subject: Re: mris_register external atlas
External Email - Use Caution
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
________________________________
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on behalf of Fischl, Bruce R.,PHD
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Sent: Monday, March 31, 2025 4:41 PM
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Cc: Zollei, Lilla,Ph.D.
<lzol...@mgh.harvard.edu<mailto:lzol...@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:
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<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Stefanie Bradley
Sent: Monday, March 31, 2025 4:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mris_register external atlas
External Email - Use Caution
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
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