Sorry, I defer to Doug…
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Stefanie Bradley
*Sent:* Wednesday, April 2, 2025 3:52 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. The command seems to stall when I try to run it following
mri_surf2surf.
It ends like this: "calling annotation2labelV2() ..." And then doesn't
create any labels. Not sure if this is a bug?
Stef
------------------------------------------------------------------------
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce
R.,PHD <bfis...@mgh.harvard.edu>
*Sent:* Wednesday, April 2, 2025 3:42 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
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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
------------------------------------------------------------------------
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce
R.,PHD <bfis...@mgh.harvard.edu>
*Sent:* Wednesday, April 2, 2025 3:22 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
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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
<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>; Freesurfer
support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mris_register external atlas
* External Email - Use Caution *
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>
*Sent:* Wednesday, April 2, 2025 10:59 AM
*To:* Stefanie Bradley <stefanie.brad...@mail.utoronto.ca>; Freesurfer
support list <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>
*Sent:* Wednesday, April 2, 2025 10:49 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Cc:* Zollei, Lilla,Ph.D. <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
------------------------------------------------------------------------
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce
R.,PHD <bfis...@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. <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:*freesurfer-boun...@nmr.mgh.harvard.edu
<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
*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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