How did you create the new MNI chimp average surface?
On 12/5/2021 11:08 AM, Trisanna Sprung-Much wrote:
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Hi Bruce
So I have 77 chimp scans reconstructed in FS (NOT registered to MNI
space, but rather a chimp volume template, to avoid scaling). After a
lot of trial and error, we got some really nice surfaces.
I tried to use make_average_surface this summer and I was running into
one problem after the next and unfortunately no one answered my
questions. So, we have a new MNI chimp average surface and I would
like to know if I can somehow implement this average surface into FS
to perform surface registration of my individual labels to the average
surface.
Thanks!
Trisanna
--
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*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce
<bfis...@mgh.harvard.edu>
*Sent:* Sunday, December 5, 2021 12:03 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] question about surface registration to an
average surface
I’m not really sure what you are trying to do, but I guess you will
want to make your own average. I think there is a new script for this,
so someone else will have to comment
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Trisanna
Sprung-Much
*Sent:* Saturday, December 4, 2021 10:00 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] question about surface registration to an
average surface
* External Email - Use Caution *
Thanks Bruce Yes I am working with chimp data.
Any other things I could try?
Trisanna
Sent from my Galaxy
-------- Original message --------
From: "Fischl, Bruce" <bfis...@mgh.harvard.edu>
Date: 2021-12-04 11:12 a.m. (GMT-05:00)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] question about surface registration to an
average surface
Oh, then no, that won’t work
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Trisanna
Sprung-Much
*Sent:* Saturday, December 4, 2021 10:48 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] question about surface registration to an
average surface
* External Email - Use Caution *
Hi Bruce, I will try mris_sphere! But since this is a chimp average,
when you say then register it to your atlas- is this something I
should do?
Trisanna
Sent from my Bell Samsung device over Canada's largest network.
-------- Original message --------
From: "Fischl, Bruce" <bfis...@mgh.harvard.edu>
Date: 2021-12-04 10:27 a.m. (GMT-05:00)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] question about surface registration to an
average surface
Hi Trisanna
Can you run mris_sphere on it to create a spherical surface? You could
then register that to our atlas using mris_register. You will need to
create a bunch of files that we expect though like ?h.curv, ?h.sulc,
etc… You might also need to specify a volume, but I expect any
conformed one will be ok
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Trisanna
Sprung-Much
*Sent:* Friday, December 3, 2021 6:42 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] question about surface registration to an
average surface
* External Email - Use Caution *
Hi there
I have a bunch of labels on individual subjects and would like to
register them to an average surface that we have created here at the
MNI. So, this average has not gone through recon-all and there are no
freesurfer recon-all files associated with it. There is no volume
associated with it to run in recon-all.
According to the instructions for mri_surf2surf I need the sphere.reg
file, which is generated during recon-all. I wonder if there is a way
to undergo surface registration in my situation? I found the following
documentation, but this seems to be for creating a new average. I have
the average already.
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The output from registration is yet another version of the subject's
surface mesh, typically named ?h.sphere.reg, with the x,y,z vertex
positions still on a sphere, but warped so that the subject's
curvature pattern best aligns with the template data.Here is the same
convexity data, now plotted on the lh.sphere.reg surface. Similar
pattern, but "stretched around".
surfer.nmr.mgh.harvard.edu
Thank you,
Trisanna
--
/Trisanna Sprung-Much, PhD/
/Research Associate/
/McGill University/
/Montreal Neurological Institute/
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