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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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

 

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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" <BFISCHL@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

 

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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" <BFISCHL@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

 

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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.

 

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

 

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Trisanna Sprung-Much, PhD

Research Associate

McGill University

Montreal Neurological Institute