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-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
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-------- 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.
*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates https://secure-web.cisco.com/1hQ9hS6yFMKayjbN2TstCM6s3-2VxHitXzaDRkJ6eA1mJJTp3IxsLYdnBDBQOyDFVpelzHXtlwVfs0-GXekG7piJHu1rfxNSV4fH2ZN9m4WW3xaAyR1jFH1opEVpeilrgGv2stuEp2X8p-fsPhsGBkJQs-X-WgzKgILLyXqSbIdjUFirnl1gFFdbEz-qbegHI38k27LekUKBEfYAgybD9WfDL2MAsT7126KhikYz-6ShmLI_qdjZM7QasrzNlss9WNl2J62oq8GjqLIr-8rLois_vdzT1W1emHKj7pQ78wKHCtr4vTX7ttPb8hlRohBvj/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates
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/
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