question about surface registration to an average surface

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Trisanna Sprung-Much

3 Dec 2021 3 Dec '21

6:42 p.m.

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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.

https://secure-web.cisco.com/1hQ9hS6yFMKayjbN2TstCM6s3-2VxHitXzaDRkJ6eA1mJJT... SurfaceRegAndTemplates - Free Surfer Wikihttps://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

Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

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Fischl, Bruce

4 Dec 4 Dec

10:27 a.m.

New subject: 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

External Email - Use Caution Hi there

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 SurfaceRegAndTemplates - Free Surfer Wikihttps://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

Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

Trisanna Sprung-Much

10:47 a.m.

New subject: 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" 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

External Email - Use Caution Hi there

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Xi2lcpZACDikuDU8pSzKMt-Dtjs_Y2CYuQRXl20Tw2-Jmf...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 SurfaceRegAndTemplates - Free Surfer Wikihttps://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

Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

Fischl, Bruce

11:12 a.m.

New subject: 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

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" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Date: 2021-12-04 10:27 a.m. (GMT-05:00) To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] question about surface registration to an average surface

Hi Trisanna

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] question about surface registration to an average surface

External Email - Use Caution Hi there

Thank you, Trisanna

Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

Trisanna Sprung-Much

9:59 p.m.

New subject: 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" 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

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.

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

External Email - Use Caution Hi there

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1JoFFWUwURIT9QWgPmGPEnw6MLYHphGQE-pZ0Cqw9PL8mID...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 SurfaceRegAndTemplates - Free Surfer Wikihttps://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

Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

Fischl, Bruce

5 Dec 5 Dec

11:03 a.m.

New subject: 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

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" <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Date: 2021-12-04 11:12 a.m. (GMT-05:00) To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.

Hi Trisanna

Cheers Bruce

External Email - Use Caution Hi there

Thank you, Trisanna

Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

Trisanna Sprung-Much

11:08 a.m.

New subject: question about surface registration to an average surface

External Email - Use Caution

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

________________________________ 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

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" <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU>

Date: 2021-12-04 11:12 a.m. (GMT-05:00)

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu>

Date: 2021-12-04 10:27 a.m. (GMT-05:00)

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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

External Email - Use Caution

Hi there

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ppm0q2LDxoGwh_MrfaHaTdx84YY-m-Ubv2X9R5fF6eWa1c...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

SurfaceRegAndTemplates - Free Surfer Wikihttps://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

Trisanna Sprung-Much, PhD

Research Associate

McGill University

Montreal Neurological Institute

Douglas N. Greve

10 Dec 10 Dec

6:37 p.m.

New subject: question about surface registration to an average surface

How did you create the new MNI chimp average surface?

On 12/5/2021 11:08 AM, Trisanna Sprung-Much wrote:

...

External Email - Use Caution

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

--

*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

*        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" 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

*        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" 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

*        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.

*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

SurfaceRegAndTemplates - Free Surfer Wiki 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

--

/Trisanna Sprung-Much, PhD/

/Research Associate/

/McGill University/

/Montreal Neurological Institute/

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Douglas N. Greve
Fischl, Bruce
Trisanna Sprung-Much