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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@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. LZOLLEI@mgh.harvard.edu Subject: Re: [Freesurfer] mris_register external atlas

You don't often get email from bfischl@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1gfZqDzKiIh98-4loRHB8fue6dQ_jnxXo5n2w7h846SlYcgpxMjc9u62e5zahp8l7audxi8JSthX6_G351MThRHeIF0ndVpt_jDvG35dQMizKVLeMXO827wmmBRm6mXjxW44X1rfv9_mJ4EAYPWlcaHwhKB5UXaU2QCRgMPtvcmqctXurEnzR88F_CYQFwni5zW4XylTiGTRvchAVa7GAJC6T48ij5PE6nk2o5wJJeHb9DThUlA5j95CjNY92G_M8phv0nJYgjkpqo5tI_RCQmBAphIm4y4UaO-4tOpJogz21WlsRBQdTxnWZjHihJ6TG-IU1cCe510_kGB2POAOBgw/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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

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. LZOLLEI@mgh.harvard.edu Sent: Wednesday, April 2, 2025 10:59 AM To: Stefanie Bradley stefanie.bradley@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.bradley@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. LZOLLEI@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@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. LZOLLEI@mgh.harvard.edu Subject: Re: [Freesurfer] mris_register external atlas

You don't often get email from bfischl@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1n0q7-5_MhqbUSwkqp2HOBEIE7J1N5o81-5sI0KTIRelu5dtsw02GGIa7ZQbo_xr9PNQyZLwgvE46oy4uQJH6BSTE1x_LKUh5xmZI-Tt01VunoTH0vebamBTHMkXj8bEil6JxHVIQnwGFze7ul1CcxNA1u1Bdb0A8Knwc6jvBneBUqnd6k9qyGC7Gxy42TdLvs69x4ieiAtIBvJzAewTH4Co9L-st1rUpaJkU4j9fOgqXa3Xy4GGH5VT6oIr56JjyX_xzzxpsutgq7vZQ_VZY5hjDRFxx-Cwww8UZNpEzlqY0XEfB8OJEpt6JVvRJA2xc/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Sent: Wednesday, April 2, 2025 3:22 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Subject: Re: [Freesurfer] mris_register external atlas

You don't often get email from bfischl@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1PHsQ4AJTr3NeL3Z8kKkcYAZNHaEFv2VA26WYTyGOiprAYUaf-fj2MoWXnqDv60_GqB2593Q0QqrCXPKPUDm7uevUOnOF48dz8-HxPiSe6lzxsk4N5XuepTF_b6uHy0QLkOYQml7qYlYCVB2H2bBeSbKHwy7BL0scE5EtH2Spe5NHJyKK-lIVeRtwEXNzoH9xXFGjxjjsWwWEQ5PhPXqmM4k9EACI0UjrfWZYdvNjAM5zJM8X-lSwEEtB7wvp9F-MhEz99IeTQyU76pcd0ynE_8c-u-cx-KjsHnLcdYSgtCX0u03dT-3qsChsAYLglnRFjNH3XLee3Sn43nGIXFPigA/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification

You should be able to use mri_annotation2label to extract all the labels in the annot as separate label files

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Stefanie Bradley Sent: Wednesday, April 2, 2025 3:15 PM To: Zollei, Lilla,Ph.D. LZOLLEI@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. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@mgh.harvard.edu> Sent: Wednesday, April 2, 2025 10:59 AM To: Stefanie Bradley <stefanie.bradley@mail.utoronto.camailto:stefanie.bradley@mail.utoronto.ca>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.bradley@mail.utoronto.camailto:stefanie.bradley@mail.utoronto.ca> Sent: Wednesday, April 2, 2025 10:49 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@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-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 Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Monday, March 31, 2025 4:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@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-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 Stefanie Bradley Sent: Monday, March 31, 2025 4:35 PM To: freesurfer@nmr.mgh.harvard.edumailto: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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1CIUyWzyYeYEL7prwBUhFmyondWgS41KFPlTABwO4ESk3oU...https://secure-web.cisco.com/1ruPZtHe-DvH7xKxJ3I50hZaZi3VyU1fu423FdNI1u9oPMnPCzVs5552xzbsfNnpKELcnifKxrYI-n73Iz7njLB6H_FDxxE8xIfKMPV31qUKkJQNUV3KkhVx0raU2w7ZJMr7xij7agNa6hJB1kI6O3-lZU6Y3r2HntFA_dmmuGCgTpKvNGw_xuEwuhRM6pBl38MSP7S8J77MmgrnAXQUYgT-rreMPpdKGvmpEqvXCsO8PFuABSWpTR-jAsIyK7jXjU72WMP1TnQewPtlUqG1PuwvKGhE7_sdKJJ-jQizzqmmdyyKyGHo18dago7SSRYpM/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Sent: Wednesday, April 2, 2025 3:42 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Subject: Re: [Freesurfer] mris_register external atlas

You don't often get email from bfischl@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1llLLHRQT4Ocsy9plBnLn3G9NrXEhwmYaNDsSKY9oWlK9xWsLCzbtmndGWKK-V_6nuVyK7qor_aJAmQN4u16ceBenO30Mw_lvDa0ghLkB0KIerSw4YUt6P4Lk7P9PFAJlGIi3qr9P1wjYgu0FIoCVDLRqkgYgnkxP-VjPWg2vnQ3Y6rW2nKbgeL7InTNVSLg-w2u9N-0FOT7A-bm2lNrW3DZFODzGHxOpCKvf5VZsVr5Dt-dTvdMcF1lX4dSSVzFLGE5sSqstOwJTpb3HuRlpfK2nxOR1GNbXLhzpOEGncDLboFe8PD9yM3lIOV58fN7ruMJtsbauFYswpZApAPIk_Q/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification

Hi Stef

I would do it at the end on whichever annot you want to convert into labels

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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. LZOLLEI@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-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 Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Wednesday, April 2, 2025 3:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@mgh.harvard.edu> Subject: Re: [Freesurfer] mris_register external atlas

You don't often get email from bfischl@mgh.harvard.edumailto:bfischl@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1PHsQ4AJTr3NeL3Z8kKkcYAZNHaEFv2VA26WYTyGOiprAYUaf-fj2MoWXnqDv60_GqB2593Q0QqrCXPKPUDm7uevUOnOF48dz8-HxPiSe6lzxsk4N5XuepTF_b6uHy0QLkOYQml7qYlYCVB2H2bBeSbKHwy7BL0scE5EtH2Spe5NHJyKK-lIVeRtwEXNzoH9xXFGjxjjsWwWEQ5PhPXqmM4k9EACI0UjrfWZYdvNjAM5zJM8X-lSwEEtB7wvp9F-MhEz99IeTQyU76pcd0ynE_8c-u-cx-KjsHnLcdYSgtCX0u03dT-3qsChsAYLglnRFjNH3XLee3Sn43nGIXFPigA/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification

You should be able to use mri_annotation2label to extract all the labels in the annot as separate label files

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 Stefanie Bradley Sent: Wednesday, April 2, 2025 3:15 PM To: Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@mgh.harvard.edu> Sent: Wednesday, April 2, 2025 10:59 AM To: Stefanie Bradley <stefanie.bradley@mail.utoronto.camailto:stefanie.bradley@mail.utoronto.ca>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.bradley@mail.utoronto.camailto:stefanie.bradley@mail.utoronto.ca> Sent: Wednesday, April 2, 2025 10:49 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@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-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 Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Monday, March 31, 2025 4:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@mgh.harvard.edu> Subject: Re: [Freesurfer] mris_register external atlas

You don't often get email from bfischl@mgh.harvard.edumailto:bfischl@mgh.harvard.edu. Learn why this is importanthttps://secure-web.cisco.com/1n0q7-5_MhqbUSwkqp2HOBEIE7J1N5o81-5sI0KTIRelu5dtsw02GGIa7ZQbo_xr9PNQyZLwgvE46oy4uQJH6BSTE1x_LKUh5xmZI-Tt01VunoTH0vebamBTHMkXj8bEil6JxHVIQnwGFze7ul1CcxNA1u1Bdb0A8Knwc6jvBneBUqnd6k9qyGC7Gxy42TdLvs69x4ieiAtIBvJzAewTH4Co9L-st1rUpaJkU4j9fOgqXa3Xy4GGH5VT6oIr56JjyX_xzzxpsutgq7vZQ_VZY5hjDRFxx-Cwww8UZNpEzlqY0XEfB8OJEpt6JVvRJA2xc/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification

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-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 Stefanie Bradley Sent: Monday, March 31, 2025 4:35 PM To: freesurfer@nmr.mgh.harvard.edumailto: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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What is the command you are running? Also include the terminal output

On 4/2/2025 3:56 PM, Fischl, Bruce R.,PHD wrote:

Sorry, I defer to Doug…

*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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. LZOLLEI@mgh.harvard.edu *Subject:* Re: [Freesurfer] mris_register external atlas

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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

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*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu *Sent:* Wednesday, April 2, 2025 3:42 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Zollei, Lilla,Ph.D. LZOLLEI@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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. LZOLLEI@mgh.harvard.edu *Subject:* Re: [Freesurfer] mris_register external atlas

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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

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*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu *Sent:* Wednesday, April 2, 2025 3:22 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Zollei, Lilla,Ph.D. LZOLLEI@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Stefanie Bradley *Sent:* Wednesday, April 2, 2025 3:15 PM *To:* Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mris_register external atlas

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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

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*From:*Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu *Sent:* Wednesday, April 2, 2025 10:59 AM *To:* Stefanie Bradley stefanie.bradley@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

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*From:*Stefanie Bradley stefanie.bradley@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. LZOLLEI@mgh.harvard.edu *Subject:* Re: mris_register external atlas

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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

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*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@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. LZOLLEI@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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

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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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