External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <bfis...@mgh.harvard.edu> Sent: Wednesday, April 2, 2025 3:42 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Zollei, Lilla,Ph.D. <lzol...@mgh.harvard.edu> Subject: Re: [Freesurfer] mris_register external atlas You don't often get email from bfis...@mgh.harvard.edu. Learn why this is important<https://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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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. <lzol...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce R.,PHD <bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> Sent: Wednesday, April 2, 2025 3:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>; Zollei, Lilla,Ph.D. <lzol...@mgh.harvard.edu<mailto:lzol...@mgh.harvard.edu>> Subject: Re: [Freesurfer] mris_register external atlas You don't often get email from bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>. Learn why this is important<https://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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Stefanie Bradley Sent: Wednesday, April 2, 2025 3:15 PM To: Zollei, Lilla,Ph.D. <lzol...@mgh.harvard.edu<mailto:lzol...@mgh.harvard.edu>>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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. <lzol...@mgh.harvard.edu<mailto:lzol...@mgh.harvard.edu>> Sent: Wednesday, April 2, 2025 10:59 AM To: Stefanie Bradley <stefanie.brad...@mail.utoronto.ca<mailto:stefanie.brad...@mail.utoronto.ca>>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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.brad...@mail.utoronto.ca<mailto:stefanie.brad...@mail.utoronto.ca>> Sent: Wednesday, April 2, 2025 10:49 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: Zollei, Lilla,Ph.D. <lzol...@mgh.harvard.edu<mailto:lzol...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce R.,PHD <bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> Sent: Monday, March 31, 2025 4:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: Zollei, Lilla,Ph.D. <lzol...@mgh.harvard.edu<mailto:lzol...@mgh.harvard.edu>> Subject: Re: [Freesurfer] mris_register external atlas You don't often get email from bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>. Learn why this is important<https://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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Stefanie Bradley Sent: Monday, March 31, 2025 4:35 PM To: freesurfer@nmr.mgh.harvard.edu<mailto: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. 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