External Email - Use Caution
Dear freesurfer experts,
I was wondering if ?h.sphere.reg files have any coordinates in space tagged to them? What I actually mean is I'm using TRACULA which itself use the following files from mri and surf folder (all created by running recon-all on T1 image): aparc+aseg.mgz, brain.mgz, brainmask.mgz, orig.mg, T1.mgz and ThalamicNuclei.v12.Ta.FSvoxelSpace.mgzlh.thickness,rh.thickness,lh.white,rh.white,lh.sphere.reg,rh.shere.reg. I have all these files (except ?h.thickness and ?h.sphere.reg) in new coordinates in space created by co-registration. The pipeline we use to create recon-all results is almost the same as freesurfer pipeline with a slight difference in autorecon1 step, so the final results are almost always the same but the coordinate of the brain in 3D space is different, so we usually end up co-register one's reconstruction result (from our pipeline) with oneself T1.nii (come from mri_convert T1.dcm) so the structural mri reconstruction and dwi dcm files are in the same coordinate and can overlay. My understanding is that there is no coordinate tagged to ?h.sphere.reg files in 3D space, rather they are regulatory files which include some information about x,y,z vertices in regard to the surface of a hypothetical sphere (and the xyz are coming from the curvature of one's brain). As a result, I can use ?h.sphere.reg files as they are without any need to make any changes to match my files after they are coregistered. Is my understanding correct?
I'm sorry if my language is not clear enough. I tried my best to describe the situation, but I'm not sure if my description is clear enough.
Thank you for your help and time. Ela
The ?h.sphere.reg xyz coordinates are coordinates on the sphere. To apply a spherical registration, a point on one spherical mesh is mapped to the closest point on the other spherical mesh. not sure if that answers your question ...
On 7/21/2022 5:26 PM, Salar Dini, Elaheh wrote:
External Email - Use Caution
Dear freesurfer experts,
I was wondering if ?h.sphere.reg files have any coordinates in space tagged to them? What I actually mean is I'm using TRACULA which itself use the following files from mri and surf folder (all created by running recon-all on T1 image): aparc+aseg.mgz, brain.mgz, brainmask.mgz, orig.mg, T1.mgz and ThalamicNuclei.v12.Ta.FSvoxelSpace.mgzlh.thickness,rh.thickness,lh.white,rh.white,lh.sphere.reg,rh.shere.reg. I have all these files (except ?h.thickness and ?h.sphere.reg) in new coordinates in space created by co-registration. The pipeline we use to create recon-all results is almost the same as freesurfer pipeline with a slight difference in autorecon1 step, so the final results are almost always the same but the coordinate of the brain in 3D space is different, so we usually end up co-register one's reconstruction result (from our pipeline) with oneself T1.nii (come from mri_convert T1.dcm) so the structural mri reconstruction and dwi dcm files are in the same coordinate and can overlay. My understanding is that there is no coordinate tagged to ?h.sphere.reg files in 3D space, rather they are regulatory files which include some information about x,y,z vertices in regard to the surface of a hypothetical sphere (and the xyz are coming from the curvature of one's brain). As a result, I can use ?h.sphere.reg files as they are without any need to make any changes to match my files after they are coregistered. Is my understanding correct?
I'm sorry if my language is not clear enough. I tried my best to describe the situation, but I'm not sure if my description is clear enough.
Thank you for your help and time. Ela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Douglas, It does. Thank you. Can you also help me with something else? If we coregister bunch of volume and surfaces using the same reg.lta for one subject, is there a way to safely reflect these changes in label files like rh.cortex.label or in transformation fies like talairach.xfm? In other words, can we make any changes to rh.cortex.label and talairach.xfm from pre co-registeration to make them usable with post co-registration files? Thanks
Douglas N. Grevehttps://secure-web.cisco.com/1ihiy9xLc9u1yyF8DQ1uOVgvZt_RRMNCUkxXo527aY3PFbUXS3sfC31bcx11dGxVlTccZYSThLDEdA1-3FGQ1CRTg7XrTBcJhZLLtaE0sj3xsYQuQhsTIcoXEHc80x65wcAwmwzAQhBjtjU7gSRcvRovhlCWIQpbERg4NaELK39aLmAdyzCW6rcv0uS1vZXVVEKZpjbIClaZc0KvKcon0XBFT2EnE8V8WnmbZFA0Ms_Ajk2yCM4wEA-7EDHvdugmdMATHvEeQPqsHB6ENdIMYKfIMnLuuC5f1jPWqeO-ve2V1a2AkfCiwwnI0UyGL51Wq7nwq4gghSRQwhaImVRrJoQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BN.%2BGreve%2522 Sun, 24 Jul 2022 19:20:57 -0700https://secure-web.cisco.com/1e1fNuakNR9rUdATXJzSZ_w-tcuJBuKAh2t_dACTgCH1j5-4VUvtc5rvIZCJFKOlPbGXowSq_6kruiE2CsHDduor_EB8P0u7msIv7b6emi5-qXTO4AoZNtQTQqDVE11xqp9oDDo4cd6tXFfkSrOTLtWA442PBdZAdcqU7Fd7wz1CHXGUUNHszhAlSZ3AA6c3hbUr_6ixRbFwjz4iXIDW8IMMII2EEUfKEt9AEnXMOhtwsfG9FIw4gw8vk19UKnZvNodvU6bIcdaLavEDXunsu65KfnqeVc0LAfE8Y-qW-DWvTg91JOJFCjU_5sgZdZtPVFYHCUuqrlvYOP4mjqiHUIQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220724
The ?h.sphere.reg xyz coordinates are coordinates on the sphere. To apply a spherical registration, a point on one spherical mesh is mapped to the closest point on the other spherical mesh. not sure if that answers your question ... ________________________________ From: Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Thursday, July 21, 2022 5:26 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Understanding ?h.sphere.reg
Dear freesurfer experts,
I was wondering if ?h.sphere.reg files have any coordinates in space tagged to them? What I actually mean is I'm using TRACULA which itself use the following files from mri and surf folder (all created by running recon-all on T1 image): aparc+aseg.mgz, brain.mgz, brainmask.mgz, orig.mg, T1.mgz and ThalamicNuclei.v12.Ta.FSvoxelSpace.mgzlh.thickness,rh.thickness,lh.white,rh.white,lh.sphere.reg,rh.shere.reg. I have all these files (except ?h.thickness and ?h.sphere.reg) in new coordinates in space created by co-registration. The pipeline we use to create recon-all results is almost the same as freesurfer pipeline with a slight difference in autorecon1 step, so the final results are almost always the same but the coordinate of the brain in 3D space is different, so we usually end up co-register one's reconstruction result (from our pipeline) with oneself T1.nii (come from mri_convert T1.dcm) so the structural mri reconstruction and dwi dcm files are in the same coordinate and can overlay. My understanding is that there is no coordinate tagged to ?h.sphere.reg files in 3D space, rather they are regulatory files which include some information about x,y,z vertices in regard to the surface of a hypothetical sphere (and the xyz are coming from the curvature of one's brain). As a result, I can use ?h.sphere.reg files as they are without any need to make any changes to match my files after they are coregistered. Is my understanding correct?
I'm sorry if my language is not clear enough. I tried my best to describe the situation, but I'm not sure if my description is clear enough.
Thank you for your help and time. Ela
The surface labels are independent of the coordinates. If it is just the tal.xfm, you might be able to convert it to lta (lta_convert), then concatenate with your other reg (mri_concatenate_lta), then convert it back to xfm, but you're on your own after this -- I can't spend time supporting it
On 7/26/2022 12:45 PM, Salar Dini, Elaheh wrote:
External Email - Use Caution
Hi Douglas,
It does. Thank you. Can you also help me with something else? If we coregister bunch of volume and surfaces using the same reg.lta for one subject, is there a way to safely reflect these changes in label files like rh.cortex.label or in transformation fies like talairach.xfm? In other words, can we make any changes to rh.cortex.label and talairach.xfm from pre co-registeration to make them usable with post co-registration files?
Thanks
Douglas N. Greve https://secure-web.cisco.com/1ihiy9xLc9u1yyF8DQ1uOVgvZt_RRMNCUkxXo527aY3PFbUXS3sfC31bcx11dGxVlTccZYSThLDEdA1-3FGQ1CRTg7XrTBcJhZLLtaE0sj3xsYQuQhsTIcoXEHc80x65wcAwmwzAQhBjtjU7gSRcvRovhlCWIQpbERg4NaELK39aLmAdyzCW6rcv0uS1vZXVVEKZpjbIClaZc0KvKcon0XBFT2EnE8V8WnmbZFA0Ms_Ajk2yCM4wEA-7EDHvdugmdMATHvEeQPqsHB6ENdIMYKfIMnLuuC5f1jPWqeO-ve2V1a2AkfCiwwnI0UyGL51Wq7nwq4gghSRQwhaImVRrJoQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BN.%2BGreve%2522Sun, 24 Jul 2022 19:20:57 -0700 https://secure-web.cisco.com/1e1fNuakNR9rUdATXJzSZ_w-tcuJBuKAh2t_dACTgCH1j5-4VUvtc5rvIZCJFKOlPbGXowSq_6kruiE2CsHDduor_EB8P0u7msIv7b6emi5-qXTO4AoZNtQTQqDVE11xqp9oDDo4cd6tXFfkSrOTLtWA442PBdZAdcqU7Fd7wz1CHXGUUNHszhAlSZ3AA6c3hbUr_6ixRbFwjz4iXIDW8IMMII2EEUfKEt9AEnXMOhtwsfG9FIw4gw8vk19UKnZvNodvU6bIcdaLavEDXunsu65KfnqeVc0LAfE8Y-qW-DWvTg91JOJFCjU_5sgZdZtPVFYHCUuqrlvYOP4mjqiHUIQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220724
The ?h.sphere.reg xyz coordinates are coordinates on the sphere. Toapply a spherical registration, a point on one spherical mesh is mappedto the closest point on the other spherical mesh. not sure if thatanswers your question ...
*From:* Salar Dini, Elaheh elaheh.salardini@yale.edu *Sent:* Thursday, July 21, 2022 5:26 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Understanding ?h.sphere.reg Dear freesurfer experts,
I was wondering if ?h.sphere.reg files have any coordinates in space tagged to them? What I actually mean is I'm using TRACULA which itself use the following files from mri and surf folder (all created by running recon-all on T1 image): aparc+aseg.mgz, brain.mgz, brainmask.mgz, orig.mg, T1.mgz and ThalamicNuclei.v12.Ta.FSvoxelSpace.mgzlh.thickness,rh.thickness,lh.white,rh.white,lh.sphere.reg,rh.shere.reg. I have all these files (except ?h.thickness and ?h.sphere.reg) in new coordinates in space created by co-registration. The pipeline we use to create recon-all results is almost the same as freesurfer pipeline with a slight difference in autorecon1 step, so the final results are almost always the same but the coordinate of the brain in 3D space is different, so we usually end up co-register one's reconstruction result (from our pipeline) with oneself T1.nii (come from mri_convert T1.dcm) so the structural mri reconstruction and dwi dcm files are in the same coordinate and can overlay. My understanding is that there is no coordinate tagged to ?h.sphere.reg files in 3D space, rather they are regulatory files which include some information about x,y,z vertices in regard to the surface of a hypothetical sphere (and the xyz are coming from the curvature of one's brain). As a result, I can use ?h.sphere.reg files as they are without any need to make any changes to match my files after they are coregistered. Is my understanding correct?
I'm sorry if my language is not clear enough. I tried my best to describe the situation, but I'm not sure if my description is clear enough.
Thank you for your help and time. Ela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug,
I found the solution to my problem, so please ignore my previous message. Thanks so much for always helping out anyway. In case, this question ever comes up for anyone else, here is the solution:
I just used freesurfer auto-recon steps to create the files I want using co-registered images. I needed the following files:
talairach.xfm and rh.cortex.label for my pipeline, so I just the following steps of recon-all on my co-registered files:
recon-allhttps://secure-web.cisco.com/1HfPVktnUOgRTFJY-mCNGr4GpEo8x9TCztlgWlyEX2jjfspgViDhhEGC-Z9f4umHvbY9N9NJ8wzYhH45BFSQmPbgu57qlA6M95j24bRmV7U6YMZXLNtPT3SRJsRC1yevK40Z11yKeAFyPBhSrREgiOVEA-UAi2Fv9ge9sXOptEx1EYbwYe_z8stAZT5A5IT-T4RCMd0k4YWBJzC8kuNH-G-SA4JxTL64rDjpSB583pXLlmoeJmxAWAK16s-ZAHEMU7zTRQC5ITfcs9ydcbqjluJuvQaBZBqmOD1hzhdLfhcASN2T1Q4Y4KFqo5uXU5IEfrcfYfmAptThmFq7NAiSKHQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all -autorecon1 -subjid <subjid> -talairachhttps://secure-web.cisco.com/1yX40e-pKgP2O3tNH6hEKcPzjb7Dn8B5ij5MN3lio02Uo-I_SFidef7xvuP4qAbiqAKx8zOlqxqX1YY1jcWzctzt1kJKDk1OQeUSVnYHg4SImkQsG5wcDMiS_bxqOLe1VIP0IrfIENSYbcqCwNNPJVpUCrefl3JvkIgFABRwgFQNTFdyMwuqMPJ84hKBdnx9z1Apqn2SGuY0HBWZwzWEjwcIldDkI6pJxgHlJbtMolJPZuNsg9hnbUxO280IFnwGavWzlPSGiRbGSsnXa0h6YVly-Z3-VB8g7O6ryVL0GEzyylIF2kRwwZD6KMmeuIDX0MV2IlwGcRD3CGUFEzHC8Zw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Ftalairach on post-co-registerated orig.mgz to get talairach.xfm
and recon-allhttps://secure-web.cisco.com/1HfPVktnUOgRTFJY-mCNGr4GpEo8x9TCztlgWlyEX2jjfspgViDhhEGC-Z9f4umHvbY9N9NJ8wzYhH45BFSQmPbgu57qlA6M95j24bRmV7U6YMZXLNtPT3SRJsRC1yevK40Z11yKeAFyPBhSrREgiOVEA-UAi2Fv9ge9sXOptEx1EYbwYe_z8stAZT5A5IT-T4RCMd0k4YWBJzC8kuNH-G-SA4JxTL64rDjpSB583pXLlmoeJmxAWAK16s-ZAHEMU7zTRQC5ITfcs9ydcbqjluJuvQaBZBqmOD1hzhdLfhcASN2T1Q4Y4KFqo5uXU5IEfrcfYfmAptThmFq7NAiSKHQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all -autorecon2 -subjid <subjid> -white on post-co-registerated aseg.presurf.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz and ?h.orig to get ?h.cortex.label
Thanks and all the best, Ela
________________________________ From: Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Tuesday, July 26, 2022 12:45 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: Understanding ?h.sphere.reg
Hi Douglas, It does. Thank you. Can you also help me with something else? If we coregister bunch of volume and surfaces using the same reg.lta for one subject, is there a way to safely reflect these changes in label files like rh.cortex.label or in transformation fies like talairach.xfm? In other words, can we make any changes to rh.cortex.label and talairach.xfm from pre co-registeration to make them usable with post co-registration files? Thanks
Douglas N. Grevehttps://secure-web.cisco.com/1Sa9geD9Pn3WQS7pXoIgFzUzwLTkndP52ZiOFFA74ycdRqO4IwNK1Wy_Ed3fUyZd48SU7PTEl2on_isy_xY-UXnhkhp2NmqaoOMXHhNZeVItHidCoNqjAdO_0pF2s5GPOB31QrdS9iU5NfWrzJUs6eJCDKtjPZ3cG8blbykryh1DdEQQ_o0KCG-MLbK3VNBqkHBkqYdsCWuQI6FukiUCcXCDI1rBLKyARdu-jalsR0BjxUGrO_hUFQRuLtfja9MsG5jTpi5B95FDXtSMbPdcpp4WkYMeErmXElxacngYqyYkuS8Sm5lKAUWna5BqnhS8NpH0uVWM-10s-Mtxyf287tQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Douglas%2BN.%2BGreve%2522 Sun, 24 Jul 2022 19:20:57 -0700https://secure-web.cisco.com/1CZTg3v8StwDIz8ldgeKmmXwRWzysyMwI4k2NQwCM1Rkdk-ER_E0eARDrF6UsFzFRICrgy9fB7fglQV2lCsdTKeBwgofgbD49SVMC0dn-qWpVWTLkSnBiZNq1UXyHoE_wQqKNPIkkjbXsdUt0TVD1lvdl2eMY9Jsp8WkXS7YQTtJod3SOkpga1NYGz-yY8t1BIyI2kNGvEX1N9995ME9YUWM9lkt_rjFCePu2AFq5xO2zlwn8_bFx748WcZSNKlQvLpqE_DH90o3Y9lAIbwFAlryqIIEV2kMyWZ50MPg8gLU6gxfZfcWiEGxTgRHpl_CZ-zBb3E2pbEhLA0f1LQ3qog/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220724
The ?h.sphere.reg xyz coordinates are coordinates on the sphere. To apply a spherical registration, a point on one spherical mesh is mapped to the closest point on the other spherical mesh. not sure if that answers your question ... ________________________________ From: Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Thursday, July 21, 2022 5:26 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Understanding ?h.sphere.reg
Dear freesurfer experts,
I was wondering if ?h.sphere.reg files have any coordinates in space tagged to them? What I actually mean is I'm using TRACULA which itself use the following files from mri and surf folder (all created by running recon-all on T1 image): aparc+aseg.mgz, brain.mgz, brainmask.mgz, orig.mg, T1.mgz and ThalamicNuclei.v12.Ta.FSvoxelSpace.mgzlh.thickness,rh.thickness,lh.white,rh.white,lh.sphere.reg,rh.shere.reg. I have all these files (except ?h.thickness and ?h.sphere.reg) in new coordinates in space created by co-registration. The pipeline we use to create recon-all results is almost the same as freesurfer pipeline with a slight difference in autorecon1 step, so the final results are almost always the same but the coordinate of the brain in 3D space is different, so we usually end up co-register one's reconstruction result (from our pipeline) with oneself T1.nii (come from mri_convert T1.dcm) so the structural mri reconstruction and dwi dcm files are in the same coordinate and can overlay. My understanding is that there is no coordinate tagged to ?h.sphere.reg files in 3D space, rather they are regulatory files which include some information about x,y,z vertices in regard to the surface of a hypothetical sphere (and the xyz are coming from the curvature of one's brain). As a result, I can use ?h.sphere.reg files as they are without any need to make any changes to match my files after they are coregistered. Is my understanding correct?
I'm sorry if my language is not clear enough. I tried my best to describe the situation, but I'm not sure if my description is clear enough.
Thank you for your help and time. Ela
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Salar Dini, Elaheh