External Email - Use Caution
Dear Freesurfer experts,
Is there a way to move lh.white of a subject to a new coordinate? Something quite similar as volumetric co-registration but for surfaces. To be exact, I have moved a subject's brainmask.mgz, orig.mgz, aparc+aseg.mgz, and T1 mgz to a new coordinate using mri_coreg and subsequently vol2vol, but the surfaces are still in the original coordinate and doesn't match the volumes. Is there a way to move the surface files to the new coordinate?
OS: Centos 7, Freesurfer version: 7.2.0
Thank you for your time and help. Kindly, Ela
If you have an LTA file, you can run mris_apply_reg --lta lh.white your.lta lh.white.newcoords
On 3/16/2022 4:15 PM, Salar Dini, Elaheh wrote:
External Email - Use Caution
Dear Freesurfer experts,
Is there a way to move lh.white of a subject to a new coordinate? Something quite similar as volumetric co-registration but for surfaces. To be exact, I have moved a subject's brainmask.mgz, orig.mgz, aparc+aseg.mgz, and T1 mgz to a new coordinate using mri_coreg and subsequently vol2vol, but the surfaces are still in the original coordinate and doesn't match the volumes. Is there a way to move the surface files to the new coordinate?
OS: Centos 7, Freesurfer version: 7.2.0
Thank you for your time and help. Kindly, Ela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks Douglas. I have read the freesurfer official page on surface co-registration, but I still can't grasp where the .lta file comes from in case of surface co-registration. I suspect that you can't use the same lta file that you used for vol2vol. Is that correct? Where can I obtain the .lta file from then?
Also, on another note, may I ask if I have a correct understanding of lh.thickness file? My understanding is that this specific file doesn't have any specific defined coordinate attached to it? It's just the cortical thickness information at each point? Or am I wrong and there are x,y,z coordinates signature for each spatial point? If the latter is correct, is there a way to change those coordinates to the new ones as well?
I appreciate your time and help as always.
Ela
_____________________________________________________________________________________________________________________
To: elaheh.saladini@yale.edu
If you have an LTA file, you can run mris_apply_reg --lta lh.white your.lta lh.white.newcoords
________________________________ From: Salar Dini, Elaheh Sent: Wednesday, March 16, 2022 4:15 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: lh.white surface co-registration
Dear Freesurfer experts,
Is there a way to move lh.white of a subject to a new coordinate? Something quite similar as volumetric co-registration but for surfaces. To be exact, I have moved a subject's brainmask.mgz, orig.mgz, aparc+aseg.mgz, and T1 mgz to a new coordinate using mri_coreg and subsequently vol2vol, but the surfaces are still in the original coordinate and doesn't match the volumes. Is there a way to move the surface files to the new coordinate?
OS: Centos 7, Freesurfer version: 7.2.0
Thank you for your time and help. Kindly, Ela
On 3/28/2022 2:39 PM, Salar Dini, Elaheh wrote:
External Email - Use Caution
Thanks Douglas. I have read the freesurfer official page on surface co-registration, but I still can't grasp where the .lta file comes from in case of surface co-registration. I suspect that you can't use the same lta file that you used for vol2vol. Is that correct? Where can I obtain the .lta file from then?
Yes, same as vol2vol. Use bbregister to get the lta
Also, on another note, may I ask if I have a correct understanding of lh.thickness file? My understanding is that this specific file doesn't have any specific defined coordinate attached to it? It's just the cortical thickness information at each point? Or am I wrong and there are x,y,z coordinates signature for each spatial point? If the latter is correct, is there a way to change those coordinates to the new ones as well?
It is just the thickness values at each point. They xyz is implicitly associated with the point.
I appreciate your time and help as always.
Ela
To: elaheh.saladini@yale.edu
If you have an LTA file, you can run mris_apply_reg --lta lh.white your.lta lh.white.newcoords
*From:* Salar Dini, Elaheh *Sent:* Wednesday, March 16, 2022 4:15 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* lh.white surface co-registration Dear Freesurfer experts,
Is there a way to move lh.white of a subject to a new coordinate? Something quite similar as volumetric co-registration but for surfaces. To be exact, I have moved a subject's brainmask.mgz, orig.mgz, aparc+aseg.mgz, and T1 mgz to a new coordinate using mri_coreg and subsequently vol2vol, but the surfaces are still in the original coordinate and doesn't match the volumes. Is there a way to move the surface files to the new coordinate?
OS: Centos 7, Freesurfer version: 7.2.0
Thank you for your time and help. Kindly, Ela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Salar Dini, Elaheh