[Freesurfer] lh.white surface co-registration

2022-03-16 Thread Salar Dini, Elaheh 
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





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Re: [Freesurfer] lh.white surface co-registration

2022-03-17 Thread Douglas N. Greve 

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






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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] lh.white surface co-registration

2022-03-28 Thread Salar Dini, Elaheh 
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





_

From: Douglas N. 
Greve

Sent: Thu, 17 Mar 2022 19:45:36 
-0700

To: elaheh.salad...@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 
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





___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] lh.white surface co-registration

2022-04-04 Thread Douglas N. Greve 



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





_

From: Douglas N. Greve 



Sent: Thu, 17 Mar 2022 19:45:36 -0700 



To: elaheh.salad...@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 
*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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.