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
Re: [Freesurfer] Understanding ?h.sphere.reg
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Douglas N. Greve
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24 Jul 2022 19:20:57 -0700
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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.salard...@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
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