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On 8/14/2023 12:38 PM, Qian Chu wrote:
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Correction: tal_mat is 3x4. Sorry for the typo.
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*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Qian Chu
<qian....@mail.utoronto.ca>
*Sent:* Monday, August 14, 2023 12:36
*To:* Freesurfer@nmr.mgh.harvard.edu <Freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] Native coordinate to MNI305 to MNI152
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Dear list,
I'm working on intracranial electrode localization and am developing a
pipeline to map electrode coordinates in the native RAS space to brain
templates like fsaverage/MNI305 and MNI152. I would like to check
whether my workflow is correct and would appreciate any input on the
validity! The steps are described below:
1. Obtain electrode coordinates (in mm) on the native orig.mgz as an
array [R A S]
2. Read the 4x3 matrix (tal_mat) in mri/transforms/talairach.xfm.
Obtain the new coordinates in MNI305 = tal_mat * [R A S 1]'
I'm not sure this is right. Why not just read the MNI305 coordinates
when viewing the orig.mgz? They should be in the freeview window just
below "RAS" and "TkRegRAS".
1. Use the MNI305 to MNI152 matrix (305_152_mat) mentioned in
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(8^th Use case). Obtain the new coordinates in MNI152 =
305_152_mat* [R_305 A_305 S_305 1]'. Where R/A/S_305 is the output
from step 2.
Thank you very much in advance!
Best regards,
Qian
--------
*QIAN CHU*(he/him/his) | qian.chu@{mail.utoronto.ca, ae.mpg.de} |
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