From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Qian Chu <qian.chu@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

External Email - Use Caution

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:

Obtain electrode coordinates (in mm) on the native orig.mgz as an array [R A S]
Read the 4x3 matrix (tal_mat) in mri/transforms/talairach.xfm. Obtain the new coordinates in MNI305 = tal_mat * [R A S 1]'

Use the MNI305 to MNI152 matrix (305_152_mat) mentioned in MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems (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

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QIAN CHU (he/him/his) | qian.chu@{mail.utoronto.ca, ae.mpg.de} | Website

PhD Student, Max Planck - University of Toronto Centre for Neural Science and Technology

- Neural Circuits, Consciousness, and Cognition Research Group

Max Planck Institute for Empirical Aesthetics

- Neuron to Brain laboratory

Institute of Biomedical Engineering and Krembil Brain Institute, University of Toronto