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Correction: tal_mat is 3x4. Sorry for the typo.
________________________________
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]'
3. 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://secure-web.cisco.com/1u3gROO93WuSMDsPIjpBxqLizdPGwHGIPnujW3vULRzbDp5l4AcftKFOPcKFJGwMDidADlmKQfa95d3LKhLILGm6wmxQqO0GQgAPG41WIZWJKNX3-BjswXvHflOH_3Crtbiop8GHZ4RU9waT1-1Iul-ywYQiYvGtlvtyvXQFI5zDYwzEYajAjkyR8_l9lgMCTbXIvaUuao8ePo5hvG94w4HeHsx-iL0edODVZCFY2R3Kb3pSNzS9kQHVGf6c9hdKRs2PEmxNym3WEUukrhPdvYjkx3et2mzU48qxSiqfiOY1k8TIAeU_Jwr_ArOLyPvHNUcBKYss0eYobn7uXXcz3pA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCoordinateSystems<https://secure-web.cisco.com/1KBgpyl2eUHbe3JJquLznCmUPf5H6Y6u32jsqi9JO-tyM4nXJV7lP--un21IWVUlF4OdqiCWzzNf7N2RxTI-k3ByEsy111v0oyVcDVRwYX9_5fl9CjJaeVAOTEVDBoK88J794eGg4DZVHiMutPI1fcP49RZU79QNk8fPx2Cwo8u70NixWssbpKyM5GnH7qf5a9muDnyjr-cF-ud2BrjBE7OYh_-4ofvqu09liwmmZfrioZXw3RlzZIVhM3H6mai0eHc0OYs8A4B9Bv2DkENdZNM-jjVEGjuXkv5yJ6ZiD7fcsHgHONtp9GzezXnY66QGbNqMQjnibwbTyxbHPW_YnIg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCoordinateSystems>
(8th 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} |
Website<https://secure-web.cisco.com/1sSvt_8iF8TDt6AOi7fpFSVomBHHihzVXzlD8iQRtgls4npi42gTOrc0v-owOr03Gopc4tDolUebvc2_DfdHuXwjonUsYpJ_W0oIFjlDjQuN2OTy23YSk9tSEPw7uqs5hU84A6YKXhDLx9RJ6dLsp-og_Y9uxdtRP5ebxgsvnEvKLdcgKA5RXugd8AMeLPQjErlVatVL1BoJYMa0c-SGZO1f_qBCU6uADgpER55y0LqX-0nLNyT_W6hZAUI1Svkn_Souq4W-i2eGCHRoFZ9I8w4KzGRg7zyWrKOwa9V8iqAfyMymwnbC6MdcpkIrZDzgHPfoSmihFa0_CvvlCJx3Z_A/https%3A%2F%2Fqian-chu.github.io%2F>
PhD Student, Max Planck - University of Toronto Centre for Neural Science and
Technology
- Neural Circuits, Consciousness, and Cognition Research
Group<https://secure-web.cisco.com/12q0YRBUXUV2R0upgxdIxqSAdxXp93zy9YPIQn5p4K4-u8tPIr44CBlHadxMiUX_J8-QZ04ZLAGZo8FjwvVXhLf29JrihGIBtRP5xPQKvQAiVvNYcoGJwIy2M9t2h82cqjAWzsejF7yQjES5nKfWb_pBAKZ41OIcYUmh2JQMKCDBSfO9UUSCB5vHCBdsMQpoXTV6lZE-2Xy_qeYUDcULZgWEQ3G_157eLJLZC_qL_Tls9RYI10He_949v-o4KfT2LB-uN1LANRSmuW26nac6xdN01mECyoZbZp6y0awIT7_UFzZCrDmzanm-Wah_SFJL_RswTMDkIF6SSGyGliSCMjw/https%3A%2F%2Fwww.aesthetics.mpg.de%2Fen%2Fresearch%2Fresearch-group-neural-circuits-consciousness-and-cognition.html>
Max Planck Institute for Empirical Aesthetics
- Neuron to Brain
laboratory<http://secure-web.cisco.com/1YurU9IJfcJ0-OPOy4t2cSOIsEPbKHXN3-14v8LYQEBcrC8S1ChXGb6srTTLibpHnENhNLlL6extC7GeXXVe--Yp-_R_4BXDv-1Bm_Ez1hC6XFRohBM0Ss7eJAJ8M0mwDD3O3GWwle0fNoAlxK7iJcJMpMJEKWFV9hkHCI7m5XRPmxrwwoxOc2TBgz0VnC__7DG8z9xSfrUvvdg8EHIqrcpUWibNgpuSMBwtsiG95xDaYVXgabPnugN9V61fdrg5lui3YOZdIRlXcLulsoEKaR-TE1yVU3gtIP72P4qkbRHgAOCvs0RArdP3cpGyETse1/http%3A%2F%2Fwww.neurontobrainlaboratory.ca%2F>
Institute of Biomedical Engineering and Krembil Brain Institute, University
of Toronto
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