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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 https://secure-web.cisco.com/1KBgpyl2eUHbe3JJquLznCmUPf5H6Y6u32jsqi9JO-tyM4n... (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} | Websitehttps://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 Grouphttps://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 laboratoryhttp://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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Correction: tal_mat is 3x4. Sorry for the typo. ________________________________ 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:
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/1u3gROO93WuSMDsPIjpBxqLizdPGwHGIPnujW3vULRzbDp5...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} | Websitehttps://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 Grouphttps://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 laboratoryhttp://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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On 8/14/2023 12:38 PM, Qian Chu wrote:
External Email - Use Caution
Correction: tal_mat is 3x4. Sorry for the typo.
*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]'
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".
- 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/1Fnkjj78IAl7JavWJF9ZzoT1vKi7FUzB00w4fhFhM1aldP5... 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 (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} | 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
- Neuron to Brain laboratory
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Qian Chu