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Hello, I am conducting research using ECoG. I want to accurately track the location of electrodes. I am inputting data from a NIfTI file (size: 512, 512, 360, 1). I already know the exact electrode location within the NIfTI file, e.g., (182, 274, 260). The x, y, z values of this coordinate correspond to the raw fMRI scan, with x ranging from 0-512, y from 0-512, and z from 0-360.
I extracted the --vox2ras matrix from the 001.mgz file using mri_info. I attempted to project the coordinates from the NIfTI file onto the generated pial surface, but I found a significant discrepancy.
What I need is not Talairach coordinates, but a precise transformation of the electrode coordinates in the NIfTI space to their exact location on the subject's pial surface. How can I achieve this?
Additionally, I noticed that the origin (0,0,0) of the generated pial surface does not align with the anterior commissure (AC). I am curious about the coordinate system of the final mesh – is it simply the voxel-based x, y, z system, or is it in the RAS coordinate system?
Thank you. Best regards, Yonghyeon Gwon
Have you seen this page? https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 12/22/2024 11:05 PM, 권용현 wrote:
External Email - Use Caution
Hello, I am conducting research using ECoG. I want to accurately track the location of electrodes. I am inputting data from a NIfTI file (size: 512, 512, 360, 1). I already know the exact electrode location within the NIfTI file, e.g., (182, 274, 260). The x, y, z values of this coordinate correspond to the raw fMRI scan, with x ranging from 0-512, y from 0-512, and z from 0-360.
I extracted the --vox2ras matrix from the 001.mgz file using |mri_info|. I attempted to project the coordinates from the NIfTI file onto the generated pial surface, but I found a significant discrepancy.
What I need is not Talairach coordinates, but a precise transformation of the electrode coordinates in the NIfTI space to their exact location on the subject's pial surface. How can I achieve this?
Additionally, I noticed that the origin (0,0,0) of the generated pial surface does not align with the anterior commissure (AC). I am curious about the coordinate system of the final mesh – is it simply the voxel-based x, y, z system, or is it in the RAS coordinate system?
Thank you. Best regards, Yonghyeon Gwon
-- Yongheyon Gwon Interdisciplinary Program in Neuroscience, Seoul National University, Human Brain Function Laboratory, Seoul National University Hospital Seoul, Korea
E-mail: gngyong@hbf.re.kr , gyh0321@naver.com Phone: +82-10-9706-3814
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