Have you seen this page
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems ?
On 12/10/2023 8:55 AM, Hyunchul Lee wrote:
External Email - Use Caution
Hello,
I've just started using Freesurfer this week and I'm quite confused
about coordinate systems.
Specifically, I have SEEG electrode locations that have been digitized
in MRI RAS space, and I'm trying to apply a transform matrix so that
these electrodes will be registered with the same brain that I
performed recon-all on using Freesurfer, so that I can do further
analysis in MNE python.
I understand that voxel space to MRI RAS space transform matrix is
stored in vox2ras and the transform for voxel space to Freesurfer's
surface RAS is in vox2ras_tkr of T1.mgz in my subject folder. Since
the electrodes are in MRI RAS space, I am applying a transform matrix
that is a matrix product of inverse(vox2ras) and vox2ras_tkr. However,
this doesn't work out in real life, and I end up with electrodes half
way outside the head.
Am I using the correct matrices? Also, T1.affine appears similar to
vox2ras but very slightly different. Just hoping that there would be
an easier way..
Best regards,
*
*
*Hyunchul Lee* MBBS PhD
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