Re: [Freesurfer] Help with transform matrix for SEEG

[Douglas N. Greve]

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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[Freesurfer] Help with transform matrix for SEEG

[Hyunchul Lee]

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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