Problem in FreesurferRAS

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1
  • MNE version: 1.6.1
  • operating system: Windows 10

Hi, I am currently curious about the vertex coordinates of the source space. I used src[0]['rr'] to get the FreesurferRAS coordinates of vertices.
Here is the code I used:

import mne
import numpy as np
src_fname = “./src/surface_oct6-src.fif”
src = mne.read_source_spaces(src_fname)
ras = np.concatenate(
[
src[0][‘rr’][src[0][‘vertno’]],
src[1][‘rr’][src[1][‘vertno’]]
],
axis=0
)

I tested this code on two subjects and reconstructed the surfaces. And I found that one subject’s reconstructed surface did not coincide well with the Freesurfer results, while another subject could. Like:

ed8d0f421516889cd97b15adcff0812
ed8d0f421516889cd97b15adcff0812715×609 335 KB

However simple translation could help with this situation. I suppose this has to do with the origin of the coordinates. I noticed that "The origin of this coordinate system is at the center of the conformed FreeSurfer MRI volumes (usually 256 x 256 x 256 isotropic 1-mm3 voxels) and the axes are oriented along the axes of this volume.".

Would this be caused by the T1w MRI if it is not "256 x 256 x 256 isotropic 1-mm3 voxels"?

2

Sorry it was a bit unclear how you are generating these two images. One was using the script but the other was using freesurfer which I’m not sure what that means. If you’re using freesurfer surfaces through the mne plot functions like mne.viz.Brain or mne.viz.plot_alignment then it could be because they are using surface RAS (like scan RAS but different origin that freesurfer uses because it helps with their analysis pipeline and also for historical backward compatibility reasons). So you’d just need to pass coord_frame=‘ras’.