Aligning volume source space with mri

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  • MNE version: 1.8.0
  • operating system: Debian GNU/Linux 9.8 (stretch)

Dear MNE community,
I’m writing you about some difficulty I am experiencing on aligning properly the volume source space (created using MNE) and the T1 image used to create the source space.

src = mne.setup_volume_source_space(subject, bem=bem_sol, pos=5)
fwd = mne.make_forward_solution(
        raw.info, src=src, bem=bem_sol, trans=trans_sol, meg=True, eeg=False
)
mri_img = nib.load(f"{subjects_dir}/{subject}/mri/T1.mgz")
src_pts = fwd['src'][0]['rr'] * 1e3
trans_coords = mne.transforms.apply_trans(trans, src_pts)
voxel_coords = nib.affines.apply_affine(
    np.linalg.inv(mri_img.affine),
    trans_coords
)

current_ornt = io_orientation(mri_img.affine)
ras_ornt = axcodes2ornt(('R', 'A', 'S'))
transform = ornt_transform(current_ornt, ras_ornt)
img_ras = nib.as_closest_canonical(mri_img)
mri_ras_data = img_ras.get_fdata()

subset = voxel_coords[(voxel_coords[:, 0] > 110) & (voxel_coords[:, 0] < 120)].copy().round()
x = subset[:, 1]
y = subset[:, 2]
mri_slice = mri_ras_data[118, :, :]
fig, ax = plt.subplots(figsize=(6, 6))
ax.imshow(mri_slice)
ax.scatter(x, y)

With this code I’m able to plot both, the src positions and mri slice at the same place but they don’t align perfectly. I’d say there is like a 15-20% missalignement whereas when I use

mne.viz.plot_bem(src=src, subjects_dir=subjects_dir, subject=subject, brain_surfaces='white', orientation='coronal')

The aligment is absolutely perfect but I can’t seem to reproduce the same transformations to get to the same result.
Thank you,

2

I finally soved my problem it was due to some transpose missing on the mri slice because of how imshow works (inversing cols and rows (y, x) instead of (x, y)). Also I’ve figured that using the src[‘rr’] directly is faster as it is in MRI coords already. Hope that will help someone one day

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