[Mne_analysis] alignment inner_skull mri

[Eric Larson]

        External Email - Use Caution        

>
> what did you try?
>
> you can use plot_bem in mne-python to check things and you can write a
> surface file in .surf format.
>

Keep in mind you need to know what coordinate frame the surface that is
created by fieldtrip/spm lives in. If it's MRI voxels (?), then you'd want
a MRI voxel (just called "vox" in MNE) to FreeSurfer Surface RAS MRI (just
called "mri" in MNE) transformation. In nibabel this would be something
like:

rr, tris = mne.read_surface('inner_skull.surf')  # in mm
mri = nibabel.load('SUBJECTS_DIR/SUBJECT/mri/T1.mgz')
xform = mri.header.get_vox2ras_tkr()  # in mm
rr = mne.transforms.apply_trans(rr, xform)
mne.write_surface('inner_skull_fixed.surf', rr, tris)

This might or might not work depending on the coordinate frame that
fieldtrip/spm actually uses. For example, if the volume is in just
MRI/Scanner RAS coordinates (probably more likely?), you'll need to take
the points and convert them from MRI/scanner RAS to FreeSurfer surface RAS,
which would involve something like:

a = mri.header.affine  # vox->ras
b = mri.header.get_vox2ras_tkr()  # vox->mri
xform = b @ np.linalg.inv(a)  # ras->mri

and apply this xform instead and save as above. For more information, see:

https://mne.tools/dev/auto_tutorials/source-modeling/plot_background_freesurfer_mne.html#mri-coordinate-frames

Eric
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