ENH: Use something other than FreeSurfer for BEM extraction

Dear MNE expert,

I am working with a EEG dataset and I wish to run source on that. Unfortunately the T1w are not FLASH and I know that in the absence of FLASH images, MNE offers a somewhat less accurate solution based on the watershed algorithm (see Jas et al., 2018).

Indeed for some subjects in my dataset (see attached 1) I got the following error when I am going to run make_bem_model.

RuntimeError: Surface inner skull is not completely inside surface outer skull

For other subject instead the surfaces are simply wrong (see attached 2), even though make_bem_model hadn’t give me any error

I was wondering whether if you have some tips on how to fix them.

Thanks

Dave

[larsoner]

Some exploration so far – I’ve had decent luck with FieldTrip + SPM (worked on 157/158 subjects), but this requires MATLAB so it’s a bit of a no-go.

I then tried brainsuite and fsl using this gist. brainsuite skullfinder is very fast (1-2 sec) but produces a questionable output, whereas fsl seems to work well in about a minute of run-time.

Subject 1

brainsuite skullfinder:

$ freeview -v T1.mgz -f bs_inner_skull.surf:edgecolor=red -f bs_outer_skull.surf:edgecolor=yellow -f bs_outer_skin.surf:edgecolor=255,170,128:hide_in_3d=true

fsl bet:

FieldTrip + SPM could not process this subject because it couldn’t determine the orientation (the head is tilted about the Z axis is probably the issue?).

Subject 2

brainsuite:

fsl:

FieldTrip + SPM + Python mesh code to marching_cubes + smooth + decimate:

Overall I think I like the idea of adding a mne fsl_bem function that uses fsl to generate BEM surfaces. It already puts out ones that are smoothed and 5120 triangles, writes to a standard format (vtk) that can by read by pyvista, etc. It even makes sure that the meshes don’t intersect:

the mesh is self-intersecting 
thus will rerun with higher smoothness constraint

[hoechenberger]

Amazing work, @larsoner!! Would very much love to see this added to MNE