ENH: Bem editing?

[larsoner]

@kingjr recently asked (but is probably too wary of opening issues to do it):

is there a way to quickly edit BEMs? I have some intersections between inner and outer skulls but they're tiny, and a manual dragging of the points would really help.

My suggestion would be to:

1. Find some nice triangulated mesh editing software (3D program of some sort, maybe CAD or blender?)
2. Figure out what file format it needs
3. Convert the surf to that format (it should be simple, if it's not, open MNE-Python issue and I'll help there)
4. Document the process in the docs

Does anyone know of a better way? If not, then we can make a recommendation for how people can fix minor BEM surface issues if necessary.

[kingjr]

Relatedly, I am currently trying to see whether I can fix the tiny surface intersections problem by:

• Detecting the points outside the outer surface (e.g. inner skull point out of outer skull)
• Changing the xyz of these points by a param k toward the center of the surface

EDIT: in any case we'd need to wait for nipy/nibabel#458 to be merged.

[dgwakeman]

1. Make sure people know they should be using good quality MR sequences including MEFLASH if they have EEG
2. If they just have MEG they should just use a single layer
3. in lucky cases mne_surf2bem can shift the surfaces to avoid simple problems

[larsoner]

@kingjr you know we have code for detecting whether points are inside a surface already right?

[kingjr]

@Eric89GXL Yes, I'm now trying to understand how it works :)

[larsoner]

Follow the trail of the surface topology checks in _check_surfaces

[dgwakeman]

Seriously though, is there a problem with getting an MEFLASH or with mri_make_bem_surfaces (it has never failed for me)?

[kingjr]

@dgwakeman It's not always possible to acquire MRI, sometimes you have to retrieve from archive data.

[kingjr]

[i.e. you don't always have the adequate MRI sequence, hence the unstable segmentation]

[dgwakeman]

Ok, in that case the one cheap easy step to solve the intersection problem with the watershed BEM is to just binarize and smooth/expand the 3d volume of the aseg volume from FreeSurfer, and then just fit an icosahedral surface to it. That should avoid all intersections. This would be totally automatable, and easy. I had some hacks to do this back in the day (hacking calls to mri_watershed: the code is pretty entrenched in a particular naming directory structure). Note, the watershed is still not recommended for EEG.

I did that to generate the inner skull surface for the SPM BEM. Then I did way crazier hacks to get the outer skull, but that is a ton of work.

[kingjr]

@dgwakeman that seems like a better fix than what I was suggesting. Would you be ok sharing your script and opening a PR?

[dgwakeman]

I can try to dig it up, but it doesn't really belong in mne-python (unless we got icosahedral meshing and I missed it), because it uses FreeSurfer commands. I'm happy to help. I'm in the middle of moving (to Philadelphia if anyone knows of labs looking for someone, or wants to hire a consultant to work remotely), but I should be able to look into it late next week. I'm setting an alarm now to look at it on Friday afternoon. hth d