[Mne_analysis] Pial and inner skull surfaces intersecting

[Christopher Bailey]

Hi Kambiz, Alex and Dan,

In the occipital regions particularly, FLASH-based BEM's seem to be consistently "tight", and in some cases we've even seen inner skull-WM-intersections (admittedly pathological and rare). Omitting such points using mindist is perhaps an option, but doesn't seem very elegant. Furthermore, the inner skull boundary is guaranteed to be wrong, which is not a good outset for forward modelling.

@Kambiz Our experience indicates that the freesurfer-based brainmask is pretty aggressive in the occipital region, which might have some impact on mne_flash_bem. I can see that the brain.mgz-file is often "better" in that it includes a hint of dura outside the pia, but it's very faint and may not be picked up by mri_make_bem_surfaces. Perhaps the use of the -wsthresh parameter to recon-all would help? Do you also see this occipitally?

May not, could not, whatnot... I'm just guessing, of course, since the inner workings of the bem creation are hidden.

I feel this is a suitable opportunity to advocate for some clever person out there to implement a new (and tweakable) BEM surface creation tool. According to the FS website (http://freesurfer.net/fswiki/mri_make_bem_surfaces), we are relying on closed-source code written 15 years ago... Any takers? ;)

@Alex Could you write a few words on how the --atlas option might help here?

/Chris
--
Christopher Bailey, MSc
MEG Engineer, MINDLab Core Experimental Facility
Center of Functionally Integrative Neuroscience (CFIN)
Aarhus University, Denmark

tel. cell: +45-2674-9927
tel. office: +45-7846-9942

On Nov 4, 2014, at 1:24 AM, dgw <dgwakeman at gmail.com<mailto:dgwakeman at gmail.com>>
 wrote:

Alex,

Don't you think this is less of a problem, since we don't use the pial
surface as the source space? Plus the mindist requirement throws out
points too close?

There are not any automated available tools to do this.

D

On Mon, Nov 3, 2014 at 5:15 PM, Alexandre Gramfort
<alexandre.gramfort at telecom-paristech.fr<mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:
Hi Kambiz,

The pial and inner skull surfaces intersecting is not a problem given
the coarseness of our forward models.

I don't have a solution for you but I would not be so convinced that it
has low influence. If 2 vertices/triangles are too close then you can numerical
errors with BEM models. I would try to correct for it. Isn't there a way to use
an atlas to avoid this?

otherwise use MEG and a single layer :)

Alex
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