[Mne_analysis] Pial and inner skull surfaces intersecting

[dgw]

Hi Chris,

On Tue, Nov 4, 2014 at 4:50 AM, Christopher Bailey <cjb at cfin.au.dk> wrote:
> 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.

This is very surprising. Usually, the inner_skull surface generated by
mri_make_bem_surfaces does an excellent job hugging the flash 5. Can
you send an image showing the surface on the flash 5? I have seen some
small clipping of the pial surface due to the sharpness at the brain
at the tip of the occipital lobe, but I have never seen it cross the
white matter.

It is also important to note that MPRAGE type sequence are virtually
useless for determining the skull boundary, as they don't provide any
contrast between cortical bone and CSF.

With regards to the inner skull boundary being wrong, in practice this
is a visualization issue, because the underlying math with which the
BEM is calculated is not sensitive to these minor changes. We would
need a new BEM solver (first, and then fix the mesh issues) to make
these small surface changes have an effect on our solutions.

>
> @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? ;)

I nominate you ;)

HTH,
D
>
> @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>
>  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> 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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