[Mne_analysis] Pial and inner skull surfaces intersecting

dgw dgwakeman at gmail.com
Wed Nov 5 09:27:46 EST 2014
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Hi Chris,

I'm sorry, but at the moment there are no better options. I have some long
term goals in the pipeline, but the big barrier for me is the BEM code.
Until we get a better BEM solver there isn't much incentive to solve this
problem (will not be publishable to say we get prettier images). If I get
some time over the holidays, I may take a look and see what i can do.

Dan

On Wed, Nov 5, 2014 at 6:15 AM, Christopher Bailey <cjb at cfin.au.dk> wrote:

>  Hi Dan,
>
>  Here are images of the inner skull intersecting WM in occipital regions,
> on the T1 and "flash5_reg.mgz". For comparison, a frontal view is also
> attached. NB: we only ran the 5 deg FLASH sequence on this subject. It's
> clear that something's gone wrong, and that the performance is worst in the
> occipital region.
>
>  This isn't something I see a lot, but it would be nice to do something
> about it (and /please/ don't say "Seglab" ;). I do understand that the T1
> isn't any help, but is the brain extraction not used by
> mri_make_bem_surfaces for anything, then? Like a starting point for
> shrink-wrapping the inner skull on the ("synthetic" or "average") flash5?
> If the brain extraction is not used, then it's at least pointless to spend
> time tweaking recon-all.
>
>  I accept your point about the error made in less-than-perfect inner
> skull delineation being something we can usually live with when dealing
> with real data (and real sources of error). And thanks for the nomination,
> but note that I did say "clever" ;)
>
>  Best,
>
>  Chris
>
>
>    On Nov 4, 2014, at 7:53 PM, dgw <dgwakeman at gmail.com> wrote:
>
> 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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