[Mne_analysis] Current dipole moment densities

[Emily Stephen]

Hi Alex,

Are you saying that MNE-python does that?

When I run standard MNE solutions in python (no depth-weighting, fixed
orientation sources) using patch_stats=True (or False) in
mne_read_source_spaces, I get exactly the same forward solution and source
estimates. If the code were normalized by patch area for patch_stats=True,
I would have expected them to be quite different.

Code is attached. I've also included a version of the src file where the
patch statistics were computed using MNE-C (eeganes07-ico-3p-src.fif). It
produces a different forward solution, but the resulting stcs are nearly
identical (I think this comes from using the patch statistics in the
surface normal decision, which doesn't happen if the patches were computed
using mne-python, possibly because 'patch_inds' is never set in the
SourceEstimates). Sorry for the large download size (it's the BEM file).
​
 patch_stats.zip
<https://drive.google.com/file/d/0B8PjVL8SDL7IQUhLWjhLWUpiMFU/view?usp=drive_web>
​
Emily



On Fri, Apr 1, 2016 at 4:01 AM, Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr> wrote:

> hi Emily,
>
> > I'm trying to plot current dipole moment densities (e.g. Murakami and
> Okada
> > 2015 NeuroImage) in mne_analyze and mne-python, and it all seems rather
> > confusing.
> >
> > As far as I can tell based on the manual, MNE-C can compute densities if
> the
> > cortical patch statistics are available.
> >
> > But I'm confused about when the
> > cortical patch statistics are used after they are calculated. What do I
> need
> > to do to specify that I want current moment densities rather than
> > unnormalized moments?
>
> the forward BEM code makes use of it. It basically yields surface
> weighted forward fields.
>
> see
>
>
> https://github.com/mne-tools/mne-python/blob/master/mne/forward/forward.py#L451
>
> https://github.com/mne-tools/mne-python/blob/master/mne/minimum_norm/inverse.py#L1294
>
> so when you use MNE or a sparse solver that returns source amplitudes
> you should get source densities when the patch info is present.
>
> ok?
>
> ALex
>
> > Then when it comes to MNE-python I can't find any references to current
> > densities. Will I need to implement this myself? I think I can see how
> to do
> > it using the 'tri-area' field combined with the 'pinfo' vertices in the
> > SourceSpaces, and the current dipole moments from the SourceEstimate.
> I'm a
> > bit worried that I'm not understanding the relationship between the
> > vertices/patches in the SourceSpaces and the SourceEstimate (since the
> stc
> > doesn't have all of the patches from the src), and that this might affect
> > how I compute the area. Can I just forget about the patches in the
> > SourceSpaces that aren't in the SourceEstimate?
> >
> > Thanks,
> > Emily
> >
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