[Mne_analysis] Current dipole moment densities

[Alexandre Gramfort]

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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