[Mne_analysis] Morph dipole to fsaverage brain

[Marijn van Vliet]

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Hi Eric,

if I morph the dipoles to MNI space (mne.head_to_mni(dip.pos)) and throw them on 
top of an fsaverage brain with brain.add_foci(morphed_dip_pos), I don't get 
reasonable results, points are floating way outside of the brain. They are sort 
of aligned on the brain, so origin point may be reasonable, but the scaling I 
wouldn't exactly call close enough.

Making compute_source_morph work for discrete source spaces would be a great 
solution. But that sounds hard :)

best,
Marijn.

On 26/08/2020 15.45, Eric Larson wrote:
>          External Email - Use Caution
> 
> fsaverage is in MNI space, so you should be able to use that affine if you want. 
> If they don't land in the right place it suggests some problem with how you're 
> applying the transformation or a problem return the transformation itself, which 
> you could manually adjust using tkregister (then probably rerun the subsequent 
> recon steps) or something similar.
> 
> If you want to go beyond affine, you could use the SDR volumetric transformation 
> code in compute_source_morph. You could try using a full 1mm MRI resolution, but 
> this might run into memory problems. You could code it yourself if you want to 
> try it from reading the MNE code, but you have to be careful about the 
> coordinate frames.
> 
> We could extend compute_source_morph to work with discrete source spaces using 
> this full-resolution MRI intermediate approach. Then you could set up each 
> subjects one dipole (or as many ECDs add you have) as a discrete source space 
> with one element, and morph it/them.
> 
> Eric
> 
> On Wed, Aug 26, 2020, 07:52 Alexandre Gramfort <alexandre.gramfort at inria.fr 
> <mailto:alexandre.gramfort at inria.fr>> wrote:
> 
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> 
>     hi,
> 
>     how do you want to visualize this? you can go from MNI to fsaverage
>     surface RAS but the dipole will not be positioned on the surface.
> 
>     Alex
> 
>     On Wed, Aug 26, 2020 at 1:47 PM Christian Kiefer
>     <ch.kiefer at fz-juelich.de <mailto:ch.kiefer at fz-juelich.de>> wrote:
>      >
>      >         External Email - Use Caution
>      >
>      > Hi Marijn,
>      >
>      > Is morph = mne.compute_source_morph() and morph.apply() what you are
>      > looking for?
>      >
>      > Best,
>      >
>      > Christian
>      >
>      > On 26.08.20 13:41, Marijn van Vliet wrote:
>      > >          External Email - Use Caution
>      > >
>      > > Dear MNE-Python community,
>      > >
>      > > I have a bunch of dipoles that were fitted in the brains of several
>     subjects.
>      > > Now I want to visualize the locations of all these dipoles in a shared
>     brain.
>      > > Is there a way to morph the positions of the dipoles from the individual
>      > > subjects to a template brain, for example fsaverage?
>      > >
>      > > I see that there is a head_to_mni function that will convert the
>     position to MNI
>      > > space. That is close, but does not match fsaverage space. Or is there a
>     way to
>      > > visualize the MNI brain in a 3d sort of way (not MRI image slices)?
>      > >
>      > > best,
>      > > Marijn.
>      > >
>      >
>      >
>      >
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