[Mne_analysis] Morph dipole to fsaverage brain

[Eric Larson]

        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>
wrote:

>         External Email - Use Caution
>
> 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> 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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