[Mne_analysis] Morph dipole to fsaverage brain

[Jean-Remi KING]

        External Email - Use Caution        

Hi Marijn,

Have you tried to pick the closest subject surface to your dipole location
and use the morph_surface to get the alignment? Not know how the morph
works, ny hack would something like this:

elec_xyz = np.random.randn(3)*50
surf_xyz, _ = nibabel.freesurfer.read_geometry('sub-0001/surf/lh.pial')

distances = np.sum((surf_xyz - elec_xyz[None,:])**2, 1)
closest = np.argmin(distances)
data = np.zeros(len(surf_xyz))
data[closest] = 1.

stc = mne.SourceEstimate(data, vertices=range(len(surf_xyz)), tmin=0.,
tstep=1., subject='sub-0001')
morph = mne.compute_source_morph(stc, subject_to='fsaverage',
subjects_dir='./')
stc_morph = morph.apply(stc)
vert_idx = stc_morph.vertices[np.argmax(stc_morph.data)]  # fixme deal with
left and right hemi

surf_xyz, _ = nibabel.freesurfer.read_geometry('fsaverage/surf/lh.pial')

plt.plot(*surf_xyz[vert_idx])

JR

On Wed, 26 Aug 2020 at 15:43, Marijn van Vliet <w.m.vanvliet at gmail.com>
wrote:

>         External Email - Use Caution
>
> 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:
> >
> >              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 <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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