[Mne_analysis] MNI Coords from SourceSpaces

[Eric Larson]

        External Email - Use Caution        

vertex_to_mni is only really designed to work for surface-based source
estimates. So in this case you can instead look at
`src[0]['rr'][src[0]['vertno'][whichever]]` and this will give you an array
of shape (N, 3) corresponding to the points in the subject's MRI coordinate
frame.

For now you can use `mne.source_space._read_talxfm` to get the affine
transformation matrix that will convert these points to MNI space:

https://github.com/mne-tools/mne-python/blob/master/mne/source_space.py#L1286

But it's private so the API can change at any time. Then you can use
`mne.transformns.apply_trans` to apply it to your points.

Feel free to open an MNE issue about making this function public, it's
probably worthwhile for applications like these. Also we should update the
`vertex_to_mni` doc to mention that it's only designed to work with surface
source spaces.

Eric


On Wed, Jan 9, 2019 at 1:36 PM Bear, Joshua <JOSHUA.BEAR at ucdenver.edu>
wrote:

> Hi MNE Folks,
>
> I am trying to identify the MNI coordinates from a SourceSpaces object
> from a specific individual (i.e. not fsaverage).
>
> If src is the result from mne.set_volume_source_space():
> I found that I can identify the indices of the relevant vertices from:
> src[0][‘vertno’]
> I can then use vertex_to_mni for the vertex; however, I cannot figure out
> how to identify which hemisphere a vertex belongs to, and vertex_to_mni
> requires a selection.
> My source space has coordinate_frame=MRI (surface RAS).
>
> Does anyone know how to extract the MNI coordinates for the sources in a
> volume source space?
>
> Thanks for any help,
> Josh
>
>
>         External Email - Use Caution
>
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