[Mne_analysis] MNI Coords from SourceSpaces

[Bear, Joshua]

Hi Eric, 

Thank you for these details! I had to shift focus for a minute but will get back to this shortly. I’ll open an MNE issue after I’ve had a chance to work it out. 

I also want to comment on how awesome the MNE team is for all of the timely support and thoughtful responses, not to mention the software itself! 

Josh



> On Jan 11, 2019, at 8:26 AM, Eric Larson <larson.eric.d at gmail.com> wrote:
> 
>         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 <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 <mailto: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
> 
> 
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> 
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