<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div dir="ltr"><div>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.</div><div><br></div><div>For now you can use `mne.source_space._read_talxfm` to get the affine transformation matrix that will convert these points to MNI space:</div><div><br></div><div><a href="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</a><br></div><div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>Eric</div><div><br></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Jan 9, 2019 at 1:36 PM Bear, Joshua <<a href="mailto:JOSHUA.BEAR@ucdenver.edu">JOSHUA.BEAR@ucdenver.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi MNE Folks, <br>
<br>
I am trying to identify the MNI coordinates from a SourceSpaces object from a specific individual (i.e. not fsaverage). <br>
<br>
If src is the result from mne.set_volume_source_space(): <br>
I found that I can identify the indices of the relevant vertices from: src[0][‘vertno’]<br>
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. <br>
My source space has coordinate_frame=MRI (surface RAS).<br>
<br>
Does anyone know how to extract the MNI coordinates for the sources in a volume source space?<br>
<br>
Thanks for any help,<br>
Josh<br>
<br>
<br>
<p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p>_______________________________________________<br>
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