[Mne_analysis] how to use viz.plot_alignment() on SEEG data?

[Alexandre Gramfort]

hi Larry,

indeed sEEG were ignored in plot_alignment.

This PR should fix it: https://github.com/mne-tools/mne-python/pull/4903

let us know directly on github if it does the job for you.

thanks for reporting the issue.

Best,
Alex


On Sat, Jan 27, 2018 at 12:05 AM, Eisenman, Lawrence
<leisenman at wustl.edu> wrote:
> To clarify, I have been using the data from the ECOG demo (https://martinos.org/mne/stable/auto_examples/visualization/plot_3d_to_2d.html#sphx-glr-auto-examples-visualization-plot-3d-to-2d-py) in my demo notebooks since other MNE users have easy access to that data.
>
> To facilitate my attempts to use the Brainstorm demo, I have run the pre-implantation MRI from the Brainstorm demo (http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity) through freesurfer as that seemed the path of least resistance to using the data in MNE. I'm not using that scan in these demos because it is not mine to share and I don't think anyone else wants to run it through freesurfer just to try my demo.
>
> I think my issue is that I have electrode coordinates in the MRI coordinate system as suggested by the observation that they make sense when plotted using pysurfer. However MNE seems to use a different default coordinate system ('head'?) and I haven't figured out how to convert or make MNE recognize that the coordinates are not in the default system. I have created yet another demo notebook using the MRI from the ECOG demo ('sample') with some electrode coordinates in the MRI coordinate system. As shown, they can be plotted with pysurfer but viz.plot_alignment doesn't work.
>
> https://gist.github.com/lneisenman/38ca9cf2e4075776f8476cebb114d2a1
>
> How do I find/create the transform to convert the coordinates to the default system? The coordinates included in the ECOG demo clearly are not in the MRI coordinate system.
>
>
> Larry
>
> ---------------------------------------------------------------------------------------------------------------------
> From: Alexandre Gramfort <alexandre.gramfort at m4x.org>
>
> did you run freesurfer on this subject? these notebooks suggest you used data from the MNE example?
>
>
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