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

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1

Hi all,

Using the ECOG tutorial (Page Redirection) as a starting point, I'm trying to import some SEEG data. I can get the EEG data loaded and create a DigMontage, but I am unable to view/confirm electrode location. Viz.plot_alignment does not seem to work with SEEG data. Am I missing something?

As an alternative, I tried a kludge with PySurfer.

from surfer import Brain
%gui qt

brain = Brain(subject_id, "lh", "pial", subjects_dir=subjects_dir, cortex='ivory', alpha=0.6)
coords = [[seeg.x[i], seeg.y[i], seeg.z[i]] for i in range(len(seeg))]
brain.add_foci(coords, color='red', scale_factor=0.2)
brain.show_view('lateral')

If this results in positions that look correct, does that imply that the electrode positions are probably correct?

Thanks for your help.

Larry

2

hi Larry,

did you properly set the sEEG electrode locations in the measurement info?
ie in the right coordinate system? if sEEG has never been tested you
can set the electrodes
as EEG channels and avoid the projection on scalp surface during plotting.

Let us know if it works

Alex

3

Thanks for the suggestion. Now I think I have two issues. The first is that I still don't think plot_alignment shows 'seeg' electrodes. To test this, I used the ECOG demo to confirm that with 'ecog' electrodes, things work as expected. I then switched to 'eeg' electrodes and that also worked but switching to 'seeg' no longer works. Here is a gist of a notebook showing how I tested.

https://gist.github.com/lneisenman/c133e19c32faced76b9434f53dace7f6

In the process of testing all this, it became clear to me that my electrode locations are not in the correct coordinate system. They seem correct when using PySurfer to display the MRI and the plot_foci() function to display the electrodes but not when using MNE even with the electrode type set to 'ecog'. Can you point me to the relevant MNE docs so I can understand what coordinate system(s) is/are being used and where/how MNE moves between them.

Thanks for your help.

Larry

4

yes there is so far no sEEG option in plot_alignment see:

https://github.com/mne-tools/mne-python/blob/master/mne/viz/_3d.py#L537

also you can set the coordinate frame to mri to have the same coordinate
system as pysurfer.

it's hard to help you more without having access to the data :frowning:

5

Thanks. It helps to know that I'm not missing something. The data is from a Brainstorm SEEG tutorial (http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity )

I can't tell that setting the coord_frame parameter in either channel.DigMontage or in viz.plot_alignment makes any difference

https://gist.github.com/lneisenman/c133e19c32faced76b9434f53dace7f6 (2nd file)

Larry

6

did you run freesurfer on this subject? these notebooks suggest you
used data from the MNE example?

7

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