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

Eisenman, Lawrence leisenman at wustl.edu
Fri Jan 19 13:03:24 EST 2018
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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

-----Original Message-----
From: mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Alexandre Gramfort
Sent: Friday, January 19, 2018 3:09 AM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] how to use viz.plot_alignment() on SEEG data?

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

On Thu, Jan 18, 2018 at 12:08 AM, Eisenman, Lawrence <leisenman at wustl.edu> wrote:
> Hi all,
>
>
>
> Using the ECOG tutorial
> (https://martinos.org/mne/stable/auto_examples/visualization/plot_3d_t
> o_2d.html) 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
>
>
>
>
>
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