[Mne_analysis] Sources and labels for reconstruct time course label from EEG

Victor Ferat victor.ferat at fcbg.ch
Wed Aug 14 08:43:41 EDT 2019
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Hi,

Thanks for you answer Eric,

If I understand well, in the connectivity source space exemple<https://martinos.org/mne/stable/auto_examples/connectivity/plot_mixed_source_space_connectivity.html#sphx-glr-auto-examples-connectivity-plot-mixed-source-space-connectivity-py>, the volume sources are not taken into account when using mne.extract_label_time_course<https://martinos.org/mne/stable/generated/mne.extract_label_time_course.html#mne.extract_label_time_course> ?
It may be confusing because in the previous exemple, we provide both Volume and Surface sources to compute the label time course.  If it's the case perhaps the name of the example is misleading as the connectivity is only evaluated on the surface source space.

About assigning label for volume source space, I proposed a workaround on this issue<https://github.com/mne-tools/mne-python/issues/6155>,

Thanks again,

Regards,
Victor<https://github.com/mne-tools/mne-python/issues/6155>
________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Eric Larson <larson.eric.d at gmail.com>
Sent: Tuesday, August 13, 2019 7:05 PM
To: Discussion and support forum for the users of MNE Software <mne_analysis at nmr.mgh.harvard.edu>
Subject: Re: [Mne_analysis] Sources and labels for reconstruct time course label from EEG


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    - Is it possible to create a volume source space which does not creates sources inside white matter ? ( I followed this exemple <https://martinos.org/mne/stable/auto_tutorials/source-modeling/plot_forward.html#sphx-glr-auto-tutorials-source-modeling-plot-forward-py> and had a look at the  API, but I didn't find a way to do what I want )

Implicitly, yes. You can choose which volume labels to use (and thus not include cortex), see for example https://mne.tools/dev/auto_examples/inverse/plot_mixed_source_space_inverse.html

    - When using mne.extract_label_time_course<https://martinos.org/mne/stable/generated/mne.extract_label_time_course.html#mne.extract_label_time_course> , how MNE assigns label for volume source space ? I'm working with a custom atlas,  should I use my specific atlas aparc+asef:mgz when setting the volume sources<https://martinos.org/mne/stable/generated/mne.setup_volume_source_space.html#mne.setup_volume_source_space> as volume label ?

We do not currently have an API for this so you'll need to write custom code. See the ongoing discussion (and some usable code snippets) in:

https://github.com/mne-tools/mne-python/issues/6278
https://github.com/mne-tools/mne-python/issues/6155

HTH,
Eric

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