[Mne_analysis] Connectivity calculation using PLI

[Denis-Alexander Engemann]

        External Email - Use Caution        

Hi Fleur,

our spectral connectivity code does not implement single-trial
connectivity, it implements phase statistics across trials.
If you want source-level connectivity, you need epochs in source space.
To do that in a memory-efficient manner, you can use
`return_generator=True` in
https://mne.tools/dev/generated/mne.minimum_norm.apply_inverse_epochs.html
and then for loop by source localizing one epoch at a time.

Best,
Denis

On Fri, Mar 6, 2020 at 11:30 AM Fleur GAUDFERNAU
<fleur.gaudfernau at pasteur.fr> wrote:
>
>         External Email - Use Caution
>
> Hello,
>
> Thanks a lot for your help!
>
> I actually want to z score connectivities for each subject. Is there a way to compute connectivity for each epoch in the source space? (I mean: a more efficient way than iterating over all epochs)
>
> ________________________________
> De : mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> de la part de Alexandre Gramfort <alexandre.gramfort at inria.fr>
> Envoyé : mercredi 4 mars 2020 20:08:09
> À : Discussion and support forum for the users of MNE Software
> Objet : Re: [Mne_analysis] Connectivity calculation using PLI
>
>         External Email - Use Caution
>
> hi Fleur,
>
> you cannot really transfer PLI from sensor to source. You need to estimate
> PLI directly in source space eg using parcels.
>
> here an example
>
> https://mne.tools/stable/auto_examples/connectivity/plot_mne_inverse_label_connectivity.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-label-connectivity-py
>
> or
>
> https://mne.tools/stable/auto_examples/connectivity/plot_mne_inverse_psi_visual.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-psi-visual-py
>
> note that the choice of the parcellation and metric has been the topic
> of many papers
> with various recommendations.
>
> HTH
> Alex
>
> On Wed, Mar 4, 2020 at 11:35 AM Fleur GAUDFERNAU
> <fleur.gaudfernau at pasteur.fr> wrote:
> >
> >         External Email - Use Caution
> >
> > Hi,
> >
> > I want to compute connectivity between sources using the PLI metric.
> > As far as I understand it, PLI is computed at the electrode level and
> > not at the source level. Does anyone know how to transform the
> > connectivity matrix between channels into a connectivity matrix
> > between sources? (I've looked at the inverse operator but I have no
> > idea how to apply it to the connectivity matrix).
> >
> > Thanks,
> >
> > Fleur
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis