[Mne_analysis] Connectivity calculation using PLI

[Denis-Alexander Engemann]

        External Email - Use Caution        

Hi Fleur,

The code in spectral connectivity does not yield any meaningful
single-epoch results.
At this point, the only valid usage of the function is to compute
connectivity across trials.

Denis

On Mon, Mar 9, 2020 at 12:25 PM Fleur GAUDFERNAU
<fleur.gaudfernau at pasteur.fr> wrote:
>
>         External Email - Use Caution
>
> Hello,
>
> I tried source localizing one epoch at a time, and then computing connectivity for each epoch.
>
> However, when I average the connectivity matrices over epochs, I do not obtain the same matrix as the one obtained by computing directly connectivity over all epochs in source space. Connectivity matrices for one epoch are made only of 0 and 1.
>
> Is there something I'm missing ?
>
>
> ________________________________
> De : mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> de la part de Denis-Alexander Engemann <denis.engemann at gmail.com>
> Envoyé : vendredi 6 mars 2020 16:09:23
> 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,
>
> 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
> > >
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