[Mne_analysis] Resting state connectivity

Fri Feb 3 16:02:06 EST 2017

Noam,

can you tell me more about your use case? Why would you want to compute
connectivity for one window only? If you have some real-time application
you would need to create "mini-epochs" of a few samples and then aggregate
over them using the epochs-oriented API, but you would run into estimator
problems as all these measures scale get more stable with more trials.
With the existing API, single-trial connectivity does not seem easy to
realise.

Sheraz,
I have a power envelopes implementation on one of my MNE-Python branches
and plan to commit it soon after some final validation is done. Pinging me
on this may speed up things. But also here you would go across trials.

Avniel, yes that's a nice paper, they managed to put together some nice
materials and making explicit intuitions that had been circulating for
quite some time without tapping into the absolute CFC bashing game; indeed
they are rather constructive. I also liked their idea that the notion of
spurious CFC maybe spurious itself. If CFC is due to harmonics it would at
least suggest non-sinusoidal waveforms. Curious to see where this goes.
Denis

On Fri, Feb 3, 2017 at 9:49 PM Sheraz Khan, PhD <sheraz at nmr.mgh.harvard.edu>
wrote:

> Hi Noam,
>
> Did you try envelope correlations or its flavors like orthogonal
> correlations (Hipp or Brookes) ?
>
> They are found to be most reliable for resting state connectivity.
>
> http://www.sciencedirect.com/science/article/pii/S1053811916301914
>
> HTH
>
> Sheraz
>
>
>
>
> > Yep, this is my problem :)
> > Do you know any other approach for resting state connectivity?
> >
> > Thanks,
> > Noam
> > ________________________________
> > From: mne_analysis-bounces at nmr.mgh.harvard.edu
> > [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Denis-Alexander
> > Engemann [denis.engemann at gmail.com]
> > Sent: Friday, February 03, 2017 2:22 PM
> > To: Discussion and support forum for the users of MNE Software
> > Subject: Re: [Mne_analysis] Resting state connectivity
> >
> > Ah no the assumption here is that you aggregate over trials. If you just
> > send one window you cannot get a meaningful score.
> >
> > On Fri, Feb 3, 2017 at 8:13 PM Peled, Noam
> > <NPELED at mgh.harvard.edu<mailto:NPELED at mgh.harvard.edu>> wrote:
> > Hey Denis!
> > Thanks for the answer!
> > My problem isn't creating the events (actually I didn't know about this
> > function and now I can delete the code I wrote for that), but how to send
> > one window to the mne.connectivity.spectral_connectivity (one of the PLI
> > methods) without getting all zeros or nans.
> >
> > Thanks,
> > Noam
> > ________________________________
> > From:
> > mne_analysis-bounces at nmr.mgh.harvard.edu<mailto:
> mne_analysis-bounces at nmr.mgh.harvard.edu>
> > [mne_analysis-bounces at nmr.mgh.harvard.edu<mailto:
> mne_analysis-bounces at nmr.mgh.harvard.edu>]
> > on behalf of Denis-Alexander Engemann
> > [denis.engemann at gmail.com<mailto:denis.engemann at gmail.com>]
> > Sent: Friday, February 03, 2017 1:51 PM
> > To: Discussion and support forum for the users of MNE Software
> > ý[mne_analysis at nmr.mgh.harvard.edu<mailto:
> mne_analysis at nmr.mgh.harvard.edu>]ý
> > Subject: Re: [Mne_analysis] Resting state connectivity
> >
> > Hi Noam,
> >
> > checkout `mne.make_fixed_length_events`,
> >
> > Denis
> >
> > On Fri, Feb 3, 2017 at 7:50 PM Peled, Noam
> > <NPELED at mgh.harvard.edu<mailto:NPELED at mgh.harvard.edu>> wrote:
> > Hey all,
> > What is the best approach for resting state connectivity analysis?
> > It seems that mne.connectivity.spectral_connectivity is design for evoked
> > data.
> > In resting state, the different 'epochs' are sliding windows in time, so
> > for each calculation I can send only one epoch, which yields to zeros
> > (pli2_unbiased).
> >
> > Thanks,
> > Noam
> >
> >
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>
> -------------------------
> Sheraz Khan, M.Eng, Ph.D.
> Instructor in Neurology
>
> Athinoula A. Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Harvard Medical School
>
> McGovern Institute for Brain Research
> Massachusetts Institute of Technology
>
> Tel:   +1 617-643-5634 <+1%20617-643-5634>
> Fax:   +1 617-948-5966 <+1%20617-948-5966>
> Email: sheraz at nmr.mgh.harvard.edu
>        sheraz at mit.edu
> Web:   http://sheraz.mit.edu
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