<div dir="ltr">Noam, <div><br></div><div>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.<div><div>With the existing API, single-trial connectivity does not seem easy to realise.</div><div><br></div></div><div>Sheraz,<br></div><div>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.<br><div><br></div></div><div>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.</div><div>Denis</div></div></div><br><div class="gmail_quote"><div dir="ltr">On Fri, Feb 3, 2017 at 9:49 PM Sheraz Khan, PhD <<a href="mailto:sheraz@nmr.mgh.harvard.edu">sheraz@nmr.mgh.harvard.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Noam,<br class="gmail_msg">
<br class="gmail_msg">
Did you try envelope correlations or its flavors like orthogonal<br class="gmail_msg">
correlations (Hipp or Brookes) ?<br class="gmail_msg">
<br class="gmail_msg">
They are found to be most reliable for resting state connectivity.<br class="gmail_msg">
<br class="gmail_msg">
<a href="http://www.sciencedirect.com/science/article/pii/S1053811916301914" rel="noreferrer" class="gmail_msg" target="_blank">http://www.sciencedirect.com/science/article/pii/S1053811916301914</a><br class="gmail_msg">
<br class="gmail_msg">
HTH<br class="gmail_msg">
<br class="gmail_msg">
Sheraz<br class="gmail_msg">
<br class="gmail_msg">
<br class="gmail_msg">
<br class="gmail_msg">
<br class="gmail_msg">
> Yep, this is my problem :)<br class="gmail_msg">
> Do you know any other approach for resting state connectivity?<br class="gmail_msg">
><br class="gmail_msg">
> Thanks,<br class="gmail_msg">
> Noam<br class="gmail_msg">
> ________________________________<br class="gmail_msg">
> From: <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" class="gmail_msg" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a><br class="gmail_msg">
> [<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" class="gmail_msg" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a>] on behalf of Denis-Alexander<br class="gmail_msg">
> Engemann [<a href="mailto:denis.engemann@gmail.com" class="gmail_msg" target="_blank">denis.engemann@gmail.com</a>]<br class="gmail_msg">
> Sent: Friday, February 03, 2017 2:22 PM<br class="gmail_msg">
> To: Discussion and support forum for the users of MNE Software<br class="gmail_msg">
> Subject: Re: [Mne_analysis] Resting state connectivity<br class="gmail_msg">
><br class="gmail_msg">
> Ah no the assumption here is that you aggregate over trials. If you just<br class="gmail_msg">
> send one window you cannot get a meaningful score.<br class="gmail_msg">
><br class="gmail_msg">
> On Fri, Feb 3, 2017 at 8:13 PM Peled, Noam<br class="gmail_msg">
> <<a href="mailto:NPELED@mgh.harvard.edu" class="gmail_msg" target="_blank">NPELED@mgh.harvard.edu</a><mailto:<a href="mailto:NPELED@mgh.harvard.edu" class="gmail_msg" target="_blank">NPELED@mgh.harvard.edu</a>>> wrote:<br class="gmail_msg">
> Hey Denis!<br class="gmail_msg">
> Thanks for the answer!<br class="gmail_msg">
> My problem isn't creating the events (actually I didn't know about this<br class="gmail_msg">
> function and now I can delete the code I wrote for that), but how to send<br class="gmail_msg">
> one window to the mne.connectivity.spectral_connectivity (one of the PLI<br class="gmail_msg">
> methods) without getting all zeros or nans.<br class="gmail_msg">
><br class="gmail_msg">
> Thanks,<br class="gmail_msg">
> Noam<br class="gmail_msg">
> ________________________________<br class="gmail_msg">
> From:<br class="gmail_msg">
> <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" class="gmail_msg" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a><mailto:<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" class="gmail_msg" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a>><br class="gmail_msg">
> [<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" class="gmail_msg" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a><mailto:<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" class="gmail_msg" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a>>]<br class="gmail_msg">
> on behalf of Denis-Alexander Engemann<br class="gmail_msg">
> [<a href="mailto:denis.engemann@gmail.com" class="gmail_msg" target="_blank">denis.engemann@gmail.com</a><mailto:<a href="mailto:denis.engemann@gmail.com" class="gmail_msg" target="_blank">denis.engemann@gmail.com</a>>]<br class="gmail_msg">
> Sent: Friday, February 03, 2017 1:51 PM<br class="gmail_msg">
> To: Discussion and support forum for the users of MNE Software<br class="gmail_msg">
> ý[<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" class="gmail_msg" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a><mailto:<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" class="gmail_msg" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a>>]ý<br class="gmail_msg">
> Subject: Re: [Mne_analysis] Resting state connectivity<br class="gmail_msg">
><br class="gmail_msg">
> Hi Noam,<br class="gmail_msg">
><br class="gmail_msg">
> checkout `mne.make_fixed_length_events`,<br class="gmail_msg">
><br class="gmail_msg">
> Denis<br class="gmail_msg">
><br class="gmail_msg">
> On Fri, Feb 3, 2017 at 7:50 PM Peled, Noam<br class="gmail_msg">
> <<a href="mailto:NPELED@mgh.harvard.edu" class="gmail_msg" target="_blank">NPELED@mgh.harvard.edu</a><mailto:<a href="mailto:NPELED@mgh.harvard.edu" class="gmail_msg" target="_blank">NPELED@mgh.harvard.edu</a>>> wrote:<br class="gmail_msg">
> Hey all,<br class="gmail_msg">
> What is the best approach for resting state connectivity analysis?<br class="gmail_msg">
> It seems that mne.connectivity.spectral_connectivity is design for evoked<br class="gmail_msg">
> data.<br class="gmail_msg">
> In resting state, the different 'epochs' are sliding windows in time, so<br class="gmail_msg">
> for each calculation I can send only one epoch, which yields to zeros<br class="gmail_msg">
> (pli2_unbiased).<br class="gmail_msg">
><br class="gmail_msg">
> Thanks,<br class="gmail_msg">
> Noam<br class="gmail_msg">
><br class="gmail_msg">
><br class="gmail_msg">
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<br class="gmail_msg">
<br class="gmail_msg">
-------------------------<br class="gmail_msg">
Sheraz Khan, M.Eng, Ph.D.<br class="gmail_msg">
Instructor in Neurology<br class="gmail_msg">
<br class="gmail_msg">
Athinoula A. Martinos Center for Biomedical Imaging<br class="gmail_msg">
Massachusetts General Hospital<br class="gmail_msg">
Harvard Medical School<br class="gmail_msg">
<br class="gmail_msg">
McGovern Institute for Brain Research<br class="gmail_msg">
Massachusetts Institute of Technology<br class="gmail_msg">
<br class="gmail_msg">
Tel: <a href="tel:+1%20617-643-5634" value="+16176435634" class="gmail_msg" target="_blank">+1 617-643-5634</a><br class="gmail_msg">
Fax: <a href="tel:+1%20617-948-5966" value="+16179485966" class="gmail_msg" target="_blank">+1 617-948-5966</a><br class="gmail_msg">
Email: <a href="mailto:sheraz@nmr.mgh.harvard.edu" class="gmail_msg" target="_blank">sheraz@nmr.mgh.harvard.edu</a><br class="gmail_msg">
<a href="mailto:sheraz@mit.edu" class="gmail_msg" target="_blank">sheraz@mit.edu</a><br class="gmail_msg">
Web: <a href="http://sheraz.mit.edu" rel="noreferrer" class="gmail_msg" target="_blank">http://sheraz.mit.edu</a><br class="gmail_msg">
_______________________________________________<br class="gmail_msg">
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</blockquote></div>