[Mne_analysis] spectral_connectivity function in MNE Python Library

Bear, Joshua JOSHUA.BEAR at cuanschutz.edu
Mon Feb 10 10:44:45 EST 2020
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That makes sense. Thank you for those clarifications!

Best,
Josh





Joshua Bear, MD, MA | Assistant Professor, Pediatric Neurology and Epilepsy
University of Colorado and Children’s Hospital Colorado
13123 East 16th Avenue, Box B-155 | Aurora, CO 80045 | Phone: 720-777-6138 | Fax: 720-777-7285 

> On Feb 10, 2020, at 8:31 AM, Denis A. Engemann <denis-alexander.engemann at inria.fr> wrote:
> 
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> 
> Hi,
> 
> I think there are two things going on here.
> 
> Our function does support resting-state analysis by considering equally spaced peudo-epochs with or without overlap.
> But computing a value for one single trial is not implemented by our function as it is now.
> The averaging implied in the expectations that you find in the notations inside the documentation is indeed phase-locking across epochs,
> not averaging across time.
> To support a variant that gives you meaningful outputs in single-epoch mode, e.g., slimilar to a single-trial correlation or covariance matrix, the could would need to be extended.
> It's perhaps worthwhile to open a related issue on github.
> 
> Denis
> 
>> On Feb 10, 2020, at 3:51 PM, Bear, Joshua <JOSHUA.BEAR at cuanschutz.edu> wrote:
>> 
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>> Hi Denis and Sudhakar, 
>> 
>> This is an interesting point. Sudhakar, depending on which spectral connectivity method you are using, you can pass it a single epoch as a list of length 1, i.e. [epoch], to get a matrix of values.
>> 
>> Denis, several of these connectivity methods have been used to meaningful effect on single epochs of resting state data (see, for example, Englot et al., Brain, 2016, using imaginary coherence). Is there something specific about MNE’s implementation that would make it less reliable for resting state data calculations, or is this more a debate of the utility of resting state information in the first place? 
>> 
>> FWIW, I would favor throwing a warning rather than an error since people (myself included) might intentionally use a single epoch if there isn’t some reason why MNE’s implementation is different from others. 
>> 
>> Thanks,
>> Josh
>> 
>> 
>> 
>> 
>> 
>> Joshua Bear, MD, MA | Assistant Professor, Pediatric Neurology and Epilepsy
>> University of Colorado and Children’s Hospital Colorado
>> 13123 East 16th Avenue, Box B-155 | Aurora, CO 80045 | Phone: 720-777-6138 | Fax: 720-777-7285 
>> 
>>> On Feb 10, 2020, at 3:37 AM, Denis A. Engemann <denis-alexander.engemann at inria.fr> wrote:
>>> 
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>>> 
>>> Hi Sudhakar,
>>> 
>>> what you experience is expected as the spectral connectivity metrics implemented in that function are defined as statistics across epochs/trials.
>>> See notes here: https://mne.tools/stable/generated/mne.connectivity.spectral_connectivity.html
>>> 
>>> We should probably include a warning or even throw an error in when a single epoch is passed.
>>> I’d  be even careful  when using only few epochs.
>>> You need data to estimate these metrics.
>>> 
>>> Hope that helps,
>>> Denis
>>> 
>>>> On Feb 8, 2020, at 2:40 PM, sudhakar Mishra <rs163 at iiita.ac.in> wrote:
>>>> 
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>>>> 
>>>> 
>>>> Hi all,
>>>> 
>>>> I am using MNE library for cross confirming my results on connectivity. While using the library I noticed something peculiar. When I provide data with more than one epoch the spectral_connectivity function seems to work fine. But, when the data with only one epoch is provided, I get the connectivity matrix with all one in the lower triangle. I am unable to comprehend the issue. Please help me with this.
>>>> 
>>>> For your reference I am providing the modified example taken from the website only.
>>>> 
>>>> Looking eagerly for your reply.
>>>> 
>>>> Thanks,
>>>> Sudhakar Mishra
>>>> Research Scholar
>>>> IIIT-Allahabad
>>>> Website
>>>> 
>>>> 
>>>> Is the nothingness lack of differentiation?
>>>> सर्वद्वारेषु देहेऽस्मिन्प्रकाश उपजायते । ज्ञानं यदा तदा विद्याद्विवृद्धं सत्त्वमित्युत ॥
>>>> श्रद्धावाँल्लभते ज्ञानं तत्परः संयतेन्द्रियः। ज्ञानं लब्ध्वा परां शान्तिमचिरेणाधिगच्छति।।
>>>> योगश्चित्तवृत्तिनिरोधः
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