[Mne_analysis] spectral_connectivity function in MNE Python Library

[Bear, Joshua]

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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।।
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>> <plot_sensor_connectivity.py>_______________________________________________
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