[Mne_analysis] Mne_analysis Digest, Vol 145, Issue 15

sudhakar Mishra rs163 at iiita.ac.in
Mon Feb 10 10:52:17 EST 2020
Search archives:

        External Email - Use Caution        

Hi,

Actually, I implemented PLV using hilbert transform as per the method
mentioned in [Bruña, R., Maestú, F., & Pereda, E. (2018). Phase locking
value revisited: teaching new tricks to an old dog. *Journal of neural
engineering*, *15*(5), 056011.] for single Epoch.

Thanks,
Sudhakar Mishra
Research Scholar
IIIT-Allahabad
Website <https://modelingemotion.wixsite.com/emotion>


Is the nothingness lack of differentiation?
*सर्वद्वारेषु देहेऽस्मिन्प्रकाश उपजायते । ज्ञानं यदा तदा विद्याद्विवृद्धं
सत्त्वमित्युत ॥*
*श्रद्धावाँल्लभते ज्ञानं तत्परः संयतेन्द्रियः। ज्ञानं लब्ध्वा परां
शान्तिमचिरेणाधिगच्छति।।*
*योगश्चित्तवृत्तिनिरोधः*


On Mon, Feb 10, 2020 at 9:18 PM <mne_analysis-request at nmr.mgh.harvard.edu>
wrote:

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> Today's Topics:
>
>    1. Re: spectral_connectivity function in MNE Python Library
>       (Bear, Joshua)
>    2. Re: Mne_analysis Digest, Vol 145, Issue 14 (sudhakar Mishra)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 10 Feb 2020 15:44:45 +0000
> From: "Bear, Joshua" <JOSHUA.BEAR at cuanschutz.edu>
> Subject: Re: [Mne_analysis] spectral_connectivity function in MNE
>         Python Library
> To: Discussion and support forum for the users of MNE Software
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID: <0DE8333A-8BDA-49B0-969C-A8BB0D156AAF at cuanschutz.edu>
> Content-Type: text/plain; charset="utf-8"
>
>         External Email - Use Caution
>
> 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:
> >
> >        External Email - Use Caution
> >
> > 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:
> >>
> >>       External Email - Use Caution
> >>
> >> 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:
> >>>
> >>>      External Email - Use Caution
> >>>
> >>> 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:
> >>>>
> >>>>      External Email - Use Caution
> >>>>
> >>>>
> >>>> 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?
> >>>> ???????????? ????????????????? ??????? ? ?????? ??? ???
> ???????????????? ????????????? ?
> >>>> ???????????????? ?????? ?????? ?????????????? ?????? ??????? ????
> ???????????????????????
> >>>> ??????????????????????
> >>>>
> <plot_sensor_connectivity.py>_______________________________________________
> >>>> Mne_analysis mailing list
> >>>> Mne_analysis at nmr.mgh.harvard.edu
> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>>
> >>>
> >>> _______________________________________________
> >>> Mne_analysis mailing list
> >>> Mne_analysis at nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >>
> >> _______________________________________________
> >> Mne_analysis mailing list
> >> Mne_analysis at nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 10 Feb 2020 21:17:16 +0530
> From: sudhakar Mishra <rs163 at iiita.ac.in>
> Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 145, Issue 14
> To: mne_analysis at nmr.mgh.harvard.edu
> Message-ID:
>         <CAPVJSdcgBiek_wvnqN3b=
> 1+OWJwGj5hTP0-J2_9jHXfaw+cywA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
>         External Email - Use Caution
>
> Thanks for responding.
>
> Sudhakar Mishra
> Research Scholar
> IIIT-Allahabad
> Website <https://modelingemotion.wixsite.com/emotion>
>
>
> Is the nothingness lack of differentiation?
> *???????????? ????????????????? ??????? ? ?????? ??? ??? ????????????????
> ????????????? ?*
> *???????????????? ?????? ?????? ?????????????? ?????? ??????? ????
> ???????????????????????*
> *??????????????????????*
>
>
> On Mon, Feb 10, 2020 at 9:02 PM <mne_analysis-request at nmr.mgh.harvard.edu>
> wrote:
>
> > Send Mne_analysis mailing list submissions to
> >         mne_analysis at nmr.mgh.harvard.edu
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >         https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > or, via email, send a message with subject or body 'help' to
> >         mne_analysis-request at nmr.mgh.harvard.edu
> >
> > You can reach the person managing the list at
> >         mne_analysis-owner at nmr.mgh.harvard.edu
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Mne_analysis digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: spectral_connectivity function in MNE Python Library
> >       (Denis A. Engemann)
> >    2. Re: spectral_connectivity function in MNE Python Library
> >       (Bear, Joshua)
> >    3. Re: spectral_connectivity function in MNE Python Library
> >       (Denis A. Engemann)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 10 Feb 2020 11:37:24 +0100
> > From: "Denis A. Engemann" <denis-alexander.engemann at inria.fr>
> > Subject: Re: [Mne_analysis] spectral_connectivity function in MNE
> >         Python Library
> > To: Discussion and support forum for the users of MNE Software
> >         <mne_analysis at nmr.mgh.harvard.edu>
> > Message-ID: <3511B9F2-61DA-49EA-A76F-336D692487F0 at inria.fr>
> > Content-Type: text/plain; charset="utf-8"
> >
> >         External Email - Use Caution
> >
> > 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:
> > >
> > >         External Email - Use Caution
> > >
> > >
> > > 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?
> > > ???????????? ????????????????? ??????? ? ?????? ??? ???
> ????????????????
> > ????????????? ?
> > > ???????????????? ?????? ?????? ?????????????? ?????? ??????? ????
> > ???????????????????????
> > > ??????????????????????
> > >
> >
> <plot_sensor_connectivity.py>_______________________________________________
> > > Mne_analysis mailing list
> > > Mne_analysis at nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 10 Feb 2020 14:51:09 +0000
> > From: "Bear, Joshua" <JOSHUA.BEAR at cuanschutz.edu>
> > Subject: Re: [Mne_analysis] spectral_connectivity function in MNE
> >         Python Library
> > To: Discussion and support forum for the users of MNE Software
> >         <mne_analysis at nmr.mgh.harvard.edu>
> > Message-ID: <3693595F-E23D-44F7-99E6-1785BD4580DA at cuanschutz.edu>
> > Content-Type: text/plain; charset="utf-8"
> >
> >         External Email - Use Caution
> >
> > 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:
> > >
> > >        External Email - Use Caution
> > >
> > > 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:
> > >>
> > >>        External Email - Use Caution
> > >>
> > >>
> > >> 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?
> > >> ???????????? ????????????????? ??????? ? ?????? ??? ???
> > ???????????????? ????????????? ?
> > >> ???????????????? ?????? ?????? ?????????????? ?????? ??????? ????
> > ???????????????????????
> > >> ??????????????????????
> > >>
> >
> <plot_sensor_connectivity.py>_______________________________________________
> > >> Mne_analysis mailing list
> > >> Mne_analysis at nmr.mgh.harvard.edu
> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >
> > >
> > > _______________________________________________
> > > Mne_analysis mailing list
> > > Mne_analysis at nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Mon, 10 Feb 2020 16:31:23 +0100
> > From: "Denis A. Engemann" <denis-alexander.engemann at inria.fr>
> > Subject: Re: [Mne_analysis] spectral_connectivity function in MNE
> >         Python Library
> > To: Discussion and support forum for the users of MNE Software
> >         <mne_analysis at nmr.mgh.harvard.edu>
> > Message-ID: <B3CAB11D-8094-4CDA-B116-CD9479C0B7F7 at inria.fr>
> > Content-Type: text/plain; charset="utf-8"
> >
> >         External Email - Use Caution
> >
> > 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:
> > >
> > >        External Email - Use Caution
> > >
> > > 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:
> > >>
> > >>       External Email - Use Caution
> > >>
> > >> 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:
> > >>>
> > >>>       External Email - Use Caution
> > >>>
> > >>>
> > >>> 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?
> > >>> ???????????? ????????????????? ??????? ? ?????? ??? ???
> > ???????????????? ????????????? ?
> > >>> ???????????????? ?????? ?????? ?????????????? ?????? ??????? ????
> > ???????????????????????
> > >>> ??????????????????????
> > >>>
> >
> <plot_sensor_connectivity.py>_______________________________________________
> > >>> Mne_analysis mailing list
> > >>> Mne_analysis at nmr.mgh.harvard.edu
> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >>
> > >>
> > >> _______________________________________________
> > >> Mne_analysis mailing list
> > >> Mne_analysis at nmr.mgh.harvard.edu
> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >
> > >
> > > _______________________________________________
> > > Mne_analysis mailing list
> > > Mne_analysis at nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> > End of Mne_analysis Digest, Vol 145, Issue 14
> > *********************************************
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