[Mne_analysis] Mne_analysis Digest, Vol 150, Issue 16

Abdallah Qusaibe abdallah.qusaibe at gmail.com
Thu Jul 9 11:03:21 EDT 2020
Search archives:

        External Email - Use Caution        

Thank you Alex,

Thank you so much @sylvain <https://neuroimage.usc.edu/forums/u/sylvain>,
Infact I just found it in mne VERY INTERESTING!
but I do not know how can I switch now to mne (because I am dealing with
BST),

With BST I just modified the channel (by exporting it to matlab and make
some modification)
the issue as i see that mne accept fif file and BST do not export to fif
file.
and I do not know how I can modify the channel in mne,

On Thu, 9 Jul 2020 at 16:40, <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: Average over channels (Alexandre Gramfort)
>    2. Sensitivity of MEG and EEG to Source Orientation
>       (Abdallah Qusaibe)
>    3. Re: Sensitivity of MEG and EEG to Source Orientation
>       (Alexandre Gramfort)
>    4. Re: mn.time_frequency.tfr_array_stockwell (Alexandre Gramfort)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 9 Jul 2020 13:26:43 +0200
> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> Subject: Re: [Mne_analysis] Average over channels
> To: Discussion and support forum for the users of MNE Software
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
>         <CADeotZreg3GTtTf0-SRnEKgSGNmNidLrmrjPkYs=
> y2MEvo5ZwQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
>         External Email - Use Caution
>
> hi,
>
> yes create an issue to we can exchange ideas more easily
>
> thx
>
> A
>
> On Thu, Jul 9, 2020 at 12:30 PM Johann Benerradi
> <Johann.Benerradi at nottingham.ac.uk> wrote:
> >
> >         External Email - Use Caution
> >
> > Hi Alex,
> >
> > Alright, thank you. Is that something users would be interested in, and
> worth creating a GitHub issue for feature request? I personally would like
> to do such a thing to average channels by ROI before classification with
> fNIRS (in addition to having this for visualisation)... I can eventually
> work on an implementation, but as for now I'll keep doing this with
> get_data() and np.mean().
> >
> > Thanks,
> > Johann
> > ________________________________
> > From: mne_analysis-bounces at nmr.mgh.harvard.edu <
> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Alexandre Gramfort
> <alexandre.gramfort at inria.fr>
> > Sent: 09 July 2020 07:47
> > To: Discussion and support forum for the users of MNE Software <
> mne_analysis at nmr.mgh.harvard.edu>
> > Subject: Re: [Mne_analysis] Average over channels
> >
> >         External Email - Use Caution
> >
> > hi Johann,
> >
> > no it's not possible presently.
> >
> > you can group channel when plotting though
> >
> >
> https://mne.tools/stable/generated/mne.viz.plot_compare_evokeds.html#mne.viz.plot_compare_evokeds
> >
> > Alex
> >
> > On Wed, Jul 8, 2020 at 11:43 PM Johann Benerradi
> > <Johann.Benerradi at nottingham.ac.uk> wrote:
> > >
> > >         External Email - Use Caution
> > >
> > > Hello MNE users,
> > >
> > > I was wondering if there is an easy way to do an average over channels
> on a Raw or Epochs object. I've seen a few plotting functions with a
> "combine" parameter but is it possible to create a new Raw/Epochs object
> with combined channels (for example a new object with pseudo-channels
> representing ROIs)? I would like to avoid extracting a data array and doing
> it with NumPy if there is easier...
> > >
> > > Thanks a lot!
> > >
> > > Best wishes,
> > >
> > > Johann Benerradi
> > > -------------------------
> > > PhD Student
> > > School of Computer Science
> > > University of Nottingham, UK
> > > -------------------------
> > > https://hanbnrd.gitlab.io/
> > >
> > >
> > > This message and any attachment are intended solely for the addressee
> > > and may contain confidential information. If you have received this
> > > message in error, please contact the sender and delete the email and
> > > attachment.
> > >
> > > Any views or opinions expressed by the author of this email do not
> > > necessarily reflect the views of the University of Nottingham. Email
> > > communications with the University of Nottingham may be monitored
> > > where permitted by law.
> > >
> > >
> > >
> > > _______________________________________________
> > > 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
> >
> > This message and any attachment are intended solely for the addressee
> > and may contain confidential information. If you have received this
> > message in error, please contact the sender and delete the email and
> > attachment.
> >
> > Any views or opinions expressed by the author of this email do not
> > necessarily reflect the views of the University of Nottingham. Email
> > communications with the University of Nottingham may be monitored
> > where permitted by law.
> >
> >
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 9 Jul 2020 12:27:33 +0200
> From: Abdallah Qusaibe <abdallah.qusaibe at gmail.com>
> Subject: [Mne_analysis] Sensitivity of MEG and EEG to Source
>         Orientation
> To: mne_analysis at nmr.mgh.harvard.edu
> Message-ID:
>         <
> CAAj1RLs2uUnOy7++H1LpPg1eGgpW77h5q+888xrEnaEBSXJXjQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
>         External Email - Use Caution
>
> Dear All,
>
> Is there in mne tool, a function to measure the Sensitivity of MEG and EEG
> to Source Orientation?
>
> Best,
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200709/52c4c544/attachment-0001.html
>
> ------------------------------
>
> Message: 3
> Date: Thu, 9 Jul 2020 16:07:01 +0200
> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> Subject: Re: [Mne_analysis] Sensitivity of MEG and EEG to Source
>         Orientation
> To: Discussion and support forum for the users of MNE Software
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
>         <
> CADeotZr_9rCzSh1fw6cqtr3zDhZ3hqNnefZEfKxB0ayNgiG+SQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
>         External Email - Use Caution
>
> hi,
>
> you can have a look at:
>
> https://mne.tools/stable/generated/mne.sensitivity_map.html
>
> Alex
>
> On Thu, Jul 9, 2020 at 3:11 PM Abdallah Qusaibe
> <abdallah.qusaibe at gmail.com> wrote:
> >
> >         External Email - Use Caution
> >
> > Dear All,
> >
> > Is there in mne tool, a function to measure the Sensitivity of MEG and
> EEG to Source Orientation?
> >
> > Best,
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 9 Jul 2020 16:38:32 +0200
> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> Subject: Re: [Mne_analysis] mn.time_frequency.tfr_array_stockwell
> To: Discussion and support forum for the users of MNE Software
>         <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
>         <CADeotZr_ceXp5BPvhkf=bBR=
> fHR2_8v95okR+JUNJqBNh8+C2A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
>         External Email - Use Caution
>
> hi Paul,
>
> try:
>
> import numpy as np
> import mne
>
> raw = mne.io.read_raw_edf('/Users/fishbacp/Desktop/EEG_file.edf',
> preload=True)
> Fs = raw.info['sfreq']
> data, times=raw[:, :]
> signal = data[[0]]
> min_freq = 5
> max_freq = 100
> st_power, itc, freqs = mne.time_frequency.tfr_array_stockwell(signal,
> Fs, fmin=min_freq, fmax=max_freq)
>
> --
>
> signal must be a 2d array with dimensions: channel x time
>
> Alex
>
>
>
> ------------------------------
>
> _______________________________________________
> 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 150, Issue 16
> *********************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200709/0e5b8610/attachment-0001.html 


More information about the Mne_analysis mailing list