[Mne_analysis] Digitization and Channel Positions

Alexandre Gramfort alexandre.gramfort at inria.fr
Fri Sep 27 03:15:11 EDT 2019
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        External Email - Use Caution        

Dear Jason,

if you now use version 0.19 you should be using:

https://mne.tools/stable/generated/mne.channels.read_dig_polhemus_isotrak.html#mne.channels.read_dig_polhemus_isotrak

something like:

montage = mne.channels.read_dig_polhemus_isotrak(fname)
raw.set_montage(montage)

should just work. If not please open an issue on github

Alex


On Fri, Sep 27, 2019 at 12:50 AM Geller, Jason <jason-geller at uiowa.edu>
wrote:

>         External Email - Use Caution
>
> Hello,
>
> I am creating digitization montage files I obtained from a Polhemus system
> using the read_dig_montage and setting it with set_montage(rawfile,
> set_dig=True). When I go to run ICA, I get this warning:
>
> WARNING:root:Did not find any electrode locations (in the info object),
> will attempt to use digitization points instead. However, if digitization
> points do not correspond to the EEG electrodes, this will lead to bad
> results. Please verify that the sensor locations in the plot are accurate.
>
> My question is: how do I set the channel positions for a dig montage? Any
> help would be greatly appreciated.
>
> Thanks,
>
> J
>
>
> > On Sep 26, 2019, at 5:35 PM, mne_analysis-request at nmr.mgh.harvard.edu
> wrote:
> >
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> >
> > Today's Topics:
> >
> >   1. Re: mne.minimum_norm.compute_source_psd (Dan McCloy)
> >   2. Re: mne.minimum_norm.compute_source_psd (Vivek Sharma)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 26 Sep 2019 11:30:04 -0700
> > From: Dan McCloy <dan.mccloy at gmail.com>
> > Subject: Re: [Mne_analysis] mne.minimum_norm.compute_source_psd
> > To: Discussion and support forum for the users of MNE Software
> >       <mne_analysis at nmr.mgh.harvard.edu>
> > Message-ID:
> >       <CAOE0pYk7QJxJvsOD5QR1pg0HNObfDjnLh=
> CnCwB_roJ07DZt3A at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> >        External Email - Use Caution
> >
> > Ah, Victor is right.  Sorry Vivek for giving you the wrong advice; I
> looked
> > only at the repr of the object, which had a tmin, tmax, and tstep; I
> didn't
> > dig through the example that got you there.
> >
> > On Thu, Sep 26, 2019 at 3:30 AM Victor Ferat <victor.ferat at fcbg.ch>
> wrote:
> >
> >>        External Email - Use Caution
> >>
> >> It should be the number of frequencies.
> >> For each source (8064) you have 1025 values of power density, one per
> >> frequency . (frequencies ranging from 0 Hz to 100Hz with 97.65625mHz
> step).
> >> This tutorial
> >> <
> https://www.nmr.mgh.harvard.edu/mne/stable/auto_examples/time_frequency/plot_source_power_spectrum.html#sphx-glr-auto-examples-time-frequency-plot-source-power-spectrum-py
> >
> >> should help you understand how it works ( especially the last plot)
> >>
> >>
> >> Best,
> >> Victor
> >> ------------------------------
> >> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
> >> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Vivek Sharma <
> >> vivek.sharma1510 at gmail.com>
> >> *Sent:* Thursday, September 26, 2019 8:17 AM
> >> *To:* Discussion and support forum for the users of MNE Software <
> >> mne_analysis at nmr.mgh.harvard.edu>
> >> *Subject:* Re: [Mne_analysis] mne.minimum_norm.compute_source_psd
> >>
> >>
> >>        External Email - Use Caution
> >>
> >> The total time I have considered is 574 seconds so how it is related to
> >> 1025 time points.
> >>
> >> On Wed, Sep 25, 2019 at 8:46 PM Daniel McCloy <dan.mccloy at gmail.com>
> >> wrote:
> >>
> >>        External Email - Use Caution
> >>
> >> It is the number of time points.
> >>
> >> On September 25, 2019 2:27:52 AM PDT, Vivek Sharma <
> >> vivek.sharma1510 at gmail.com> wrote:
> >>>       External Email - Use Caution
> >>>
> >>> In continuation of the above thread, I unable to understand what does
> >>> 1025
> >>> mean in data shape.
> >>> <SourceEstimate  |  8064 vertices, subject : Collin, tmin : 0.0 (ms),
> >>> tmax
> >>> : 100000.0 (ms), tstep : 97.65625 (ms),
> >>> *data shape : (8064, 1025)>*
> >>>
> >>>
> >>> On Fri, Jun 14, 2019 at 4:33 PM Vivek Sharma
> >>> <vivek.sharma1510 at gmail.com>
> >>> wrote:
> >>>
> >>>> Thank You.
> >>>>
> >>>> On Wed, Jun 12, 2019 at 11:53 AM Alexandre Gramfort <
> >>>> alexandre.gramfort at inria.fr> wrote:
> >>>>
> >>>>>        External Email - Use Caution
> >>>>>
> >>>>> hi,
> >>>>>
> >>>>> this function hacks a SourceEstimate object : stc_psd to store PSDs.
> >>> So
> >>>>> what you read
> >>>>> with time:
> >>>>>
> >>>>> <SourceEstimate  |  8064 vertices, subject : Collin, tmin : 0.0
> >>> (ms),
> >>>>> tmax : 100000.0 (ms), tstep : 97.65625 (ms), data shape : (8064,
> >>> 1025)>
> >>>>>
> >>>>> should be:
> >>>>>
> >>>>> <SourceEstimate  |  8064 vertices, subject : Collin, fmin : 0.0
> >>> (Hz),
> >>>>> fmax : 100000.0 (mHz), fstep : 97.65625 (mHz), data shape : (8064,
> >>> 1025)>
> >>>>>
> >>>>> HTH
> >>>>> Alex
> >>>>>
> >>>>> _______________________________________________
> >>>>> Mne_analysis mailing list
> >>>>> Mne_analysis at nmr.mgh.harvard.edu
> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Vivek Sharma
> >>>>
> >>>
> >>>
> >>> --
> >>> Vivek Sharma
> >>
> >> _______________________________________________
> >> Mne_analysis mailing list
> >> Mne_analysis at nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >>
> >>
> >> --
> >> Vivek Sharma
> >> _______________________________________________
> >> Mne_analysis mailing list
> >> Mne_analysis at nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 27 Sep 2019 04:05:30 +0530
> > From: Vivek Sharma <vivek.sharma1510 at gmail.com>
> > Subject: Re: [Mne_analysis] mne.minimum_norm.compute_source_psd
> > To: Discussion and support forum for the users of MNE Software
> >       <mne_analysis at nmr.mgh.harvard.edu>
> > Message-ID:
> >       <CAKzh67FKy0ShTSUCEO496cZF7K-7QJbzNT6fmKC_7=
> KVY6v31Q at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> >        External Email - Use Caution
> >
> > Hi,
> > Thanks for the information.
> >
> > On Fri, Sep 27, 2019 at 12:00 AM Dan McCloy <dan.mccloy at gmail.com>
> wrote:
> >
> >>        External Email - Use Caution
> >>
> >> Ah, Victor is right.  Sorry Vivek for giving you the wrong advice; I
> >> looked only at the repr of the object, which had a tmin, tmax, and
> tstep; I
> >> didn't dig through the example that got you there.
> >>
> >> On Thu, Sep 26, 2019 at 3:30 AM Victor Ferat <victor.ferat at fcbg.ch>
> wrote:
> >>
> >>>        External Email - Use Caution
> >>>
> >>> It should be the number of frequencies.
> >>> For each source (8064) you have 1025 values of power density, one per
> >>> frequency . (frequencies ranging from 0 Hz to 100Hz with 97.65625mHz
> step).
> >>> This tutorial
> >>> <
> https://www.nmr.mgh.harvard.edu/mne/stable/auto_examples/time_frequency/plot_source_power_spectrum.html#sphx-glr-auto-examples-time-frequency-plot-source-power-spectrum-py
> >
> >>> should help you understand how it works ( especially the last plot)
> >>>
> >>>
> >>> Best,
> >>> Victor
> >>> ------------------------------
> >>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
> >>> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Vivek Sharma <
> >>> vivek.sharma1510 at gmail.com>
> >>> *Sent:* Thursday, September 26, 2019 8:17 AM
> >>> *To:* Discussion and support forum for the users of MNE Software <
> >>> mne_analysis at nmr.mgh.harvard.edu>
> >>> *Subject:* Re: [Mne_analysis] mne.minimum_norm.compute_source_psd
> >>>
> >>>
> >>>        External Email - Use Caution
> >>>
> >>> The total time I have considered is 574 seconds so how it is related to
> >>> 1025 time points.
> >>>
> >>> On Wed, Sep 25, 2019 at 8:46 PM Daniel McCloy <dan.mccloy at gmail.com>
> >>> wrote:
> >>>
> >>>        External Email - Use Caution
> >>>
> >>> It is the number of time points.
> >>>
> >>> On September 25, 2019 2:27:52 AM PDT, Vivek Sharma <
> >>> vivek.sharma1510 at gmail.com> wrote:
> >>>>       External Email - Use Caution
> >>>>
> >>>> In continuation of the above thread, I unable to understand what does
> >>>> 1025
> >>>> mean in data shape.
> >>>> <SourceEstimate  |  8064 vertices, subject : Collin, tmin : 0.0 (ms),
> >>>> tmax
> >>>> : 100000.0 (ms), tstep : 97.65625 (ms),
> >>>> *data shape : (8064, 1025)>*
> >>>>
> >>>>
> >>>> On Fri, Jun 14, 2019 at 4:33 PM Vivek Sharma
> >>>> <vivek.sharma1510 at gmail.com>
> >>>> wrote:
> >>>>
> >>>>> Thank You.
> >>>>>
> >>>>> On Wed, Jun 12, 2019 at 11:53 AM Alexandre Gramfort <
> >>>>> alexandre.gramfort at inria.fr> wrote:
> >>>>>
> >>>>>>        External Email - Use Caution
> >>>>>>
> >>>>>> hi,
> >>>>>>
> >>>>>> this function hacks a SourceEstimate object : stc_psd to store PSDs.
> >>>> So
> >>>>>> what you read
> >>>>>> with time:
> >>>>>>
> >>>>>> <SourceEstimate  |  8064 vertices, subject : Collin, tmin : 0.0
> >>>> (ms),
> >>>>>> tmax : 100000.0 (ms), tstep : 97.65625 (ms), data shape : (8064,
> >>>> 1025)>
> >>>>>>
> >>>>>> should be:
> >>>>>>
> >>>>>> <SourceEstimate  |  8064 vertices, subject : Collin, fmin : 0.0
> >>>> (Hz),
> >>>>>> fmax : 100000.0 (mHz), fstep : 97.65625 (mHz), data shape : (8064,
> >>>> 1025)>
> >>>>>>
> >>>>>> HTH
> >>>>>> Alex
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Mne_analysis mailing list
> >>>>>> Mne_analysis at nmr.mgh.harvard.edu
> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Vivek Sharma
> >>>>>
> >>>>
> >>>>
> >>>> --
> >>>> Vivek Sharma
> >>>
> >>> _______________________________________________
> >>> Mne_analysis mailing list
> >>> Mne_analysis at nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>>
> >>>
> >>>
> >>> --
> >>> Vivek Sharma
> >>> _______________________________________________
> >>> 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
> >
> >
> >
> > --
> > Vivek Sharma
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