[Mne_analysis] mne_browse_raw

Wed Nov 30 16:24:10 EST 2016

Certo, con piacere!

In my experience your values are a bit low, we typically use those for
rejection of EOG/ECG. So this is not what you want because your ICA is
supposed to learn EOG/ECG pattern by exposure to their corresponding
topographies.

Best,
Denis

On Wed, Nov 30, 2016 at 10:20 PM <pascarel at dima.unige.it> wrote:

> Ciao Denis,
>
> thks a lot, also for the useful links.
> I know quite well the webpage but I miss ever something :)
>
> In my experience, the dict(mag=4e-12, grad=4000e-13)
> works well, it is the first time I met this problem.
> I'll look to this tutorial.
>
> Thks again!
> best
> Annalisa
>
> Denis-Alexander Engemann <denis.engemann at gmail.com> ha scritto:
>
> > I see where you want to go. In my experience the values I recommended to
> > you work pretty well on many data. Just take a look at average EOG/ECG
> > artefact scales and then add some room above to make sure you don't
> reject
> > data because of biological artifacts you intend to regress out using ICA.
> > Have a look at the last section here:
> >
> http://martinos.org/mne/stable/auto_tutorials/plot_artifacts_detection.html
> >
> > Hope this helps,
> > Denis
> >
> > On Wed, Nov 30, 2016 at 4:25 PM <pascarel at dima.unige.it> wrote:
> >
> >> Hi Denis,
> >>
> >> thks for your fast response!
> >>
> >>
> >> >> RuntimeError: No clean segment found. Please consider updating your
> >> > rejection thresholds
> >> >
> >> > It means that your reject parameters are too strict. You want to make
> >> sure
> >> > that data segments contaminated by strong environmental magnetic
> fields
> >> are
> >> > ignored, but you don't want to reject ECG or EOG since these need to
> be
> >> > kept in order to find corresponding components.
> >> >
> >>
> >> Thks, I supposed it was related to the reject dict and
> >> I wonder if I could get this thresholds by inspecting the data
> >> but with raw.plot() I didn't see the MEG field amplitudes o.O
> >>
> >> I attached what I see by using raw.plot().
> >>
> >> >> Try dict(mag=5e-12, grad=5000e-13)
> >>
> >> I'll try with this dict!
> >>
> >> Thks again!
> >> best
> >> Annalisa
> >>
> >>
> >>
> >> > What is wrong with raw.plot()?
> >> > It should give you exactly what you want.
> >> >
> >> > I hope this helps,
> >> > Denis
> >> >
> >> > On Tue, Nov 29, 2016 at 11:56 PM <pascarel at dima.unige.it> wrote:
> >> >
> >> >> Dear Mne users,
> >> >>
> >> >> is there in MNE python a way to interactively plot
> >> >> the raw data as in mne_browse_raw?
> >> >>
> >> >> If I use raw.plot() is there a way to visualize the
> >> >> intensity of the magnetic field?
> >> >>
> >> >> I'm applying ICA to a raw dataset and I'm using this
> >> >> reject dict
> >> >> reject = dict(mag=4e-12, grad=4000e-13)
> >> >>
> >> >> but ICA doesn't perform and I get this message
> >> >>
> >> >> RuntimeError: No clean segment found. Please consider updating your
> >> >> rejection thresholds
> >> >>
> >> >> since I'm asking how inspect the raw data by MNE python to see how to
> >> set
> >> >> the reject thresholds.
> >> >>
> >> >> Thks!
> >> >> best
> >> >> Annalisa
> >> >>
> >> >>
> >> >> --
> >> >> Dott. Annalisa Pascarella
> >> >> Istituto per le Applicazioni del Calcolo "M. Picone"
> >> >> Consiglio Nazionale delle Ricerche
> >> >> Via dei Taurini 19, 00185 Roma (Italy)
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> >> >>
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> >> Dott. Annalisa Pascarella
> >> Istituto per le Applicazioni del Calcolo "M. Picone"
> >> Consiglio Nazionale delle Ricerche
> >> Via dei Taurini 19, 00185 Roma (Italy)
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> --
> Dott. Annalisa Pascarella
> Istituto per le Applicazioni del Calcolo "M. Picone"
> Consiglio Nazionale delle Ricerche
> Via dei Taurini 19, 00185 Roma (Italy)
> Ph.:+39-0649270946 <+39%2006%204927%200946>; Fax:+39-064404306
> <+39%2006%20440%204306>
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