[Mne_analysis] mne_browse_raw

Wed Nov 30 16:55:48 EST 2016

ok!

grazie del consiglio!:)

best,
Annalisa

Denis-Alexander Engemann <denis.engemann at gmail.com> ha scritto:

> 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)
>>>> >> Ph.:+39-0649270946 <+39%2006%204927%200946>
>> <+39%2006%204927%200946> <+39%2006%204927%200946>;
>>>> Fax:+39-064404306 <+39%2006%20440%204306> <+39%2006%20440%204306>
>>>> >> <+39%2006%20440%204306>
>>>> >>
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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> <+39%2006%204927%200946>;
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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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-- 
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; Fax:+39-064404306

----- Fine messaggio inoltrato. -----

-- 
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; Fax:+39-064404306
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Subject: Re: [Mne_analysis] mne_browse_raw
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