[Mne_analysis] Mne_analysis Digest, Vol 143, Issue 14

Sophie Herbst ksherbst at googlemail.com
Thu Dec 19 05:50:42 EST 2019
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        External Email - Use Caution        

Thank you, Denis & Alex for your quick replies!
What we were trying to clarify is whether adding ssp-projections computed
from emptyrooms
to Neuromag data to which Maxfilter and SSS have been applied should have
additional benefits, theoretically and practically.
Related, a quick side question: the system-based projectors that appear in
the raw.fif after recording, are they just discarded during Maxfilter, or
have they been applied?

Thanks!
Sophie





On Thu, Dec 19, 2019 at 10:40 AM Denis A. Engemann <
denis-alexander.engemann at inria.fr> wrote:

>         External Email - Use Caution
>
> I would add: one single cardiac / occular SSP vector is often good enough
> and safe.
>
> For empty room SSS it really depends on your data. I think on some sites
> people include up to 16 vectors for the magnetometers.
> My impression is that empty room SSP is much less critical and being
> generous with it is not a bad idea.
> But always do plots to analyze the impact of your preprocessing.
>
> Denis
>
> > On 19 Dec 2019, at 10:32, Alexandre Gramfort <
> alexandre.gramfort at inria.fr> wrote:
> >
> >        External Email - Use Caution
> >
> > hi Harish,
> >
> > my suggestion is to look at the data before and after SSP, including the
> evoked
> > response. Pre-processing is all about increasing SNR so you need to
> remove noise
> > making sure that you don't loose too much signal by doing this.
> >
> > with mne you can use proj="interactive" option is evoked.plot to see how
> SSPs
> > affect the data. Make sure the projections are not already applied
> though.
> >
> > HTH
> > Alex
> >
> > On Thu, Dec 19, 2019 at 10:14 AM Harish Gunasekaran
> >
> > <ngharish18 at gmail.com> wrote:
> >>
> >>        External Email - Use Caution
> >>
> >> Hi Denis,
> >> Thanks for your reply. I am concerned about the empty room noise
> removal during the pre-processing stage (artifacts removal using SSP) as
> recommended in the MNE website (
> https://mne.tools/stable/auto_tutorials/preprocessing/plot_50_artifact_correction_ssp.html).
> Another related question: How to choose the number of noise components or
> projectors (empty room,ecg,eog) during artifact removal when using SSP? Is
> there any automated way or setting any threshold to automatically remove
> depending upon the subjects?
> >>
> >> Thanks in advance.
> >>
> >> Harish
> >>
> >>
> ------------------------------------------------------------------------------------------
> >> Harish Gunasekaran,
> >> NUMERICS Ph.D. fellow under Marie Skłodowska-Curie actions (2019-22),
> >> Cognition & Brain Dynamics team, Cognitive Neuroimaging Unit (UNICOG),
> >> NeuroSpin, CEA/DRF/Joliot, CEA Paris Saclay,
> >> Bât 145 PC 156 , Gif s/ Yvette F-91190 FRANCE.
> >>
> ------------------------------------------------------------------------------------------
> >>
> >>
> >>
> >>> On Wed, Dec 18, 2019 at 11:02 PM <
> mne_analysis-request at nmr.mgh.harvard.edu> wrote:
> >>>
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> >>>
> >>> Today's Topics:
> >>>
> >>>   1. using the command line interface of mne (Neeraj Sharma)
> >>>   2. Empty room SSP vs. Maxwell filtering (Harish Gunasekaran)
> >>>   3. Re: Empty room SSP vs. Maxwell filtering
> >>>      (Denis-Alexander Engemann)
> >>>
> >>>
> >>> ----------------------------------------------------------------------
> >>>
> >>> Message: 1
> >>> Date: Wed, 18 Dec 2019 13:50:16 -0500
> >>> From: Neeraj Sharma <neerajww at gmail.com>
> >>> Subject: [Mne_analysis] using the command line interface of mne
> >>> To: Mne_analysis at nmr.mgh.harvard.edu
> >>> Message-ID:
> >>>        <
> CACcKo1A9YbXnkXSUb9O1b7sQPmKq4hAXRYN2iAYVDSvy9QqcWg at mail.gmail.com>
> >>> Content-Type: text/plain; charset="utf-8"
> >>>
> >>>        External Email - Use Caution
> >>>
> >>> Hi Community,
> >>>
> >>> I am interested in doing some of the continuous-time data (that is,
> before
> >>> epoching) pre-processing using the command line interface. I am hoping
> this
> >>> will be less time consuming as it will use the C libraries (?)
> compared to
> >>> using the python functions with the code.
> >>> Can you help me with the functions available? I see the link here
> >>> https://mne.tools/stable/generated/commands.html but got some doubts
> in the
> >>> underlying functionality when the options are used.
> >>>
> >>> To start, I will like to do a bandpass filter of EEG data from 0.1 to
> 40
> >>> Hz. I see that there is the -filterorder option but does it use:
> >>> mne.filter.filter_data(data, Fs, l_freq, h_freq, picks=None,
> >>>                              filter_length='auto',
> >>> l_trans_bandwidth='auto',
> >>>                              h_trans_bandwidth='auto', n_jobs=1,
> >>> method='fir',
> >>>                              iir_params=None, copy=True, phase='zero',
> >>>                              fir_window='hamming', fir_design='firwin',
> >>> pad='reflect_limited', verbose=False)
> >>> If yes, then how can we specify the other arguments of the function,
> >>> especially, those related to phase delay.
> >>>
> >>>
> >>> Cheers,
> >>> Neeraj
> >>> -------------- next part --------------
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> >>> ------------------------------
> >>>
> >>> Message: 2
> >>> Date: Wed, 18 Dec 2019 19:52:12 +0100
> >>> From: Harish Gunasekaran <ngharish18 at gmail.com>
> >>> Subject: [Mne_analysis] Empty room SSP vs. Maxwell filtering
> >>> To: mne_analysis at nmr.mgh.harvard.edu
> >>> Message-ID:
> >>>        <
> CAGqhYKUAA3nCTJEuQaCwop97+zJwztsO278ZSpmQmrTdSjZBTA at mail.gmail.com>
> >>> Content-Type: text/plain; charset="utf-8"
> >>>
> >>>        External Email - Use Caution
> >>>
> >>> Dear Alex and Denis,
> >>> Could you tell us what is the importance of removing the empty room
> noise
> >>> component using SSP? Wouldn't the maxwell filtering remove the empty
> room
> >>> noise component by default?
> >>>
> >>> Thanks in advance,
> >>> Harish
> >>>
> >>>
> *------------------------------------------------------------------------------------------*
> >>> *Harish Gunasekaran,*
> >>> NUMERICS
> >>> <
> http://numerics.cea.fr/Pages/Numerics/Numerics%20program/Numerics-PhD.aspx
> >
> >>> Ph.D. fellow under Marie Sk?odowska-Curie actions (2019-22),
> >>> Cognition & Brain Dynamics team <https://brainthemind.com/team2/>,
> >>> Cognitive Neuroimaging Unit (UNICOG <http://www.unicog.org/site_2016/
> >),
> >>> NeuroSpin, CEA/DRF/Joliot, CEA Paris Saclay,
> >>> B?t 145 PC 156 , Gif s/ Yvette F-91190 FRANCE.
> >>>
> *------------------------------------------------------------------------------------------*
> >>> -------------- next part --------------
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> >>>
> >>> ------------------------------
> >>>
> >>> Message: 3
> >>> Date: Wed, 18 Dec 2019 23:00:55 +0100
> >>> From: Denis-Alexander Engemann <denis.engemann at gmail.com>
> >>> Subject: Re: [Mne_analysis] Empty room SSP vs. Maxwell filtering
> >>> To: Discussion and support forum for the users of MNE Software
> >>>        <mne_analysis at nmr.mgh.harvard.edu>
> >>> Message-ID:
> >>>        <CA+MN3Ot6=
> 9DAWX+QOMd-pznd3-9UAPex7Fr+LOGzeY859okuvg at mail.gmail.com>
> >>> Content-Type: text/plain; charset="utf-8"
> >>>
> >>>        External Email - Use Caution
> >>>
> >>> Well I guess you're asking why one should process the empty room
> recording
> >>> like one processes the data?
> >>> You simply want to make sure the rank of the data is the same and the
> only
> >>> difference is in the content of the signal, not the processing applied.
> >>>
> >>> Does that make sense?
> >>> Denis
> >>>
> >>> On Wed, Dec 18, 2019 at 7:52 PM Harish Gunasekaran <
> ngharish18 at gmail.com>
> >>> wrote:
> >>>
> >>>>        External Email - Use Caution
> >>>>
> >>>> Dear Alex and Denis,
> >>>> Could you tell us what is the importance of removing the empty room
> noise
> >>>> component using SSP? Wouldn't the maxwell filtering remove the empty
> room
> >>>> noise component by default?
> >>>>
> >>>> Thanks in advance,
> >>>> Harish
> >>>>
> >>>>
> >>>>
> *------------------------------------------------------------------------------------------*
> >>>> *Harish Gunasekaran,*
> >>>> NUMERICS
> >>>> <
> http://numerics.cea.fr/Pages/Numerics/Numerics%20program/Numerics-PhD.aspx
> >
> >>>> Ph.D. fellow under Marie Sk?odowska-Curie actions (2019-22),
> >>>> Cognition & Brain Dynamics team <https://brainthemind.com/team2/>,
> >>>> Cognitive Neuroimaging Unit (UNICOG <http://www.unicog.org/site_2016/
> >),
> >>>> NeuroSpin, CEA/DRF/Joliot, CEA Paris Saclay,
> >>>> B?t 145 PC 156 , Gif s/ Yvette F-91190 FRANCE.
> >>>>
> >>>>
> *------------------------------------------------------------------------------------------*
> >>>>
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-- 
*Dr. Sophie K. Herbst*
CEA Researcher
NeuroSpin, CEA Saclay, DRF/Joliot
Inserm Cognitive Neuroimaging Unit
Bât 145, Gif s/ Yvette F-91190 FRANCE
Phone: +33 (0)1 6908 7938
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