[Mne_analysis] Mne_analysis Digest, Vol 143, Issue 14

Denis A. Engemann denis-alexander.engemann at inria.fr
Thu Dec 19 05:57:59 EST 2019
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        External Email - Use Caution        

Ah. No they are discarded.
To me either you do empty room SSP or you do SSS.

> On 19 Dec 2019, at 11:50, Sophie Herbst <ksherbst at googlemail.com> wrote:
> 
>         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
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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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>> >>> End of Mne_analysis Digest, Vol 143, Issue 14
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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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