[Mne_analysis] Mne_analysis Digest, Vol 143, Issue 14

Eric Larson larson.eric.d at gmail.com
Fri Dec 20 14:13:01 EST 2019
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        External Email - Use Caution        

In case you are interested in combining SSS and empty-room projectors, you
can try this branch from this PR I just opened:

https://github.com/mne-tools/mne-python/pull/7156

It uses the extended SSS (eSSS) method to improve the external SSS basis
during Maxwell filtering. This method was originally presented back in 2016
-- if you're curious to learn more about it, there is a poster link in the
PR above.

Eric


On Fri, Dec 20, 2019 at 8:37 AM Virginie van Wassenhove <
virginie.van.wassenhove at gmail.com> wrote:

>         External Email - Use Caution
>
> Hi there, I am not sure to follow entirely what the question is (but it
> may be my jetlag)?
>
> 1)  If you wish to know the environmental/site noise level, this is given
> by the set of SSP that we read when maxfiltering (cf config in the pipeline)
> 2) for your purpose, you may be interested in ER (sensor) noise which
> Merlin is currently investigating so you may want to chat with him
> 3) in addition to the site noise, you apply SSP or ICA for biological
> artifacts (as previously mentioned 2 to 3 components are typically far
> enough per biological artifact, e.g. 2 for EOG and 2 for ECG)
>
> Cheers,
>
>
> Virginie van Wassenhove
> *https://brainthemind.com/ <https://brainthemind.com/>*
>
>
>
>
>
> On Thu, Dec 19, 2019 at 11:58 AM ENGEMANN Denis <
> denis-alexander.engemann at inria.fr> wrote:
>
>>         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:
>>> >>>
>>> >>> Send Mne_analysis mailing list submissions to
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>>> >>> When replying, please edit your Subject line so it is more specific
>>> >>> than "Re: Contents of Mne_analysis digest..."
>>> >>>
>>> >>>
>>> >>> 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.
>>> >>>
>>> *------------------------------------------------------------------------------------------*
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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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