<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div>Hi Denis,</div><div>Thanks for your reply. I am concerned about the empty room noise removal during the <b>pre-processing stage (artifacts removal using SSP)</b> as recommended in the MNE website (<a href="https://mne.tools/stable/auto_tutorials/preprocessing/plot_50_artifact_correction_ssp.html">https://mne.tools/stable/auto_tutorials/preprocessing/plot_50_artifact_correction_ssp.html</a>). <b>Another related question: </b>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?</div><div><br></div><div>Thanks in advance.<br></div><div><br></div><div>Harish<br></div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><br></div><div dir="ltr"><b style="font-family:"trebuchet ms",sans-serif"><i><font size="2">------------------------------------------------------------------------------------------</font></i></b><font face="trebuchet ms, sans-serif"><b><i><font size="2"><br></font></i></b></font></div><div dir="ltr"><font face="trebuchet ms, sans-serif"><b><i><font size="2">Harish Gunasekaran,</font></i></b></font><div dir="ltr"><font face="trebuchet ms, sans-serif"><a href="http://numerics.cea.fr/Pages/Numerics/Numerics%20program/Numerics-PhD.aspx" target="_blank">NUMERICS</a> Ph.D. </font>fellow under Marie Skłodowska-Curie actions <font face="trebuchet ms, sans-serif">(2019-22),</font></div><div dir="ltr"><a href="https://brainthemind.com/team2/" target="_blank">Cognition & Brain Dynamics team</a>, Cognitive Neuroimaging Unit (<a href="http://www.unicog.org/site_2016/" target="_blank">UNICOG</a>), <br></div><div>NeuroSpin, CEA/DRF/Joliot, CEA Paris Saclay, </div><div dir="ltr">Bât 145 PC 156 , Gif s/ Yvette F-91190 FRANCE.<font face="trebuchet ms, sans-serif"><br></font></div></div><div dir="ltr"><div><div dir="ltr"><font face="trebuchet ms, sans-serif"><b><i>------------------------------------------------------------------------------------------</i></b></font></div><div dir="ltr"><b style="font-family:"trebuchet ms",sans-serif"><i><br></i></b></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Dec 18, 2019 at 11:02 PM <<a href="mailto:mne_analysis-request@nmr.mgh.harvard.edu">mne_analysis-request@nmr.mgh.harvard.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send Mne_analysis mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. using the command line interface of mne (Neeraj Sharma)<br>
2. Empty room SSP vs. Maxwell filtering (Harish Gunasekaran)<br>
3. Re: Empty room SSP vs. Maxwell filtering<br>
(Denis-Alexander Engemann)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 18 Dec 2019 13:50:16 -0500<br>
From: Neeraj Sharma <<a href="mailto:neerajww@gmail.com" target="_blank">neerajww@gmail.com</a>><br>
Subject: [Mne_analysis] using the command line interface of mne<br>
To: <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
Message-ID:<br>
<<a href="mailto:CACcKo1A9YbXnkXSUb9O1b7sQPmKq4hAXRYN2iAYVDSvy9QqcWg@mail.gmail.com" target="_blank">CACcKo1A9YbXnkXSUb9O1b7sQPmKq4hAXRYN2iAYVDSvy9QqcWg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
External Email - Use Caution <br>
<br>
Hi Community,<br>
<br>
I am interested in doing some of the continuous-time data (that is, before<br>
epoching) pre-processing using the command line interface. I am hoping this<br>
will be less time consuming as it will use the C libraries (?) compared to<br>
using the python functions with the code.<br>
Can you help me with the functions available? I see the link here<br>
<a href="https://mne.tools/stable/generated/commands.html" rel="noreferrer" target="_blank">https://mne.tools/stable/generated/commands.html</a> but got some doubts in the<br>
underlying functionality when the options are used.<br>
<br>
To start, I will like to do a bandpass filter of EEG data from 0.1 to 40<br>
Hz. I see that there is the -filterorder option but does it use:<br>
mne.filter.filter_data(data, Fs, l_freq, h_freq, picks=None,<br>
filter_length='auto',<br>
l_trans_bandwidth='auto',<br>
h_trans_bandwidth='auto', n_jobs=1,<br>
method='fir',<br>
iir_params=None, copy=True, phase='zero',<br>
fir_window='hamming', fir_design='firwin',<br>
pad='reflect_limited', verbose=False)<br>
If yes, then how can we specify the other arguments of the function,<br>
especially, those related to phase delay.<br>
<br>
<br>
Cheers,<br>
Neeraj<br>
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Message: 2<br>
Date: Wed, 18 Dec 2019 19:52:12 +0100<br>
From: Harish Gunasekaran <<a href="mailto:ngharish18@gmail.com" target="_blank">ngharish18@gmail.com</a>><br>
Subject: [Mne_analysis] Empty room SSP vs. Maxwell filtering<br>
To: <a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a><br>
Message-ID:<br>
<<a href="mailto:CAGqhYKUAA3nCTJEuQaCwop97%2BzJwztsO278ZSpmQmrTdSjZBTA@mail.gmail.com" target="_blank">CAGqhYKUAA3nCTJEuQaCwop97+zJwztsO278ZSpmQmrTdSjZBTA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
External Email - Use Caution <br>
<br>
Dear Alex and Denis,<br>
Could you tell us what is the importance of removing the empty room noise<br>
component using SSP? Wouldn't the maxwell filtering remove the empty room<br>
noise component by default?<br>
<br>
Thanks in advance,<br>
Harish<br>
<br>
*------------------------------------------------------------------------------------------*<br>
*Harish Gunasekaran,*<br>
NUMERICS<br>
<<a href="http://numerics.cea.fr/Pages/Numerics/Numerics%20program/Numerics-PhD.aspx" rel="noreferrer" target="_blank">http://numerics.cea.fr/Pages/Numerics/Numerics%20program/Numerics-PhD.aspx</a>><br>
Ph.D. fellow under Marie Sk?odowska-Curie actions (2019-22),<br>
Cognition & Brain Dynamics team <<a href="https://brainthemind.com/team2/" rel="noreferrer" target="_blank">https://brainthemind.com/team2/</a>>,<br>
Cognitive Neuroimaging Unit (UNICOG <<a href="http://www.unicog.org/site_2016/" rel="noreferrer" target="_blank">http://www.unicog.org/site_2016/</a>>),<br>
NeuroSpin, CEA/DRF/Joliot, CEA Paris Saclay,<br>
B?t 145 PC 156 , Gif s/ Yvette F-91190 FRANCE.<br>
*------------------------------------------------------------------------------------------*<br>
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Message: 3<br>
Date: Wed, 18 Dec 2019 23:00:55 +0100<br>
From: Denis-Alexander Engemann <<a href="mailto:denis.engemann@gmail.com" target="_blank">denis.engemann@gmail.com</a>><br>
Subject: Re: [Mne_analysis] Empty room SSP vs. Maxwell filtering<br>
To: Discussion and support forum for the users of MNE Software<br>
<<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a>><br>
Message-ID:<br>
<CA+MN3Ot6=<a href="mailto:9DAWX%2BQOMd-pznd3-9UAPex7Fr%2BLOGzeY859okuvg@mail.gmail.com" target="_blank">9DAWX+QOMd-pznd3-9UAPex7Fr+LOGzeY859okuvg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
External Email - Use Caution <br>
<br>
Well I guess you're asking why one should process the empty room recording<br>
like one processes the data?<br>
You simply want to make sure the rank of the data is the same and the only<br>
difference is in the content of the signal, not the processing applied.<br>
<br>
Does that make sense?<br>
Denis<br>
<br>
On Wed, Dec 18, 2019 at 7:52 PM Harish Gunasekaran <<a href="mailto:ngharish18@gmail.com" target="_blank">ngharish18@gmail.com</a>><br>
wrote:<br>
<br>
> External Email - Use Caution<br>
><br>
> Dear Alex and Denis,<br>
> Could you tell us what is the importance of removing the empty room noise<br>
> component using SSP? Wouldn't the maxwell filtering remove the empty room<br>
> noise component by default?<br>
><br>
> Thanks in advance,<br>
> Harish<br>
><br>
><br>
> *------------------------------------------------------------------------------------------*<br>
> *Harish Gunasekaran,*<br>
> NUMERICS<br>
> <<a href="http://numerics.cea.fr/Pages/Numerics/Numerics%20program/Numerics-PhD.aspx" rel="noreferrer" target="_blank">http://numerics.cea.fr/Pages/Numerics/Numerics%20program/Numerics-PhD.aspx</a>><br>
> Ph.D. fellow under Marie Sk?odowska-Curie actions (2019-22),<br>
> Cognition & Brain Dynamics team <<a href="https://brainthemind.com/team2/" rel="noreferrer" target="_blank">https://brainthemind.com/team2/</a>>,<br>
> Cognitive Neuroimaging Unit (UNICOG <<a href="http://www.unicog.org/site_2016/" rel="noreferrer" target="_blank">http://www.unicog.org/site_2016/</a>>),<br>
> NeuroSpin, CEA/DRF/Joliot, CEA Paris Saclay,<br>
> B?t 145 PC 156 , Gif s/ Yvette F-91190 FRANCE.<br>
><br>
> *------------------------------------------------------------------------------------------*<br>
><br>
> _______________________________________________<br>
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</blockquote></div>