[Eeglablist] EEGLAB

Makoto Miyakoshi mmiyakoshi at ucsd.edu
Thu Dec 5 08:24:20 PST 2024 

Hi David,

My understanding is that when we say 'clean dataset', it does not mean to
'reject' independent components (ICs). Instead, we mean to perform ASR,
window rejection, etc.. Epoch rejection is fine.

About 'components with 20-40% of non-EEG', first of all how do you know
such a quantity? If you are referring to IC Label's class probability, it
does not exactly represent that. IC Label's class probability is like a
'prediction of result of the election'; IC Label extrapolates human
'voting' patterns (vote for one of the seven classes) to unseen results.

 > Am I correct in assuming the PCA spatial filter from dataset2 only
retains these same components in the original set 1 that was minimally
processed and therefore contains many artifacts?

I do not mean to run ICA twice.
My point is that you may run ICA on heavily-cleaned data and use it for
lightly-cleaned data. The idea is the same as Stefan Debener's trick i.e.
ICA on 2.0-Hz high-passed data, then copy the weight matrices to 0.1-Hz
high-passed data.

That being said, I'm less dependent on ICA these days. ICA is probably only
good for low-frequency phenomena such as ERP because of its bias to power,
and EEG data have 1/f power distributions. Basically, your theta band
signals are closer to independence, but your gamma band signals are not
independent across ICs

Makoto



On Tue, Nov 26, 2024 at 6:02 PM Gilbert, David G <dgilbert at siu.edu> wrote:

> Makoto,
> I have a question about your suggestion for bad data to be used for LPP
> and P3 data.
>
> With a low-quality ICA decomposition, you can try filtering the data as
> indicated in the previous section. Another strategy is to clean the data
> aggressively of artifacts before running ICA as explained below:
>
>    1. Start with an unfiltered (or minimally filtered) dataset (dataset 1)
>    2. Aggressively clean dataset either manually or using the automated
>    tools provided in EEGLAB to obtain dataset 2
>    Can epochs be removed during this aggressive cleaning? Should
>    components with 20 or 40% non-eeg be removed?
>    3. Run ICA on dataset 2
>    Am I correct in assuming the PCA spatial filter from dataset2 only
>    retains these same components in the original set 1 that was minimally
>    processed and therefore contains many artifacts?
>
> Thanks for any help you can provide!
> David Gilbert
>
>
> ------------------------------
> *From:* eeglablist <eeglablist-bounces at sccn.ucsd.edu> on behalf of Makoto
> Miyakoshi via eeglablist <eeglablist at sccn.ucsd.edu>
> *Sent:* Monday, November 25, 2024 2:25 PM
> *To:* eeglab list <eeglablist at sccn.ucsd.edu>
> *Subject:* Re: [Eeglablist] EEGLAB Orientation
>
> [EXTERNAL EMAIL ALERT]: Verify sender before opening links or attachments.
>
> Hi Arno and all
>
> Thanks for your input.
> I recommend people posted here try that plugin and tell me what it does.
>
> eegfiltnew() and fir_filt() are close enough, if you just
> need band-specific powers.
>
> Makoto
>
> On Sun, Nov 24, 2024 at 12:43 AM Arnaud Delorme via eeglablist <
> eeglablist at sccn.ucsd.edu> wrote:
>
> > For extracting brainwaves at specific frequencies, I would advise using
> > the eegstats EEGLAB plugin.
> >
> > Best wishes,
> >
> > Arno
> >
> > > On Nov 22, 2024, at 22:09, Meha Fatima via eeglablist <
> > eeglablist at sccn.ucsd.edu> wrote:
> > >
> > > Hi. Thank you for this opportunity. I'd like to join in, too. Can you
> > > please share the Zoom link?
> > >
> > > On Fri, 22 Nov 2024 at 23:34, Makoto Miyakoshi via eeglablist <
> > > eeglablist at sccn.ucsd.edu> wrote:
> > >
> > >> Hi Devvarta,
> > >>
> > >>> Could you please open this zoom session for others as well?
> > >>
> > >> Sure, gather as many participants as you want and let them ask as many
> > >> questions as necessary.
> > >> I'll be available after 7:00 am in New York time (EST) which is 5:30
> pm
> > in
> > >> Bangalore. I prefer it in the morning rather than the evening/night.
> > >>
> > >> I notice that there has been a large and constant need for extracting
> > EEG
> > >> power using EEGLAB, which is only partially supported by GUI.
> > >> After our discussion, maybe I can summarize the requested
> > functionalities
> > >> into a solution in the form of EEGLAB plugin. It should be pretty
> easy.
> > >> What I want to know is the type of output format you need most. Is it
> > ascii
> > >> or Excel? Do you want a result in linear scale (microV^2) or in dB? Do
> > you
> > >> want a mean power within a frequency band (with SD across sliding
> > windows)
> > >> or full freq bin resolution (which is already available in EEGLAB
> > spectopo)
> > >> etc..
> > >>
> > >> I like the idea of robust PSD proposed by Melman and Victor (2016) so
> > that
> > >> you do not need to worry too much about data cleaning.
> > >>
> > >>
> >
> https://urldefense.com/v3/__https://nam11.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fpmc.ncbi.nlm.nih.gov*2Farticles*2FPMC4903894*2F__*3B!!Mih3wA!Hc_qvUxHKj94lakBpoAoDLDmyqzks4elWCUSSecAgiLfWsompHx83bc4_GJA8f1FYPh9Rceqb8iycYCC-UFVaSR4uL8*24&data=05*7C02*7Cdgilbert*40siu.edu*7Cb7c49d490128497da23f08dd0d9bc90e*7Cd57a98e7744d43f9bc9108de1ff3710d*7C0*7C0*7C638681684954144017*7CUnknown*7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ*3D*3D*7C0*7C*7C*7C&sdata=61CfqcMQU7UG*2BLoV0b5rnW3SLyUtpmP8Gz1Rz1E1w3k*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!AyMqmAwXErs-Qb2LRE6o4en-I2qAhwg1xupeyZ3KE3xYmitAYUbklI8qayVJsFO8XxBh7vGFUdEfK-eV0rtlajdmUqE$ 
> <https://urldefense.com/v3/__https://pmc.ncbi.nlm.nih.gov/articles/PMC4903894/__;!!Mih3wA!Hc_qvUxHKj94lakBpoAoDLDmyqzks4elWCUSSecAgiLfWsompHx83bc4_GJA8f1FYPh9Rceqb8iycYCC-UFVaSR4uL8$>
> > >> I have long thought that the averaging process in Welch's method
> should
> > be
> > >> replaced with median because EEG recordings can contain pretty bad
> > >> outliers. At least, outcomes from Welch's method by mean and median
> can
> > be
> > >> compared to evaluate the window-mean PSD's deviation from the
> > window-median
> > >> PSD.
> > >>
> > >> Grace, if this selection of time does not work for you, we can set a
> > >> separate Zoom meeting. Tell me what time zone you are in.
> > >>
> > >> Makoto
> > >>
> > >>
> > >> On Fri, Nov 22, 2024 at 3:42 AM Devvarta Kumar <
> > devvarta.k at nimhans.ac.in>
> > >> wrote:
> > >>
> > >>> Hi Mokoto
> > >>> I assume many of us would be interested in understanding the process
> of
> > >>> calculating power in different bands in raw EEG. Could you please
> open
> > >> this
> > >>> zoom session for others as well?
> > >>> Regards
> > >>>
> > >>> Devvarta Kumar, Ph.D.
> > >>>
> > >>> Professor
> > >>> Department of Clinical Psychology
> > >>> M. V. Govindaswamy Building
> > >>> National Institute of Mental Health and Neurosciences,
> > >>> Hosur Road,
> > >>> Bangalore,
> > >>> Karnataka-560029
> > >>> India
> > >>>
> > >>> Ph: +91-80-26995188
> > >>>
> > >>>
> > >>
> >
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> > >>>
> > >>> ResearchGate:
> > >>>
> > >>
> >
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> > >>>
> > >>> ----- Original Message -----
> > >>> From: eeglablist at sccn.ucsd.edu
> > >>> To: eeglablist at sccn.ucsd.edu
> > >>> Sent: Friday, November 22, 2024 1:51:05 AM
> > >>> Subject: Re: [Eeglablist] EEGLAB Orientation
> > >>>
> > >>> Hi Grace,
> > >>>
> > >>> If your group wants to Zoom with me, I'll be available. Which time
> zone
> > >> are
> > >>> you in?
> > >>>
> > >>> Makoto
> > >>>
> > >>> On Thu, Nov 21, 2024 at 2:50 PM Grace Bang via eeglablist <
> > >>> eeglablist at sccn.ucsd.edu> wrote:
> > >>>
> > >>>> Hello!
> > >>>>
> > >>>> We are 3rd year medical students trying to conduct research where we
> > >>>> collect brain wave activity data using the CGX Patch 2-channel EEG.
> > >> We've
> > >>>> been having a lot of issues trying to navigate how to use EEGLAB to
> > >>> process
> > >>>> the data. We just want to be able to quantify the number of alpha
> and
> > >>> beta
> > >>>> waves present in the raw data. The resources we've read online have
> > >> been
> > >>>> somewhat helpful, but we are looking for someone who can jump on a
> > >>>> Zoom/phone call to help fill some gaps of knowledge. Neither of us
> > >> have a
> > >>>> background in more complicated softwares/coding/EEGs so any guidance
> > >>> would
> > >>>> be greatly appreciated!
> > >>>>
> > >>>> - Grace Bang, OMS-3
> > >>>> _______________________________________________
> > >>>> Eeglablist page:
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> > >
> > >
> > > --
> > >
> > > *  Dr. Meha Fatima BSMT, Ph.D.*
> > >                                         Assistant Professor
> > >                                         Dow Institute of Medical
> > Technology
> > >                                         Dow University of Health
> Sciences
> > >                                          *mehafatima1 at gmail.com
> > > <mehafatima1 at gmail.com>.*
> > > _______________________________________________
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