[Eeglablist] [Fwd: Eye Movement Artifacts and Filtering]
Bradley Voytek
btvoytek at berkeley.edu
Mon Jun 30 09:20:02 PDT 2008
Viviane:
You can open eeglab, and then just loop the file load function across files.
To load in a bunch of files in the pwd, you could do something like:
for i = 1:length(FILENAMECELL)
EEG = pop_loadset('filename', FILENAMECELL{i}, 'filepath', pwd);
[ALLEEG, EEG, CURRENTSET] = eeg_store(ALLEEG, EEG, 0);
end
::brad
Bradley Voytek
PhD Candidate: Neuroscience
University of California, Berkeley
Helen Wills Neuroscience Institute
Berkeley, CA 94720-3190
On Fri, Jun 27, 2008 at 10:39 AM, Viviane Monteiro Braconi
<viviane at sarah.br> wrote:
> Hi
>
> I want write to Matlab script to call the eeg functions.....I don't want to use the EEGLAB menu. But the first command that I need is >>eeglab....and the menun is open.....I would like that the menu is not open......Do you know if it is possible?
>
> Example:
>
>>> eeglab
>>>eeg = pop_loadset()
>>> and so on
>
> And......I don't want to open a eeglab menu. I would like to make everything using script...
>
> Thanks
> Viviane
>> ----------
>> From: eeglablist-bounces at sccn.ucsd.edu[SMTP:eeglablist-bounces at sccn.ucsd.edu] on behalf of Timothy O'Keefe [BROWN][SMTP:timothy_okeefe at brown.edu]
>> Sent: quinta-feira, 15 de maio de 2008 09:56
>> To: eeglablist at sccn.ucsd.edu
>> Subject: Re: [Eeglablist] [Fwd: Eye Movement Artifacts and Filtering]
>>
>> EEGLAB Users,
>>
>> I might try to "inject" my opinion here, for whatever it's worth.
>>
>> Among other endeavors involving ICA, I've had significant dealings with
>> ocular artifact "correction" using EEGLAB/ICA. Now, while I'm not an
>> "expert" by any means, I would like to provide some food for thought.
>> What it will feed has yet to be determined :)
>>
>> So far as introducing bipolar electrodes - or anything for that matter -
>> into the input matrix, I was always under the assumption that it should
>> not matter as ICA should not determine any relationships which include
>> these nonsense(?) data.
>>
>> As for "cleaning" EEG data. This is one problem that I've found
>> particularly frustrating. My inner demon has me questioning *exactly*
>> which components EOG - or the influences of EOG - manifest?
>> How does one test this with a measurable degree of certainty? Better
>> yet, how does one test this without making assumptions? How good of an
>> indicator of "cleanliness" is a "flat" EOG ERP anyways? Pretty good?
>> Good enough? Is it enough to bet your life on (where some of us might
>> be!!)?
>>
>> Best,
>> Tim
>>
>> Scott Makeig wrote:
>> > ICA can decompose common reference and bipolar channel pairs
>> > simultaneously, since the sources sum linearly at all these channels
>> > proportional to the difference in source projection strengths to the
>> > 'active' and 'reference' channels. However, plotting the scalp maps of
>> > ICA components including both types of channels is not apt to be wholly
>> > accurate, since the baselines for the two channel types are
>> > different.However, iIt should be possible to reconstruct the full
>> > component scalp maps (at least for 'dipolar' components) using a forward
>> > (BEM) head model... In the absence of such a procedure, one can always
>> > remove the bipolar channels *after* running ICA decomposition, using the
>> > EEGLAB 'remove channels' function. This will allow plotting the
>> > component maps based on the (common reference) montage.
>> >
>> > Scott Makeig
>> >
>> > On Sun, Apr 20, 2008 at 3:45 PM, Nicolas Robitaille
>> > <nicolas.robitaille at umontreal.ca
>> > <mailto:nicolas.robitaille at umontreal.ca>> wrote:
>> >
>> > Dear Arno,
>> >
>> > Just a related idea:
>> >
>> > Would it be a better practice to simply include the EOG channels as
>> > if they were just others EEG electrodes (if they were all recorded
>> > with say a left-earlobe reference, as the others EEG channels, or
>> > reference-free using a Biosemi system) instead of bipolar channels,
>> > when possible? In my mind, this would help ICA to isolate these
>> > signals (which is not always trivial for horizontal eye movements,
>> > which are smaller and can be less frequent than eye blinks),
>> > according that at least some channels would have clear eye-related
>> > signals. This would also avoid the difference in referencing methods
>> > across channels you mentionned.
>> >
>> > Nicolas
>> >
>> > > Date: Sun, 20 Apr 2008 23:13:52 +0200
>> > > From: arno at ucsd.edu <mailto:arno at ucsd.edu>
>> > > To: modestino at ccs.fau.edu <mailto:modestino at ccs.fau.edu> >
>> > > CC: eeglablist at sccn.ucsd.edu <mailto:eeglablist at sccn.ucsd.edu>
>> > > Subject: Re: [Eeglablist] [Fwd: Eye Movement Artifacts and Filtering]
>> >
>> > >
>> > > Dear Justin,
>> > >
>> > > > I am planning to use ICA in EEGLAB to remove eye movement
>> > artifacts. I
>> > > > know that ICA does not use EOG channels locate the component
>> > associated
>> > > > with eye movements. However, my advisor will want me to show
>> > ERP averages
>> > > > of the EOG channels as evidence that the eye movements have
>> > been removed
>> > > > using ICA. So, I will be including the EOG channels (bipolar, but
>> > > > represented as individual difference waves as one channel, for
>> > HEO and
>> > > > VEO).
>> > > >
>> > >
>> > > It is OK to include bipolar channels for that purpose. ICA should be
>> > > able to detect the difference in reference (although you might
>> > have to
>> > > search for the component that accounts for that). Then you may
>> > compute
>> > > ERP for your EOG channels. A better idea though would be to do
>> > that for
>> > > frontal channels such as FPz.
>> > >
>> > > > Finally, I need to run an acausal FIR high pass filter at 1 Hz.
>> > [which
>> > > > will not change the temporal components of the EEG] on the data
>> > before
>> > > > running ICA, as there is an extreme trend in the data that made
>> > automated
>> > > > and even manual eye movement removal inadequate using the raw
>> > data outside
>> > > > of EEGLAB. Also, the trend needs to be removed anyway. However,
>> > removing
>> > > > the linear trend will not adequately alter the tend in the
>> > continuous data
>> > > > as the FIR filter will. So, I wish to use such a filter. [I may
>> > remove
>> > > > the linear trend once the data is epoched per condition, but
>> > not on the
>> > > > continuous data.] What sort of filters does EEGLAB have built
>> > in? Is this
>> > > > filter already available?
>> > > >
>> > >
>> > > Yes, there are 2 types of filters available in EEGLAB by default. I
>> > > would advise to use the non-linear IIR filter which has better
>> > design
>> > > than the linear FIR filter (and does not introduce phase distortion
>> > > because it is applied in both directions). There is also an
>> > additional
>> > > plugin that allows more advanced filtering.
>> > >
>> > >
>> > http://www.uni-leipzig.de/~biocog/content/widmann/eeglab-plugins/#firfilt
>> > <http://www.uni-leipzig.de/%7Ebiocog/content/widmann/eeglab-plugins/#firfilt>
>> > >
>> > > Sorry for the late answer. Answer do come in time if you are patient.
>> > >
>> > > Best regards,
>> > >
>> > > Arno
>> > >
>> > > _______________________________________________
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>> >
>> > ------------------------------------------------------------------------
>> > Branchez-vous aujourd'hui. Jusqu'au 12 mai, lorsque vous vous
>> > connectez à Windows Live Messenger, vous courez la chance de gagner
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>> >
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>> >
>> >
>> >
>> >
>> > --
>> > Scott Makeig, Research Scientist and Director, Swartz Center for
>> > Computational Neuroscience, Institute for Neural Computation, University
>> > of California San Diego, La Jolla CA 92093-0961,
>> > http://sccn.ucsd.edu/~scott
>> >
>> >
>> > ------------------------------------------------------------------------
>> >
>> > _______________________________________________
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>>
>> --
>> --------------------------
>> Timothy M. O'Keefe
>> Brown University
>> Department of Neuroscience
>> 185 Meeting Street
>> Providence, RI 02912
>>
>> Voice: +1.401.863.1258
>> --------------------------
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