[Eeglablist] Average Reference after measuring 128 Ch using one of the 128 channels as reference (Cz)?

Wed Dec 2 10:19:35 PST 2015

Dear Ernesto,

> Should I remove the reference channel from my data (select data->remove)
before processing the average reference, even if it is part of my data?

If you have reference channel in your data, the recorded signal is (ref
chan) - (ref chan) = 0, so it should be flat. You want to remove this flat
channel, of course.

After average referencing, you may want to discard *any* one channel to
make the data full-ranked.

Makoto

On Wed, Dec 2, 2015 at 3:11 AM, Ernesto Gonzalez Trejo <gonzalez at snn-unit.de
> wrote:

> Dear Makoto,
>
> thank you for your answer.
>
> There is no problem when importing the data and setting Cz (ch 30) as
> reference
> when i set the channel locations. But i don't know if it is valid for
> EEGLAB if
> i assign one of my existing 128 channels as reference (by edit->channel
> locations->set reference-> Channel Indices 1:128, Reference Cz).  There is
> no
> exclusive reference channel appended at the end. Is this refrence
> assignment
> only a label? does it matter when computing the average reference?
>
> I can "synthesize" my question as follows: Should I remove the reference
> channel
> from my data (select data->remove) before processing the average
> reference, even
> if it is part of my data?
>
> From the 128 acquired electrodes, 63 and 64 are earlobes (so i remove
> them) and
> 30 (cz)  is used as a reference, while channel 30 itself is measured
> against the
> ground. Unfortunately our setup has no option to use a dedicated reference
> electrode, so either EEG has to be measured against ground (no reference)
> or one
> of the 128 channels.
>
> So in order to get an accurate average-referenced EEG, should i remove the
> reference before calculating it?
>
> Thanks again!
>
> Ernesto
>
>
> > On December 1, 2015 at 9:17 PM Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> wrote:
> >
> > Dear Ernesto,
> > > i have a brief question
> >
> > I thought it was quite long, which is why I did not understand the
> > question.Let me start from here: What's the problem of importing the
> data and
> > apply average reference?
> > REST is a good solution but I've never been used it myself. Does REST has
> > Matlab code? If it's available I'd love to try it out.
> > Another approach is Nima Bigdely-Shamlo's PREP. It'll do conscientious
> channel
> > cleaning before average
> > referencing.
> http://journal.frontiersin.org/article/10.3389/fninf.2015.00016/abstract
> > Makoto
> > On Thu, Nov 26, 2015 at 7:14 AM, Ernesto Gonzalez Trejo <
> gonzalez at snn-unit.de>
> > wrote:
> > > Hi everyone,
> > >
> > > i have a brief question regarding a correct average referencing in
> EEGLAB,
> > > that until now i've been unable to solve. I've read the EEGLAB
> tutorial and
> > > also searched for some answers in the EEGLAB list but until now i
> didn't
> > > find one that helps me solve the problem.
> > >
> > > I am doing EEG measurements with 128 Channels, using the channel in the
> > > position Cz as reference(ch. 30 in my cap). During the acquisition, the
> > > amplifier properties have Cz set as reference for all electrodes, and
> the
> > > Cz electrode is then measured then against the ground. Additionally,
> two
> > > more channels (63-64) are on the earlobes and are usually discarded
> since
> > > i'm not using them as reference or for data analysis.
> > >
> > > Given the nature of the measurement I consider the average reference
> the way
> > > to go in order to represent better the brain activity.
> > >
> > > The acquisition is done through SIMULINK and saved into a MAT file, for
> > > post-processing in MATLAB. (The output is a 128xL matrix, where L is
> the
> > > length of the measurement in samples).
> > >
> > > The problem i have is that i can't seem to indicate correctly to
> EEGLAB that
> > > the reference used in my measurement is also part of the channels.
> When i
> > > import the mat file, i cannot give explicitely the channel (as stated
> on the
> > > import window's help:
> > >
> > > "Ref. channel indices or mode" - [edit box] current reference. This
> edit box
> > >  cannot be edited. To change data reference, use menu
> > >  Tools > Re-reference calling function pop_reref(). The reference
> > >  can be a string, 'common' indicating an unknow common reference,
> > >  'averef' indicating average reference, or an array of integer
> > >  containing the indices of the reference channels."
> > >
> > > Then, after I import the data without a reference, I select the channel
> > > locations (using a self-made loc file for the cap i use). Here, each
> one of
> > > the 128 channels has a label (10-10 system names for electrodes 1-64
> and
> > > just the electrode number for 65-128). Once loaded, i click on "Set
> > > Reference" and write 1:128 as channel indices and Cz as "Reference".
> > > (Channel 30 has the label Cz and was the reference in the measurement).
> > > After the locations are set, i remove channels 63 and 64, since i
> don't want
> > > to use them for AR.
> > >
> > > So far, so good. After this i can just go and compute the average
> reference
> > > using the tools from EEGLAB. I wanted to validate the results so i kept
> > > doing some tests, and i realized that if i clicked on
> tools-rereference and
> > > then to "add current reference channel back to the data", the error :
> > >
> > > "There are no Reference channel defined, add it using the channel
> location
> > > editor"
> > >
> > > appeared, although in the main EEGLAB window the Reference is stated
> to be
> > > Cz and Channel locations as "Yes".
> > >
> > > Question 1:
> > >
> > > Could it be that i am giving the Reference wrong in the channel
> locations?
> > > After reading the tutorials i only got that the reference is usually
> given
> > > as an extra channel, which is appended to the locations. In this case,
> it is
> > > not an extra channel, but channel 30 of 128. Is it wrong then, to
> input this
> > > channel as i did in the channel locations?
> > >
> > > Question 2:
> > >
> > > Since i wanted to see how exactly the average referencing was working,
> I
> > > checked also the reref.m function from EEGLAB and tried to run it
> standalone
> > > as follows:
> > >
> > > output=reref(eeg,30,'exclude',[63 64],'keepref','on');,
> > >
> > > where i am only interesed on the average-referenced EEG (output) and i
> give
> > > a 128xL matrix (my EEG measurement), I indicate my reference was the
> channel
> > > (row) 30, and i exclude the earlobes (63 64).
> > >
> > > The output is however very different to the one i obtain with the
> method
> > > explained above in EEGLAB.
> > >
> > > In order to obtain the (mostly) same result as in EEGLAB i have to
> input the
> > > following:
> > >
> > > output=reref(eeg,30,'exclude',[30 63 64],'keepref','on');
> > >
> > > So, what exactly am i doing wrong here? I am probably specifying the
> > > reference in a wrong way. How should one manage such a reference system
> > > within EEGLAB or in the reref function? As i understand the
> calculation of
> > > average referencing, i should NOT use the values of the reference to
> > > calculate the mean of all electrodes, which would be afterwards
> subtracted
> > > from each one. And if i wanted to see the signal of Cz post-AR, i
> would have
> > > it by inverting the mean of all electrodes. If so, then the right way
> to go
> > > here would be to exclude also the channel 30 in the reref function. Is
> that
> > > right?
> > >
> > > I am using currently EEGLAB v13.4.4b on MATLAB R2013a
> > >
> > > Thanks in advance!
> > >
> > > EG
> > >
> > > _______________________________________________
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> >
> > --
> > Makoto Miyakoshi
> > Swartz Center for Computational Neuroscience
> > Institute for Neural Computation, University of California San Diego
>

-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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