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

Fri Dec 4 10:20:02 PST 2015

Dear Ernesto,

> the channel chosen as a reference will be measured against Ground

If that's the case, why don't you exclude it from average reference. You
can use whatever interpolation method afterwords. Again, I recommend you
check Nima's PREP.

Makoto

On Fri, Dec 4, 2015 at 1:33 AM, Ernesto Gonzalez Trejo <gonzalez at snn-unit.de
> wrote:

> Dear Makoto,
>
> thanks again for your answer. Still:
>
> > 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.
>
> As i mentioned on the previous emails, the reference channel in the
> recorded
> signal is NOT zero, due to the manufacturer (g.tec) settings (since there
> are no
> dedicated reference electrodes, the channel chosen as a reference will be
> measured against Ground and not against itself, in order not to lose the
> channel).  That's why i was not sure if this channel should be used within
> the
> averaging or if EEGLAB ignores it for the calculation of AR.
>
> It seems then, that EEGLAB ignores the reference channel (since
> theoretically
> should be 0) so from now on i will remove it pre-AR, and afterwards i will
> write
> the inverted mean of all electrodes into the reference channel (as it
> should be
> (ref chan-ref chan)-(average of all channels)).
>
> Thanks,
>
> Ernesto
>
>
>
>
> > On December 2, 2015 at 7:19 PM Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> wrote:
> >
> > Dear Ernesto,
> >
> > > Should I remove the reference channel from my data (select>
> > 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>
> > >
> > > > 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
>

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