[Eeglablist] epoch baseline removal experience?

Scott Makeig smakeig at gmail.com
Fri May 11 20:09:51 PDT 2012


Even whole-epoch baseline removal is not ideal.  It is better to
zero-baseline the data after major artifact-period removal but before
epoching (and, typically, high-pass filtering above ~1 Hz). Only then
extract epochs for ICA decomposition (IF you do not want to decompose the
continuous data -- our more typical procedure). After ICA decomposition,
data epochs can be individually baseline-zeroed without affecting the ICA
account of them.

Scott

On Fri, May 11, 2012 at 12:31 PM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>wrote:

> Dear Ida and Scott,
>
> > As I understood, the purpose of Baseline Removal is for me/us to have
> > better insight when event in observed epoch happened, so the value around
> > corresponding marker is expected to be zero. Right?
>
> That sounds right, although I may not understand you perfectly.
> ERP show up usually after the event (unless it is expectation-related
> nature), so it makes sense to set the baseline period before stimulus
> onset during which brain activity is supposed to be neutral, and
> whatever ERP can be compared against it.
>
> > I have one more question regarding this - does it matter if I Remove
> > Baseline for example (-1000ms to 0ms) if I have epoch that is longer (-4
> > secs to 4 secs)? I read in Q&A list Arno's answer regarding similar
> question
> > where he said that ICA can be unstable if the epochs baseline is too
> short,
> > so he suggests longer baselines (i.e 1 sec).
>
> Although I don't know what Arno meant in that specific context, I
> guess he was probably referring to the finding reported by Groppe,
> Makeig, and Kutas (2009). In the paper, the authors reports
> whole-epoch baseline produced better ICA results compared to short
> pre-stimulus baseline. Therefore, for ICA purpose, it's even better to
> use an entire epoch for a baseline. The authors says 'It is not clear
> what causes this difference.' in the paper (pp.1208), though I heard
> Scott say a brief explanation. What do you think, Scott?
>
> Makoto
>
>
>
> 2012/5/10 ida miokovic <ida.miokovic at gmail.com>:
> > Dear Makoto,
> >
> > thank you for your answer, it cleared the doubts in my head regarding
> this
> > =). As I understood, the purpose of Baseline Removal is for me/us to have
> > better insight when event in observed epoch happened, so the value around
> > corresponding marker is expected to be zero. Right?
> >
> > I have one more question regarding this - does it matter if I Remove
> > Baseline for example (-1000ms to 0ms) if I have epoch that is longer (-4
> > secs to 4 secs)? I read in Q&A list Arno's answer regarding similar
> question
> > where he said that ICA can be unstable if the epochs baseline is too
> short,
> > so he suggests longer baselines (i.e 1 sec).
> >
> > Thanks,
> >
> > Ida
> >
> >
> > On Thu, May 10, 2012 at 9:45 PM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> > wrote:
> >>
> >> Dear Ida,
> >>
> >> The consequence would be that you may not have near-zero potential
> >> at/around time zero (and this time zero which should be an onset of
> >> whatever event). Usually people want to reset their data to zero
> >> microvolt at/around time zero, so they subtract mean of short time
> >> period immediately before it (for example, -200 ms to 0 ms as a
> >> baseline period). Am I answering to your question? If not, let me
> >> know.
> >>
> >> Makoto
> >>
> >> 2012/5/10 ida miokovic <ida.miokovic at gmail.com>:
> >> > Hello everyone,
> >> >
> >> > Since I do not have experience in eeg signal processing, I am asking
> you
> >> > for
> >> > the opinion regarding epoch baseline removal (a window for this pops
> up
> >> > after I do the data epoching). Epochs I am extracting are quite long:
> -4
> >> > secs before and 4 secs after Marker of my interest.
> >> >
> >> > Why is following suggested in tutorial:
> >> >
> >> > "Using the mean value in the pre-stimulus period (the pop_rmbase()
> >> > default)
> >> > is effective for many datasets, if the goal of the analysis is to
> define
> >> > transformations that occur in the data following the time-locking
> >> > events."
> >> >
> >> > What are the consequences if I leave the fields in pop up window
> (Epoch
> >> > Baseline Removal) empty and therefore have the whole epoch used as a
> >> > baseline?
> >> >
> >> > Thank you in advance,
> >> >
> >> > All the best,
> >> >
> >> > Ida
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > _______________________________________________
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> >>
> >>
> >>
> >> --
> >> Makoto Miyakoshi
> >> JSPS Postdoctral Fellow for Research Abroad
> >> Swartz Center for Computational Neuroscience
> >> Institute for Neural Computation, University of California San Diego
> >
> >
>
>
>
> --
> Makoto Miyakoshi
> JSPS Postdoctral Fellow for Research Abroad
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>



-- 
Scott Makeig, Research Scientist and Director, Swartz Center for
Computational Neuroscience, Institute for Neural Computation; Prof. of
Neurosciences (Adj.), University of California San Diego, La Jolla CA
92093-0559, http://sccn.ucsd.edu/~scott
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