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.<div>
<br></div><div>Scott<br><br><div class="gmail_quote">On Fri, May 11, 2012 at 12:31 PM, Makoto Miyakoshi <span dir="ltr"><<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Ida and Scott,<br>
<br>
> As I understood, the purpose of Baseline Removal is for me/us to have<br>
> better insight when event in observed epoch happened, so the value around<br>
> corresponding marker is expected to be zero. Right?<br>
<br>
That sounds right, although I may not understand you perfectly.<br>
ERP show up usually after the event (unless it is expectation-related<br>
nature), so it makes sense to set the baseline period before stimulus<br>
onset during which brain activity is supposed to be neutral, and<br>
whatever ERP can be compared against it.<br>
<br>
> I have one more question regarding this - does it matter if I Remove<br>
> Baseline for example (-1000ms to 0ms) if I have epoch that is longer (-4<br>
> secs to 4 secs)? I read in Q&A list Arno's answer regarding similar question<br>
> where he said that ICA can be unstable if the epochs baseline is too short,<br>
> so he suggests longer baselines (i.e 1 sec).<br>
<br>
Although I don't know what Arno meant in that specific context, I<br>
guess he was probably referring to the finding reported by Groppe,<br>
Makeig, and Kutas (2009). In the paper, the authors reports<br>
whole-epoch baseline produced better ICA results compared to short<br>
pre-stimulus baseline. Therefore, for ICA purpose, it's even better to<br>
use an entire epoch for a baseline. The authors says 'It is not clear<br>
what causes this difference.' in the paper (pp.1208), though I heard<br>
Scott say a brief explanation. What do you think, Scott?<br>
<br>
Makoto<br>
<br>
<br>
<br>
2012/5/10 ida miokovic <<a href="mailto:ida.miokovic@gmail.com">ida.miokovic@gmail.com</a>>:<br>
> Dear Makoto,<br>
><br>
> thank you for your answer, it cleared the doubts in my head regarding this<br>
> =). As I understood, the purpose of Baseline Removal is for me/us to have<br>
> better insight when event in observed epoch happened, so the value around<br>
> corresponding marker is expected to be zero. Right?<br>
><br>
> I have one more question regarding this - does it matter if I Remove<br>
> Baseline for example (-1000ms to 0ms) if I have epoch that is longer (-4<br>
> secs to 4 secs)? I read in Q&A list Arno's answer regarding similar question<br>
> where he said that ICA can be unstable if the epochs baseline is too short,<br>
> so he suggests longer baselines (i.e 1 sec).<br>
><br>
> Thanks,<br>
><br>
> Ida<br>
><br>
><br>
> On Thu, May 10, 2012 at 9:45 PM, Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu">mmiyakoshi@ucsd.edu</a>><br>
> wrote:<br>
>><br>
>> Dear Ida,<br>
>><br>
>> The consequence would be that you may not have near-zero potential<br>
>> at/around time zero (and this time zero which should be an onset of<br>
>> whatever event). Usually people want to reset their data to zero<br>
>> microvolt at/around time zero, so they subtract mean of short time<br>
>> period immediately before it (for example, -200 ms to 0 ms as a<br>
>> baseline period). Am I answering to your question? If not, let me<br>
>> know.<br>
>><br>
>> Makoto<br>
>><br>
>> 2012/5/10 ida miokovic <<a href="mailto:ida.miokovic@gmail.com">ida.miokovic@gmail.com</a>>:<br>
<div><div class="h5">>> > Hello everyone,<br>
>> ><br>
>> > Since I do not have experience in eeg signal processing, I am asking you<br>
>> > for<br>
>> > the opinion regarding epoch baseline removal (a window for this pops up<br>
>> > after I do the data epoching). Epochs I am extracting are quite long: -4<br>
>> > secs before and 4 secs after Marker of my interest.<br>
>> ><br>
>> > Why is following suggested in tutorial:<br>
>> ><br>
>> > "Using the mean value in the pre-stimulus period (the pop_rmbase()<br>
>> > default)<br>
>> > is effective for many datasets, if the goal of the analysis is to define<br>
>> > transformations that occur in the data following the time-locking<br>
>> > events."<br>
>> ><br>
>> > What are the consequences if I leave the fields in pop up window (Epoch<br>
>> > Baseline Removal) empty and therefore have the whole epoch used as a<br>
>> > baseline?<br>
>> ><br>
>> > Thank you in advance,<br>
>> ><br>
>> > All the best,<br>
>> ><br>
>> > Ida<br>
>> ><br>
>> ><br>
>> ><br>
>> ><br>
>> ><br>
>> ><br>
</div></div>>> > _______________________________________________<br>
>> > Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>
>> > To unsubscribe, send an empty email to<br>
>> > <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>
>> > For digest mode, send an email with the subject "set digest mime" to<br>
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>><br>
>><br>
<span class="HOEnZb"><font color="#888888">>><br>
>> --<br>
>> Makoto Miyakoshi<br>
>> JSPS Postdoctral Fellow for Research Abroad<br>
>> Swartz Center for Computational Neuroscience<br>
>> Institute for Neural Computation, University of California San Diego<br>
><br>
><br>
<br>
<br>
<br>
--<br>
Makoto Miyakoshi<br>
JSPS Postdoctral Fellow for Research Abroad<br>
Swartz Center for Computational Neuroscience<br>
Institute for Neural Computation, University of California San Diego<br>
</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>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, <a href="http://sccn.ucsd.edu/%7Escott" target="_blank">http://sccn.ucsd.edu/~scott</a><br>
</div>