<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Yes, Steve is right. Baseline correction might offset the potential of some electrodes compared to other electrodes, and if there is a source projecting linearly to several data channels (as it should), the projection might not be linear after baseline correction. Consistent with this, David Groppe who has done formal testing on ICA data quality decompositions and showed that ICA quality degrades when using short baseline prior to doing ICA. <div><br></div><div><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062525/">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062525/</a><br><div><br></div><div>Arno</div><div><br><div><div>On Sep 13, 2012, at 11:23 AM, Steve Luck wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Eren and Joe: I'm not an expert on using ICA -- this is just the advice I received many years ago from Arno and Scott. The idea is that baseline correction might change the scalp distribution of various components on each trial, which would prevent ICA from working properly. However, I don't know whether baseline correction ends up being worthwhile on balance despite this potential problem. It may, as Joe suggests, depend on factors such as whether the data have been high-pass filtered and the nature of the slow drifts.<div><br></div><div>In general, we need more sophisticated simulation studies to answer questions like this. (This is a hint for you technically inclined graduate students and postdocs!)</div><div><br></div><div>Steve</div><div><br></div><div><br><div><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Joseph Dien <<a href="mailto:jdien07@mac.com">jdien07@mac.com</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: [Eeglablist] On ICA based artifact rejection</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">September 12, 2012 6:56:29 PM PDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">"Gunseli, E." <<a href="mailto:e.gunseli@vu.nl">e.gunseli@vu.nl</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>Cc: </b></span><span style="font-family:'Helvetica'; font-size:medium;">"<a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a>" <<a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a>><br></span></div><br><br>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>All due respect to Steve (who runs a great course), I'd need some persuading to follow this advice. The entire reason we baseline correct is that without it we can't actually be sure what the true zero is due to slow drifts in the data. Much of the relative values that are being removed we want to remove because they reflect these slow but, over time, substantial drifts. In my own data, I've found that I get better results (in terms of clean removal of blink artifacts) with ICA artifact correction of epoched data if it is baseline corrected first because it helps minimize the effects of these drifts. I haven't subjected this question to systematic evaluation however. I imagine it would also depend on the characteristics of the recording equipment and filter settings and so forth.</div><div><br></div><div>Joe</div><br><div><div>On Sep 12, 2012, at 7:02 AM, "Gunseli, E." <<a href="mailto:e.gunseli@vu.nl">e.gunseli@vu.nl</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="NL" link="blue" vlink="purple" style="font-family: Courier; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="WordSection1" style="page: WordSection1; "><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Dear all,<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">I have a question about the steps that should be taken before running ICA.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">If we are going to epoch the data (step 5), why are we manually rejecting the extra noisy parts earlier (step 2).<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Since these extra noisy portions are mostly at beginning and end of trial blocks, they will be gone away during epoching anyway.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">So, epoching the critical time window can save a fair amount of time that else we would have spent on manual inspection.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">At this point I have another question; I have read that, it is better to run ICA on continuous, non-epoched data.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">One of the problems of running ICA on epoched data is that, “the baseline correction changes relative values across channels” (S. Luck, ERP Boot Camp Lecture Slides). But probably that is not the only reason to run ICA on continuous data because this problem can easily be overcome via removing the baseline after running ICAs.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">So I guess there should be other problems related to running ICAs on epoched data.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Can anyone provide information about these potential problems?<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Kind regards,<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Eren<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div></div></div></blockquote></div></div></blockquote></div><br><div apple-content-edited="true">
--------------------------------------------------------------------<br>Steven J. Luck, Ph.D.<br>Director, Center for Mind & Brain<br>Professor, Department of Psychology<br>University of California, Davis<br>Room 109<br>267 Cousteau Place<br>Davis, CA 95618<br>(530) 297-4424<br>E-Mail: <a href="mailto:sjluck@ucdavis.edu">sjluck@ucdavis.edu</a><br>Web: <a href="http://mindbrain.ucdavis.edu/people/sjluck">http://mindbrain.ucdavis.edu/people/sjluck</a><br>Calendar: <a href="http://www.google.com/calendar/embed?src=stevenjluck%40gmail.com&ctz=America/Los_Angeles">http://www.google.com/calendar/embed?src=stevenjluck%40gmail.com&ctz=America/Los_Angeles</a><br>--------------------------------------------------------------------<br><br><br><br><br><br><br>
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