<div>in addition to my response further below, here are</div><div>some other eeglab discussions I found via google (searcing PCA, ICA, eeglab)</div><div>that seem related to some of your questions, and that you may find useful:</div>
<div><br></div><span style="color:rgb(34,34,34);line-height:15px;font-family:arial,sans-serif"><h3 style="font-size:medium;font-weight:normal;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;display:block;overflow-x:hidden;overflow-y:hidden;text-overflow:ellipsis;white-space:nowrap">
<a href="http://www.google.com/url?sa=t&rct=j&q=site%3Asccn.ucsd.edu%20running%20ica%20with%20pca%20eeglab&source=web&cd=14&ved=0CC8QFjADOAo&url=http%3A%2F%2Fsccn.ucsd.edu%2Fpipermail%2Feeglablist%2F2012%2F004652.html&ei=5Vh3UOXCDMbiiAKIzIDoCA&usg=AFQjCNFrJ_1rUMANWhgYkho9LdIAFfYTmg&sig2=b6FCefIns3Du6J3o8CxbTA" style="color:rgb(17,34,204)" target="_blank">[<em style="font-weight:bold;font-style:normal">Eeglablist</em>] Problems with rank computation - <em style="font-weight:bold;font-style:normal">ICA</em></a></h3>
<div style="max-width:42em;color:rgb(34,34,34)"><div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><a href="http://sccn.ucsd.edu/pipermail/" target="_blank">sccn.ucsd.edu/pipermail/</a><b>eeglablist</b>/<a href="tel:2012%2F004652" value="+12012004652" target="_blank">2012/004652</a>.html</cite></div>
<div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><br></cite></div></div></span><span style="color:rgb(34,34,34);line-height:15px;font-family:arial,sans-serif"><h3 style="font-size:medium;font-weight:normal;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;display:block;overflow-x:hidden;overflow-y:hidden;text-overflow:ellipsis;white-space:nowrap">
<a href="http://sccn.ucsd.edu/pipermail/eeglablist/2006/001475.html" style="color:rgb(17,34,204)" target="_blank">[<em style="font-weight:bold;font-style:normal">Eeglablist</em>] value of <em style="font-weight:bold;font-style:normal">PCA</em> pre-processing before <em style="font-weight:bold;font-style:normal">running ICA</em> on EEG <b>...</b></a></h3>
<div style="max-width:42em;color:rgb(34,34,34)"><div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><a href="http://sccn.ucsd.edu/pipermail/" target="_blank">sccn.ucsd.edu/pipermail/</a><b>eeglablist</b>/2006/001475.html</cite></div>
<div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><br></cite></div></div></span><span style="color:rgb(34,34,34);line-height:15px;font-family:arial,sans-serif"><h3 style="font-size:medium;font-weight:normal;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;display:block;overflow-x:hidden;overflow-y:hidden;text-overflow:ellipsis;white-space:nowrap">
<a href="http://sccn.ucsd.edu/pipermail/eeglablist/2011/003768.html" style="color:rgb(17,34,204)" target="_blank">[<em style="font-weight:bold;font-style:normal">Eeglablist</em>] The number of the <em style="font-weight:bold;font-style:normal">ICA</em> components is smaller than the <b>...</b></a></h3>
<div style="max-width:42em;color:rgb(34,34,34)"><div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><a href="http://sccn.ucsd.edu/pipermail/" target="_blank">sccn.ucsd.edu/pipermail/</a><b>eeglablist</b>/2011/003768.html</cite></div>
<div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><br></cite></div></div></span><span style="color:rgb(34,34,34);line-height:15px;font-family:arial,sans-serif"><h3 style="font-size:medium;font-weight:normal;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;display:block;overflow-x:hidden;overflow-y:hidden;text-overflow:ellipsis;white-space:nowrap">
<a href="http://sccn.ucsd.edu/pipermail/eeglablist/2011/004269.html" style="color:rgb(17,34,204)" target="_blank">[<em style="font-weight:bold;font-style:normal">Eeglablist</em>] A second <em style="font-weight:bold;font-style:normal">ICA</em> after removing components?</a></h3>
<div style="max-width:42em;color:rgb(34,34,34)"><div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><a href="http://sccn.ucsd.edu/pipermail/" target="_blank">sccn.ucsd.edu/pipermail/</a><b>eeglablist</b>/2011/004269.html</cite></div>
<div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><br></cite></div></div></span><span style="line-height:15px;font-family:arial,sans-serif"><h3 style="color:rgb(34,34,34);font-size:medium;font-weight:normal;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;display:block;overflow-x:hidden;overflow-y:hidden;text-overflow:ellipsis;white-space:nowrap">
<a href="http://sccn.ucsd.edu/pipermail/eeglablist/2008/002541.html" style="color:rgb(17,34,204)" target="_blank">[<em style="font-weight:bold;font-style:normal">Eeglablist</em>] Computing a second <em style="font-weight:bold;font-style:normal">ICA</em> on a dataset (Conny Kranczioch)</a></h3>
<div style="max-width:42em"><div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><a href="http://sccn.ucsd.edu/pipermail/" target="_blank">sccn.ucsd.edu/pipermail/</a><b>eeglablist</b>/2008/002541.html</cite></div>
<div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><br></cite></div><div style="display:block;margin-bottom:1px">
<cite style="font-style:normal;display:inline-block;margin-bottom:1px">and I assume you have already read through the tutorials, worked with the sample data provided, have done some exploring on your own, and that you have read at least </cite></div>
<div style="display:block;margin-bottom:1px"><cite style="font-style:normal;display:inline-block;margin-bottom:1px">10 articles that use the methods you are using. See Google Scholar for help.</cite></div><div style="display:block;margin-bottom:1px">
<cite style="font-style:normal;display:inline-block;margin-bottom:1px">See also this recent article from the EEGLAB group:</cite></div><div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><br>
</cite></div></div></span><span style="color:rgb(34,34,34);line-height:15px;font-family:arial,sans-serif"><h3 style="font-size:medium;font-weight:normal;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;display:block;overflow-x:hidden;overflow-y:hidden;text-overflow:ellipsis;white-space:nowrap">
<a href="http://www.google.com/url?sa=t&rct=j&q=eeg%20source%20dipolar%20makeig&source=web&cd=1&ved=0CCQQFjAA&url=http%3A%2F%2Fwww.plosone.org%2Farticle%2Finfo%253Adoi%252F10.1371%252Fjournal.pone.0030135&ei=el13UKycGILOiwLi_IDQAw&usg=AFQjCNEe9tgWzzASZLrsCdwcHCN5Guc6aQ&sig2=qwyYy38Vv57pW11aXBvxjw" style="color:rgb(17,34,204)" target="_blank">PLOS ONE: Independent <em style="font-weight:bold;font-style:normal">EEG Sources</em> Are <em style="font-weight:bold;font-style:normal">Dipolar</em></a></h3>
<div style="max-width:42em;color:rgb(34,34,34)"><div style="color:rgb(102,102,102);display:block;margin-bottom:1px"><cite style="color:rgb(0,153,51);font-style:normal;display:inline-block;margin-bottom:1px"><a href="http://www.plosone.org/.../info%3Adoi%2F10.1371%2Fjournal.pone.0030." target="_blank">www.plosone.org/.../info%3Adoi%2F10.1371%2Fjournal.pone.0030.</a>..</cite></div>
</div></span><br>
<br><br><div class="gmail_quote">On Thu, Oct 11, 2012 at 4:44 PM, Tarik S Bel-Bahar <span dir="ltr"><<a href="mailto:tarikbelbahar@gmail.com" target="_blank">tarikbelbahar@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>Greetings M,</div><div><br></div><div>***we could use an opinion from an ICA/PCA expert here, but here are some thoughts. *******</div><div>I have tried to keep it as clear, simple, and (hopefully) useful as possible.</div>
<div><br></div><div>I assume you have done some cleaning before running your first ICA, </div><div>as per general pre-ICA guidelines.</div><div>If so, then your sequence of </div><div>first ICA, then reject some epochs using IC data, </div>
<div>then second ICA, then remove some bad components...</div><div>seems OK. This seems like a normal processing procedure.</div><div><br></div><div>So now you can analyze specific ICs,</div><div>or you can "reconstruct" your eeg data using only the remaining ICs, </div>
<div>and have "cleaner" EEG data for "normal" EEG analyses.</div><div><br></div><div>imho, I don't see why you want to re-run the ICA again now for the third time.</div><div>If you do, you might get a slightly better decomposition, </div>
<div>but there should not be a significant change of ICs.</div><div><br></div><div>on your question about PCA, perhaps one of the experts can make a suggestion,</div><div>but from my understanding, the PCA option is used when </div>
<div>A. the "dimensionality" and/or the "rank" of the data has been reduced via some method, </div><div>and you want ICA to know this before running a new decomposiiton</div><div>B. or you want to "reduce" the total number of dimensions that ICA generates, </div>
<div>for some other good reason. [see published articles on this point]</div><div><br></div><div>Last, I want you to know I am not 100% sure about whether or not you "have to" run ICA with PCA options</div><div>
when you are re-running ICA after having "dropped/removed" some components. </div><div>one previous eeglab list discussion:</div><div><a href="http://sccn.ucsd.edu/pipermail/eeglablist/2012/004543.html" target="_blank">http://sccn.ucsd.edu/pipermail/eeglablist/2012/004543.html</a></div>
<div><br></div><div>Good luck and let the list know of your success.</div><div><br></div><div><br></div><div><br></div>
</blockquote></div><br>