<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"></head><body><span class="Apple-style-span" style="background-color: transparent;">Thank <span class="Apple-style-span" style="background-color: transparent;">you! <span class="Apple-style-span" style="background-color: transparent;">This <span class="Apple-style-span" style="background-color: transparent;">is <span class="Apple-style-span" style="background-color: transparent;">very <span class="Apple-style-span" style="background-color: transparent;">helpfull </span></span></span></span></span></span><div><span class="Apple-style-span" style="background-color: transparent;">Regards <span class="Apple-style-span" style="background-color: transparent;">Veerle</span></span></div><br><br><br> Arnaud Delorme <arno@ucsd.edu> schreef: <br><br><br><html><head><base href="x-msg://1753/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Veerle,<div><br></div><div>I was just reviewing a PhD thesis (<a href="http://infosci.otago.ac.nz/carl-leichter-phd">http://infosci.otago.ac.nz/carl-leichter-phd</a>) that showed using simulations and real data that removing PCA components creates artifacts in the data, especially in the power spectrum.</div><div><br></div><div>This thesis shows that it is not OK to remove "noise" using PCA when processing data channels. So it is even worse when using a statistical algorithm like ICA. Removing PCA components alters the linear projection of EEG sources to scalp sensors that ICA sought to extract. </div><div><br></div><div>Arno</div><div><br><div><div>On 25 Feb 2013, at 01:16, Veerle ROSS wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; 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-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div lang="NL-BE" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 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); ">Dear Arno<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 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); ">Thank you for the advice. May I ask why it’s a problem to run ICA with PCA? There are some references available that recommend to use PCA before ICA.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 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); ">See for instance;<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 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); ">Leonid Zhukov, David Weinstein and Chris Johnson (2000): Independent Component Analysis For EEG Source Localization In Realistic Head Models.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 36pt; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; text-indent: -18pt; "><span lang="EN-US" style="font-size: 11pt; font-family: Wingdings; color: rgb(31, 73, 125); "><span>è<span style="font: normal normal normal 7pt/normal 'Times New Roman'; "><span class="Apple-converted-space"> </span></span></span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">The EEG data is first decomposed into signal and noise subspaces using a Principal Component Analysis (PCA) decomposition. This partitioning allows us to easily discard the noise subspace, which has two primary benefits: the remaining signal is less noisy, and it has lower dimensionality. After PCA, we apply Independent Component Analysis (ICA) on the signal subspace.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 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); ">That’s why we thought that we could use ICA the first time to remove the noise and a second time to remove the remaining artifacts.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 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); ">Best Veerle<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 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); "><o:p> </o:p></span></div><div><div style="border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding-top: 3pt; padding-right: 0cm; padding-bottom: 0cm; padding-left: 0cm; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span class="Apple-converted-space"> </span>Arnaud Delorme [mailto:arno@ucsd.edu]<span class="Apple-converted-space"> </span><br><b>Sent:</b><span class="Apple-converted-space"> </span>maandag 25 februari 2013 2:19<br><b>To:</b><span class="Apple-converted-space"> </span>Veerle ROSS<br><b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:eeglablist@sccn.ucsd.edu" style="color: blue; text-decoration: underline; ">eeglablist@sccn.ucsd.edu</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [Eeglablist] running ICA a second time<o:p></o:p></span></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">Dear Veerle,<o:p></o:p></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">you can run ICA twice in a row and use the first ICA to detect bad portion of data or bad channels (because it is often easier to detect these when looking at ICA components). After you have removed bad portion of data or bad channels, you may rerun ICA.<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">But you should not remove ICA components, then rerun ICA (the data dimension would be reduced and this will force ICA to run PCA first - assuming it is able to automatically detect the dimension reduction). In other words, do not do it.<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">Thanks,<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">Arno<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">On 19 Feb 2013, at 01:36, Veerle ROSS wrote:<o:p></o:p></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><br><br><o:p></o:p></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">Hi all</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">For a current study we are applying ICA. Because our lab was not free of noise we wanted to run ICA 2 times and we hope to obtain cleaner components the second time.</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">After searching the internet and the literature we are still not sure what the limits of such a second ICA run are.</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">Therefore we were wondering:</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div style="margin-left: 36pt; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; text-indent: -18pt; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">1.</span><span lang="EN-US" style="font-size: 7pt; "> <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">Is it even possible to indicate ICA components in both the first and second ICA</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div style="margin-left: 72pt; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; text-indent: -18pt; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">a.</span><span lang="EN-US" style="font-size: 7pt; "> <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">We read that you can use the PCA option for this to reduce the dimensions</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div style="margin-left: 72pt; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; text-indent: -18pt; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">b.</span><span lang="EN-US" style="font-size: 7pt; "> <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">However why can’t we use ICA the second time?</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div style="margin-left: 72pt; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; text-indent: -18pt; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">c.</span><span lang="EN-US" style="font-size: 7pt; "> <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">Other sites mention that you shouldn’t indicate components in the first ICA</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div style="margin-left: 36pt; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; text-indent: -18pt; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">2.</span><span lang="EN-US" style="font-size: 7pt; "> <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">If we run ICA 2 times</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div style="margin-left: 72pt; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; text-indent: -18pt; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">a.</span><span lang="EN-US" style="font-size: 7pt; "> <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">Should we only remove the noise the first time?</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div style="margin-left: 72pt; "><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; text-indent: -18pt; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">b.</span><span lang="EN-US" style="font-size: 7pt; "> <span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">Or should we also already indicated components such as blinks, bad channels, etc.</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">Thanks in advance.</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">Regards, Veerle Ross</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; "> </span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; ">_______________________________________________<br>Eeglablist page:<span class="apple-converted-space"> </span><a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" style="color: blue; text-decoration: underline; ">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>To unsubscribe, send an empty email to<span class="apple-converted-space"> </span><a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" style="color: blue; text-decoration: underline; ">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>For digest mode, send an email with the subject "set digest mime" to<span class="apple-converted-space"> </span><a href="mailto:eeglablist-request@sccn.ucsd.edu" style="color: blue; text-decoration: underline; ">eeglablist-request@sccn.ucsd.edu</a><o:p></o:p></span></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div></div></div></span></blockquote></div><br></div></body></html>