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</o:shapelayout></xml><![endif]--></head><body lang=NL-BE link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Dear Arno<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>See for instance;<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Leonid Zhukov, David Weinstein and Chris Johnson (2000): Independent Component Analysis For EEG Source Localization In Realistic Head Models.<o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><span lang=EN-US style='font-size:11.0pt;font-family:Wingdings;color:#1F497D'><span style='mso-list:Ignore'>è<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best Veerle<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Arnaud Delorme [mailto:arno@ucsd.edu] <br><b>Sent:</b> maandag 25 februari 2013 2:19<br><b>To:</b> Veerle ROSS<br><b>Cc:</b> eeglablist@sccn.ucsd.edu<br><b>Subject:</b> Re: [Eeglablist] running ICA a second time<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Dear Veerle,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Thanks,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Arno<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On 19 Feb 2013, at 01:36, Veerle ROSS wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Hi all</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;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:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;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:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Therefore we were wondering:</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div style='margin-left:36.0pt'><p class=MsoNormal style='text-indent:-18.0pt'><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>1.</span><span lang=EN-US style='font-size:7.0pt'> <span class=apple-converted-space> </span></span><span lang=EN-US style='font-size:11.0pt;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:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div style='margin-left:72.0pt'><p class=MsoNormal style='text-indent:-18.0pt'><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>a.</span><span lang=EN-US style='font-size:7.0pt'> <span class=apple-converted-space> </span></span><span lang=EN-US style='font-size:11.0pt;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:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div style='margin-left:72.0pt'><p class=MsoNormal style='text-indent:-18.0pt'><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>b.</span><span lang=EN-US style='font-size:7.0pt'> <span class=apple-converted-space> </span></span><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>However why can’t we use ICA the second time?</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div style='margin-left:72.0pt'><p class=MsoNormal style='text-indent:-18.0pt'><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>c.</span><span lang=EN-US style='font-size:7.0pt'> <span class=apple-converted-space> </span></span><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Other sites mention that you shouldn’t indicate components in the first ICA</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div style='margin-left:36.0pt'><p class=MsoNormal style='text-indent:-18.0pt'><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>2.</span><span lang=EN-US style='font-size:7.0pt'> <span class=apple-converted-space> </span></span><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>If we run ICA 2 times</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div style='margin-left:72.0pt'><p class=MsoNormal style='text-indent:-18.0pt'><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>a.</span><span lang=EN-US style='font-size:7.0pt'> <span class=apple-converted-space> </span></span><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Should we only remove the noise the first time?</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div style='margin-left:72.0pt'><p class=MsoNormal style='text-indent:-18.0pt'><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>b.</span><span lang=EN-US style='font-size:7.0pt'> <span class=apple-converted-space> </span></span><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Or should we also already indicated components such as blinks, bad channels, etc.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Thanks in advance.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Regards, Veerle Ross</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><p class=MsoNormal><span 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