<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Hannah,<div class=""><br class=""></div><div class="">I would like to try to replicate this behavior. Could you please make available one of the affected datasets and the relevant parts of the code used for pre-processing and ICA, e.g. via the bugtracker or Dropbox? Are there possibly data discontinuities without boundary markers? Did you keep MATLAB version constant?</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Andreas</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">Am 19.01.2017 um 09:41 schrieb Hiebel, Hannah (<a href="mailto:hannah.hiebel@uni-graz.at" class="">hannah.hiebel@uni-graz.at</a>) <<a href="mailto:hannah.hiebel@uni-graz.at" class="">hannah.hiebel@uni-graz.at</a>>:</div><br class="Apple-interchange-newline"><div class=""><div style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;" class=""><span class="">Dear Alberto and Tarik,</span></div><p class="MsoNormal" style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;"><span class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;" class=""><span class="">thank you very much for your suggestions. I work on a computer with i7 3.60 GHz processor, 8 GB RAM or notebook with i7 2.5 GHz and 8GB Ram – this should be okay.</span></div><div style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;" class=""><span class="">Gladly, the ICA eventually finds a solution and the IC maps look good. However, the question for me is still why does the ICA become >10 times slower after changing the pre-processing routine. I’ve continued testing and indeed the high-pass filter seems to be responsible for the differences.</span></div><p class="MsoNormal" style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;"><span class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;" class=""><span class="">In my recent routine I used the eeglab windowed sinc FIR filter with 1 Hz cut-off frequency, 1 Hz transition bandwidth, 0.001 passband ripple, Kaiser window. When I change the filter (settings) while keeping all other steps the same, I see huge differences in ICA runtime in some subjects. That is, when using a 0.1 Hz Butterworth filter instead, ICA is running fast again (< 1h for the subjects where it took > 30h before). With the eeglab basic FIR filter with 1 Hz passband edge and default settings defined by the internal heuristic (resulting in 0.5 Hz cut-off, 1 Hz trans. bandwidth) it’s also running much faster in most subjects but already takes >20h in the “problematic” cases.<span class="Apple-converted-space"> </span></span></div><p class="MsoNormal" style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;"><span class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;" class=""><span class="">This gives me the impression that the higher cut-off frequency causes the problems (or maybe stopband edge and attenuation are more decisive?).</span></div><div style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;" class=""><span class="">That's very surprising as I would not have expected the filter to have such an impact and a higher cut-off is normally recommended.</span></div><p class="MsoNormal" style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;"><span class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;" class=""><span class="">I’d be very grateful if anyone could provide more insight!</span></div><p class="MsoNormal" style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;"><span class=""> </span></p><div style="margin-top: 0px; margin-bottom: 0.0001pt; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); line-height: normal;" class=""><span class="">Best,<br class="">Hannah</span><span class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><br class=""></div><div id="Signature" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><div name="divtagdefaultwrapper" style="margin: 0px; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div class="BodyFragment"><font size="2" class=""><div class="PlainText">Hannah Hiebel, Mag.rer.nat.<br class="">Cognitive Psychology & Neuroscience</div><div class="PlainText">Department of Psychology, University of Graz</div><div class="PlainText">Universitätsplatz 2, 8010 Graz, Austria<br class=""><br class=""></div></font></div></div></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); color: rgb(33, 33, 33);" class=""><hr tabindex="-1" style="display: inline-block; width: 565.453125px;" class=""><div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">Von:</b><span class="Apple-converted-space"> </span>Alberto Sainz <<a href="mailto:albertosainzc@gmail.com" class="">albertosainzc@gmail.com</a>><br class=""><b class="">Gesendet:</b><span class="Apple-converted-space"> </span>Mittwoch, 18. Jänner 2017 04:29<br class=""><b class="">An:</b><span class="Apple-converted-space"> </span>Hiebel, Hannah (<a href="mailto:hannah.hiebel@uni-graz.at" class="">hannah.hiebel@uni-graz.at</a>)<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:eeglablist@sccn.ucsd.edu" class="">eeglablist@sccn.ucsd.edu</a><br class=""><b class="">Betreff:</b><span class="Apple-converted-space"> </span>Re: [Eeglablist] ICA running very slowly</font><div class=""> </div></div><div class=""><div dir="ltr" class="">I would suggest to try in a different computer. I have been applying ICA in a 14 electrode 30min continuous EEG recording (around 40mb) in two different computers. 2Ghz dual core computer took 1h. 2.2Ghz i7 takes around 5 minutes.<br class=""><br class="">I know your data is larger but just to say that the processor (and probably the RAM if is too small) matters a lot.<br class=""><br class="">Good luck</div><div class="gmail_extra"><br class=""><div class="gmail_quote">2017-01-16 20:26 GMT+01:00 Hiebel, Hannah (<a href="mailto:hannah.hiebel@uni-graz.at" class="">hannah.hiebel@uni-graz.at</a>)<span dir="ltr" class=""><<a href="mailto:hannah.hiebel@uni-graz.at" target="_blank" class="">hannah.hiebel@uni-graz.at</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div dir="ltr" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class="">Dear all,<br class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class="">I am using ICA to clean my EEG data for eye-movement related artifacts. I’ve already done some testing in the past to see how certain pre-processing steps affect the quality of my decomposition (e.g. filter settings). In most cases, it took approximately 1-2 hours to run ICA for single subjects (62 channels: 59 EEG, 3 EOG channels).<br class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class="">Now that I run ICA on my final datasets it suddenly takes hours over hours to do only a few steps. It still works fine in some subjects but in others runica takes up to 50 hours. I observed that in some cases the weights blow up (learning rate is lowered many times); in others it starts right away without lowering the learning rate but every step takes ages.</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class="">I’ve done some troubleshooting to see if a specific pre-processing step causes this behavior but I cannot find a consistent pattern. It seems to me though that (at least in some cases) the high-pass filter played a role – can anyone explain how this is related? Could a high-pass filter potentially be too strict?<br class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class="">On the eeglablist I could only find discussions about rank deficiency (mostly due to using average reference) as a potential reason. I re-referenced to linked mastoids – does this also affect the rank? When I check with<span class="Apple-converted-space"> </span><em class=""><span style="font-family: Verdana, sans-serif;" class="">rank(EEG.data(:, :))<span class="Apple-converted-space"> </span></span></em>it returns 62 though, which is equal to the number of channels. For some of the “bad” subjects I nonehteless tried without re-referencing – no improvement. Also, reducing dimensionality with pca ("pca, 61") didn’t help.<br class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class="">Any advice would be very much appreciated!<br class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class="">Many thanks in advance,</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class="">Hannah</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="m_-9147620952188609437Signature" class=""><div name="divtagdefaultwrapper" style="margin: 0px; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div class="m_-9147620952188609437BodyFragment"><font size="2" class=""><div class="m_-9147620952188609437PlainText">Hannah Hiebel, Mag.rer.nat.<br class="">Cognitive Psychology & Neuroscience</div><div class="m_-9147620952188609437PlainText">Department of Psychology, University of Graz</div><div class="m_-9147620952188609437PlainText">Universitätsplatz 2, 8010 Graz, Austria</div></font></div></div></div></div><br class="">______________________________<wbr class="">_________________<br class="">Eeglablist page:<span class="Apple-converted-space"> </span><a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" rel="noreferrer" target="_blank" class="">http://sccn.ucsd.edu/eeglab/<wbr class="">eeglabmail.html</a><br class="">To unsubscribe, send an empty email to<span class="Apple-converted-space"> </span><a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" class="">eeglablist-unsubscribe@sccn.<wbr class="">ucsd.edu</a><br class="">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" class="">eeglablist-request@sccn.ucsd.<wbr class="">edu</a><br class=""></blockquote></div><br class=""></div></div></div><span style="font-family: Calibri, Arial, Helvetica, sans-serif; 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