<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=""><div>Hi Angel, </div><div><br class=""></div><div>I’ve not used the clustering implemented in EEGLAB itself, but I’ve been very pleased with the spatiotemporal clustering and permutation tests implemented in the CosmoMVPA toolbox. This clusters across both sensors and time, which is what I think you want, and uses low-assumption approaches like TFCE. There is basic support for the EEGLAB ‘set’ data format. </div><div><br class=""></div><div><a href="http://cosmomvpa.org" class="">cosmomvpa.org</a></div><div><br class=""></div><div>this function in particular: </div><div><br class=""></div><div><a href="http://www.cosmomvpa.org/matlab/cosmo_montecarlo_cluster_stat.html#cosmo-montecarlo-cluster-stat" class="">http://www.cosmomvpa.org/matlab/cosmo_montecarlo_cluster_stat.html#cosmo-montecarlo-cluster-stat</a></div><div><br class=""></div><div>The package is developed and maintained by Nick Oosterhof and Andrew Connolly, and I know Nick spent a lot of time and thought on exactly your issue (if I correctly understand what you mean). </div><div><br class=""></div><div>best, clayton</div><div><br class=""></div><div><br class=""></div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class=""><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">From:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">Angel Caputi <<a href="mailto:caputiangel@gmail.com" class="">caputiangel@gmail.com</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><b class="">Re: [Eeglablist] Cluster-based permutation tests for 3 conditions</b><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Date:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">September 11, 2017 at 8:56:14 PM GMT+2<br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">Stephen Politzer-Ahles <<a href="mailto:politzerahless@gmail.com" class="">politzerahless@gmail.com</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">"<a href="mailto:eeglablist@sccn.ucsd.edu" class="">eeglablist@sccn.ucsd.edu</a>" <<a href="mailto:eeglablist@sccn.ucsd.edu" class="">eeglablist@sccn.ucsd.edu</a>><br class=""></span></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div dir="ltr" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">I wonder What kind of post-hoc test can be used for testing that the cluster site (i.e. combination of times and channels) we need to use for spatio-temporal localization. Would not be the use a sencond test on the cluster region a kind of double dipping? What would the correct procedure for testing where the spatio-temporal pattern differ? <div class="">Sincerely </div><div class="">Angel</div><div class=""><br class=""></div></div><div class="gmail_extra" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><br class=""><div class="gmail_quote">2017-09-09 9:49 GMT-03:00 Stephen Politzer-Ahles<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:politzerahless@gmail.com" target="_blank" class="">politzerahless@gmail.com</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr" class="">Cluster-based permutation tests are not necessarily between two conditions. They operate on any test statistic; this test statistic can be an F test from an ANOVA with three conditions. Just like with a two-condition permutation test, if the test comes out significant this will tell you that the three conditions differ in this dataset (whatever selection of channels, times, and frequency bands you looked at), and the cluster extent can give you an idea of what channel/time/frequency cluster is driving that difference. With an F-test, you would need to do follow-up comparisons to see which particular conditions are driving the difference.<br class=""></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_-4158992315510138863gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><br class=""></div><span class=""><div class="">---<br class=""></div>Stephen Politzer-Ahles<br class="">The Hong Kong Polytechnic University<br class="">Department of Chinese and Bilingual Studies<br class=""><a href="http://www.mypolyuweb.hk/~sjpolit/" target="_blank" class="">http://www.mypolyuweb.hk/~<wbr class="">sjpolit/</a></span><a href="http://www.nyu.edu/projects/politzer-ahles/" target="_blank" class=""></a></div></div></div></div></div></div></div></div></div><div class=""><div class="h5"><br class=""><div class="gmail_quote">On Thu, Sep 7, 2017 at 9:43 AM, 時本真吾<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:tokimoto@mejiro.ac.jp" target="_blank" class="">tokimoto@mejiro.ac.jp</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">Dear EEGLAB users,<br class=""><br class="">I usually perform cluster-based permutation tests for my EEG analyses. I understand permutation tests are tests between two conditions. However, I have realized that the test results can be presented for the comparison of three conditions, as is shown by the image file below. I usually perform the test from the GUI of EEGLAB. Could anyone tell me how I should understand the test results? Thank you in advance.<br class=""><br class=""><a href="http://tokimoto.o.oo7.jp/ERSP_sample.jpg" rel="noreferrer" target="_blank" class="">http://tokimoto.o.oo7.jp/ERSP_<wbr class="">sample.jpg</a><br class=""><br class="">******************************<wbr class="">************<br class="">Shingo Tokimoto, Ph.D.<br class="">in Linguistics and Psychology<br class="">Department of Foreign Languages<br class="">Mejiro University<br class="">4-31-1, Naka-Ochiai, Shinjuku, Tokyo,<br class="">161-8539, Japan<br class=""><a href="mailto:tokimoto@mejiro.ac.jp" target="_blank" class="">tokimoto@mejiro.ac.jp</a><br class="">******************************<wbr class="">************<br class=""><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/ee<wbr class="">glabmail.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" target="_blank" class="">eeglablist-unsubscribe@sccn.uc<wbr class="">sd.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" target="_blank" class="">eeglablist-request@sccn.ucsd.e<wbr class="">du</a><br class=""></blockquote></div><br class=""></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><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">From:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">Baris Demiral <<a href="mailto:demiral.007@gmail.com" class="">demiral.007@gmail.com</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><b class="">[Eeglablist] (no subject)</b><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Date:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">September 11, 2017 at 9:28:11 PM GMT+2<br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">eeglablist <<a href="mailto:eeglablist@sccn.ucsd.edu" class="">eeglablist@sccn.ucsd.edu</a>><br class=""></span></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div dir="ltr" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><p class="MsoNormal" style="margin-top: 0px; margin-bottom: 12pt;">Statistician is needed for Sleep studies. Please see below:</p><p class="MsoNormal" style="margin-top: 0px; margin-bottom: 12pt;"><a href="https://www.linkedin.com/jobs/view/423167080/" target="_blank" class="">https://www.linkedin.com/jobs/view/423167080/</a><span class=""></span></p><div class=""><br class=""></div><div class="">Best,</div><div class="">Baris</div><br class=""></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">From:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">lmm226 <<a href="mailto:laura.morett@yale.edu" class="">laura.morett@yale.edu</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><b class="">[Eeglablist] Open source data acquisition software for ANT Neuro</b><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Date:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">September 12, 2017 at 3:50:17 AM GMT+2<br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">"<a href="mailto:eeglablist@sccn.ucsd.edu" class="">eeglablist@sccn.ucsd.edu</a>" <<a href="mailto:eeglablist@sccn.ucsd.edu" class="">eeglablist@sccn.ucsd.edu</a>><br class=""></span></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Dear colleagues:</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I'm writing to inquire into whether anyone knows of open source data acquisition software that works with ANT Neuro's hardware. I have an amplifier manufactured by TMSi that was purchased in 2015 and appears to have been manufactured in 2014. It came with ANT Neuro's proprietary data acquisition software, but it requires a dongle to use, and the group that I acquired it from needs their dongle for another system that they're currently using to collect data. I did find one open source option called OpenVIBE, but it isn't clear whether it works with this system. Does anyone have any experience using this or any other open source acquisition software, particularly with ANT Neuro's hardware? If so, I would be interested in hearing about your experience using it.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Best wishes,</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Laura Morett</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="Signature" class=""><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols;" class=""><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><p class="p1" style="margin-top: 0px; margin-bottom: 0px;"><span class="s1"><span id="ms-rterangepaste-start" class=""></span></span></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">********************************************************</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">Laura M. Morett</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">Hilibrand Postdoctoral Fellow</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1"></span><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">Yale Child Study Center</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">320 S. Frontage Rd.</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">New Haven, CT 06520</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1"></span><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s1">Email:<span class="Apple-converted-space"> </span><a href="mailto:laura.morett@yale.edu" class="">laura.morett@yale.edu</a></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s2">Phone: (</span><span class="s1">203) 737-4586</span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="s3">Web: <a href="http://lauramorettphd.wix.com/home" id="LPNoLP" class=""><span class="s4">http://lauramorettphd.wix.com/home</span></a></span></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><p class="p1" style="margin-top: 0px; margin-bottom: 0px;"><span class="s1"><span id="ms-rterangepaste-end" class=""></span></span></p><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p></div></div></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">From:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">Stephen Politzer-Ahles <<a href="mailto:politzerahless@gmail.com" class="">politzerahless@gmail.com</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><b class="">Re: [Eeglablist] Cluster-based permutation tests for 3 conditions</b><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Date:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">September 12, 2017 at 4:32:09 AM GMT+2<br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">Angel Caputi <<a href="mailto:caputiangel@gmail.com" class="">caputiangel@gmail.com</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">"<a href="mailto:eeglablist@sccn.ucsd.edu" class="">eeglablist@sccn.ucsd.edu</a>" <<a href="mailto:eeglablist@sccn.ucsd.edu" class="">eeglablist@sccn.ucsd.edu</a>><br class=""></span></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div dir="ltr" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">As far as I understand, double-dipping (in the form of non-independent analysis, e.g. Baker, Hutchison, & Kanwisher 2007) is when you use the same test statistic to identify an analysis region and to test it. e.g., if you do a cluster-based permutation t-test, find a p=.2 cluster, and then do a regular t-test on the average activation within that cluster and get p=.00001, that's double-dipping. Using a different analysis to identify a cluster than what you look at within the cluster is not double-dipping --- e.g., you can use some control manipulation to identify a cluster, and then look at the manipulation of interest just within this cluster. The issue described above is I guess kind of halfway in between, so I'm not totally sure. Using an omnibus F-test to find a cluster and then testing the pairwise comparisons in it is not using the exact same test twice; on the other hand, though, the F-test is not totally independent of the pairwise comparisons within it. My intuition is that it should be ok to look at these pairwise comparisons as long as your interpretation of them is "there was a significant omnibus ANOVA effect<span class="Apple-converted-space"> </span><i class="">and it was driven by a difference between these conditions</i>", rather than saying directly "there was a difference between these conditions" (because the latter is technically not what was tested in the cluster-based permutation test). I have done this before and gotten away with it (although that doesn't mean it's right; all kinds of bad stats stuff gets published, maybe my analysis was more of that). I'd be interested learn what others think.<br class=""></div><div class="gmail_extra" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><br class=""></div><span class=""><div class="">---<br class=""></div>Stephen Politzer-Ahles<br class="">The Hong Kong Polytechnic University<br class="">Department of Chinese and Bilingual Studies<br class=""><a href="http://www.mypolyuweb.hk/~sjpolit/" target="_blank" class="">http://www.mypolyuweb.hk/~sjpolit/</a></span><a href="http://www.nyu.edu/projects/politzer-ahles/" target="_blank" class=""></a></div></div></div></div></div></div></div></div></div><br class=""><div class="gmail_quote">On Tue, Sep 12, 2017 at 2:56 AM, Angel Caputi<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:caputiangel@gmail.com" target="_blank" class="">caputiangel@gmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr" class="">I wonder What kind of post-hoc test can be used for testing that the cluster site (i.e. combination of times and channels) we need to use for spatio-temporal localization. Would not be the use a sencond test on the cluster region a kind of double dipping? What would the correct procedure for testing where the spatio-temporal pattern differ? <div class="">Sincerely </div><span class="HOEnZb"><font color="#888888" class=""><div class="">Angel</div><div class=""><br class=""></div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">2017-09-09 9:49 GMT-03:00 Stephen Politzer-Ahles<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:politzerahless@gmail.com" target="_blank" class="">politzerahless@gmail.com</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr" class="">Cluster-based permutation tests are not necessarily between two conditions. They operate on any test statistic; this test statistic can be an F test from an ANOVA with three conditions. Just like with a two-condition permutation test, if the test comes out significant this will tell you that the three conditions differ in this dataset (whatever selection of channels, times, and frequency bands you looked at), and the cluster extent can give you an idea of what channel/time/frequency cluster is driving that difference. With an F-test, you would need to do follow-up comparisons to see which particular conditions are driving the difference.<br class=""></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_1090400672654858293m_-4158992315510138863gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><br class=""></div><span class=""><div class="">---<br class=""></div>Stephen Politzer-Ahles<br class="">The Hong Kong Polytechnic University<br class="">Department of Chinese and Bilingual Studies<br class=""><a href="http://www.mypolyuweb.hk/~sjpolit/" target="_blank" class="">http://www.mypolyuweb.hk/~sjpo<wbr class="">lit/</a></span><a href="http://www.nyu.edu/projects/politzer-ahles/" target="_blank" class=""></a></div></div></div></div></div></div></div></div></div><div class=""><div class="m_1090400672654858293h5"><br class=""><div class="gmail_quote">On Thu, Sep 7, 2017 at 9:43 AM, 時本真吾<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:tokimoto@mejiro.ac.jp" target="_blank" class="">tokimoto@mejiro.ac.jp</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">Dear EEGLAB users,<br class=""><br class="">I usually perform cluster-based permutation tests for my EEG analyses. I understand permutation tests are tests between two conditions. However, I have realized that the test results can be presented for the comparison of three conditions, as is shown by the image file below. I usually perform the test from the GUI of EEGLAB. Could anyone tell me how I should understand the test results? Thank you in advance.<br class=""><br class=""><a href="http://tokimoto.o.oo7.jp/ERSP_sample.jpg" rel="noreferrer" target="_blank" class="">http://tokimoto.o.oo7.jp/ERSP_<wbr class="">sample.jpg</a><br class=""><br class="">******************************<wbr class="">************<br class="">Shingo Tokimoto, Ph.D.<br class="">in Linguistics and Psychology<br class="">Department of Foreign Languages<br class="">Mejiro University<br class="">4-31-1, Naka-Ochiai, Shinjuku, Tokyo,<br class="">161-8539, Japan<br class=""><a href="mailto:tokimoto@mejiro.ac.jp" target="_blank" class="">tokimoto@mejiro.ac.jp</a><br class="">******************************<wbr class="">************<br class=""><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/ee<wbr class="">glabmail.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" target="_blank" class="">eeglablist-unsubscribe@sccn.uc<wbr class="">sd.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" target="_blank" class="">eeglablist-request@sccn.ucsd.e<wbr class="">du</a><br class=""></blockquote></div><br class=""></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/ee<wbr class="">glabmail.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" target="_blank" class="">eeglablist-unsubscribe@sccn.uc<wbr class="">sd.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" target="_blank" class="">eeglablist-request@sccn.ucsd.e<wbr class="">du</a><br class=""></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">From:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">Samran <<a href="mailto:samranasghar@gmail.com" class="">samranasghar@gmail.com</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><b class="">Re: [Eeglablist] ICA pipeline questions</b><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Date:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">September 12, 2017 at 9:14:40 AM GMT+2<br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><a href="mailto:tarikbelbahar@gmail.com" class="">tarikbelbahar@gmail.com</a><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">eeglablist <<a href="mailto:eeglablist@sccn.ucsd.edu" class="">eeglablist@sccn.ucsd.edu</a>><br class=""></span></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div dir="ltr" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class="">Hi Tarik,<br class=""><br class=""></div>Thanks a lot for the detailed response. Really helpful. :)<br class=""><br class=""></div>*The data is not PREPed again, it's the same data loaded in step1 of the pipelines. It was not clear earlier.<br class=""><br class=""></div>*It seems reasonable to move downsampling at step2. It will likely reduce the filtering time as well.<br class=""><br class=""></div>*You have suggested to drop a channel, instead of using PCA. Can you please recommend the criteria for selection of channel to be dropped, or it can be any channel? As per Makoto's pipeline, it is reasonable to drop the reference channel, but the data I have is not referenced. Although I can reference it to a particular channel offline in EEGLAB, but I would like to go with average reference, as given by PREP pipeline.<br class=""><br class=""></div>*Do you have any suggestions of using ICA with PREP pipeline (because of the interpolation step)? Here's what I have come up with: Use PREP pipeline to clean_line and identifying the bad channels. For ICA, use the clean_lined data having only the good channels (chans_G) referenced to the average of chans_G. After removing bad ICs (and rejecting any leftover bad epochs), interpolate and average reference the data. However, I think the data will not be referenced to the 'true' average now, one of the targets of PREP, since good channels were already referenced to average of chans_G. Is there a better way of doing ICA with PREP?<br class=""></div><br class=""></div>Thanks.<br class=""></div><div class="gmail_extra" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><br class=""><div class="gmail_quote">On Tue, Sep 12, 2017 at 7:22 AM, Tarik S Bel-Bahar<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:tarikbelbahar@gmail.com" target="_blank" class="">tarikbelbahar@gmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr" class=""><div class="gmail_default" style="color: rgb(51, 51, 153);">Some followup points here for your Samran:</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">1. many researchers use and trust near fully automatic or fully automatic pipelines. See for example TAPEEG. It really depends on their biases (e.g., being programmers/engineers versus EEG researchers) and their needs (e.g., having dozens versus thousands of files). Further, automated pipeleines can be tweaked to your satisfaction, and can also provide "quality metrics" to know when there are issues in the pipeline.</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">2. Your "Drop artifactual ICs" step can be complex. Some researchers only keep neural ICs, some researchers only remove artifactual ICs, some researchers fully trust the results of ICA classifcation plugins such as Adjust, MARA, IC-MARA, and SASICA. If you haven't had a chance to use/test the results form those plugins, please be sure to do so.</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">3. If you haven't had a chance to yet, make sure to avail yourself of the excellent IC classification site from Luca at the following link. I usually recommend to students and beginners to do at least 500 classifications there. </div><div class="gmail_default"><font color="#333399" class=""><a href="http://reaching.ucsd.edu:8000/tutorial/overview" target="_blank" class="">http://reaching.ucsd.edu:8000/<wbr class="">tutorial/overview</a></font><br class=""></div><div class=""><div class="h5"><div class="gmail_default"><font color="#333399" class=""><br class=""></font></div><div class="gmail_default"><font color="#333399" class=""><br class=""></font></div><div class="gmail_default"><font color="#333399" class=""><br class=""></font></div><div class="gmail_default"><font color="#333399" class=""><br class=""></font></div><div class="gmail_default"><font color="#333399" class=""><br class=""></font></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Mon, Sep 11, 2017 at 11:55 AM, Tarik S Bel-Bahar<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:tarikbelbahar@gmail.com" target="_blank" class="">tarikbelbahar@gmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<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" class=""><div style="color: rgb(51, 51, 153);" class="">Hello Samran, here's notes for you below, good luck on your eeg adventures!</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">******NOTES FOR SAMRAN********</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">*you need to understand/know exactly what PREP is doing, and if you want comments on that, you should list the steps you think PREP is doing.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">*your pipeline 1 seems okay. One can drop channels instead of PCA.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">*Note It's generally not recommended to interpolate channels before ICA.</div><div style="color: rgb(51, 51, 153);" class="">*Not sure why you are running PREP again (I guess it's okay if it does exactly the same thing as earlier.</div><div style="color: rgb(51, 51, 153);" class="">*Reject epochs at step 13 after reviewing the data, unless for some reason you trust that A) you have removed all artifactual ICs and B) there are no remaining artifactual periods in the epoched data </div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">*In your Pipeline 2, it's up to users whether or not they run a second ICA after pruning the data of Bad ICs. I would not recommend that, but you can look in past eeglablist answers, and in Makoto's processing suggestions, and in publications using ICA for EEG.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">*Double check that you don't need to move the resampling to the be first or second step.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">Your question #1</div><div style="color: rgb(51, 51, 153);" class="">***ICA in eeglab does not care if there are discontinuities in the data, so it does not matter if you give it continuous data with breaks, or epoched data. It mixes up the time points and focuses on spatial patterns (not temporal patterns).</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">your question #2</div><div style="color: rgb(51, 51, 153);" class="">I've specified above that the Data Analyst (you) needs to be sure there is no dirty data going into your averages and metrics. That is regardless of whether or not you already pruned your data by rejecting ICs. Be careful to NOT DO everything automatically until you have checked the results of your pipelines (at the epoch level and averaging level), and your are sure really sure that you don't need to go extra cleaning after bad IC rejection.</div><div style="color: rgb(51, 51, 153);" class="">In short, there may still be dirt in the data after rejecting artifactual ICs. You need to personally check whether there is or is not remaining dirt in the data, and you need to be careful not to "assume" that things are working, but rather "check fully" that things are working.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">Your question #3b</div><div style="color: rgb(51, 51, 153);" class="">The PCA correction is correct. Personally I've had better success with "dropping a channel before ICA to account fix average referencing's drop in rank" instead of the PCA flag in runica. In other words, after average referecing, and before ICA, I drop 1 channel rather than use the PCA reduction.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">Your Question $3b</div><div style="color: rgb(51, 51, 153);" class="">Don't interpolate before ICA.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div></div></blockquote></div><br class=""></div></div></div></div></blockquote></div><br class=""><br clear="all" class=""><br class="">--<span class="Apple-converted-space"> </span><br class=""><div class="gmail_signature" data-smartmail="gmail_signature">Regards,<br class=""><br class=""><br class="">M. Samran Navid.<br class=""></div></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">From:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">Tarik S Bel-Bahar <<a href="mailto:tarikbelbahar@gmail.com" class="">tarikbelbahar@gmail.com</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><b class="">Re: [Eeglablist] ICA pipeline questions</b><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Date:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">September 11, 2017 at 8:55:02 PM GMT+2<br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">Samran <<a href="mailto:samranasghar@gmail.com" class="">samranasghar@gmail.com</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">eeglablist <<a href="mailto:eeglablist@sccn.ucsd.edu" class="">eeglablist@sccn.ucsd.edu</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Reply-To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><a href="mailto:tarikbelbahar@gmail.com" class="">tarikbelbahar@gmail.com</a><br class=""></span></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div dir="ltr" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class="gmail_default" style="color: rgb(51, 51, 153);">Hello Samran, here's notes for you below, good luck on your eeg adventures!</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">******NOTES FOR SAMRAN********</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">*you need to understand/know exactly what PREP is doing, and if you want comments on that, you should list the steps you think PREP is doing.</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">*your pipeline 1 seems okay. One can drop channels instead of PCA.</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">*Note It's generally not recommended to interpolate channels before ICA.</div><div class="gmail_default" style="color: rgb(51, 51, 153);">*Not sure why you are running PREP again (I guess it's okay if it does exactly the same thing as earlier.</div><div class="gmail_default" style="color: rgb(51, 51, 153);">*Reject epochs at step 13 after reviewing the data, unless for some reason you trust that A) you have removed all artifactual ICs and B) there are no remaining artifactual periods in the epoched data </div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">*In your Pipeline 2, it's up to users whether or not they run a second ICA after pruning the data of Bad ICs. I would not recommend that, but you can look in past eeglablist answers, and in Makoto's processing suggestions, and in publications using ICA for EEG.</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">*Double check that you don't need to move the resampling to the be first or second step.</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">Your question #1</div><div class="gmail_default" style="color: rgb(51, 51, 153);">***ICA in eeglab does not care if there are discontinuities in the data, so it does not matter if you give it continuous data with breaks, or epoched data. It mixes up the time points and focuses on spatial patterns (not temporal patterns).</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">your question #2</div><div class="gmail_default" style="color: rgb(51, 51, 153);">I've specified above that the Data Analyst (you) needs to be sure there is no dirty data going into your averages and metrics. That is regardless of whether or not you already pruned your data by rejecting ICs. Be careful to NOT DO everything automatically until you have checked the results of your pipelines (at the epoch level and averaging level), and your are sure really sure that you don't need to go extra cleaning after bad IC rejection.</div><div class="gmail_default" style="color: rgb(51, 51, 153);">In short, there may still be dirt in the data after rejecting artifactual ICs. You need to personally check whether there is or is not remaining dirt in the data, and you need to be careful not to "assume" that things are working, but rather "check fully" that things are working.</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">Your question #3b</div><div class="gmail_default" style="color: rgb(51, 51, 153);">The PCA correction is correct. Personally I've had better success with "dropping a channel before ICA to account fix average referencing's drop in rank" instead of the PCA flag in runica. In other words, after average referecing, and before ICA, I drop 1 channel rather than use the PCA reduction.</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">Your Question $3b</div><div class="gmail_default" style="color: rgb(51, 51, 153);">Don't interpolate before ICA.</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">From:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">Tarik S Bel-Bahar <<a href="mailto:tarikbelbahar@gmail.com" class="">tarikbelbahar@gmail.com</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><b class="">Re: [Eeglablist] ICA pipeline questions</b><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Date:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">September 11, 2017 at 9:22:17 PM GMT+2<br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">Samran <<a href="mailto:samranasghar@gmail.com" class="">samranasghar@gmail.com</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class="">eeglablist <<a href="mailto:eeglablist@sccn.ucsd.edu" class="">eeglablist@sccn.ucsd.edu</a>><br class=""></span></div><div style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; margin: 0px;" class=""><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Reply-To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, 'Helvetica Neue', Helvetica, sans-serif;" class=""><a href="mailto:tarikbelbahar@gmail.com" class="">tarikbelbahar@gmail.com</a><br class=""></span></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div dir="ltr" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class="gmail_default" style="color: rgb(51, 51, 153);">Some followup points here for your Samran:</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">1. many researchers use and trust near fully automatic or fully automatic pipelines. See for example TAPEEG. It really depends on their biases (e.g., being programmers/engineers versus EEG researchers) and their needs (e.g., having dozens versus thousands of files). Further, automated pipeleines can be tweaked to your satisfaction, and can also provide "quality metrics" to know when there are issues in the pipeline.</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">2. Your "Drop artifactual ICs" step can be complex. Some researchers only keep neural ICs, some researchers only remove artifactual ICs, some researchers fully trust the results of ICA classifcation plugins such as Adjust, MARA, IC-MARA, and SASICA. If you haven't had a chance to use/test the results form those plugins, please be sure to do so.</div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);">3. If you haven't had a chance to yet, make sure to avail yourself of the excellent IC classification site from Luca at the following link. I usually recommend to students and beginners to do at least 500 classifications there. </div><div class="gmail_default"><font color="#333399" class=""><a href="http://reaching.ucsd.edu:8000/tutorial/overview" class="">http://reaching.ucsd.edu:8000/tutorial/overview</a></font><br class=""></div><div class="gmail_default"><font color="#333399" class=""><br class=""></font></div><div class="gmail_default"><font color="#333399" class=""><br class=""></font></div><div class="gmail_default"><font color="#333399" class=""><br class=""></font></div><div class="gmail_default"><font color="#333399" class=""><br class=""></font></div><div class="gmail_default"><font color="#333399" class=""><br class=""></font></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_default" style="color: rgb(51, 51, 153);"><br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Mon, Sep 11, 2017 at 11:55 AM, Tarik S Bel-Bahar<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:tarikbelbahar@gmail.com" target="_blank" class="">tarikbelbahar@gmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<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" class=""><div style="color: rgb(51, 51, 153);" class="">Hello Samran, here's notes for you below, good luck on your eeg adventures!</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">******NOTES FOR SAMRAN********</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">*you need to understand/know exactly what PREP is doing, and if you want comments on that, you should list the steps you think PREP is doing.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">*your pipeline 1 seems okay. One can drop channels instead of PCA.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">*Note It's generally not recommended to interpolate channels before ICA.</div><div style="color: rgb(51, 51, 153);" class="">*Not sure why you are running PREP again (I guess it's okay if it does exactly the same thing as earlier.</div><div style="color: rgb(51, 51, 153);" class="">*Reject epochs at step 13 after reviewing the data, unless for some reason you trust that A) you have removed all artifactual ICs and B) there are no remaining artifactual periods in the epoched data </div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">*In your Pipeline 2, it's up to users whether or not they run a second ICA after pruning the data of Bad ICs. I would not recommend that, but you can look in past eeglablist answers, and in Makoto's processing suggestions, and in publications using ICA for EEG.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">*Double check that you don't need to move the resampling to the be first or second step.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">Your question #1</div><div style="color: rgb(51, 51, 153);" class="">***ICA in eeglab does not care if there are discontinuities in the data, so it does not matter if you give it continuous data with breaks, or epoched data. It mixes up the time points and focuses on spatial patterns (not temporal patterns).</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">your question #2</div><div style="color: rgb(51, 51, 153);" class="">I've specified above that the Data Analyst (you) needs to be sure there is no dirty data going into your averages and metrics. That is regardless of whether or not you already pruned your data by rejecting ICs. Be careful to NOT DO everything automatically until you have checked the results of your pipelines (at the epoch level and averaging level), and your are sure really sure that you don't need to go extra cleaning after bad IC rejection.</div><div style="color: rgb(51, 51, 153);" class="">In short, there may still be dirt in the data after rejecting artifactual ICs. You need to personally check whether there is or is not remaining dirt in the data, and you need to be careful not to "assume" that things are working, but rather "check fully" that things are working.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">Your question #3b</div><div style="color: rgb(51, 51, 153);" class="">The PCA correction is correct. Personally I've had better success with "dropping a channel before ICA to account fix average referencing's drop in rank" instead of the PCA flag in runica. In other words, after average referecing, and before ICA, I drop 1 channel rather than use the PCA reduction.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class="">Your Question $3b</div><div style="color: rgb(51, 51, 153);" class="">Don't interpolate before ICA.</div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div><div style="color: rgb(51, 51, 153);" class=""><br class=""></div></div></blockquote></div><br class=""></div></div><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; 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