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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Dear Bingshuo,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I am forwarding your e-mail to the Fieldtrip mailinglist so that others can benefit and/or contribute from our discussion. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>The reason why I like to postpone the interpolation to after the ICA is that I noticed that when interpolating before ICA the interpolated data would load onto one component. Removing this component did not make sense as it would leave a flat line in the TEP, keeping it in did not make sense either because the interpolation was done with, for example, the decay artifact still in the data. After removing the decay artifact with ICA you would be left with a sharp peak in the interpolated segment. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I see that it is difficult to reject trials and channels before interpolation but keep in mind that before having done ICA large amounts of variance of the data can be explained by the TMS related artifacts, these will most likely cloud the detection of other types of artifacts with functions such as ft_rejectvisual. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>In my experience bad channels show up as separate independent components anyway and can be removed after having run the ICA, but that may depend on a number of factors I’m not aware of. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>If you would like to reject bad channels prior to running ICA you could also try to run ft_rejectvisual and specify cfg.latency to contain only your pre-TMS period or a period post-TMS that does not contain any large artifacts. That way you should at least be able to run metrics on your data to remove bad channels. In any case you can always run ft_databrowser on your data to visually inspect your channel time courses for bad channels prior to running the ICA.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>In any case you are of course free to try running the ICA after interpolation yourself and share your experiences, perhaps this works fine for you </span><span style='font-size:11.0pt;font-family:Wingdings;color:#1F497D'>J</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Jim<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Bingshuo Li [mailto:bingshuo.li@cin.uni-tuebingen.de] <br><b>Sent:</b> donderdag 10 april 2014 16:36<br><b>To:</b> j.herring@fcdonders.ru.nl<br><b>Subject:</b> Question re: TMS-EEG FT Tutorial<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'>Dear Jim, <o:p></o:p></p></div><p class=MsoNormal style='margin-bottom:12.0pt'>I inquired you about a TMS-EEG question a while ago and you referred me to the TMS-EEG tutorial on Fieldtrip's website. As I was following the steps of the tutorial, there is a new question that come up to me -- Is it really necessary to postpone the interpolation of the TMS artifact until the ICA is done? Would there be any bad consequences if I interpolate first and then run the ICA over the entire interpolated trial(s)? The reason I am asking this question is that I would like to visually inspect my data first and remove bad channels or trials (if any) prior to ICA. If the artifact is not interpolated, it is really difficult to run visual inspection or metrics on the data.. Following the logic of the tutorial, I can only visual inspection after the ICA, which I think might not be a good idea as I was told that a bad channel can easily bias the ICA result..<o:p></o:p></p></div><p class=MsoNormal>Do you have any insights in this? Thank you very much for your time in advance! <br><br>Sincerely, <o:p></o:p></p><div><div><div><div><div><p class=MsoNormal><br clear=all><o:p></o:p></p><div><div><div><p class=MsoNormal>-----<br>Bingshuo Li (MSc. candidate)<br>Systems Neurophysiology Group<br>Centre for Integrative Neuroscience<br>University of Tuebingen<br>Otfried-Mueller-Str. 25<br>D-72076 Tuebingen, Germany<o:p></o:p></p></div><p class=MsoNormal><a href="mailto:bingshuo.li@cin.uni-tuebingen.de" target="_blank">bingshuo.li@cin.uni-tuebingen.de</a><o:p></o:p></p><div><p class=MsoNormal>+49-7071-29-89029<o:p></o:p></p></div></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On Mon, Feb 10, 2014 at 3:24 PM, Herring, J.D. (Jim) <<a href="mailto:j.herring@fcdonders.ru.nl" target="_blank">j.herring@fcdonders.ru.nl</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Dear Bingshuo,</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Please have a look at the following tutorial: <a href="http://fieldtrip.fcdonders.nl/tutorial/tms-eeg" target="_blank">http://fieldtrip.fcdonders.nl/tutorial/tms-eeg</a></span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>It deals with a number of TMS-EEG related artifacts including the ‘evil’ decay artifact.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best,</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Jim </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> <a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a> [mailto:<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a>] <b>On Behalf Of </b>Bingshuo Li<br><b>Sent:</b> maandag 10 februari 2014 15:06<br><b>To:</b> FieldTrip discussion list<br><b>Subject:</b> [FieldTrip] TMS-EEG Decay Artifact</span><o:p></o:p></p></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'>Dear FT users and developers, <o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'>Does anyone have any experience in dealing with the so-called decay artifacts found in TMS-EEG? It is a relatively long lasting (up to 100ms) artifact that follows a waveform similar to exponential decay and it occurs sporadically in certain recording channels.<o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'>Any tips/hints/recommendations are greatly appreciated! Thank you! <o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Regards, <o:p></o:p></p><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><br><br clear=all><o:p></o:p></p><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>-----<br>Bingshuo Li (MSc. candidate)<br>Systems Neurophysiology Group<br>Centre for Integrative Neuroscience<br>University of Tuebingen<br>Otfried-Mueller-Str. 25<br>D-72076 Tuebingen, Germany<br><a href="mailto:bingshuo.li@student.uni-tuebingen.de" target="_blank">bingshuo.li@student.uni-tuebingen.de</a><br><a href="tel:%2B49-152-06054831" target="_blank">+49-152-06054831</a><o:p></o:p></p></div></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></div></div></div></div></div></body></html>