<div dir="ltr"><div><div><div><div>Hi Jim,<br><br></div>Thanks for the quick reply, this is really helpful.<br></div><div>I will try your suggestion for number three.<br><br>Regarding the second criteria, we indeed want to exclude changes of more than 3uV between t and t+200ms.</div>So if you have any suggestion of how we might be able to implement this as well, that would be great!<br><br></div>Thanks!<br>Ricarda<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Nov 18, 2015 at 2:14 PM, Herring, J.D. (Jim) <span dir="ltr"><<a href="mailto:j.herring@donders.ru.nl" target="_blank">j.herring@donders.ru.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Ricarda,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">All three criteria have a certain threshold that has to be met in order for a trial to be marked as containing artifacts so for all criteria you could use ft_artifact_threshold
(or ft_artifact_zvalue). The difference will be how you preprocess the signal. You would need to transform the signal so that for criteria nr. 2 the signal represents the potential difference over a 200ms window?, and for nr. 3 the potential difference per
sampling point. <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Number 3 is relatively easy, you can calculate the first temporal derivative (ie. the difference between two consecutive samples) with cfg.artfctdef.threshold.derivative
= ‘yes’ (or ….threshold.absdiff = ‘yes’, if you want the absolute difference). So something like this should work:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">cfg.artfctdef.threshold.channel = cell-array with channel labels<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">cfg.artfctdef.threshold.bpfilter = 'no';<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">cfg.artfctdef.threshold.absdiff = ‘yes’;
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">cfg.artfctdef.threshold.max = 50;<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Number 2 is slightly more difficult because you want to integrate over a larger window. I don’t fully understand what you want to avoid, should the signal at
time X stay within 3uV of the signal at time X + 200ms? <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Best,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Jim<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<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""> <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>Ricarda Braukmann<br>
<b>Sent:</b> woensdag 18 november 2015 12:58<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> [FieldTrip] Automatized artifact rejection in FT<u></u><u></u></span></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Hi everyone,<u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">I would like to implement an automatized artifact rejection procedure for my EEG data and compare this to manual rejection.<br>
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I would like to use the following criteria for rejection of a segment:<br>
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1. amplitudes below -150 or above 150 µV<br>
2. a difference of 3 µV per 200 ms, <br>
3. or a voltage change of 50 µV per sampling point<u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Is there a function in fieldtrip that I can use for implementing these different criteria?<u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">I know that FT_ARTIFACT_THRESHOLD can reject segments on basis of the first criteria but I am unsure how to implement the second two.<u></u><u></u></p>
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<p class="MsoNormal">Any help would be highly appreciated.<u></u><u></u></p>
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<p class="MsoNormal">Thanks!<u></u><u></u></p>
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<p class="MsoNormal">Ricarda<u></u><u></u></p>
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-- <u></u><u></u></p>
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Ricarda Braukmann, MSc<br>
PhD student<br>
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Radboud University Medical Centre & Baby Research Center <br>
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Donders Institute for Brain, Cognition and Behaviour, <br>
Centre for Neuroscience & Centre for Cognition<br>
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Room B.01.22<br>
Phone: +31 (0) 24 36 12652<br>
Email: <a href="mailto:r.braukmann@donders.ru.nl" target="_blank">r.braukmann@donders.ru.nl</a>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Website: <a href="http://www.zebra-project.nl/" target="_blank">
http://www.zebra-project.nl/</a><u></u><u></u></p>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr"><div><span></span><span><br>Ricard</span><span>a Braukmann, </span>MSc<br>
PhD student<br> <br>Radboud University Medical Centre & Baby Research Center <br><br>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Neuroscience & Centre for Cognition<br><br>Room B.01.22<br>
Phone: +31 (0) 24 36 12652<br>Email: <a href="mailto:r.braukmann@donders.ru.nl" target="_blank">r.braukmann@donders.ru.nl</a> <br></div>Website: <a href="http://www.zebra-project.nl/" target="_blank">http://www.zebra-project.nl/</a><br><br></div></div>
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