<div dir="ltr">Hi Jerry,<div><br></div><div>If you're using average reference, bad channels should definitely be taken care of first, otherwise they'll affect the reference. I've also heard it recommended that referencing should be done before ICA (see e.g. <a href="http://sccn.ucsd.edu/pipermail/eeglablist/2013/006511.html">http://sccn.ucsd.edu/pipermail/eeglablist/2013/006511.html</a>). I've heard mixed things about channel interpolation and ICA (see e.g. the message linked above). </div>
<div><br></div><div>As for removing bad epochs, it depends what you mean by bad epochs. ICA shouldn't include some kinds of noise, so for example you should remove periods of data where the participant was resting between blocks or things like that. But typical artifacts, like blinks, can probably be left in since they will probably result in a separate ICA component (especially if you mean to remove that component later). So my recommended order would probably be: interpolate channels, re-reference, run ICA, remove bad epochs.</div>
<div><br></div><div>Best,</div><div>Steve</div></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><div><br><br></div>Stephen Politzer-Ahles<br>New York University, Abu Dhabi<br>Neuroscience of Language Lab<br>
<a href="http://www.nyu.edu/projects/politzer-ahles/" target="_blank">http://www.nyu.edu/projects/politzer-ahles/</a><br></div></div>
<br><br><div class="gmail_quote">On Thu, Jun 19, 2014 at 2:45 AM, Jerry Zhu <span dir="ltr"><<a href="mailto:jerryzhu@siu.edu" target="_blank">jerryzhu@siu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div><div><div><div><div><div><div><div><div><div>Hi Makoto,<br></div>Thank you again for your reply.<br><br></div>Did you mean "averaging AFTER removing bad epoches" in your sentence "you should apply average referencing AFTER removing bad channels."?<br>
<br></div>So here are my processing:<br></div>1) re-reference (from Cz to average in my case)<br></div>2) remove bad epoches<br></div>3) interpolate bad channels<br></div>4) ICA<br><br></div>Sounds like you would recommend the order: 2143?<br>
<br></div>Looking forward to your and others inputs!<br></div>Thanks all!<br>Jerry<br></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><div><span style="font-family:times new roman,serif">--<br>Jian Zhu, M.A.<br>
Brain and Cognitive Sciences<br>Department of Psychology<br>Southern Illinois University Carbondale<br></span></div><span style="font-family:times new roman,serif">Web: <a href="http://zhupsy.com" target="_blank">http://zhupsy.com</a><br>
</span><div><span style="font-family:times new roman,serif"><br>We have two halves in the brain: left and right. Nothing is right in the left. Nothing is left in the right.</span></div></div></div>
<br><br><div class="gmail_quote">On Wed, Jun 18, 2014 at 1:38 PM, Makoto Miyakoshi <span dir="ltr"><<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Dear Jason,<div><br></div><div>I remember you said that average reference should be applied before ICA, but I did not understand exactly why. Could you comment on this?</div><div><br></div><div>Jerry, you should apply average referencing AFTER removing bad channels.</div>
<div><br></div><div>I don't think it makes big differences between average referencing before or after interpolation. However we don't necessarily recommend interpolation before ICA.</div><div><br></div><div>Makoto</div>
<div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On Tue, Jun 17, 2014 at 12:20 PM, Jerry Zhu <span dir="ltr"><<a href="mailto:jerryzhu@siu.edu" target="_blank">jerryzhu@siu.edu</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div>
<div dir="ltr"><div><div><div>Hi all,<br></div>At which stage do you re-reference your data? It was suggested do re-ref before ICA (<a href="http://sccn.ucsd.edu/pipermail/eeglablist/2011/003795.html" target="_blank">http://sccn.ucsd.edu/pipermail/eeglablist/2011/003795.html</a>). How about re-ref before/after bad epochs rejection and bad channel interpolation? The note here (<a href="ftp://ftp.egi.com/pub/documentation/technotes/SplineInterpolation.pdf" target="_blank">ftp://ftp.egi.com/pub/documentation/technotes/SplineInterpolation.pdf</a>) suggests after interpolation. ("Since the interpolated potentials can be used to better approximate the average reference (Junghofer et al., 1999), it may be somewhat advantageous to compute the interpolated potentials directly from the measured data, in which case the voltages below are best thought of as referring to these measured potentials")<br>
<br></div>What is your experience? Thanks for your sharing and suggestions!<br><br></div>Jerry<br clear="all"><div><div><div><div><div><div><div><div dir="ltr"><div><span style="font-family:times new roman,serif">--<br>Jian Zhu, M.A.<br>
Brain and Cognitive Sciences<br>Department of Psychology<br>Southern Illinois University Carbondale<br></span></div><span style="font-family:times new roman,serif">Web: <a href="http://zhupsy.com" target="_blank">http://zhupsy.com</a><br>
</span><div><span style="font-family:times new roman,serif"><br>We have two halves in the brain: left and right. Nothing is right in the left. Nothing is left in the right.</span></div></div></div>
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