<div dir="ltr">Dear Jerry,<div><br></div><div>> Well, this wiki page says average referencing before ICA could reduce the rank by 1, which seems to be a bad thing. <br></div><div class="gmail_extra"><br></div><div class="gmail_extra">
Yeah, I thought so too. But I hear Jason Palmer, who wrote AMICA, say data should be average referenced before ICA... I add Jason here again, expecting to hear from him on this issue.</div><div class="gmail_extra"><br></div>
<div class="gmail_extra">Makoto<br><br><div class="gmail_quote">On Thu, Jun 26, 2014 at 1:55 PM, 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: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"><div>Well, this wiki page says average referencing before ICA could reduce the rank by 1, which seems to be a bad thing. <br></div><div>So I guess, average reference should go after ICA.<br></div><div><br>
<a href="http://sccn.ucsd.edu/wiki/Chapter_09:_Decomposing_Data_Using_ICA" target="_blank">http://sccn.ucsd.edu/wiki/Chapter_09:_Decomposing_Data_Using_ICA</a><br>
</div>close to the end of page<br>"When computing average reference on n-channel data, the rank of the data
is reduced to n-1. Why? Because the sum of the potential is 0 at all
time points, the last channel activity is equal to minus the sum of the
others. ICA does not behave well in this (<b>rank-deficient</b>) condition."</div><div class="gmail_extra"><div class=""><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><div><div class="h5"><div class="gmail_quote">On Mon, Jun 23, 2014 at 11:56 AM, 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: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">Dear Brian,<div><br></div><div>The average referencing is not affected by epoch rejection (assuming that bad EEG is restricted to the epochs that are rejected) or component rejection. In your case, average referencing can be done either before or after two ICAs.</div>
<div><br></div><div>I'm still waiting to hear from Jason though whether it's better to do average referencing before ICA and if so, why.</div><span><font color="#888888"><div><br></div></font></span><div>
<span><font color="#888888">Makoto</font></span><div><div><br><div class="gmail_extra"><br><br><div class="gmail_quote">
On Thu, Jun 19, 2014 at 8:37 AM, Brian Scally <span dir="ltr"><<a href="mailto:scallybrian@gmail.com" target="_blank">scallybrian@gmail.com</a>></span> wrote:<br><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"><div>Hi there,</div><div> </div><div>I have been following the discussion. So it is recommended to re-reference to average after removing channels/epochs and right before running ICA. Suppose I plan on running ICA twice: the first time to identify epochs that are affected by improbable components, after which the epochs will be removed. The second time would be to remove actual components. Do I need to re-reference before the first, or will before the second suffice?</div>
<div> </div><div>Cheers,</div><div>Brian</div></div><div class="gmail_extra"><div><div><br><br><div class="gmail_quote">On 19 June 2014 00:56, 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: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">yes.</div><div><div><div class="gmail_extra">
<br><br><div class="gmail_quote">
On Wed, Jun 18, 2014 at 3:45 PM, 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:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><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!<span><font color="#888888"><br>Jerry<br></font></span></div><div class="gmail_extra"><div><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><div><div><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:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid">
<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:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><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>
</div></div></div></div></div></div></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">Makoto Miyakoshi<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego<br></div>
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<br>-- <br></div></div><span><font color="#888888">Brian Scally
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">Makoto Miyakoshi<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego<br></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">Makoto Miyakoshi<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego<br></div>
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