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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:black'>It should also be noted that for Active electrodes like Biosemi, referencing is considered crucial to realizing the significant attenuation in line noise (50/60 Hz) of active electrodes. I have found average reference (assuming good channels kept) to be adequate for attenuation of line noise with Biosemi. This essentially assumes line noise is additive at each channel with the same amplitude, which is approximately correct. If you get an ICA map that has a very prominent 50 or 60 Hz peak, then the map is usually “almost flat” on the scalp map. It is very difficult to completely remove line noise with referencing or ICA for the data, due I believe to slight phase variation in the channels. Channel specific methods filtering methods, like Cleanline, can be used prior to ICA if you are insistent on removing all line noise.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Jason<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></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"'> Makoto Miyakoshi [mailto:mmiyakoshi@ucsd.edu] <br><b>Sent:</b> Monday, October 06, 2014 1:09 PM<br><b>To:</b> Iman M.Rezazadeh; Simon Finnigan<br><b>Cc:</b> Jason Palmer; eeglablist; Eric HG<br><b>Subject:</b> Re: [Eeglablist] Rereference<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Thank you Iman. Did I tell you this page too?<br><a href="http://sccn.ucsd.edu/wiki/Linear_Representations_and_Basis_Vectors#Singular_Value_Decomposition_.28SVD.29">http://sccn.ucsd.edu/wiki/Linear_Representations_and_Basis_Vectors#Singular_Value_Decomposition_.28SVD.29</a><br><br>However, the wikipage linked above does not explain what's good about doing the re-referencing as a pre-ICA preprocess. Hence I was happy to hear the clear explanation for the reason.<br><br>Simon, I appreciate your honest opinion. I agree that the conclusion may look damn, but I am happy to find it rather simple. After all, that's the only thing ICA users want to care.<br><br>Jason, I agree to this:<br><br>> I would still of course suggest removing bad channels first for practical reasons.<br><br>and I would say this is an optimism; <br><br>> However the change is just a linear addition of one noise direction along the channel, which can be easily undone by ICA, at the cost of using one of the ICA sources to contain this noise channel.<br><br>It would only hold for the cases of eye-blink, EOG, and EMG.<o:p></o:p></p><div><p class=MsoNormal>Artifacts with very high level amplitude (>10^4 uV), channels with continuous zeros, or saturated channels can destroy ICA results or terminates the converging process. We should protect ICA from these artifacts rather than letting it handle them to fail (maybe this is a different topic from the average referencing.)<br><br>Jason, I suggest we update the wiki page about the average referencing, since this is a recurring topic on the list... if you don't mind I'll edit your replies and prepare the draft for your check.<br><br>Makoto<o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>On Sun, Oct 5, 2014 at 9:36 PM, Iman M.Rezazadeh <<a href="mailto:irezazadeh@ucdavis.edu" target="_blank">irezazadeh@ucdavis.edu</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'>I would like to suggest you read also the following archive :</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'><a href="http://sccn.ucsd.edu/pipermail/eeglablist/2014/007810.html" target="_blank">http://sccn.ucsd.edu/pipermail/eeglablist/2014/007810.html</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'><a name="148e3bf422ddcb34__MailEndCompose"><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span></a><o:p></o:p></p><div><div style='border:none;border-top:solid #E1E1E1 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:11.0pt;font-family:"Calibri","sans-serif"'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <a href="mailto:eeglablist-bounces@sccn.ucsd.edu" target="_blank">eeglablist-bounces@sccn.ucsd.edu</a> [mailto:<a href="mailto:eeglablist-bounces@sccn.ucsd.edu" target="_blank">eeglablist-bounces@sccn.ucsd.edu</a>] <b>On Behalf Of </b>Jason Palmer<br><b>Sent:</b> Sunday, October 5, 2014 5:33 PM<br><b>To:</b> 'Simon Finnigan'; <a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a></span><o:p></o:p></p><div><div><p class=MsoNormal><br><b>Cc:</b> 'eeglablist'; 'Eric HG'<br><b>Subject:</b> Re: [Eeglablist] Rereference<o:p></o:p></p></div></div></div></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <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:black'>Dear Eric, Simon, et al.,</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:black'> </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:black'>This issue has been discussed several times before and you can check the archives for more discussion. I have argued before, mainly from a linear algebra point of view, that any referencing using a linear combination some of the other channels is essentially projecting the data onto an space of dimension (nchan-1), where sources along a particular direction become invisible. In the case of average reference, this direction is the source that equally increases or decreases all the channel potentials by the same amount, i.e. [1 1 1 1 …. 1], and in consequence, all the learned ICA maps are orthogonal to this direction, and any sources along that direction are lost. But if there is any part of the source map that is not constant, this part will be retained and can be extracted by ICA.</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:black'> </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:black'>Using average reference makes all ICA sources have zero total potential. I have argued before that zero total potential makes sense for brain sources assuming approximately complete surrounding of head by electrode array, by a charge conservation argument. This will of course not hold exactly in practice, and there will be some shunting, so the learned ICA maps must be assumed to have an unknown constant potential added to each electrode for localization purposes.</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:black'> </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:black'>What I said to Makoto was that the reference didn’t really matter ultimately as long as you choose a combination of channels that cannot likely represent a real source. I suggest average reference because this makes all the maps sum to zero, clearly indicating dipolarity/directionality by having negative (blue) and positive (red) values in each map, rather than having maps that have dark blue background and light blue source “blob” (or dark red and light red). As I said, there must be assumed to be an unknown constant added to each map. My natural default for display purposes would be the total potential, and using average reference does this for you “automatically” with little risk of losing any sources of interest.</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:black'> </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:black'>People often worry that including a bad channel in the average reference will contaminate everything by adding noise to every channel. However the change is just a linear addition of one noise direction along the channel, which can be easily undone by ICA, at the cost of using one of the ICA sources to contain this noise channel. I would still of course suggest removing bad channels first for practical reasons.</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:black'> </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:black'>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:black'>Jason</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:black'> </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:black'> </span><o:p></o:p></p><div><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:eeglablist-bounces@sccn.ucsd.edu" target="_blank">eeglablist-bounces@sccn.ucsd.edu</a> [<a href="mailto:eeglablist-bounces@sccn.ucsd.edu" target="_blank">mailto:eeglablist-bounces@sccn.ucsd.edu</a>] <b>On Behalf Of </b>Simon Finnigan<br><b>Sent:</b> Saturday, October 04, 2014 2:51 AM<br><b>To:</b> <a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a><br><b>Cc:</b> eeglablist; Eric HG<br><b>Subject:</b> Re: [Eeglablist] Rereference</span><o:p></o:p></p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hi All<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Firstly I must say that as a scientist, I find the rationale from Jason via Makoto to be un-scientific and unsatisfactory.<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Second - This will only partly answer your question I think, but here goes: it all depends on how you're analysing your data [what you're looking at/for] and particularly, whether or not scalp topographies are of interest to you - but in general and in brief, the consensus seems to be that common-average referencing is preferable over mastoid referencing, at least - and probably other references sites too [e.g. vertex; nasion]. [Also are your data referenced to one or both mastoids? and if both - were they linked, or averaged together after recording?]<o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>My 2002 paper in 'Neuropsychologia' addressed this issue scientifically, at least in part - e.g. see final figure [albeit we weren't doing ICA back then either!].<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Regards, Simon<o:p></o:p></p></div></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><br>On 04/10/2014, at 8:21, Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>> wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Here is update.<o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I asked the question to Jason. He told me that t<span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>he main reason avg reference is useful is that it returns brain maps that look like nice localized sources inside the head with red blob and slight negative (aqua/green) background. This makes sense.</span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <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:black'>Makoto</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><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Thu, Oct 2, 2014 at 10:00 AM, Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>> wrote:<o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear Eric,<o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I have the same question for long time. In my case, because I run ICA and remain in IC analysis and almost never come back to channels, I really wonder if I need re-referencing at all.<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I've heard Jason Palmer, who wrote AMICA for EEGLAB, say average reference before ICA is necessary, but he did not give me a clear explanation for that. Scott wanted to know it too, but we were interrupted at that time. Next time I'll ask it to him (when I ever see him in the lab...)<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Makoto <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><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Tue, Sep 30, 2014 at 2:44 PM, Eric HG <<a href="mailto:erichg2013@gmail.com" target="_blank">erichg2013@gmail.com</a>> wrote:<o:p></o:p></p></div></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt'><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear list,<o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I have read the tutorial on the site and it says: "<span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>Converting data, before analysis, from fixed or common reference (for example, from a common earlobe or other channel reference) to 'average reference' is advocated by some researchers, particularly when the electrode montage covers nearly the whole head (as for some high-density recording systems)." </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Arial","sans-serif";color:black'>I have data collected with a mastoid reference and I was wondering in which cases it would be considered best to rereference to the average? Are there any specific papers about rereferencing that anyone would recommend?</span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Arial","sans-serif";color:black'>Regards,</span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Arial","sans-serif";color:black'>Eric </span><o:p></o:p></p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>_______________________________________________<br>Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>To unsubscribe, send an empty email to <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" target="_blank">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>For digest mode, send an email with the subject "set digest mime" to <a href="mailto:eeglablist-request@sccn.ucsd.edu" target="_blank">eeglablist-request@sccn.ucsd.edu</a><o:p></o:p></p></blockquote></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#888888'><br><br clear=all></span><o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#888888'>-- </span><o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#888888'>Makoto Miyakoshi<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego</span><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><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>-- <o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Makoto Miyakoshi<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego<o:p></o:p></p></div></div></div></blockquote><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>_______________________________________________<br>Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>To unsubscribe, send an empty email to <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" target="_blank">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>For digest mode, send an email with the subject "set digest mime" to <a href="mailto:eeglablist-request@sccn.ucsd.edu" target="_blank">eeglablist-request@sccn.ucsd.edu</a><o:p></o:p></p></div></blockquote></div></div></div></div></div><p class=MsoNormal><br><br clear=all><o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>-- <o:p></o:p></p><div><p class=MsoNormal>Makoto Miyakoshi<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego<o:p></o:p></p></div></div></div></body></html>