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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The way the code scripted is to calculate the spectrum from the whole data at once
<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">[alltfX freqs timesout] = timefreq(X, g.srate, spectraloptions{:})
<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"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Not each epoch separately and then make an average from them. and yes in matters !<o:p></o:p></span></a></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">Iman
<o:p></o:p></span></p>
<p class="MsoNormal"><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"> Makoto Miyakoshi [mailto:mmiyakoshi@ucsd.edu]
<br>
<b>Sent:</b> Thursday, July 23, 2015 3:44 PM<br>
<b>To:</b> Iman Mohammad-Rezazadeh <irezazadeh@UCDAVIS.EDU><br>
<b>Cc:</b> EEGLAB List <eeglablist@sccn.ucsd.edu>; Loo, Sandra <SLoo@mednet.ucla.edu>; Scott Makeig <smakeig@ucsd.edu>; Chantelle C Kinzel <ckinzel@mednet.ucla.edu>; Michelini, Giorgia <giorgia.michelini@kcl.ac.uk><br>
<b>Subject:</b> Re: A tentative issue in coherence calculation in EEGLAB for epoched data<o:p></o:p></span></p>
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<p class="MsoNormal">Dear Iman,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I ask you this without testing it, but does the order of the averaging process makes difference in results?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Makoto<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, Jul 20, 2015 at 10:09 AM, Iman Mohammad-Rezazadeh <<a href="mailto:irezazadeh@ucdavis.edu" target="_blank">irezazadeh@ucdavis.edu</a>> wrote:<o:p></o:p></p>
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<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">Hi EEGLABERs,
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I have been looking into ‘newcrossf’ function and the way it calculates coherence for epoched data. Basically, it uses the ‘timefreq’ function to calculate the time/frequency decomposition
the data. ‘timefreq’ function treats the epoched data as a continuous one:<o:p></o:p></p>
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<span style="font-size:10.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
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<span style="font-size:10.0pt;font-family:"Courier New";color:black">X = reshape(X, g.frame, g.trials);</span><o:p></o:p></p>
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<span style="font-size:10.0pt;font-family:"Courier New";color:black">[alltfX freqs timesout] = timefreq(X, g.srate, spectraloptions{:});</span><o:p></o:p></p>
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<span style="font-size:10.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
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<span style="font-size:10.0pt;font-family:"Courier New";color:black">Y = reshape(Y, g.frame, g.trials);</span><o:p></o:p></p>
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<span style="font-size:10.0pt;font-family:"Courier New";color:black">[alltfY] = timefreq(Y, g.srate, spectraloptions{:});</span><o:p></o:p></p>
<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">and calculates the its spectrum using the whole data which is now concatenated version of all trials. So, for each of channel’s pair (X and Y , for example) the spectrum is calculated
as described above and then the joint time-freq decomposition is calculated for coherence value.<o:p></o:p></p>
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<span style="font-size:10.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
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<span style="font-size:10.0pt;font-family:"Courier New";color:black">coherres = sum(alltfX .* conj(alltfY), 3) ./ sqrt( sum(abs(alltfX).^2,3) .* sum(abs(alltfY).^2,3) );</span><o:p></o:p></p>
<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"><b>However, similar to the ERSP concept, each trial/epoch might be different than others [because of perturbations in subjects’ mental status, mental fatigue, etc] and thus I think
it is more appropriate to calculate the coherence for each trial first and then make the average across trials.</b><o:p></o:p></p>
<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">Any thoughts?<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#888888">Iman <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#888888"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#888888"> <o:p></o:p></span></p>
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<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<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>
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