<div dir="ltr">Dear Katherine,<div><br></div><div>Copy and paste below and run it. See how to set the color scales.</div><div><br></div><div>Makoto</div><div><br></div><div><div>% generate dummy data</div><div>channels = [1 2 3];</div>
<div>erspdata{1,1}=randn(50,200,3,2);</div><div>erspdata{1,1}(:,:,2,:)=erspdata{1,1}(:,:,2,:)+1;</div><div>erspdata{1,1}(:,:,3,:)=erspdata{1,1}(:,:,3,:)+2;</div><div>ersptimes = [1:200];</div><div>erspfreqs = [1:50];</div>
<div><br></div><div>% compute ersp and stats</div><div>figure('Color',[1 1 1]);</div><div>for chan=1:length(channels) </div><div> e=channels(chan);</div><div> pvals=std_stat({erspdata{1,1}(:,:,chan,:) zeros(size(erspdata{1,1}(:,:,chan,:))) }', 'method', 'permutation', 'condstats', 'on', 'correctm', 'fdr');</div>
<div> groupersp=mean(erspdata{1,1}(:,:,chan,:),4);</div><div> maxersp=max(groupersp);</div><div> tmpersp=mean(erspdata{1,1}(:,:,chan,:),4); % average ERSP for all subjects</div><div> tmpersp(pvals{1}>0.05)=0; % zero out non-significant values</div>
<div> plotData(:,:,chan)=tmpersp;<br></div><div>end</div><div><br></div><div>% compute max and min across all plots</div><div>zmax = max(plotData(:));</div><div>zmin = min(plotData(:));</div><div><br></div><div>% plot</div>
<div>for chan=1:length(channels)</div><div> subplot(1,3,chan);</div><div> imagesc(ersptimes, erspfreqs, plotData(:,:,chan), [zmin zmax])</div><div> set(gca,'ydir','normal'); xlabel('Time (ms)'); ylabel ('Frequencies (Hz)'); %cbar;</div>
<div> hold on; title(['Channel ',num2str(e)]);</div><div>end</div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/8/17 Katherine Naish <span dir="ltr"><<a href="mailto:K.R.Naish@pgr.reading.ac.uk" target="_blank">K.R.Naish@pgr.reading.ac.uk</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Dear Arno and list,
<div><br>
</div>
<div>I was hoping someone could advise on the code I am using to plot significant ERSPs for a group of subjects. Based on the code recommended to Alex previously, I am using the following code (to plot significance for a number of channels separately). <span style="font-size:10pt">It
seems to be doing what I want it to, apart from the fact that the colour scale is rather crazy (see attached). I've played around with the 'cbar' function but can't figure out how to make it consistent across the different data sets.</span></div>
<div><br>
<div>
<div>
<div>figure('Color',[1 1 1]);</div>
<div>for chan=1:length(channels) </div>
<div> e=channels(chan);</div>
<div> pvals=std_stat({erspdata{1,1}(:,:,chan,:) zeros(size(erspdata{1,1}(:,:,chan,:))) }', 'method', 'permutation', 'condstats', 'on', 'correctm', 'fdr');</div>
<div> groupersp=mean(erspdata{1,1}(:,:,chan,:),4);</div>
<div> maxersp=max(groupersp);</div>
<div> tmpersp=mean(erspdata{1,1}(:,:,chan,:),4); % average ERSP for all subjects</div>
<div> tmpersp(pvals{1}>0.05)=0; % zero out non-significant values</div>
<div> subplot(3,2,chan);</div>
<div> imagesc(ersptimes, erspfreqs, tmpersp);</div>
<div> set(gca,'ydir','normal'); xlabel('Time (ms)'); ylabel ('Frequencies (Hz)'); %cbar;</div>
<div> hold on; title(['Channel ',num2str(e)]);</div>
<div>end</div>
</div>
<div><br>
</div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt">Any help very much appreciated!</span></div>
<div><br>
</div>
<div>Many thanks,</div>
<div>katherine</div>
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<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> <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">eeglablist-bounces@sccn.ucsd.edu</a>] on behalf of Arnaud Delorme [<a href="mailto:arno@ucsd.edu" target="_blank">arno@ucsd.edu</a>]<br>
<b>Sent:</b> 14 January 2013 15:26<br>
<b>To:</b> Aleksandra Vuckovic<br>
<b>Cc:</b> eeglablist<br>
<b>Subject:</b> Re: [Eeglablist] Ploting ONLY stat stignificant ERSP ina study<br>
</font><br>
</div>
<div></div>
<div>Dear Aleksandra,
<div><br>
</div>
<div>then use the EEGLAB function imagesclogy instead of imagesc</div>
<div><br>
</div>
<div><i>imagesclogy(times, freqs, tmpersp); set(gca, 'ydir', 'log'); xlabel('Time (ms)'); ylabel('Frequencies (Hz)'); cbar; % plot ERSP<br>
</i><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Arno</div>
<div><br>
<div>
<div>On 14 Jan 2013, at 05:31, Aleksandra Vuckovic wrote:</div>
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<div lang="EN-GB" style="word-wrap:break-word">
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<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">Dear Arno,</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">Thank you very much for the code, it works but I am getting linear frequencies and logarithmic plot. When I compare ERSP figure with
the one from GUI, they look the same (apart that values for p>0.05 are missing) but frequency scales are different. I tired recalculating log10 but frequencies do no match.</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">I also tired replacing ‘nomal’ with ‘log’ in</span></font></p>
<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic"> imagesc(times, freqs, tmpersp); set(gca, 'ydir', 'log'); xlabel('Time (ms)'); ylabel('Frequencies (Hz)'); cbar; % plot ERSP</span></font></i></p>
<p class="MsoNormal"><font size="3" color="navy" face="Times New Roman"><span style="font-size:12.0pt;color:navy">but it only inverts scale from larger to smaller values</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">Could you please help me to get the right scale?</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">Many thanks,</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">Aleksandra</span></font></p>
<div>
<div class="MsoNormal" align="center" style="text-align:center"><font size="3" face="Times New Roman"><span lang="EN-US" style="font-size:12.0pt">
<hr size="2" width="100%" align="center">
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<p class="MsoNormal"><b><font face="Tahoma"><span lang="EN-US" style="font-size:10.0pt;font-family:Tahoma;font-weight:bold">From:</span></font></b><font face="Tahoma"><span lang="EN-US" style="font-size:10.0pt;font-family:Tahoma"> Arnaud
Delorme [mailto:<a href="mailto:arno@ucsd.edu" target="_blank">arno@ucsd.edu</a>] <br>
<b><span style="font-weight:bold">Sent:</span></b> 13 January 2013 15:55<br>
<b><span style="font-weight:bold">To:</span></b> Aleksandra Vuckovic<br>
<b><span style="font-weight:bold">Cc:</span></b> <a href="mailto:eeglab@sccn.ucsd.edu" target="_blank">
eeglab@sccn.ucsd.edu</a><br>
<b><span style="font-weight:bold">Subject:</span></b> Re: [Eeglablist] Ploting ONLY stat stignificant ERSP ina study</span></font><span lang="EN-US"></span></p>
</div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Glad to hear that.</span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Best regards,</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Arno</span></font></p>
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<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">On 13 Jan 2013, at 05:13, Aleksandra Vuckovic wrote:</span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><br>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Dear Arno</span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Thanks a lot I think that is exactly what I was looking for</span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Best regards</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Aleksandra<br>
<br>
Sent from my iPhone</span></font></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><br>
On 13 Jan 2013, at 06:19, "Arnaud Delorme" <<a href="mailto:arno@ucsd.edu" target="_blank">arno@ucsd.edu</a>> wrote:</span></font></p>
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<blockquote type="cite" style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Dear Aleksandra,</span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">no that does not change anything. I agree with Makoto that we should find a way to plot difference with baseline in ERSP. It is not too hard from the command line. Afer
computing ERSP in the graphic interface for your STUDY, first retrieve ERSP results on one channel.</span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic">[STUDY ersp times freqs ] = std_erspplot(STUDY,ALLEEG,'channels',{'T7'});</span></font></i></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic">size(ersp{1})</span></font></i></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic">ans =</span></font></i></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic"> 30 40 1 12</span></font></i></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">30 frequencies, 40 time points, 1 electrode, 12 subjects.</span></font></p>
</div>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Now to compare the baseline to 0, one simple way is to do this is</span></font></p>
</div>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
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<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic">% permutation statistics with FDR correction</span></font></i></p>
</div>
<div>
<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic">pvals = std_stat({ ersp{1} zeros(size(ersp{1})) }', 'method', 'permutation', 'condstats', 'on', 'correctm', 'fdr'); </span></font></i></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Or</span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic">% permutation statistics with cluster correction (note: use the latest SVN revision of EEGLAB 12)</span></font></i></p>
</div>
<div>
<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic">pvals = std_stat({ ersp{1} zeros(size(ersp{1})) }', mode', 'fieldtrip', 'fieldtripmethod', 'montecarlo', 'condstats', 'on', 'fieldtripmcorrect',
'cluster'); </span></font></i></p>
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<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Note that only surrogate method is appropriate here (the array containing zeros array has 0 variance so cannot be used in parametric tests).</span></font></p>
</div>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Now plot the ERSP masked for significance.</span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic">tmpersp = mean(ersp{1},4); % average ERSP for all subjects</span></font></i></p>
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<div>
<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic">tmpersp(pvals{1} > 0.05) = 0; % zero out non-significant values</span></font></i></p>
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<p class="MsoNormal"><i><font size="3" face="Times New Roman"><span style="font-size:12.0pt;font-style:italic">figure; imagesc(times, freqs, tmpersp); set(gca, 'ydir', 'normal'); xlabel('Time (ms)'); ylabel('Frequencies (Hz)'); cbar; % plot ERSP</span></font></i></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Best,</span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Arno</span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
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<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">On 11 Jan 2013, at 04:25, Aleksandra Vuckovic wrote:</span></font></p>
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<br>
</span></font></p>
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<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">Dear Makoto,</span></font></p>
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<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">at the moment I am working simply with EEG data not ICA components (though that will be my next step).</span></font></p>
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<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">Does that change anything?</span></font></p>
</div>
<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">Many thanks,</span></font></p>
</div>
<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">Aleksandra</span></font></p>
</div>
<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma"> </span></font></p>
</div>
<div>
<div class="MsoNormal" align="center" style="text-align:center"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">
<hr size="2" width="100%" align="center">
</span></font></div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma;font-weight:bold">From:</span></font></b><span><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma"> </span></font></span><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">Makoto
Miyakoshi [<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank"></a><a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>]<br>
<b><span style="font-weight:bold">Sent:</span></b><span> </span>10 January 2013 23:12<br>
<b><span style="font-weight:bold">To:</span></b><span> </span>Aleksandra Vuckovic<br>
<b><span style="font-weight:bold">Cc:</span></b><span> </span><a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank"></a><a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank">eeglablist@sccn.ucsd.edu</a>; Muhammad Hasan;
Arnaud Delorme; Scott Makeig<br>
<b><span style="font-weight:bold">Subject:</span></b><span> </span>Re: [Eeglablist] Ploting ONLY stat stignificant ERSP ina study</span></font></p>
</div>
<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">Dear Aleksandra,</span></font></p>
<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">So you want to show simple effect of ERSP results after significance masking. Actually it is not possible for the current STUDY scheme
(!) which is a shame. You need to write a code to extract those values from STUDY.cluster(1,x).icaersp. Type 'help std_readersp' and read the help for a start.<br>
<br>
I strongly believe that this should be doable, so I cc this to Arno and Scott to draw their attention.</span></font></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma"><br>
Makoto</span></font></p>
<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">2013/1/4 Aleksandra Vuckovic<span> </span><<a href="mailto:Aleksandra.Vuckovic@glasgow.ac.uk" target="_blank"></a><a href="mailto:Aleksandra.Vuckovic@glasgow.ac.uk" target="_blank">Aleksandra.Vuckovic@glasgow.ac.uk</a>></span></font></p>
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<div>
<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">Hi,</span></font></p>
</div>
<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">how can I plot only statistically significant ERSP<span> </span>(let's say p<0.05) in a study, in the
same way as it can be plotted for a single subject? Currently<span> </span>I can only plot a separate figure with an area of statistically significant difference between two groups rather than statistically significant ERSP<span> </span>of
a single group/single<span> </span>condition.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">Many thanks,</span></font></p>
</div>
<div>
<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">Alex</span></font></p>
</div>
</div>
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<p class="MsoNormal"><font color="black" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">--<span> </span><br>
Makoto Miyakoshi<br>
JSPS Postdoctral Fellow for Research Abroad<br>
Swartz Center for Computational Neuroscience<br>
Institute for Neural Computation, University of California San Diego</span></font></p>
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-- <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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