<html><head><base href="x-msg://1055/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Aleksandra,<div><br></div><div>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.</div><div><br></div><div><i>[STUDY ersp times freqs ] = std_erspplot(STUDY,ALLEEG,'channels',{'T7'});</i></div><div><i><br></i></div><div><div><i>size(ersp{1})</i></div><div><i><br></i></div><div><i>ans =</i></div><div><i><br></i></div><div><i> 30 40 1 12</i></div></div><div><br></div><div>30 frequencies, 40 time points, 1 electrode, 12 subjects.</div><div>Now to compare the baseline to 0, one simple way is to do this is</div><div><br></div><div><i><div style="font-style: normal; display: inline !important; "><i>% permutation statistics with FDR correction</i></div></i><i><div style="font-style: normal; "><i>pvals = std_stat({ ersp{1} zeros(size(ersp{1})) }', 'method', 'permutation', 'condstats', 'on', 'correctm', 'fdr'); </i></div></i><i></i><i></i><div style="display: inline !important; "><div style="font-style: italic; "><i><div style="font-style: normal; display: inline !important; "><i><br></i></div></i></div><div>Or</div><div style="font-style: italic; "><i><div style="font-style: normal; display: inline !important; "><i><br></i></div></i></div><i>% permutation statistics with cluster correction (note: use the latest SVN revision of EEGLAB 12)</i></div><i></i><i></i><div><i>pvals = std_stat({ ersp{1} zeros(size(ersp{1})) }', </i><i>mode', 'fieldtrip', </i><i>'fieldtripmethod', 'montecarlo', 'condstats', 'on', 'fieldtripmcorrect', 'cluster'); </i></div></div><div><i><br></i></div><div>Note that only surrogate method is appropriate here (the array containing zeros array has 0 variance so cannot be used in parametric tests).</div><div>Now plot the ERSP masked for significance.</div><div><br></div><div><div><i>tmpersp = mean(ersp{1},4); % average ERSP for all subjects</i></div><div><i>tmpersp(pvals{1} > 0.05) = 0; % zero out non-significant values</i></div><div><i>figure; imagesc(times, freqs, tmpersp); set(gca, 'ydir', 'normal'); xlabel('Time (ms)'); ylabel('Frequencies (Hz)'); cbar; % plot ERSP</i></div></div><div><br></div><div>Best,</div><div><br></div><div>Arno</div><div><br></div><div><div><div>On 11 Jan 2013, at 04:25, Aleksandra Vuckovic wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div ocsi="x"><div style="font-family: Tahoma; direction: ltr; color: rgb(0, 0, 0); font-size: x-small; "><div>Dear Makoto,</div><div><font face="tahoma">at the moment I am working simply with EEG data not ICA components (though that will be my next step<a></a>).</font></div><div><font face="tahoma">Does that change anything?</font></div><div><font face="tahoma">Many thanks,</font></div><div><font face="tahoma">Aleksandra</font></div><div dir="ltr"><font color="#000000" size="2" face="Tahoma"></font> </div><div id="divRpF684834" style="direction: ltr; "><hr tabindex="-1"><font color="#000000" size="2" face="Tahoma"><b>From:</b><span class="Apple-converted-space"> </span>Makoto Miyakoshi [<a href="mailto:mmiyakoshi@ucsd.edu">mmiyakoshi@ucsd.edu</a>]<br><b>Sent:</b><span class="Apple-converted-space"> </span>10 January 2013 23:12<br><b>To:</b><span class="Apple-converted-space"> </span>Aleksandra Vuckovic<br><b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a>; Muhammad Hasan; Arnaud Delorme; Scott Makeig<br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [Eeglablist] Ploting ONLY stat stignificant ERSP ina study<br></font><br></div><div></div><div>Dear Aleksandra,<div><br></div><div>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.</div><div><br>Makoto<br><br><div class="gmail_quote">2013/1/4 Aleksandra Vuckovic<span class="Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:Aleksandra.Vuckovic@glasgow.ac.uk">Aleksandra.Vuckovic@glasgow.ac.uk</a>></span><br><blockquote class="gmail_quote" style="border-left-color: rgb(204, 204, 204); border-left-width: 1px; border-left-style: solid; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; padding-left: 1ex; "><div><div style="font-family: Tahoma; direction: ltr; font-size: x-small; "><div></div><div dir="ltr"><font color="#000000" face="Tahoma">Hi,</font></div><div dir="ltr"><font face="tahoma">how can I plot only statistically significant ERSP<a></a><a></a><span class="Apple-converted-space"> </span>(let's say p<0.05) in a study, in the same way as it can be plotted for a single subject? Currently<a></a><span class="Apple-converted-space"> </span>I can only plot a separate figure with an area of statistically significant difference between two groups rather than statistically significant<a></a> ERSP<a></a><a></a><span class="Apple-converted-space"> </span>of a single group/single<a></a><span class="Apple-converted-space"> </span>condition.</font></div><div dir="ltr"><font face="tahoma">Many thanks,</font></div><div dir="ltr"><font face="tahoma">Alex</font></div></div></div><br>_______________________________________________<br>Eeglablist page:<span class="Apple-converted-space"> </span><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<span class="Apple-converted-space"> </span><a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>For digest mode, send an email with the subject "set digest mime" to<span class="Apple-converted-space"> </span><a href="mailto:eeglablist-request@sccn.ucsd.edu">eeglablist-request@sccn.ucsd.edu</a><br></blockquote></div><br><br clear="all"><div><br></div>--<span class="Apple-converted-space"> </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<br></div></div></div></div></blockquote></div><br></div></body></html>