<div dir="ltr"><div dir="ltr">Hi Eleonora,<div><br></div><div>A likely explanation of what you describe is that there are baseline differences between your conditions of interest. You could check this by running the statistics you used previously on the raw power in the time window that you select as a baseline (e.g. cfg.latency = [-0.5 -0.1]; cfg.avgovertime = 'yes';). The difference you are observing between your conditions are then explained by differences that already exist in the baseline. If you apply a baseline correction you get rid of this effect. </div><div><br></div><div>Best,</div><div>Tara van Viegen<br>Senior-RA (aspiring post-doc)<br>Neuroscience of Attention & Perception Lab<br>Princeton University<br></div><div><a href="mailto:tviegen@princeton.edu">tviegen@princeton.edu</a></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 7, 2019 at 12:34 PM eleonora parrotta <<a href="mailto:eleonora_p@hotmail.it">eleonora_p@hotmail.it</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">




<div dir="ltr">
<div style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<p style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:10pt;font-family:"Courier New";color:black">Dear Fieldtrippers,
</span></p>
<p style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:10pt;font-family:"Courier New";color:black">I am performing analysis of EEG data. I have two conditions of interest: A and B, and I have performed spectral decomposition
 with the wavelet method to obtain the power (frequencies from 1 to 50 Hz). </span>
</p>
<p style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:10pt;font-family:"Courier New";color:black">I performed a cluster-based permutation test to assess whether there are significant power differences between the
 two conditions of interest in the time-interval from the onset of the stimulus to 1 sec after:
</span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:forestgreen">%% clusterbased analysis</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.latency = [0 1];
</span><span style="font-size:10pt;font-family:"Courier New";color:forestgreen">% Time of Interest
</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.frequency = [8 12];
</span><span style="font-size:10pt;font-family:"Courier New";color:forestgreen">% Frequency of interest</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.channel =<span> 
</span>{</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'PO3'</span><span style="font-size:10pt;font-family:"Courier New";color:black">,
</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'P3'</span><span style="font-size:10pt;font-family:"Courier New";color:black">,
</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'O1'</span><span style="font-size:10pt;font-family:"Courier New";color:black">,
</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'P7'</span><span style="font-size:10pt;font-family:"Courier New";color:black">,</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'O2'</span><span style="font-size:10pt;font-family:"Courier New";color:black">,</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'P8'</span><span style="font-size:10pt;font-family:"Courier New";color:black">,</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'PO4'</span><span style="font-size:10pt;font-family:"Courier New";color:black">,</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'P4'</span><span style="font-size:10pt;font-family:"Courier New";color:black">};
</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.neighbours = neighbours;
</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.avgoverfreq =
</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'yes'</span><span style="font-size:10pt;font-family:"Courier New";color:black">;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.avgovertime =
</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'no'</span><span style="font-size:10pt;font-family:"Courier New";color:black">;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.avgoverchannel =
</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'no'</span><span style="font-size:10pt;font-family:"Courier New";color:black">;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.method =
</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'montecarlo'</span><span style="font-size:10pt;font-family:"Courier New";color:black">;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.statistic =
</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'ft_statfun_depsamplesT'</span><span style="font-size:10pt;font-family:"Courier New";color:black">;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">subj = 18;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">design = zeros(2,2*subj);</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:blue">for</span><span style="font-size:10pt;font-family:"Courier New";color:black"> i = 1:subj</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black"><span> 
</span>design(1,i) = i;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:blue">end</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:blue">for</span><span style="font-size:10pt;font-family:"Courier New";color:black"> i = 1:subj</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black"><span> 
</span>design(1,subj+i) = i;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:blue">end</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">design(2,1:subj)= 1;design(2,subj+1:2*subj) = 2;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.design<span>  
</span>= design;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.uvar<span>    
</span>= 1;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.ivar<span>    
</span>= 2;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.correctm<span>        
</span>= </span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'cluster'</span><span style="font-size:10pt;font-family:"Courier New";color:black">;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.clusteralpha<span>    
</span>= 0.05;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.clusterstatistic =
</span><span style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'maxsum'</span><span style="font-size:10pt;font-family:"Courier New";color:black">;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.minnbchan<span>       
</span>= 2;</span><span style="font-size:10pt;font-family:"Courier New";color:forestgreen">% specifies with which sensors other sensors can form clusters</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.tail<span>            
</span>= 0;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.clustertail<span>     
</span>= 0;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.alpha<span>           
</span>= 0.05;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">cfg.numrandomization = 1000;</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif;line-height:normal">
<span style="font-size:10pt;font-family:"Courier New";color:black">[alpha] = ft_freqstatistics(cfg, avg_pred, avg_ran);</span><span style="font-size:12pt;font-family:"Courier New""></span></p>
<p style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:10pt;font-family:"Courier New";color:black"><u></u> <u></u></span></p>
<p style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:10pt;font-family:"Courier New";color:black">When I perform the cluster-based analysis on raw power I obtain more than one negative cluster, with highly significant
 differences between my two condition (p=0.01). The problem is that when I run the cluster-based analysis on baseline-corrected power the analysis is not even able to find any cluster of electrodes that behave differently in one condition compared to the other
 one (no matter which kind of baseline I applied, I tried with both ‘absolute’ and ‘relchange’ and even different time-window).
</span></p>
<p style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:10pt;font-family:"Courier New";color:black">I am aware of the potential loss of power that can occur when we use baseline-correction (</span><a href="http://datacolada.org/39" target="_blank">http://datacolada.org/39</a>)
<span style="font-size:10pt;font-family:"Courier New";color:black">
</span></p>
<p style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:10pt;font-family:"Courier New";color:black">At the same time I am not sure how correct is to perform stats on non-baseline corrected power, as without applying
 this procedure drifts and offsets potentially present in the signal could affect the statistical test, executed on two non-normalized datasets.
</span></p>
<p style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:10pt;font-family:"Courier New";color:black">I was wondering whether I am not aware of potential ways to specify that a baseline-correction has been applied to
 the data, or if there is a correct way of doing it. </span></p>
<pre style="margin:0cm 0cm 0.0001pt;font-size:10pt;font-family:"Courier New""><span style="color:black">So far I couldn’t find any reference that explains it clearly, but if anyone has an explanation I would really appreciate.</span></pre>
<p style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:10pt;font-family:"Courier New";color:black"><u></u> <u></u></span></p>
<pre style="margin:0cm 0cm 0.0001pt;font-size:10pt;font-family:"Courier New""><span style="color:black">Thanks in advance,</span></pre>
<pre style="margin:0cm 0cm 0.0001pt;font-size:10pt;font-family:"Courier New""><span style="color:black"><u></u> <u></u></span></pre>
<pre style="margin:0cm 0cm 0.0001pt;font-size:10pt;font-family:"Courier New""><span style="color:black">Eleonora </span></pre>
<p style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:10pt;font-family:"Courier New";color:black"><u></u> <u></u></span></p>
<br>
</div>
</div>

_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<a href="https://doi.org/10.1371/journal.pcbi.1002202" rel="noreferrer" target="_blank">https://doi.org/10.1371/journal.pcbi.1002202</a><br>
</blockquote></div></div>