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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hi Jan-Mathijs,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">thank you for your quick response!<br>
I did specify this option, but I forgot to include it in the code-snipped, sorry for that!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">So it looks like that:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.channel = {'all', '-ECG'};<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.statistic = 'ft_statfun_correlationT';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.method = 'montecarlo';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.computestat = 'yes';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.computecritval = 'yes';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.computeprob = 'yes';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.alpha = 0.05;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.tail = 0;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.correcttail = 'alpha';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.numrandomization = 10000;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.correctm = 'cluster';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.clusterstatistic = 'maxsum';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.alpha = 0.025;
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.clustertail = 0;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.clusteralpha = 0.05;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.neighbours = neighbours;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> design = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> n1 = length(target); % number of subjects<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> design(1,1:n1) = fraction_ES_N;
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.design = design;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> cfg.ivar = 1;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> stat = ft_timelockstatistics(cfg, diff{:});
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">The complete error is:
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">Error using ft_statfun_correlationT<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">P-values can only be calculated if the test statistics are calculated.
<br>
Error using ft_statistics_montecarlo could not determine the parametric critical value for clustering
<br>
Error in ft_timelockstatistics (line 185) [stat, cfg] = statmethod(cfg, dat, design);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">So I found in line 66 of ft_statfun_correlationT.m, where it checks if the test stats are calculated, so that the probability can be calculated:
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">if strcmp(cfg.computeprob, 'yes') && strcmp(cfg.computestat, 'no')<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"> ft_error('P-values can only be calculated if the test statistics are calculated.');<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">end<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">But this if statement should be false, because as you can see in my configuration I defined both as ‘yes’. So my configuration might be overwritten within in the scripts or am I wrong?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">Thank you again and all the best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">Pia<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b>Von:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> <b>Im Auftrag von
</b>Schoffelen, J.M. (Jan Mathijs) via fieldtrip<br>
<b>Gesendet:</b> Samstag, 18. November 2023 17:56<br>
<b>An:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b> Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen@donders.ru.nl><br>
<b>Betreff:</b> Re: [FieldTrip] Correction for MCP using ft_statfun_correlationT<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Pia,<o:p></o:p></p>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 17 Nov 2023, at 17:55, Pia Reinfeld via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span lang="EN-GB">Dear community,</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB">I am currently working on statistically testing the correlation between EEG data (dependent variable) and quantitative data (independent variable).</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB">I'm using the ft_statfun_correlationT function to correlate and test the quantitative independent variable (e.g. reaction time), which is one value per subject, with the subject's averaged ERP data (31channelx500timepoints)
(~100 subjects). I used this configuration from the tutorial and it worked well:</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:#F0F0F0"><i><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#60A0B0">% compute statistics with correlationT</span></i><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:#F0F0F0"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">cfg<span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">=</span><span class="apple-converted-space"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">[];</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:#F0F0F0"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">cfg</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">.</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">statistic <span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">=</span><span class="apple-converted-space"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#4070A0">'ft_statfun_correlationT'</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:#F0F0F0"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">cfg</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">.</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">method <span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">=</span><span class="apple-converted-space"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#4070A0">'montecarlo'</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:#F0F0F0"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">cfg</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">.</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">numrandomization<span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">=</span><span class="apple-converted-space"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#40A070">1000</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:#F0F0F0"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:#F0F0F0"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">n1<span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">=</span><span class="apple-converted-space"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#40A070">99</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">; </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:#F0F0F0"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">design(</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#40A070">1</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">,</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#40A070">1</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">:n1) <span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">=</span><span class="apple-converted-space"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">qualitative_variable;
% e.g. [0.25, 0.22, …]</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:#F0F0F0"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">cfg</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">.</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">design <span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">=</span><span class="apple-converted-space"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">design;</span><o:p></o:p></p>
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<div>
<p class="MsoNormal" style="background:#F0F0F0"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">cfg</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">.</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">ivar <span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">=</span><span class="apple-converted-space"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#40A070">1</span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:#F0F0F0"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="background:#F0F0F0"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">stat<span class="apple-converted-space"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#666666">=</span><span class="apple-converted-space"><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529"> </span></span><span lang="EN-GB" style="font-size:10.0pt;font-family:Consolas;color:#212529">ft_freqstatistics(cfg,
data_brain{:});</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB">I saw that the t-values are calculated by using this:</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB">tstat = rho*(sqrt(nrepl-2))./sqrt((1-rho.^2))</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB">I'm afraid I don't know much about statistics. But wouldn't it be appropriate to correct for the multiple comparison problem by using a cluster-based approach?</span><o:p></o:p></p>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Yes, that should be possible.<o:p></o:p></p>
</div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span lang="EN-GB">So I tried to add this to my configuration:</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB">cfg.alpha = 0.025;<span class="apple-converted-space"> </span><br>
cfg.correcttail = 'alpha';<span class="apple-converted-space"> </span><br>
cfg.correctm = 'cluster';<span class="apple-converted-space"> </span></span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB">cfg.clustertail = 0;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB">cfg.clusteralpha = 0.05;<br>
cfg.clusterstatistic = 'maxsum';<span class="apple-converted-space"> </span><br>
cfg.neighbours = neighbours;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB">I get the error:<span class="apple-converted-space"> </span><br>
Error using ft_statistics_montecarlo could not determine the parametric critical value for clustering</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB">Error in ft_timelockstatistics (line 185)</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB">[stat, cfg] = statmethod(cfg, dat, design);</span> <o:p></o:p></p>
</div>
</blockquote>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">The error is caused by the fact that the function that is used under the hood for the computation of the (t-scored) correlation value - i.e. ft_statfun_correlationT did not properly compute the corresponding parametric p-value. This is
due to the fact that most likely, you did not specify cfg.computeprob = ‘yes’, which is needed to overrule the default value for this parameter (which happens to be ’no’).<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I hope that this helps.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Best wishes,<o:p></o:p></p>
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<p class="MsoNormal">Jan-Mathijs<o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB">Is there already a correction for MCP and am I thinking wrongly by using a cluster based approach?</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB">How is the cfg.numrandomization implemented in this statistic? I may have missed something, but it didn't look like random permutation was being used at all.</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB">Any help would be highly appreciated.</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB">Thank you very much and all the best,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB">Pia</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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</span><a href="https://doi.org/10.1371/journal.pcbi.1002202"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#954F72">https://doi.org/10.1371/journal.pcbi.1002202</span></a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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