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Hi Pia,<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 17 Nov 2023, at 17:55, Pia Reinfeld via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<span lang="EN-GB" class="">Dear community,<o:p class=""></o:p></span></div>
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<span lang="EN-GB" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-GB" class="">I am currently working on statistically testing the correlation between EEG data (dependent variable) and quantitative data (independent variable).<o:p class=""></o:p></span></div>
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<span lang="EN-GB" class=""><o:p class=""> </o:p></span></div>
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<span lang="EN-GB" class="">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:<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: rgb(240, 240, 240);" class="">
<i class=""><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(96, 160, 176);" class="">% compute statistics with correlationT</span></i><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: rgb(240, 240, 240);" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">cfg<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">=</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><span class="Apple-converted-space"> </span>[];<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: rgb(240, 240, 240);" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">cfg</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">.</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">statistic <span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">=</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(64, 112, 160);" class="">'ft_statfun_correlationT'</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">;<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: rgb(240, 240, 240);" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">cfg</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">.</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">method <span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">=</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(64, 112, 160);" class="">'montecarlo'</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">;<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: rgb(240, 240, 240);" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">cfg</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">.</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">numrandomization<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">=</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(64, 160, 112);" class="">1000</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">;<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: rgb(240, 240, 240);" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: rgb(240, 240, 240);" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">n1<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">=</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(64, 160, 112);" class="">99</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">; <o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: rgb(240, 240, 240);" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">design(</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(64, 160, 112);" class="">1</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">,</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(64, 160, 112);" class="">1</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">:n1) <span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">=</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><span class="Apple-converted-space"> </span>qualitative_variable;
% e.g. [0.25, 0.22, …]<o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">cfg</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">.</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">design <span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">=</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><span class="Apple-converted-space"> </span>design;<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: rgb(240, 240, 240);" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">cfg</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">.</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">ivar <span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">=</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(64, 160, 112);" class="">1</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">;<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: rgb(240, 240, 240);" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; background-color: rgb(240, 240, 240);" class="">
<span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class="">stat<span class="Apple-converted-space"> </span></span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(102, 102, 102);" class="">=</span><span lang="EN-GB" style="font-size: 10pt; font-family: Consolas; color: rgb(33, 37, 41);" class=""><span class="Apple-converted-space"> </span>ft_freqstatistics(cfg,
data_brain{:});<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">I saw that the t-values are calculated by using this:<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">tstat = rho*(sqrt(nrepl-2))./sqrt((1-rho.^2))<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">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></div>
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<div>Yes, that should be possible.</div>
<br class="">
<blockquote type="cite" class="">
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">So I tried to add this to my configuration:<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">cfg.alpha = 0.025;<span class="Apple-converted-space"> </span><br class="">
cfg.correcttail = 'alpha';<span class="Apple-converted-space"> </span><br class="">
cfg.correctm = 'cluster';<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">cfg.clustertail = 0;<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">cfg.clusteralpha = 0.05;<br class="">
cfg.clusterstatistic = 'maxsum';<span class="Apple-converted-space"> </span><br class="">
cfg.neighbours = neighbours;<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">I get the error:<span class="Apple-converted-space"> </span><br class="">
Error using ft_statistics_montecarlo could not determine the parametric critical value for clustering<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">Error in ft_timelockstatistics (line 185)<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">[stat, cfg] = statmethod(cfg, dat, design);</span><span style="font-size: 11pt;" class=""> </span></div>
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<div>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’).</div>
<div><br class="">
</div>
<div>I hope that this helps.</div>
<div><br class="">
</div>
<div>Best wishes,</div>
<div>Jan-Mathijs</div>
<br class="">
<blockquote type="cite" class="">
<div class="">
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">Is there already a correction for MCP and am I thinking wrongly by using a cluster based approach?<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">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.<o:p class=""></o:p></span></div>
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<span lang="EN-GB" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">Any help would be highly appreciated.<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">Thank you very much and all the best,<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-GB" class="">Pia<o:p class=""></o:p></span></div>
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