<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Monalisa,
<div class=""><br class="">
</div>
<div class="">The cfg that you used to instruct the statistics computation is somewhat ambiguous, and contains specification for options that are mutually exclusive.</div>
<div class="">Specifically, when specifying cfg.correctm = ‘fdr’, all options that pertain to clustering have become non-functional (because the thing you fill in for correctm takes precedence in determining what’s going to happen). In other words, you either
use ‘fdr’(=false discovery rate), or ‘cluster’(=for cluster-based inference + multiple comparison correction), not both. Thus, indeed, the output of the statistics computation by design will not have any information pertaining to clusters. The effect of the
false discovery rate will be visible in the ‘mask’ field, which specifies for each channel/source-time-(frequency) point whether the null hypothesis of exchangeability between conditions can be rejected with sufficient confidence. The relationship between
the p-values and mask are not so straightforward when using ‘fdr’ as a correction method. This is something that recently came up in another (unresolved, probably TLDR) thread: <a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fpipermail%2Ffieldtrip%2F2024-March%2F042417.html&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C9c4ab2b947b347f889a008dc546dd5da%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638478077945050349%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=fHqrXqfBaYWkJoGyr17Z496%2BuyCDk8gWHh31bqNDll4%3D&reserved=0" originalsrc="https://mailman.science.ru.nl/pipermail/fieldtrip/2024-March/042417.html" shash="wkb2KvYgQuWCWuDMlnUYAKinzsCSl7QPwYjKePcpTQSbSN3CIhX0c3cGhXTqDtLTLoO8H2zgdIuN1ELMg+gHKn2pMmB238lzxFLMbeRrtqQ+vmEcchJ9osDcRzr85oz+Ge1a5yU7AIaBdJQnfZv0yE7WeSYvx76dQDg4YYdlaBA=" class="">https://mailman.science.ru.nl/pipermail/fieldtrip/2024-March/042417.html</a> </div>
<div class=""><br class="">
</div>
<div class="">So, long story short, if you want to make a visualization of the effect, I would display the statistics’ value (as present in the stat-field) and creatively think of a way of highlighting the data points that survive the statistical mask.</div>
<div class=""><br class="">
</div>
<div class="">One final point: when using ‘fdr’ typically it only makes sense if you use a very large number of randomizations, in your case I would go way beyond the listed 500. If your design admits (i.e. the maximum number of randomizations will be 2^#-of-participants)
you should use at least 10000 or so. If that’s not possible, probably you’d need to consider another way of doing your inference.</div>
<div class=""><br class="">
</div>
<div class="">Good luck,</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 4 Apr 2024, at 01:08, MONALISA CHIKEZIE via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="auto" class="">Hi All,
<div dir="auto" class="">I am relatively new to Fieldtrip and I want to plot source statistics results. How do I plot the results of my parametric cluster permutation. </div>
<div dir="auto" class="">I used the following code to run the source statistics.</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">cfg.stat = [];</div>
<div dir="auto" class="">cfg.stat.method = 'analytic'; % </div>
<div dir="auto" class="">cfg.stat.statistic = 'ft_statfun_depsamplesT'; </div>
<div dir="auto" class="">cfg.stat.correctm = 'fdr'; % Analytical methods with an FDR correction</div>
<div dir="auto" class="">cfg.stat.parameter = 'pow';</div>
<div dir="auto" class="">cfg.stat.clusteralpha = 0.05;</div>
<div dir="auto" class="">cfg.stat.clustercritval = 0.05;</div>
<div dir="auto" class="">cfg.stat.clusterstatistic = 'maxsum';</div>
<div dir="auto" class="">cfg.stat.minnbchan = 2;</div>
<div dir="auto" class="">cfg.stat.tail = 0;</div>
<div dir="auto" class="">cfg.stat.clustertail = 0;</div>
<div dir="auto" class="">cfg.stat.alpha = 0.025;</div>
<div dir="auto" class="">cfg.stat.numrandomization = 500;</div>
<div dir="auto" class="">cfg.stat.computecritval = 'yes' ; % calculates the critical values of the test statistics</div>
<div dir="auto" class="">cfg.stat.computeprob = 'yes' ; %calculates the p-values</div>
<div dir="auto" class="">cfg.stat.frequency = 'all';</div>
<div dir="auto" class="">cfg.stat.ivar = 1; %conditions</div>
<div dir="auto" class="">cfg.stat.uvar = 2; %Participnts</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">I generated and saved the results as stats_results.mat.</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">The output yielded the following fields:</div>
<div dir="auto" class="">Field</div>
<div dir="auto" class="">stat</div>
<div dir="auto" class="">df</div>
<div dir="auto" class="">critval</div>
<div dir="auto" class="">prob</div>
<div dir="auto" class="">mask</div>
<div dir="auto" class="">dimord</div>
<div dir="auto" class="">dim</div>
<div dir="auto" class="">inside</div>
<div dir="auto" class="">pos</div>
<div dir="auto" class="">cfg </div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Tutorials I saw on the ft website included fields like posclusters angled negclusters when using Montecarlo method. </div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Thank you very much.</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Best,</div>
<div dir="auto" class="">Monalisa </div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class=""><br class="">
</div>
</div>
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C9c4ab2b947b347f889a008dc546dd5da%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638478077945050349%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=wnLUzMVACQZArEJRKvryu3GFIeClxkHQ8H9adWyicSk%3D&reserved=0" originalsrc="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" shash="RZWq6ZBGhcz7vcr1N1oHaCFu8HtVEvJ2eW56a+E7g05JScNBMAhLfIR6SHS7Cw/vdTj1Mp/425g4DE6CWeP8T+Vcl7sr9F96NsF2AiOIuWx03zhR0tJOP5bWVwMBcLs6K2XBat4NbkDK83l8IpFc3+c9BTxbZTG2qCyVeKsw50c=" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br class="">
https://doi.org/10.1371/journal.pcbi.1002202<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</body>
</html>