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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Hi Jan,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Of course – here’s my setup:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.latency = TIME_WINDOW;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.channel = 'eeg';<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.statistic = 'ft_statfun_depsamplesT';<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.method = 'montecarlo';<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.correctm = 'cluster';<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.neighbours = neighbours;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.clusteralpha = 0.025;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.numrandomization = n_permutations;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.tail = 0;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.design = design_matrix;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.computeprob = 'no'; <<<<< only factor I change<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.alpha = 0.05;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.correcttail = 'alpha';<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.clusterthreshold = 'nonparametric_common';<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.uvar = 1;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> cfg.ivar = 2;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> stat = ft_timelockstatistics(cfg, group_one{:}, group_two{:});<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> probs = stat.prob < if computeprob = ‘Yes’ p-values are much lower on average, when compared to computeprob = ‘No’.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">I then had a look through
<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip%2Fblob%2Fmaster%2Fstatfun%2Fft_statfun_depsamplesT.m%23L128&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C0b08a50b220f47ec2eb408ddd6655cf9%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638902453032781306%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=k8EWpTByirhUADs6MbvimvPGU4KM%2BtZYTCUaCwzKvGU%3D&reserved=0" originalSrc="https://github.com/fieldtrip/fieldtrip/blob/master/statfun/ft_statfun_depsamplesT.m#L128">
ft_statfun_depsamplesT</a> function, and it seems what actually happens is when computeprob is True, it calculates p-values from this parametric test (line 128). Then at the very end of the
<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip%2Fblob%2Fmaster%2Fft_statistics_montecarlo.m%23L528&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C0b08a50b220f47ec2eb408ddd6655cf9%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638902453032789247%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=zEGNuL%2BlmlqlRB49Jl2DO00YZYboaMXJiEJPTS05UJY%3D&reserved=0" originalSrc="https://github.com/fieldtrip/fieldtrip/blob/master/ft_statistics_montecarlo.m#L528">
ft_statistics_montcarlo</a> (line 528) if computeprob was set to true, the parametric two sample p-values are copied over the nonparametric p-values and returned.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">I have highly skewed non-gaussian data, therefore I think this is why the p-values in stat.prob are much lower across time and space when computeprob is True, vs.
when it is not.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">I just wanted to confirm if my understanding was correct.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Thank you,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Cihan<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Schoffelen,
J.M. (Jan Mathijs) via fieldtrip <fieldtrip@science.ru.nl><br>
<b>Sent:</b> Friday, August 8, 2025 11:40<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b> Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen@donders.ru.nl><br>
<b>Subject:</b> Re: [FieldTrip] Query regarding stat.prob and permutation tests</span>
<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Cihan, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Difficult to comment on this. Perhaps some example code and data might be helpful to demonstrate. <o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal">On 8 Aug 2025, at 10:53, cxd425--- via fieldtrip <fieldtrip@science.ru.nl> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Dear Jan,<br>
<br>
Thank you for the response, this is helpful.<span class="xapple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">May I ask then, if cfg.method=‘montecarlo’ and cfg.computeprob=True the p-values, are much lower in stat.prob compared to when cfg.method=‘montecarlo’ and cfg.computeprob=False – they are mostly 1s when computeprob is False. I’m not referring
to the cluster p-values (2<sup>nd</sup><span class="xapple-converted-space"> </span>level), but more so the sample (1<sup>st</sup>) level p-values.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Thank you in advance for the help,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Cihan<o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-family:"Calibri",sans-serif">From:</span></b><span style="font-family:"Calibri",sans-serif"> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip@science.ru.nl><br>
<b>Sent:</b> Wednesday, August 6, 2025 12:26 pm<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b> Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen@donders.ru.nl><br>
<b>Subject:</b> Re: [FieldTrip] Query regarding stat.prob and permutation tests</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal">Hi Cihan,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">cfg.computeprob is an option that is used by (some of) the ’statfuns’, to convert a test-statistic with a known shape into a p-value, based on the shape of the parameter, (e.g. a T or F statistic).<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">The computational algorithm with which the p-value is computed (+returned in the output of a high level function call to ft_timelock/freq/sourcestatistics) depends on a combination of the contents of cfg.method (indeed if you would use
cfg.method=‘montecarlo’, then the returned p-values are based on a permutation test, if you would use cfg.method=‘analytic’ the p-values will be based on the known distributions), and cfg.correctm.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I hope that this helps,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<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"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">On 31 Jul 2025, at 17:03, cxd425--- via fieldtrip <fieldtrip@science.ru.nl> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi FieldTrip community,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I hope you’re doing well.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I was just curious how the p-values are computed at the first level - I couldn’t find any documentation explaining the behaviour of stat.prob when cfg.computeprob is set to true or false. When I set computeprob = false, the resulting stat
object still contains p-values. Could it be that when cfg.computeprob = true, the p-values at the first level are computed using a permutation test, whereas when it’s set to false, a simpler non-permutation statistical test (e.g., a two-sample t-test) is used
instead?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Any clarification would be greatly appreciated.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Best regards,<br>
Cihan<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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