[FieldTrip] doublecheck significance cfg.alpha and cfg.clusteralpha

[Eric Maris]

Hi Hanneke,

> I am relatively new to fieldtrip, and just starting to make some
> serious use of the cluster-based permutation routines, and I would just
> like to (double)check something before I continu.
> 
> I use ft_timelockstatistics with the following configuration structure:
> cfg.parameter = 'individual';
> cfg.method = 'montecarlo';
> cfg.statistic = 'depsamplesT';
> cfg.correctm = 'cluster';
> cfg.clusteralpha = 0.05;
> cfg.clusterstatistic = 'maxsum';
> cfg.minnbchan = 2;
> cfg.tail = 0;
> cfg.clustertail = 0;
> cfg.alpha = 0.025;
> etc.
> 
> >From my understanding of the tutorial the "cfg.clusteralpha" stands
> for the alpha-value used for the initial test-statistic (in my case a
> paired t-test) for thresholding the data, 

This is correct.

and that the "cfg.alpha"
> field contains the alpha-value for the second step, i.e. selecting
> clusters after the permutation tests.

This is not correct. Actually, cfg.alpha is superfluous. In the output,
every cluster has a p-value assigned to it, and if there is one or more
cluster with a p-value less than your critical alpha-level (mostly 0.05 for
a one-sided and 0.025 for a two-sided test), then you have found a
significant difference.


Best,

Eric






> 
> However, the naming of the parameters seems rather contraintuitive to
> me. I would have expected it to be the other way around, i.e
> "cfg.clusteralpha" for my clusters (second step), and not the initial
> t-test.
> 
> Could anyone confirm (or deny) the way it is written in the tutorial?
> 
> Thanks a lot,
> 
> Hanneke Meeren
> 
> ----------------------------------
> Hanneke K.M. Meeren, PhD.
> Researcher and Lecturer
> Medical Psychology and Cognitive Neuroscience
> Tilburg University
> P.O. Box 90153
> 5000 LE Tilburg
> The Netherlands
> email: hanneke.meeren at uvt.nl
> 
> 
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