Threshold in permutation_cluster_test

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  • MNE-Python version: 0.22.0
  • operating system: win10

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Hi,

I am using the permutation_cluster_test, which is an amazing function.

However, the arg threshold in this function seems a little bit weird. Because we usually interested in the p-value instead of the F-value or t-value.

After checking the relevant code in mne package, I figured it out how to set threshold for specific p-values. However, I recommend the mne team could replace the threshold with p-values threshold. Or, maybe you guys could provide an external argument for the p-values threshold.

Hope you find my suggestion useful.
Again, thanks for your amazing work.

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Thanks for the suggestion. Normally, a new feature request will get more attention if it is posted as an issue on our GitHub page. However for this particular suggestion I doubt we will make that change… the API for the clustering functions is already complicated enough without adding alternative threshold parameters, and as you say, we do provide a formula for figuring out which t-threshold or f-threshold you need in order to yield your desired p-value.

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You might benefit from looking at our recent efforts to improve the documentation: DOC: clarify cluster-based permutation testing by sappelhoff · Pull Request #10658 · mne-tools/mne-python · GitHub