mne-tools / mne-tools/mne-python

Add that minimum number of channels for defining cluster is 0 in documentation

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Python
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Description

Proposed documentation enhancement

In mne.stats.permutation_cluster_test there is no way of defining the minimum number of neighbouring points that defines a cluster. This is a major error in the code, which makes the code invalid. This has been discussed by many of the developers for years, but nothing has been done (see issue #10604, https://github.com/mne-tools/mne-python/issues/10604). Most people 1) don't know why this is a problem; 2) blindly trust the function. The least you can do if you are not ready to change it is to add to the documentation that this is a shortcoming of the function and that it should not be used until it has been solved. To exclude clusters with less than n number of channels (as has been discussed in the above-linked thread) is not a valid way forward as the t-values for these clusters have already been part of the t-distribution for defining the threshold for what can be considered significant.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the documentation for mne.stats.permutation_cluster_test and review issue #10604 for the discussed limitation. Update the function documentation to state the minimum-channel behavior and the reported caveat, then check that the rendered text clearly reflects the issue's requested warning.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
documentation
Issue type
Documentation
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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