mne-tools / mne-tools/mne-python
[ENH] Spatio-temporal cluster permutation testing: Define minimum "nodes" to define a cluster
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Description
For spatio-temporal cluster permutation testing, it's important to consider how many "nodes" make up a cluster.
For example:
- In the time domain (considering 1 "channel"): Are two neighboring significant time points already a cluster? Or does it start with "3", "4", "N"?
- In the spatial domain: the same but for neighboring channels who have are significant at the same point in time
Currently I can only assume that in MNE-Python, any neighboring relationship (2 timepoints, or 2 channels) makes up a cluster.
It would be really nice to
- document this
- offer a parameter to customize this
In FieldTrip, this is done as so:
cfg.minnbchan = 2; % minimum number of neighborhood channels that is
% required for a selected sample to be included
% in the clustering algorithm (default=0).
https://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No implementation file or test is named. Start by locating the current spatio-temporal cluster permutation entry points and reviewing the linked FieldTrip reference; the work is done when the existing behavior is documented and the minimum-node behavior is specified, implemented, and covered by tests.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data, testing
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100