neurostuff / neurostuff/PyMARE
Revisit permutation test methodology
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- Dominant language
- Python
- Stars
- 58
- Forks
- 16
- Avg merge
- 5h 7m
- Merged PRs (30d)
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Description
In working on #101, I've come across a few things in the permutation test methods that confuse me.
First, the permutation tests loop over datasets and parallelize across permutations. This makes sense in a non-imaging context, when you won't have many, if any, parallel datasets. However, in neuroimaging meta-analyses, you'll typically have many more parallel datasets (e.g., voxels) than permutations. Would it make sense to flip the approach in PyMARE, or would that cause too many problems for non-imaging meta-analyses?
Second, I'm comparing PyMARE's approach to Nilearn's permuted_ols function. I've noticed that there are a few steps in Nilearn's procedure that aren't in PyMARE, including some preprocessing done on the target_vars (y), tested_vars (X), and confounding_vars (also X). Should we (1) adopt this step and/or (2) treat confounding variables differently from tested variables?
Contributor guide
First steps
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Research direction
Start by reviewing the permutation-test methods discussed in #101 and compare PyMARE's implementation with Nilearn's permuted_ols procedure. Investigate whether parallelizing across datasets is appropriate for neuroimaging workloads and how preprocessing should differ for target, tested, and confounding variables. Done requires an agreed methodology before implementation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Refactor
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100