neurostuff / neurostuff/PyMARE

Revisit permutation test methodology

Open
#102 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

help wanted question
Dominant language
Python
Stars
58
Forks
16
Avg merge
5h 7m
Merged PRs (30d)
4

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

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 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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.