Revisit permutation test methodology

[tsalo]

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?

[tsalo]

Here is the relevant section from permuted_ols: https://github.com/nilearn/nilearn/blob/7d04e2fa49030784c6ec5132f1f831de7c6540fd/nilearn/mass_univariate/permuted_least_squares.py#L704-L749