1. Yes. Well, to use one of the new -Clustsim or -ETAC methods, the only (current) way to do so is via 3dttest++, running one test at a time. For ANOVAs, such as with 3dMVM, then ACF clustering with 3dClustSim would be the way to go.

2. The basic cluster thresholding uses random noise, altered (blurred) to match the given ACF parameters (no permutations). Then one just counts the large clusters to get probabilities of them.

Alternatively, permutation testing permutes (typically?) subjects per group or possibly negates subjects for a single group test. Note that this is not spatial permutation, but "temporal" (cross subject) permutation.

If I understand it correctly, the 3dttest++ -Clustsim permutation method is the same, except it permutes the t-test residuals. Either way, both spatial and individual variance play a part.

Simply permuting subjects might be the most clear method, basically asking whether the current group partitioning give significant results when compared with random group partitioning.

- rick