If you are using 3dMVM, I'd say use 3dFWHMx -acf followed by 3dClustSim -acf -- there really isn't another option. However, we don't have any simulations to back this usage up, since running 1000 3dMVMs on RS data would take approximately forever.
To be clear about the covariates issue in 3dttest++ -- the main effect had proper FPR control when the analysis included a covariate, but the covariate effect (slope of the voxel data per subject vs. covariate) did not. That could be fixed -- I think -- by using the covariate t-statistics in the randomizations that go into 3dClustSim, rather than the main effect t-statistics. If you REALLY need that, I suppose I could provide such an option.
We don't have any statistics tools worthy of the name for surface-based cluster-size analyses. Considering the complexity of the 3D stuff that exists now and needs to be enhanced significantly (as discussed in the other thread), I don't see such tools coming into being in AFNI for quite some time -- if ever. We aren't exactly a big group.
