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> if I'm reading my output correctly then one of my covariates (scanner - data collected on two
> scanners) may be contributing an effect on this cluster above and beyond my variable A?
Did you center variable A? If not, the results for those two categorical variables would be interpreted as the variable A being at 0, which may or may not be meaningful. Could you provide your script? The analysis can be better done with 3dttest++ or 3dMVM.