> I am trying to compare two sets of data that have been thresholded
> by cluster size and significance (generated from alphasim).
Thresholded with each set's group analysis result?
> Is there a simple way to run comparisons (maybe 3dttest++?) between
> the two groups that includes cluster and significance thresholds?
It's not clear to me exactly what comparisons you're trying to run: their differences in effect sizes, conjunction analysis, or something else?
Gang