> I would like to run a contrast between two group mean conditions (A and B for
> simplicities sake), however I would like to threshold the data at a p value of
> 0.05 corrected before running the contrast.
Are you talking about running a two-sample t-test with 3dttest on brain volume data or something else? What kind of data are you trying to threshold, individual subject data, or each group's average?
> how I might contrast these two now thresholded conditions.
I have the same confusion with your 1st question: not clear about your intention and context.
Gang