> Looking at the between- and within- maps separately (computed using 3dttest++ with -setA),
> the distribution of t-statistics seem quite similar.

I'm lost at your description. You have the correlation coefficients (transferred z-scores for group analysis) from individual subjects, right? When you say the distribution of t-statistics, it's the distribution of t-statistics (from 3dttest++) across the brain or something else? I can see that you have the t-statistics at group level, but what t-statistics at individual level since you're comparing between- and within-maps?

> However the effect sizes are stronger in the within- than between- maps, in other words the
> between-maps show lower correlation differences (they are computed using more data) yet
> also show less variability across participants.

Less variability across subjects than the within-subject variabilities? How do you get the within-subject variability for the correlation coefficients?

> A direct comparison with 3dttest++ with -setA, setB and -paired gives a lot of blobs for the
> within>between just because it has higher mean values.

Still confused. You have two groups of subjects? What is the paired option used for in your case?

Gang