The magic function you want is 'ispositive' inside the program 3dcalc; for example
3dcalc -a Yourmask+tlrc -b Atlasmask+tlrc -expr 'ispositive(a)*b' -prefix WhateverYouWant
ispositive(x) returns 0 for x=0 or negative, and returns 1 for x > 0. Et voila!
Answers are slow this week because (a) a bunch of us were at HBM in Seattle, and (b) a bunch of us are sick, and (c) these 2 sets have nonzero intersection.