Eliana,
You can try FDR correction by running the following
3drefit -addFDR -FDRmask InputFile
Regarding family-wise error (FWE) correction, it's a little dicey. On one hand, FWE correction assumes Gaussian distribution of the data, so it may contradict with the underpinnings of the Monte Carlo simulations with 3dClustSim. However, the output from the nonparametric programs is converted into normal distribution (z-scores), therefore I think it should be fine if you correct for multiple tests based on the z-scores.
Gang