Hi Julien,
Would it be reasonable to use 3dcalc -expr 'argmax(a,b,c,...)' to get the index of a maximum R^2 result from 3dDeconvolve? That should be the same thing, but with the benefit of having all of 3dDeconvolve available. It would just take that one extra command, assuming 3dDeconvolve is run with -rout.
- rick