I'm not sure what the question is? You have 1 binary mask, anatomically based (I suppose) and manually drawn. You have created another binary mask via 3dcalc. If these are truly 0-1 valued datasets, then you could use 3dcalc to multiply them to get the 0-1 valued conjunction, then use this as a mask to 3dmaskave, etc. In fact, you could create the conjunction mask "on the fly" on the command line; for example

3dmaskave -mask '3dcalc( -a m1+orig -b m2+orig -expr m1*m2 )' ....

This will run 3dcalc for you, create a temporary dataset, read that into memory, delete it from disk, and then proceed. Thus, you don't have to explicitly create the conjunction mask on disk and keep track of it. You could even do this to create the supra-threshold mask at the same time, as in

3dmaskave -mask '3dcalc( -a m1+orig -b zork+orig[9] -expr step(b-3.2)*a )' ...

where only voxels that are greater than 3.2 in zork+orig[9] AND are nonzero in m1+orig will survive the masking operation.

bob cox