3dmaskave does have a median option and gives one number per sub-brick. So I think this might give you what you want.
% 3dmaskave -median -mask mask+orig test+orig > medianmask.1D
++ Program 3dmaskave: AFNI version=AFNI_2006_03_21_1314 [32-bit]
+++ 577496 voxels survive the mask
% more medianmask.1D
3625.69 [577496 voxels]
1607.87 [577496 voxels]
1563.36 [577496 voxels]
1596.39 [577496 voxels]
1581.9 [577496 voxels]
1580.06 [577496 voxels]
1546.82 [577496 voxels]
1593.38 [577496 voxels]
1595.6 [577496 voxels]
1568.25 [577496 voxels]
1548.16 [577496 voxels]
1525.69 [577496 voxels]
1526.89 [577496 voxels]
1519.3 [577496 voxels]
1515.96 [577496 voxels]
1601 [577496 voxels]
1540.3 [577496 voxels]
1591.41 [577496 voxels]
1525.69 [577496 voxels]
1579.77 [577496 voxels]
1588.08 [577496 voxels]
1580.24 [577496 voxels]