afni.nimh.nih.gov

I think 3dmaskave can operate on only one effective mask at a
time. However you need only loop over the mask values, not the
sub-bricks. Consider this tcsh script:

set max = 7 # number of mask regions
foreach maskval ( `count -digits 2 1 $max` )
3dmaskave -quiet -mrange $maskval $maskval -mask mask+orig \
epi+orig > rm.$maskval.1D
end
1dcat rm.??.1D > maskave.$max.1D
\rm -f rm.??.1D

1dplot maskave.$max.1D

- rick