Here is the the relevant portion of the script. Please let me know if you need to see steps before or after this.

foreach run ( `count -digits 1 1 8` )
3dAutomask -prefix mask_r{$run} {$subj}_r{$run}_vr_bl+orig
end

3dcalc -a mask_r1+orig -b mask_r2+orig -c mask_r3+orig \
-d mask_r4+orig -e mask_r5+orig -f mask_r6+orig \
-g mask_r7+orig -h mask_r8+orig \
-expr 'step(a+b+c+d+e+f+g+h)' \
-prefix full_mask

foreach run ( `count -digits 1 1 8` )
3dTstat -prefix mean_r{$run} {$subj}_r{$run}_vr_bl+orig

3dcalc -a {$subj}_r{$run}_vr_bl+orig \
-b mean_r{$run}+orig \
-c full_mask+orig \
-expr "(a/b * 100) * c" \
-prefix scaled_r{$run}

\rm mean_r{$run}+orig*

end