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Script for
Deconvolution - 3
#===============================================================
# create masks for each run
using 3dAutomask
#===============================================================
foreach run ( `count -digits
1 1 10` )
3dAutomask -prefix mask_r{$run}
{$subj}_r{$run}_vr_bl+orig
end
#===============================================================
# create a mask enveloping
masks of the individual runs
#===============================================================
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 -i mask_r9+orig
\
-j mask_r10+orig
\
-expr
'step(a+b+c+d+e+f+g+h+i+j)'
\
-prefix full_mask
Loop over
imaging runs 1..10
This mask dataset will be 1 inside the largest contiguous high
intensity EPI region, and
0 outside that region
Ñ this makes a brain mask