#!/bin/bash

# 162 slices is mulitple of 9
inc=18
for run in $( seq 1 4) ; do
    starts=( $( seq 0 $inc $( expr 162 - $inc ) ) )
    for (( gg=0; gg<${#starts[*]}; gg++ )) ; do
    	start=${starts[$gg]}
	(( end=start + inc -1 ))
	echo 3dZcutup -prefix run$( printf "%02d" $run).zcut.$( printf "%02d" ${gg} ) -keep $start $end my_brik+orig.HEAD
	## touch run$( printf "%02d" $run).zcut.$( printf "%02d" ${gg} )
    done
done

## echo gg now stores the number of cuts or groups of slices

## now that the runs are broken into groups of 18 slices you can run
## 3dTcat to get all the tuns together for analysis with 3dDecon

for (( gg=0; gg<${#starts[*]}; gg++ )) ; do
    echo 3dTcat -prefix all.runs.zcut$( printf "%02d" ${gg} ) run??.zcut.$( printf "%02d" ${gg} )
    ## touch all.runs.zcut$( printf "%02d" ${gg} )
    echo 3dDeconvolve -input all.runs.zcut$( printf "%02d" ${gg} ) -prefix stats_zcut$( printf "%02d" ${gg} )
done

## now concat all the zcuts together
## 3dZcat -prefix stats stats_zcut??+orig.HEAD