seed_corr

#!/usr/bin/env bash
set -eou pipefail
trap 'e=$?; [ $e -ne 0 ] && echo "$0 exited in error"' EXIT
SCRIPTDIR="$(cd $(dirname $0); pwd)"
[ -v DRYRUN ] && DRYRUN=echo || DRYRUN=

usage(){
 exitstat=0
 [ $# -gt 0 ] && echo "ERROR: $@" && exitstat=1
 cat <<H
 seed_corr.bash -mask XXX -o prefix -inputs a.nii.gz b.nii.gz

 save \$prefix{.1d,_missing.txt,_corrmap_r.nii.gz,_corrmat_z.nii.gz}
H

 exit $exitstat
}

while [ $# -ne 0 ]; do
 case $1 in
   -mask|-m) mask="$2"; shift 2;;
   -input|-i) input="$2"; shift 2;;
   -prefix|-o) prefix="$2"; shift 2;;
   *) usage "dont know what to do with '$1'";
 esac
done

oneD=${prefix}.1d
missingTS=${prefix}_missing_ts.txt
corrmap=${prefix}_corrmap_r.nii.gz
corrmapz=${prefix}_corrmap_z.nii.gz
# dont need to rerun if we have final output
[ -r $corrmapz ] && echo "# have '$corrmapz'; skipping (rm to redo)" && exit
[ ! -r "$mask" ] && ! 3dinfo "$mask" 2>&1 >/dev/null && echo "# mask '$mask' does not exit" && exit 1
[ ! -r $input ] && echo "# 4d input '$input' does not exist" && exit 1

# make folder if it doesn't exist
outdir="$(dirname $prefix)"
[ -n "$outdir" -a ! -d "$outdir" ] && $DRYRUN mkdir -p "$outdir"
[ -n "$DRYRUN" ] && echo "# would make '$corrmapz'" && exit

## actually do things!
# extract voxel mean timeseries of roi
3dmaskave -q -mask $mask $input > $oneD
# correlation (3d) - every voxel to extracted timeseries
! 3dTcorr1D -prefix $corrmap $input $oneD && echo "$mask $inputs" > $missingTS 
# z transform of r
3dcalc -a $corrmap -expr 'log((1+a)/(1-a))/2' -prefix $corrmapz