#!/bin/bash
# Author: Michael Hanke <michael.hanke@gmail.com>
# License: MIT

set -e
set -u

# fake test for FSL
ignore=$FSLDIR

inbold=$(readlink -f $1) || true
initref=$(readlink -f $2) || true
finalref=$(readlink -f $3) || true
finalxfm=$(readlink -f $4) || true
outbold=$(readlink -m $5)
initflirtopts=${6:--dof 6}

for f in "$inbold" "$initref" "$finalref" "$finalxfm"; do
    if [ -z "$f" ]; then
      echo "File not found '$1'"
      exit 1
    fi
done

outbolddir=$(dirname "${outbold}")
mkdir -p "$outbolddir"

wdir=$(mktemp -d --suffix=7to3reslice)
echo $wdir
trap "rm -rf $wdir" SIGINT SIGTERM
cd "$wdir"

$FSLDIR/bin/fslroi "$inbold" bold 0 1
$FSLDIR/bin/bet bold bold_brain -Z -f 0.1
$FSLDIR/bin/flirt ${initflirtopts} -in bold_brain -ref $initref -omat bold2brain.mat
$FSLDIR/bin/convert_xfm -omat bold2final.mat -concat "$finalxfm" bold2brain.mat
#$FSLDIR/bin/flirt -in bold_brain -ref "$finalref" -applyxfm -init bold2final.mat -out "$outbold" -interp sinc
$FSLDIR/bin/flirt -in "$inbold" -ref "$finalref" -applyxfm -init bold2final.mat -out "$outbold" -interp sinc

cd -
rm -rf "$wdir"