niigif

#!/usr/bin/env bash
set -euo pipefail
tmpdir=""
trap '[ -n "$tmpdir" -a -d "$tmpdir" ] && rm -r $tmpdir' EXIT SIGINT
[ -v "SCALE" ] || SCALE=200%

usage(){
  local exit=0
  [ $# -gt 0 ] && echo "ERROR: $@" && exit=1
  cat<<HD
  $0 file1 file2 ...
  $0 -help = this help

combine slicer outputs of various images to make a animated image (gif)
useful to quickly visualize warp quality or image changes
a la overlay/underlay toggle in afni

use env var e.g SCALE=200% niigif myimg1.nii.gz myimg2.nii.gz 
HD
  exit $exit
}

[ $# -eq 0 ] && usage "need at least one nifti image"
[[ "$1" =~ -h*|-useage ]] && usage

tmpdir="$(mktemp -d /tmp/niigif-XXXX)"
cnt=1
for nii in "$@"; do
  echo -n "$nii ... "
  sliceout=$tmpdir/$(printf "%02d.png" $cnt); let ++cnt;
  slicer -a $sliceout "$nii"
  convert -scale $SCALE $sliceout -background white "label:$nii" -gravity center -append $sliceout
done
echo
convert -delay 20 $tmpdir/*.png $tmpdir/all.gif
echo $tmpdir/all.gif
gifview -a $tmpdir/all.gif
# ffplay  $tmpdir/all.gif