coverage_mask

#!/usr/bin/env bash
set -eou pipefail
usage(){
cat <<HEREDOC
USAGE: 
   coverage_mask outputmask.nii.gz input1.nii.gz [input2.nii.gz input3.nii.gz ....]

 make mask of coverage.
 1) idv masks: include any voxel with any non-zero value in the individual inputfiles
 2) include only voxels in all idv masks.

 This is a wrapper for 3dTstat -absmax ...; 3dMean -mask_inter ...
 You may want 3dTstat -absmax ..; 3dMean -count ... # for a more descriptive coverage map

 Input is expected to be timeseries. If you already have mask per run, you dont need this!
 Consider:
   3dMean -prefix \$outfile -count inputs*
HEREDOC
exit 1
}

[ $# -lt 2 ] && usage

outfile="$1"; shift
[ -r $outfile ] && echo -e "# already have output file.\n\t rm '$outfile' #to redo" && exit 0
tmpd=$(mktemp -d /tmp/mkmask_XXXX)
let i=1
for f in "$@"; do
   3dTstat -absmax -prefix $tmpd/mask_$i.nii.gz $f
   let ++i
done
3dMean -prefix $outfile -mask_inter $tmpd/mask_*.nii.gz
rm -r $tmpd