maskvolume

#!/usr/bin/env bash
# use 3dROIstats nzvolume with mask as own input. reformat and transpose
# columns are
# ROI# VOLUME(mm)
#
# 20230131WF - quick look at roi volume (mm^3)
# 20231218WF - add usage and allow other 3dROIstats switches

case $1 in
   --help*|-h*)
      echo "USAGE: $0 [-nzvoxels|-nzmean|-nzvolume] atlas.nii.gz"; exit;;
   -*) measure="$1"; title="${measure/\-/}"; shift;;
   *) measure="-nzvolume"; title="Volume_mm3";;
esac

[ ! -r "${1:?roi file to report mask volume}" ] &&
   ! 3dinfo -nt "${1}" >/dev/null &&
   warn "ERROR: cannot read $1" && exit 1

[ $# -gt 1 ] &&
   warn "ERROR: $0 given more than one input ($# != 1)" && exit 1;


# NB. removed neat bash trick: "$1"{,}  same as  "$1" "$1"
echo -e "#ROI\t$title"
3dROIstats -1Dformat -nomeanout "$measure" -mask "$1" "$1"|
 sed '2s/#//;
      s/\.0\+\(\s|$\)/\1/g;
      s/[A-Za-z0-9]\+_//g;
      s/^\t\+//'|
 grep -v '#'|
 datamash transpose