automask_cnt

#!/usr/bin/env bash
#
# 3dAutomask combine(mean=>ratio) and thresholded
# as suggested by Daniel Gale Jun 18, 2023 via AP
#
# 20230724WF - init
#

[[ "${1:---help}" =~ ^--?h ]] && cat <<HERE  && exit 1
SYNOPSIS:
  3dAutomask iterations combined and masked
USAGE:
 $(basename "$0") mask_out.nii.gz input.nii.gz [-bucket] [-ratio] [-thresh=.7] [-seq=45,5,75]
  -bucket      save _bucket.nii.gz  subrick for each mask iteration
  -ratio       save _ratio.nii.gz   mean of all masks
  -thres=.5    change mask threshold to half of all automasks (default=.7)
  -seq=45,5,75 change automask clfrac sequences (default 45 to 75 by 5; csv given to 'seq')
  -noclean     don't cleanup temp files (each 3dAutomask)
   
HERE

mask_out="${1:?first argument is output name}"
[ -r "$mask_out" ] && warn "arealdy have $1; rm to redo" && exit 0
! [[ "$1" =~ .nii(.gz)?$ ]] && echo "first input should be nifti file!" && exit 1
mask_tmpdir=$(mktemp -d "${TMPDIR:-/tmp}/automask_XXXXX")

# shellcheck disable=SC2064
#trap "$(trap -p EXIT| perl -pe "s/.*?'//;s/;?' EXIT//"); test -d '$mask_tmpdir' && rm -r '$mask_tmpdir';" EXIT
[[ $* =~ -noclean ]] &&
   echo "# SAVING TO $mask_tmpdir" || 
   trap "test -d '$mask_tmpdir' && rm -r '$mask_tmpdir';" EXIT

[[ $* =~ -seq?=([,0-9]+) ]] && seq="${BASH_REMATCH[1]}" || seq=45,5,75
# shellcheck disable=SC2086 # want to split into 3
for frac in $(seq ${seq//,/ }); do
   3dAutomask -prefix "$mask_tmpdir/$frac.nii.gz"  -clfrac "0.$frac" "${2:?output name}"
done
3dMean -prefix "$mask_tmpdir/cnt.nii.gz" "$mask_tmpdir/"*.nii.gz

[[ $* =~ -bucket ]] && 3dbucket -prefix "${mask_out/.nii/_bucket.nii}" "$mask_tmpdir/"[0-9]*.nii.gz
[[ $* =~ -ratio  ]] && cp "$mask_tmpdir/cnt.nii.gz" "${mask_out/.nii/_ratio.nii}"
[[ $* =~ -thresh?=([.0-9]+) ]] && thres="${BASH_REMATCH[1]}" || thres=0.7

3dcalc -overwrite -prefix "${mask_out}" -a "$mask_tmpdir/cnt.nii.gz" -expr "step(a-$thres)"
3dNotes -h "$0 $* #git:$(gitver "$0")" "${mask_out}"