4dConcatSubBriks

#!/usr/bin/env bash
set -euo pipefail
trap 'e=$?; [ $e -ne 0 ] && echo "$0 exited in error"' EXIT
env | grep -q ^DRYRUN=. && DRYRUN=echo || DRYRUN=""
env | grep -q ^NOAFNI= || NOAFNI=1

usage(){
  cat >&2 <<HEREDOC
USAGE:
  $(basename $0) [options] output.nii.gz 'gl*ob' [subbrik]"

EXAMPLE:
  $(basename $0) allmprage.nii.gz '1*_2*/struct/*/*_G2_256x240*/mprage_warp_linear.nii.gz'
  $(basename $0) -n 2 -p '\\d' all_3rdvol.nii.gz  'file*.nii.gz'
  $(basename $0)  -p '\\d' all_3rdvol.nii.gz  -- file1.nii.gz file2.nii.gz

SYNOPSIS:
 wrap around 3dbucket and 3drefit
 extract a subbrick from a list of nifti 
 label with luna ids

 Useful for quality checking many structurals, subject masks,  or individual contrasts

OPTIONS: (are optional)
 -a                # show afni afteward
 -p '\d{5}_\d{8}'  # change id pattern
 -h                # this help
 -n SUBBRICKIDX    # use zero-index subbrick instead of first (0)
 -o output.nii.gz  # can use -o. if not assumed first argument will be output file name
 -- file1 file2 ...# instead of using 'gl*b', expliclty list input files after --

ARGUMENTS:
 output.nii.gz - final file to create
 'gl*ob' - file glob matching all images to concat. MUST BE QUOTED. 

NOTES:
  * options must come before arguments.
     good: 4dConcatSubBriks -n 2 output.nii.gz '/path/to/*nii.gz'
     bad: 4dConcatSubBriks output.nii.gz '/path/to/*nii.gz' -n 2 
  * 'gl*ob' should be quoted. if you want to expliclty enumerate files, use -- file1 file2 ....
  * cant mix '--' and '-n'
HEREDOC
  exit 1
}

[ $# -lt 2 ] && usage
PATTERN='\d{5}_\d{8}'
FILES=
prefix=
subbrik=0

while [ $# -gt 0 ]; do
   case $1 in
     -p) PATTERN="$2"; shift 2;;
     -a) NOAFNI=""; shift;;
     -h) usage;;
     -n) subbrik="$2"; shift 2;;
     -o) prefix="$2"; shift 2;;
     --) shift; FILES=("$@"); set -- ;;
      *) break;; # nothing to do. will use stuff later
   esac
done

# initially allowed prefix to be first argument (after options)
# continue allowing that if we didn't specify with -o
[ $# -eq 0 ] && [ -z "$prefix" ] && echo "output prefix not specified! For help, see $0 -h" && exit 1
[ -z "$prefix" ] && prefix="$1" && shift

if [ -z "$FILES" ]; then
   [ $# -eq 0 ] && echo "no files specified! For help, see $0 -h" && exit 1
   glob="$1"; shift
   [ $# -gt 0 ] && echo "too many input argumetns ($#)! maybe you need single quotes around the 'gl*ob'?" >&2 && exit 1
   ! [[ $prefix =~ nii$|nii.gz$|.HEAD$ ]] && echo "prefix '$prefix' must end in .nii, .nii.gz, or .HEAD" && exit 1
   [ -z "$(ls $glob)" ] && echo "bad glob provided ('$glob'). afni files? maybe add '.HEAD' to glob?" >&2 && exit 1
   ids=($(ls $glob | grep -Po "$PATTERN" || :))
   [ -z "$ids" ] && echo "could not find ID using pattern '$PATTERN' in provided glob '$glob'" >&2 && exit 1
   FILES=($(ls $glob | sed "s/$/[$subbrik]/"))
else
  [ $subbrik -ne 0 ] && echo "ERROR: -n not supported with '--' explicit file list. add it with sed if you must" && exit 1
  # check all exist -- might have [] or other afni syntax. use 3dinfo instead of just [ -f ... ]
  for f in "${FILES[@]}"; do  ! 3dinfo -space $f >/dev/null && echo "ERROR: cannot read $f" && exit 1; done
  # extract ids
  ids=($(for f in "${FILES[@]}"; do echo $f; done | grep -Po "$PATTERN" || :))
fi

echo "# Input Files: ${FILES[*]}"

[ ${#ids[@]} -ne ${#FILES[@]} ] && echo "ERROR: have ${#ids[@]} ids but ${#FILES[@]} files. Consider modifying pattern '$PATTERN' with -p."
 
if [ ! -r "$prefix" ]; then
   echo "3dbucket: combine"
   $DRYRUN 3dbucket -prefix "$prefix" "${FILES[@]}"
   echo "3drefit: relabel"
   $DRYRUN 3drefit -relabel_all_str "${ids[*]}" "$prefix"
else 
   echo "rm $prefix # to regenerate; skipping 3dbucket and 3drefit"
fi

[ -n "$DRYRUN" ] && exit 0
[ -n "$NOAFNI" ] && exit 0

afni -com 'OPEN_WINDOW axialgraph' "$prefix"  >/dev/null 2>&1

outidx=$(3dROIstats -quiet  -mask "3dcalc( -expr step(a) -a $prefix[0] )"  $prefix |
         Rscript -e 'd<-read.table("stdin");cat(paste(sep=",",collapse=",",which( abs(d$V1) > abs(mean(d$V1))+2*sd(d$V1) )-1))')
if [ -n "$outidx" ]; then
   echo "outlier idxes: $outidx"
   echo -n "outlier labels: "
   3dinfo -label "$prefix[$outidx]"
fi