preprocessMprage_fmriprep

#!/usr/bin/env bash
set -eou pipefail
env|grep -q ^DRYRUN=.&&DRYRUN=echo||DRYRUN=

# use fmriprep to make output that looks like preprocessMprage
# namely mprage_bet.nii.gz and mprage_warpcoef.nii.gz
usage_brief(){ cat <<H
USAGE:
   $0 -n mprage.nii.gz [-r MNI_2mm] [-o output_directory] [-h] [-D] [-d]
H
}
usage(){
   # show error message and usage
   # or full usage
   retcode=0
   [ $# -ne 0 ] && echo -e "***\nERROR: $*\n***" && retcode=1
   usage_brief 
   [ $retcode -ne 0 ] && exit $retcode
  [ $# -gt 1 ] && return
  cat <<H

TODO: more info

Run fmriprep --anat-only on a fake bids directory for a single structural
rewrite files to look like the output of preprocessMprage (mprage_bet.nii.gz and mprage_warpcoef.nii.gz)
used as input for preprocessFunctional
H
   exit
}

# arg parse could re-use parse_args. but intentially want to limit inputs
INPUT=""
REF="MNI_2mm"
OUTDIR="$(pwd)"
DOCKER=0

parse_args(){
 [ $# -eq 0 ] && usage "need -n INPUT"
 while [ $# -gt 0 ]; do
    case "$1" in
       -n) INPUT="$2"; shift 2;;
       -r) REF="$2"; shift 2;;
       -o) OUTDIR="$2"; shift 2;;
       -D) DOCKER=0; shift 1;;
       -d) DOCKER=1; shfit 1;;
       -h) usage;;
    esac
 done
 
 [ -z "$INPUT" ] && usage "missing -n INPUT"
 [ ! -r "$INPUT" ] && usage "cannot read $INPUT"
 [ ! -d "$OUTDIR" ] && usage "output dir '$OUTDIR' does not exist"
 return 0
}

fs_lic(){
   env|grep -q ^FS_LICENSE=. ||
      export FS_LICENSE=/opt/ni_tools/freesurfer/license.txt

   [ ! -r "$FS_LICENSE" ] && usage "cannot find '$FS_LICENSE'. fix with 'export FS_LICENSE=....'"
}

fake_bids(){
   local input="$1"
   local subjid=sub-1
   local path=bids/$subjid/anat/
   test ! -d $path  && mkdir -p $path
   out=$path/${subjid}_T1w.nii.gz
   test -r $out && return 0
   [[ ! "$input" =~ .nii.gz ]] && cmd=3dcopy || cmd="ln -s"
   $cmd  $input $out
   return 0
}
mkabs(){
   # get absolute path for a file
   # like 'readlink -f' but works even if it doesn't exist
   # will make dirname if the dir up from that exists
   # does not check file exists (arg to mkabs might be a file to create later)
   d="$(dirname "$1")"
   b="$(basename "$1")"
   [ ! -d "$d" -a -d "$(dirname "$d")" ] && mkdir "$d"
   [ ! -d "$d" ] && echo "ERROR: '$d' does not exist!" && return 1
   echo $(cd "$d"; pwd)/$b
}

get_ref(){
   local ref="$1"
   case $ref in
      MNI*) ref="MNI152NLin2009cAsym";;
      1YO*) ref="UNCInfant:cohort-2";;
      *);;
   esac
   echo "$ref"
}

main(){
   parse_args "$@"
   fs_lic
   local input="$(mkabs $INPUT)"
   local cmd="fmriprep"
   [ $DOCKER -eq 1 ] &&
      cmd="docker run  -v "$(pwd):$(pwd)" -v $FS_LICENSE:/opt/freesurfer/license.txt -it nipreps/fmriprep"
      # --user '$(id -u):$(id -g)'

   $DRYRUN cd $OUTDIR
   $DRYRUN fake_bids "$input"
   $DRYRUN $cmd  \
      --anat-only --skip_bids_validation --fs-no-reconall \
      --output-spaces $(get_ref $REF) \
      --participant-label sub-1 -- \
      $(pwd)/bids/ $(pwd)/out/ participant
   
   cat <<HERE
   # TODO
   # make files look like mprage_bet and mprage_warpcoef
   # remove fmriprep outputs?
HERE

}

[[ "$(caller)" != "0 "* ]] && set +u || main "$@"