tedana_deriv

#!/usr/bin/env bash
#
# run tendana from minimally preprocessed:
#    fmriprep --me-output-echos
# also warp
#
# 20230120WF - init
# 20230207WF - mni for both optcom and optcomDenoised 
#
tedana_from_echo1(){
  outdir=$(dirname "$f")
  prefix=$(basename "$f" _echo-1_desc-preproc_bold.nii.gz)

  ! [[ "$prefix" =~ sub-[^_]*_ses-[^_]* ]] && warn "nos sub-*_ses- in '$prefix'" && return 2
  sub_ses=${BASH_REMATCH[0]}
  tedana_mni="$outdir/${prefix}_space-MNI152NLin2009cAsym_desc-optcomDenoised_bold.nii.gz"

  test -r "$tedana_mni" &&
     warn "# already finished. have '$_'" && return 0

  ! python -c 'import tedana' &&
     warn "tedana not available! 'pip install tedana --user'" && exit 22

  # warping files
  transform_nonlin="${outdir/func/anat}/${sub_ses}_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5"
  transform_lin="$outdir/${prefix}_from-scanner_to-T1w_mode-image_xfm.txt"

  # this is high res mniref of t1 (likely 1mm^3)
  #mniref="${outdir/func/anat}/${sub_ses}_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
  # this is lower res w/epi dims. using mask for 3D. 4D preproc_bold as ref messes with transform
  mniref="${outdir}/${prefix}_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"

  # this is probably not the correct file to use!
  sdc_nonlin_all=("${outdir/func/fmap}/${sub_ses}_"fmap*_desc-coeff_fieldmap.nii.gz)
  sdc_nonlin="${sdc_nonlin_all[0]}"

  # exit early if we can't warp. dont run tedana over and over again
  # alterantively. only run tedana if we haven't?
  for v in transform_nonlin transform_lin mniref `: sdc_nonlin`; do
    test -z "${!v}" -o ! -r "${!v}" && warn "cannot find $v like '$_'" && return 3
  done

  #shellcheck disable=2206 # no spaces in fmriprep deriv path or we're in trouble
  echos=(${f/echo-1/echo-*})
  mapfile -t echotimes < <(jq .EchoTime*1000 "${echos[@]/.nii.gz/.json}")
  # todo: echos == echotimes

  tedana_epi="$outdir/${prefix}_desc-optcomDenoised_bold.nii.gz"

  dryrun \
     niinote "$tedana_epi" \
     tedana \
     --out-dir "$outdir" --prefix "$prefix" \
     --convention bids \
     -e "${echotimes[@]}" \
     -d "${echos[@]}" || return 1
  test -r tedana_report.html && dryrun mv "$_" "${prefix}_$_"


  # define function (closure -- use top level function local vars)
  warp_tedana() {
   local in="$1"; shift # tedana_epi
   local out="$1"; shift # $tedana_mni
   dryrun \
      niinote "${out}" \
      antsApplyTransforms \
         -d 3 -e 3 -v \
         -i "$in" \
         --output "$out" \
         --reference-image "$mniref" \
         --transform "$transform_nonlin" \
         --transform "$transform_lin" \
         #--transform "$sdc_nonlin" \

    dryrun 3drefit -space MNI "${out}"
  }


  # todo warp to MNI
  # https://brainhack-princeton.github.io/handbook/content_pages/04-03-registration.html

  # warping both optcomDenoised and optcom
  warp_tedana "$tedana_epi" "$tedana_mni"
  warp_tedana "$outdir/${prefix}_desc-optcom_bold.nii.gz"\
              "$outdir/${prefix}_space-MNI152NLin2009cAsym_desc-optcom_bold.nii.gz"


  # TODO: gsr, wm, csf
  #3droistats -mask 
}

tedana_main() {
  if [[ $# -eq 0 || "${1:-}" =~ ^-h ]]; then
     cat <<-EOF 
     USAGE:
        $0 all # looks in deriv/ for fmriprep output
        $0 deriv/sub-XXX/ses-YYY/func/*_task-*_run-*_echo-1_desc-preproc_bold.nii.gz 

     runs tedana for all echos in sequence of each given '*echo-1*.nii.gz' file
     OUTPUT: 
      *_space-MNI152NLin2009cAsym_desc-optcomDenoised_bold.nii.gz

     TODO:
       * confirm optcomDenoise is ideal output (continue to avoid --gscontrol mir)
       * apply SDC?
       * recalc gsr, csf, wm, ... in _desc-confounds_timeseries.tsv?

EOF
     
     exit 1
  fi

  [ "$1" == "all" ] &&
     FILES=(deriv/sub-*/ses-*/func/*_task-*_run-*_echo-1_desc-preproc_bold.nii.gz) ||
     FILES=("$@")

  for f in "${FILES[@]}"; do
     [[ ! $f =~ echo-1 ]] && warn "ERROR: bad input file. no echo-1 in '$f'" && continue
     tedana_from_echo1 "$f"
     break
  done
  return 0
}

# if not sourced (testing), run as command
eval "$(iffmain "tedana_main")"

####
# testing with bats. use like
#   bats ./01.2_tedana.bash --verbose-run
####
tedana_main_test() { #@test
   return 1
}