stroke_preproc.def

Bootstrap: docker
From: ubuntu:18.04

%setup
  # CIVET 2.1.1 binaries for Ubuntu 18.04
  # E.g. from https://github.com/aces/CIVET_Full_Project/releases/download/CIVET_2_1_1/civet-2.1.1-binaries-ubuntu-18.tar.gz
  # Assumed to be in local directory; change this path to appropriate location if it was extracted elsewhere.
  IMPORT_DIR="civet-2.1.1-binaries-ubuntu-18/Linux-x86_64/"
  rsync -r -L ${IMPORT_DIR}/* ${SINGULARITY_ROOTFS}/
	cp ./nii_slice.py ${SINGULARITY_ROOTFS}/nii_slice.py
	cp ./mask_diff.py ${SINGULARITY_ROOTFS}/mask_diff.py
	cp ./requirements.txt ${SINGULARITY_ROOTFS}/requirements.txt

%post
  # Perl dependencies for CIVET
  apt-get update
	apt-get install -y python3.8 python3-pip
	python3.8 -m pip install --upgrade pip
	python3.8 -m pip install -r /requirements.txt
  apt-get install -y perl perl-base perl-depends perl-modules-5.26
	chmod -R o+rx CIVET-2.1.1
	chmod o+rx /nii_slice.py
	chmod -R o+rx /bin/
	chmod -R o+rx /lib
	chmod -R o+rx /perl
	chmod -R o+rx /share
	
  # CIVET's init.sh
  MNIBASEPATH=/
  CIVET=CIVET-2.1.1

  echo "export LC_CTYPE=en_US.UTF-8" >> ${SINGULARITY_ENVIRONMENT}
  echo "export LC_ALL=C" >> ${SINGULARITY_ENVIRONMENT}
  echo "export PATH=\"$MNIBASEPATH/$CIVET/progs:$MNIBASEPATH/bin:\"$PATH" >> ${SINGULARITY_ENVIRONMENT}

  echo "export LD_LIBRARY_PATH=\"$MNIBASEPATH/lib:\"$LD_LIBRARY_PATH" >> ${SINGULARITY_ENVIRONMENT}

  echo "export MNI_DATAPATH=\"$MNIBASEPATH/share:\"$MNI_DATAPATH" >> ${SINGULARITY_ENVIRONMENT}
  echo "export PERL5LIB=\"$MNIBASEPATH/perl:\"$PERL5LIB" >> ${SINGULARITY_ENVIRONMENT}
  echo "export R_LIBS=\"$MNIBASEPATH/R_LIBS:\"$R_LIBS" >> ${SINGULARITY_ENVIRONMENT}
  echo "export VOLUME_CACHE_THRESHOLD=-1" >> ${SINGULARITY_ENVIRONMENT}

  echo "export BRAINVIEW=\"$MNIBASEPATH/share/brain-view\"" >> ${SINGULARITY_ENVIRONMENT}

  echo "export MINC_FORCE_V2=1" >> ${SINGULARITY_ENVIRONMENT}
  echo "export MINC_COMPRESS=4" >> ${SINGULARITY_ENVIRONMENT}

  echo "export CIVET_JOB_SCHEDULER=DEFAULT" >> ${SINGULARITY_ENVIRONMENT}

  # Add CIVET scrips to PATH
  echo 'export PATH=${PATH}:/CIVET-2.1.1/' >> ${SINGULARITY_ENVIRONMENT}

%runscript
#!/bin/bash

# This script takes in a BIDS-compatible directory and applies some of the CIVET scripts to the specified data.
#set -e -u
helpstr="$(basename $0) [-h] --subject DIR --output DIR [--session SES] [--model PATH] [--ignore-t1] [--ignore-t2] [--ignore-pd] [-q, --quiet] [--intermediate DIR]

where:
	-h,--help		Show this message.
	--subject DIR		BIDS-compliant subject directory. If defined, supercedes --cohort. Either --subject or --cohort must be specified.
	--output DIR		Directory to place pipeline output.
	--lesion-t1 PATH	Optional. Path to T1 lesion mask to co-register.
	--lesion-flair PATH	Optional. Path to FLAIR lesion mask to co-register.
	--lesion-dwi PATH	Optional. Path to DWI lesion mask to co-register.
	--qc DIR		Optional. Directory where to place QC image.
	--mask-overlap-db PATH	Optional. Path to the SQL database containing the mask overlap results. The file will be created if it doesn't exist. If not set, mask overlap will not be computed.
	--mask-overlap-csv PATH	Optional. If set, will create a CSV copy of the DB. Requires --mask-overlap-db to be set.
	--session SES		Specify the session to analyze.
	--ignore-t1		Optional. Ignore T1 image. Default: False.
	--ignore-t2		Optional. Ignore T2 image. Default: False.
	--ignore-pd		Optional. Ignore PD image. Default: False.
	-q, --quiet		Optional. Suppress text output. Default: False.
"

# Variable instantiation
session_list=()
ignore_t1=0
ignore_t2=0
ignore_pd=0
quiet=0
keep=0
lesion_list=()
model="/share/mni-models/mni_icbm152_t1_tal_nlin_sym_09a.mnc"
model_mask="/share/mni-models/mni_icbm152_t1_tal_nlin_sym_09a_mask.mnc"
model_label="MNI152NLin2009aSym"

while (( "$#" )); do
	case "$1" in
		-h|--help)
			echo "${helpstr}"
			exit 0
			;;
		--subject)
			subject_dir=`readlink -f "${2}"`
			buf="${subject_dir##*/}"
			subject_id="${buf##sub-}"
			shift 2
			;;
		--output)
			output=`readlink -f "${2}"`
			mkdir -p ${output}
			shift 2
			;;
		--input_list)
			input_list_file="${2}"
			shift 2
			;;
		--ignore-t1)
			ignore_t1=1
			shift 1
			;;
		--ignore-t2)
			ignore_t2=1
			shift 1
			;;
		--ignore-pd)
			ignore_pd=1
			shift 1
			;;
		-q|--quiet)
			quiet=1
			shift 1
			;;
		--intermediate)
			keep=1
			inter_dir="${2}"
			shift 2
			;;
		--qc)
			qc_dir="${2}"
			shift 2
			;;
		--civet-opts)
			shift 1
			civet_opts="$@"
			break
			;;
		--session)
			session="${2}"
			# Sanity check if user inputs "ses-1/" instead of "1"
			if [ "${session[@]: -1}" == "/" ]; then
			    session=${session[@]::$((${#session[@]}-1))}
			fi
			session="${session#ses-}"
			shift 2
			;;
		--lesion-t1)
			lesion_t1="${2}"
			shift 2
			;;
		--lesion-flair)
			lesion_flair="${2}"
			shift 2
			;;
		--lesion-dwi)
			lesion_dwi="${2}"
			shift 2
			;;
		--mask-overlap-db)
			mask_db="${2}"
			shift 2
			;;
		--mask-overlap-csv)
			mask_csv="${2}"
			shift 2
			;;
		*)
			>&2 echo "Unexpected argument: ${1}"
			exit 1
			;;
	esac
done

# Define quiet echo
qecho () {
if [ "${quiet}" -eq 0 ]; then
	echo "$@"
fi
}

# Define temo working dir
tmpdir=`mktemp -d`


qecho "Starting execution."
# Check session
if [ -z "${session}" ]; then
	>&2 echo "Parameter --session is undefined"
	exit 1
elif [ ! -d "${subject_dir}/ses-${session}" ]; then
  >&2 echo "Session ${session} is not defined in subject ${subject_id}"
  exit 1
fi

# Get T1 image
anat_pathlist="${subject_dir}/ses-${session}/anat"
buf=(`find ${anat_pathlist} -name "*T1w.nii*"`)
t1_img=${buf[0]}

bids_dir_out="${output}/sub-${subject_id}/ses-${session}/anat"
mkdir -p "${bids_dir_out}"
# Check if we need to gunzip T1 image; nii2mnc assumes .nii and not .nii.gz
t1_mnc="${tmpdir}/t1.mnc"
if [ ".gz" == "${t1_img[@]: -3}" ]; then
  gunzip -c -k "${t1_img}" > "${tmpdir}/t1.nii"
  nii2mnc -quiet "${tmpdir}/t1.nii" "${t1_mnc}"
else
  nii2mnc -quiet "${t1_img}" "${t1_mnc}"
fi

### Registration
qecho "Registering ${t1_mnc} to ${model}..."
transformation="${bids_dir_out}/sub-${subject_id}_ses-${session}_desc-T1${model_label}.xfm"
tmptransf="${tmpdir}/init.xfm"
t1_blur="${t1_mnc%.mnc}"
model_blur="${tmpdir}/model"
qecho "Saving to ${transformation}"
perl /CIVET-2.1.1/progs/bestlinreg.pl -clobber -lsq12 -nmi "${t1_mnc}" "${model}" "${transformation}"

### NUC
# First try do brain extraction using transformation
# Get model mask to native space
qecho "Performing non-uniformity correction"
mask_native="${tmpdir}/mask_to_native.mnc"
mincresample -clobber -quiet -transformation "${transformation}" -invert_transformation -like "${t1_mnc}" -nearest_neighbour "${model_mask}" "${mask_native}"
nu_correct -quiet -clobber -tmpdir "${tmpdir}/nu_correct/" -mask "${mask_native}" -distance 200 -mapping_dir "${tmpdir}" "${t1_mnc}" "${tmpdir}/nu_correct/t1_nuc_tmp0.mnc"
qecho "Looping..."
for i in `seq 0 2`; do
  qecho "Loop ${i}"
  nu_correct -quiet -clobber -tmpdir "${tmpdir}/nu_correct/" -mask "${mask_native}" -distance 200 -mapping_dir "${tmpdir}" "${tmpdir}/nu_correct/t1_nuc_tmp${i}.mnc" "${tmpdir}/nu_correct/t1_nuc_tmp$((i+1)).mnc"
done

### Transform nuc_image to model
qecho "Resampling."
mincresample -clobber -quiet -transformation "${transformation}" -like "${model}" -trilinear "${tmpdir}/nu_correct/t1_nuc_tmp${i}.mnc" "${tmpdir}/resampled.mnc"

### Normalize
qecho "Normalizing."
inormalize -quiet -clobber -range 1.0 -model "${model}" "${tmpdir}/resampled.mnc" "${tmpdir}/norm_reg.mnc"

# Convert to nii & gzip
qecho "Finalizing T1w image"
bids_final_name="sub-${subject_id}_ses-${session}_space-${model_label}_desc-T1FinalResampledNorm.nii.gz"
qecho "Converting ${tmpdir}/norm_reg.mnc to ${tmpdir}/norm_reg.nii"
mnc2nii "${tmpdir}/norm_reg.mnc" "${tmpdir}/norm_reg.nii"
gzip "${tmpdir}/norm_reg.nii"
mv "${tmpdir}/norm_reg.nii.gz" "${bids_dir_out}/${bids_final_name}"

### Apply transform to lesion mask
qecho "Transforming lesion mask."
lesion_filename=`basename ${lesion_t1}`
lesion_pre="${lesion_filename%space-*}"
lesion_post="${lesion_filename#*space-*_}"
lesion_outname="${lesion_pre}space-${model_label}_${lesion_post}"

if [ -n "${lesion_t1}" ]; then
  ext="${lesion_t1[*]: -3}"
  if [ "${ext}" == ".gz" ]; then
    qecho "Gunzipping ${lesion_t1}"
    lesion_file="${tmpdir}/t1_lesion.nii"
    gunzip -k -c "${lesion_t1}" > "${lesion_file}"
  else
    lesion_file="${lesion_t1}"
  fi

  qecho "Converting ${lesion_file} to mnc"
  nii2mnc "${lesion_file}" "${tmpdir}/t1_lesion.mnc"
  mincresample -clobber -quiet -transformation "${transformation}" -like "${model}" -nearest_neighbour "${tmpdir}/t1_lesion.mnc" "${tmpdir}/lesion_reg.mnc"
  mnc2nii "${tmpdir}/lesion_reg.mnc" "${tmpdir}/lesion_reg.nii"
  gzip "${tmpdir}/lesion_reg.nii"
  mv "${tmpdir}/lesion_reg.nii.gz" "${bids_dir_out}/${lesion_outname}"
fi

### QC
qc_name="${bids_dir_out}/sub-${subject_id}_ses-${session}_desc-QC.png"
model_mask_nii="${tmpdir}/model_mask.nii"
mnc2nii "${model_mask}" "${model_mask_nii}"
if [ -n "${model_mask}" ]; then
  python3.8 /nii_slice.py "${bids_dir_out}/${bids_final_name}" "${qc_name}" --mask_path ${bids_dir_out}/${lesion_outname} --nslices 9 --mask_template "${model_mask_nii}"
else
  python3.8 /nii_slice.py "${bids_dir_out}/${bids_final_name}" "${qc_name}" --mask_path ${bids_dir_out}/${lesion_outname} --nslices 9
fi

if [ -n "${qc_dir}" ]; then
  mkdir -p ${qc_dir}
  cp ${qc_name} "${qc_dir}/`basename ${qc_name}`"
fi

if [ -n "${mask_db}" ]; then
  python3.8 /mask_diff.py --mask_subject ${bids_dir_out}/${lesion_outname} --mask_ref ${model_mask} --database ${mask_db} --csv ${mask_csv}
fi