#!/bin/bash
# echo "Bash version ${BASH_VERSION}..."
# Structural Parcellation shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# $1: enquiry image
# $2: mask for enquiry image. if no mask just type "no_mask"
# $3: atlas folder. e.g. "in_vivo" or "ex_vivo"
# $4: if exist, read the file to load user defined parameters (see file under sample_parameters for examples)
if [ $# -lt 3 ]
then
echo ""
echo "********************************************************************"
echo "* CAUTION!! DO NOT use the same subject name as the atlas template *"
echo "* if it is not for leave-one-out testing *"
echo "********************************************************************"
echo "usage: bash/sh parcellation.sh <new_image> <brain_mask (type \"no_mask\" if no brainmask exist)> <atlas_folder> <[optional] user-specified-parameter-file>"
echo ""
exit
fi
# if [ ! -d job_output ]; then mkdir job_output; fi
# if [ ! -d job_error ]; then mkdir job_error; fi
# setup default value for parameters
ROOT_DIR=$(pwd)
export QSUB_CMD="qsub -l h_rt=5:00:00 -l h_vmem=4G -l tmem=4G -l s_stack=1024M -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
export QSUB_SEG_MATH="qsub -l h_rt=1:00:00 -l h_vmem=8G -l tmem=8G -l s_stack=1024M -j y -S /bin/sh -b y -cwd -V -o job_output -e job_error"
PARCELLATION_NNR="-vel" # -ln 4 -lp 4 -sx 0.6 would take much longer time
DILATE=3 # value to be dilated for the result mask
LABFUSION="-STEPS"
MASK_AFF="-ln 4 -lp 4"
# Set STEPS parameters
if [[ -z $k ]] && [[ -z $n ]]; then # if STEPS parameter is not set
# set default STEPS parameter to: "3 8 "
export k=3
export n=8
fi
export STEPS_PARAMETER="${k} ${n} "
# Read user-defined parameters
if [ ! -z $4 ]; then # check if there is a 4th argument
if [ -f $4 ]; then # check if the file specified by 4th argument exist
. $4 # if file of 4th argument exist, read the parameters from the file
fi
fi
FULL_TEST_NAME=$(basename $1)
TEST_NAME=`echo "$FULL_TEST_NAME" | cut -d'.' -f1`
echo "Creating parcellation label for: "$TEST_NAME
ATLAS=$(basename $3)
MASK=$2
if [ ! -d temp/${ATLAS} ]; then mkdir -p temp/${ATLAS}; fi
if [ ! -d mask/${ATLAS} ]; then mkdir -p mask/${ATLAS}; fi
# create dilated mask for every template image if not already exist
if [ ! -d $3/mask ]; then
echo "create mask for every template image if not done yet"
mkdir $3/mask
fi
if [ ! -d $3/mask_dilate ]; then
echo "create dilated mask for every template image if not done yet"
mkdir $3/mask_dilate
fi
for G in `ls $3/template/`
do
if [ ! -f $3/mask_dilate/$G ] && [ ! -f $3/mask_dilate/$G".nii" ] && [ ! -f $3/mask_dilate/$G".nii.gz" ] && [ ! -f $3/mask_dilate/$G".hdr" ]; then
if [ ! -f $3/mask/$G ] && [ ! -f $3/mask/$G".nii" ] && [ ! -f $3/mask/$G".nii.gz" ] && [ ! -f $3/mask/$G".hdr" ]; then
reg_tools -in $3/label/$G -bin -out $3/mask/$G
fi
seg_maths $3/mask/$G -dil ${DILATE} $3/mask_dilate/$G
fi
done
if [ ! -d label ]; then mkdir label; fi
if [ ! -d label/${ATLAS} ]; then mkdir label/${ATLAS}; fi
if [ ! -d mask ]; then mkdir mask; fi
# if no mask has been created yet, evoke mask.sh
if [ ! -f $MASK ] && [ ! -f $MASK".nii" ] && [ ! -f $MASK".nii.gz" ] && [ ! -f $MASK".hdr" ]
then
echo -e "Pre-defined mask ${MASK} NOT found, parcellation will start after the mask is generated"
# create mask for the test image first
if [ ! -z $4 ] && [ -f $4 ]; # check if there is a 4th argument# check if the file specified by 4th argument exist
then . mask.sh $1 $3 $4 # if file of 4th argument exist, read the parameters from the file
else . mask.sh $1 $3 # if there's no 4th argument or file not exist ("." eauqals to "source")
fi # if path of the script is not defined in bashrc, use "./mask.sh" instead
# Mask for the test image created
MASK=mask/${TEST_NAME}_mask_${ATLAS}_STAPLE_d${DILATE}.nii.gz
else
echo -e "Pre-defined mask ${MASK} found, start to search/generate initial affine registration from atlas to test image now"
fi
# echo "*********************************************"
# echo "* Segmentation pipeline for mouse brain MRI *"
# echo "* for ${TEST_NAME} *"
# echo "* using multi-atlas label fusion methods *"
# echo "* step 2 - structural parcellation *"
# echo "*********************************************"
# echo "usage: parcellation new_image mask atlas_type (in_vivo/ex_vivo)"
# start structural parcellation
echo "Creating label for: "$TEST_NAME
PARAMETER_NUMBER=0
TEST_NAME=`echo "$(basename $1)" | cut -d'.' -f1`
for G in `ls $3/template/`
do
NAME=`echo "$G" | cut -d'.' -f1`
jname=${jid_reg}_${TEST_NAME}_${NAME}
# Check testing image name is different from atlas template. If same, skip (for leave-one-out)
if [[ ${3}/template/${NAME} != $1 ]] && [[ ${3}/template/${NAME}.nii != $1 ]] && [[ ${3}/template/${NAME}.nii.gz != $1 ]] && [[ ${3}/template/${NAME}.hdr != $1 ]]
then
# 1)check if affine matrix exists
if [ ! -f temp/${ATLAS}/${NAME}_${TEST_NAME}_aff ]; then
# 1.1) if affine matrix not found, generate affine atlas->test
reg_aladin -flo ${3}/template/${NAME} -ref $1 -fmask ${3}/mask_dilate/${NAME} -rmask ${MASK} -res temp/${ATLAS}/${NAME}_${TEST_NAME}_aff.nii.gz -aff temp/${ATLAS}/${NAME}_${TEST_NAME}_aff ${MASK_AFF}
else
echo -e "Pre-defined affine transformation matrix ${NAME}_${TEST_NAME}_aff found, begin non-rigid registration now"
fi
# 1.2) use affine transform matrix to initialize non-rigid registration (coarse step)
reg_f3d -flo ${3}/template/${NAME} -fmask ${3}/mask_dilate/${NAME} -ref ${1} -rmask ${MASK} -aff temp/${ATLAS}/${NAME}_${TEST_NAME}_aff -res temp/${ATLAS}/${NAME}_${TEST_NAME}_f3d.nii.gz -cpp temp/${ATLAS}/${NAME}_${TEST_NAME}_cpp.nii.gz ${PARCELLATION_NNR}
# 1.3) apply control point to generate transformed mask/label from atlas to test image
reg_resample -flo ${3}/mask/${NAME} -ref ${1} -cpp temp/${ATLAS}/${NAME}_${TEST_NAME}_cpp.nii.gz -NN -res mask/${ATLAS}/${TEST_NAME}_nrr_mask_${NAME}.nii.gz
reg_resample -flo ${3}/label/${NAME} -ref ${1} -cpp temp/${ATLAS}/${NAME}_${TEST_NAME}_cpp.nii.gz -NN -res label/${ATLAS}/${TEST_NAME}_label_${NAME}.nii.gz
# 2) prepare parameters for label fusion
if (( $PARAMETER_NUMBER==0 )); then
FIRST_TEMPLATE="temp/${ATLAS}/${NAME}_${TEST_NAME}_f3d.nii.gz"
FIRST_MASK="mask/${ATLAS}/${TEST_NAME}_nrr_mask_${NAME}.nii.gz"
FIRST_LABEL="label/${ATLAS}/${TEST_NAME}_label_${NAME}.nii.gz"
else
MERGE_TEMPLATE="${MERGE_TEMPLATE} temp/${ATLAS}/${NAME}_${TEST_NAME}_f3d.nii.gz"
MERGE_MASK="${MERGE_MASK} mask/${ATLAS}/${TEST_NAME}_nrr_mask_${NAME}.nii.gz"
MERGE_LABEL="${MERGE_LABEL} label/${ATLAS}/${TEST_NAME}_label_${NAME}.nii.gz"
fi
let PARAMETER_NUMBER+=1
else
echo -e "Atlas image name ${TEST_NAME} is same as test image, skipped"
fi
done
let PARAMETER_NUMBER-=1
# Prepare 4D images for label fusion
seg_maths $FIRST_MASK -merge $PARAMETER_NUMBER 4 $MERGE_MASK mask/${ATLAS}/${TEST_NAME}_nrr_mask_4D.nii.gz
seg_maths $FIRST_LABEL -merge $PARAMETER_NUMBER 4 $MERGE_LABEL label/${ATLAS}/${TEST_NAME}_label_4D.nii.gz
# Start label fusion
# Determine which label fusion method to use
if [[ ${LABFUSION}=="-STEPS" ]]; then
seg_maths $FIRST_TEMPLATE -merge $PARAMETER_NUMBER 4 $MERGE_TEMPLATE label/${ATLAS}/${TEST_NAME}_template_4D.nii.gz
seg_LabFusion -in label/${ATLAS}/${TEST_NAME}_label_4D.nii.gz -STEPS ${k} ${n} $1 label/${ATLAS}/${TEST_NAME}_template_4D.nii.gz -out "label/${TEST_NAME}_label_${ATLAS}_STEPS_${k}_${n}.nii.gz"
# potential suffix: _NNG_${PARCELLATION_NNR} ?
# Creating NRR mask
# seg_maths label/${TEST_NAME}_label_${ATLAS}_STEPS_${k}_${n}.nii.gz -bin mask/${TEST_NAME}_mask_${ATLAS}_NRR_STEPS_${k}_${n}.nii.gz
seg_LabFusion -in mask/${ATLAS}/${TEST_NAME}_nrr_mask_4D.nii.gz -STEPS ${k} ${n} $1 label/${ATLAS}/${TEST_NAME}_template_4D.nii.gz ${LABFUSION_OPTION} -out mask/${TEST_NAME}_mask_${ATLAS}_NRR_STEPS_${k}_${n}.nii.gz
seg_maths mask/${TEST_NAME}_mask_${ATLAS}_NRR_STEPS_${k}_${n}.nii.gz -dil ${DILATE} mask/${TEST_NAME}_mask_${ATLAS}_NRR_STEPS_${k}_${n}_d${DILATE}.nii.gz
fi
