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antsLongitudinalJointLabelFusion.sh
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#!/bin/bash
VERSION="0.0.0"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
# Test availability of helper scripts.
# No need to test this more than once. Can reside outside of the main loop.
ANTS=antsRegistration
WARP=antsApplyTransforms
JLF=antsJointFusion
PEXEC=ANTSpexec.sh
SGE=waitForSGEQJobs.pl
PBS=waitForPBSQJobs.pl
XGRID=waitForXGridJobs.pl
SLURM=waitForSlurmJobs.pl
fle_error=0
for FLE in $JLF $ANTS $WARP $PEXEC $SGE $XGRID $PBS $SLURM
do
if ! command -v $FLE &> /dev/null
then
echo
echo "--------------------------------------------------------------------------------------"
echo " FILE $FLE DOES NOT EXIST -- OR -- IS NOT EXECUTABLE !!! $0 will terminate."
echo "--------------------------------------------------------------------------------------"
echo " if the file is not executable, please change its permissions. "
fle_error=1
fi
done
if [[ $fle_error = 1 ]];
then
echo "missing helper script"
exit 1
fi
#assuming .nii.gz as default file type. This is the case for ANTS 1.7 and up
function Usage {
cat <<USAGE
Usage:
`basename $0` -d ImageDimension -o OutputPrefix <other options> <images>
Compulsory arguments (minimal command line requires SGE cluster, otherwise use -c & -j options):
-d: ImageDimension: 2 or 3.
-o: OutputPrefix: A prefix that is prepended to all output files.
-t: TargetImage: Subjet Templae Target image to be labeled.
-g: Atlas: Atlas to be warped to target image.
-l: Labels: Labels corresponding to atlas (cf -g).
Optional arguments:
-m: Majority vote: Use majority vote instead of joint label fusion (default = 0).
-k: Keep files: Keep warped atlas and label files (default = 0).
-c: Control for parallel computation (default 0) -- 0 == run serially, 1 == SGE qsub,
2 == use PEXEC (localhost), 3 == Apple XGrid, 4 == PBS qsub, 5 == SLURM.
-j: Number of cpu cores to use (default 2; -- requires "-c 2").
-r: qsub options
-q: Use quick registration parameters: Either 0 or 1 (default = 1).
-p: Save posteriors: Save posteriors in specified c-style format e.g. posterior%04d.nii.gz
Need to specify output directory.
-f: Float precision: Use float precision (default = 1) -- 0 == double, 1 == float.
-u: Registration walltime (default = 20:00:00): Option for PBS/SLURM qsub specifying requested time
per pairwise registration.
-v: Registration memory limit (default = 8gb): Option for PBS/SLURM qsub specifying requested memory
per pairwise registration.
-w: JLF walltime (default = 20:00:00): Option for PBS/SLURM qsub specifying requested time
for the joint label fusion call.
-z: JLF Memory limit (default = 8gb): Option for PBS/SLURM qsub specifying requested memory
for the joint label fusion call.
-y: transform type (default = 's')
t: translation
r: rigid
a: rigid + affine
s: rigid + affine + deformable syn
sr: rigid + deformable syn
so: deformable syn only
b: rigid + affine + deformable b-spline syn
br: rigid + deformable b-spline syn
bo: deformable b-spline syn only
-x: Target mask image (default = 'otsu')
otsu: use otsu thresholding to define foreground/background
or: 'or' all the warped atlas images to defined foreground/background
<filename>: a user-specified mask
none: don't use a mask
Example:
`basename $0` -d 3 -t target.nii.gz -o malf \
-p malfPosteriors%04d.nii.gz \
-g atlas1.nii.gz -l labels1.nii.gz \
-g atlas2.nii.gz -l labels2.nii.gz \
-g atlas3.nii.gz -l labels3.nii.gz \
-b timepoint_0_dir \
-b timepoint_1_dir \
-b timepoint_2_dir
--------------------------------------------------------------------------------------
JLF was created by:
--------------------------------------------------------------------------------------
Hongzhi Wang and Paul Yushkevich
Penn Image Computing And Science Laboratory
University of Pennsylvania
Please reference http://www.ncbi.nlm.nih.gov/pubmed/22732662 when employing this script
in your studies.
Wang H, Suh JW, Das SR, Pluta J, Craige C, Yushkevich PA.
Multi-Atlas Segmentation with Joint Label Fusion.
IEEE Trans Pattern Anal Mach Intell.
--------------------------------------------------------------------------------------
script by Jeff Duda
--------------------------------------------------------------------------------------
USAGE
exit 1
}
function Help {
cat <<HELP
`basename $0` will propagate labels from a set of pre-labeled atlases using the JLF
algorithm. This occurs via a single subject template provided by antsLongitudinalCorticalThickness.
Usage:
`basename $0` -d ImageDimension -o OutputPrefix <other options> <images>
Example Case:
`basename $0` -d 3 -t target.nii.gz -o malf \
-p malfPosteriors%04d.nii.gz \
-g atlas1.nii.gz -l labels1.nii.gz \
-g atlas2.nii.gz -l labels2.nii.gz \
-g atlas3.nii.gz -l labels3.nii.gz
Compulsory arguments (minimal command line requires SGE cluster, otherwise use -c & -j options):
-d: ImageDimension: 2 or 3.
-o: OutputPrefix: A prefix that is prepended to all output files.
-t: TargetImage: Target image for registrations - single subject template.
-g: Atlas: Atlas to be warped to target image.
-l: Labels: Labels corresponding to atlas (cf -g).
Optional arguments:
-b: Timepoint directory: Single timepoint directory created by antsLongitudinalCorticalThickness.sh
-m: Majority vote: Use majority vote instead of joint label fusion (default = 0).
-k: Keep files: Keep warped atlas and label files (default = 0).
-c: Control for parallel computation (default 0) -- 0 == run serially, 1 == SGE qsub,
2 == use PEXEC (localhost), 3 == Apple XGrid, 4 == PBS qsub, 5 == SLURM.
-j: Number of cpu cores to use (default 2; -- requires "-c 2").
-q: Use quick registration parameters: Either 0 or 1 (default = 1).
-p: Save posteriors: Save posteriors in specified c-style format e.g. posterior%04d.nii.gz
Need to specify output directory.
-f: Float precision: Use float precision (default = 1) -- 0 == double, 1 == float.
-u: Registration walltime (default = 20:00:00): Option for PBS/SLURM qsub specifying requested time
per pairwise registration.
-v: Registration memory limit (default = 8gb): Option for PBS/SLURM qsub specifying requested memory
per pairwise registration.
-w: JLF walltime (default = 20:00:00): Option for PBS/SLURM qsub specifying requested time
for the joint label fusion call.
-z: JLF Memory limit (default = 8gb): Option for PBS/SLURM qsub specifying requested memory
for the joint label fusion call.
-y: Transform type (default = 's')
t: translation
r: rigid
a: rigid + affine
s: rigid + affine + deformable syn
sr: rigid + deformable syn
so: deformable syn only
b: rigid + affine + deformable b-spline syn
br: rigid + deformable b-spline syn
bo: deformable b-spline syn only
-x: Target mask image (default = 'otsu')
otsu: use otsu thresholding to define foreground/background
or: 'or' all the warped atlas images to defined foreground/background
<filename>: a user-specified mask
none: don't use a mask
Requirements:
This scripts relies on the following scripts in your $PATH. The script
will terminate prematurely if these files are not present or are not executable.
- pexec.sh
- waitForSGEQJobs.pl (only for use with Sun Grid Engine)
- waitForPBSQJobs.pl (only for use with Portable Batch System)
- ANTSpexec.sh (only for use with localhost parallel execution)
- waitForXGridJobs.pl (only for use with Apple XGrid)
- waitForSlurmJobs.pl (only for use with SLURM)
- antsRegistrationSyN.sh
- antsRegistrationSyNQuick.sh ( quick parameters )
--------------------------------------------------------------------------------------
Get the latest ANTS version at:
--------------------------------------------------------------------------------------
https://github.com/stnava/ANTs/
--------------------------------------------------------------------------------------
Read the ANTS documentation at:
--------------------------------------------------------------------------------------
http://stnava.github.io/ANTs/
--------------------------------------------------------------------------------------
JLF was created by:
--------------------------------------------------------------------------------------
Hongzhi Wang and Paul Yushkevich
Penn Image Computing And Science Laboratory
University of Pennsylvania
Please reference http://www.ncbi.nlm.nih.gov/pubmed/22732662 when employing this script
in your studies.
Wang H, Suh JW, Das SR, Pluta J, Craige C, Yushkevich PA.
Multi-Atlas Segmentation with Joint Label Fusion.
IEEE Trans Pattern Anal Mach Intell.
--------------------------------------------------------------------------------------
script by Jeff Duda
--------------------------------------------------------------------------------------
HELP
exit 1
}
function reportParameters {
cat <<REPORTPARAMETERS
--------------------------------------------------------------------------------------
Parameters
--------------------------------------------------------------------------------------
Dimensionality: $DIM
Output prefix: $OUTPUT_PREFIX
Posteriors format: $OUTPUT_POSTERIORS_FORMAT
Target image: $TARGET_IMAGE
Atlas images: ${ATLAS_IMAGES[@]}
Atlas labels: ${ATLAS_LABELS[@]}
Transformation: ${TRANSFORM_TYPE}
Keep all images: $KEEP_ALL_IMAGES
Processing type: $DOQSUB
Number of cpu cores: $CORES
--------------------------------------------------------------------------------------
REPORTPARAMETERS
}
cleanup()
{
echo "\n*** Performing cleanup, please wait ***\n"
runningANTSpids=$( ps --ppid $$ -o pid= )
for thePID in $runningANTSpids
do
echo "killing: ${thePID}"
kill ${thePID}
done
return $?
}
control_c()
# run if user hits control-c
{
echo -en "\n*** User pressed CTRL + C ***\n"
cleanup
exit $?
echo -en "\n*** Script cancelled by user ***\n"
}
#initializing variables with global scope
time_start=`date +%s`
CURRENT_DIR=`pwd`/
DIM=3
OUTPUT_DIR=${CURRENT_DIR}/tmp$RANDOM/
OUTPUT_PREFIX=${OUTPUT_DIR}/tmp
OUTPUT_SUFFIX="nii.gz"
OUTPUT_POSTERIORS_FORMAT=''
TARGET_IMAGE=''
ATLAS_IMAGES=()
ATLAS_LABELS=()
TRANSFORM='s'
TIME_IMAGES=()
TIME_DIRECTORIES=()
KEEP_ALL_IMAGES=0
DOQSUB=0
CORES=1
PRECISION=0
XGRID_OPTS=""
SCRIPT_PREPEND=""
QSUB_OPTS=""
TARGET_MASK_IMAGE="otsu"
REGISTRATION_WALLTIME="20:00:00"
REGISTRATION_MEMORY="8gb"
JLF_WALLTIME="20:00:00"
JLF_MEMORY="8gb"
##Getting system info from linux can be done with these variables.
# RAM=`cat /proc/meminfo | sed -n -e '/MemTotal/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
# RAMfree=`cat /proc/meminfo | sed -n -e '/MemFree/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
# cpu_free_ram=$((${RAMfree}/${cpu_count}))
if [[ ${OSTYPE:0:6} == 'darwin' ]];
then
cpu_count=`sysctl -n hw.physicalcpu`
else
cpu_count=`cat /proc/cpuinfo | grep processor | wc -l`
fi
# Provide output for Help
if [[ "$1" == "-h" ]];
then
Help >&2
fi
MAJORITYVOTE=0
RUNQUICK=1
TRANSFORM_TYPE="s"
# reading command line arguments
while getopts "b:c:d:f:g:h:j:k:l:m:o:p:q:r:t:u:v:w:x:y:z:" OPT
do
case $OPT in
h) #help
echo "$USAGE"
exit 0
;;
c) #use SGE cluster
DOQSUB=$OPTARG
if [[ $DOQSUB -gt 5 ]];
then
echo " DOQSUB must be an integer value (0=serial, 1=SGE qsub, 2=try pexec, 3=XGrid, 4=PBS qsub, 5=SLURM ) you passed -c $DOQSUB "
exit 1
fi
;;
d) #dimensions
DIM=$OPTARG
if [[ ${DIM} -ne 2 && $DIM -ne 3 ]];
then
echo " Dimensionality is only valid for 2 or 3. You passed -d $DIM."
exit 1
fi
;;
b) # time directory
TIME_DIRECTORIES[${#TIME_DIRECTORIES[@]}]=$OPTARG
;;
f)
PRECISION=$OPTARG
;;
g)
ATLAS_IMAGES[${#ATLAS_IMAGES[@]}]=$OPTARG
;;
j) #number of cpu cores to use
CORES=$OPTARG
;;
k)
KEEP_ALL_IMAGES=$OPTARG
;;
m) #majority voting option
MAJORITYVOTE=$OPTARG
;;
p)
OUTPUT_POSTERIORS_FORMAT=$OPTARG
;;
q)
RUNQUICK=$OPTARG
;;
r)
QSUB_OPTS=$OPTARG
;;
l)
ATLAS_LABELS[${#ATLAS_LABELS[@]}]=$OPTARG
;;
o)
OUTPUT_PREFIX=$OPTARG
OUTPUT_DIR=`dirname ${OUTPUT_PREFIX}`
;;
t)
TARGET_IMAGE=$OPTARG
;;
u)
REGISTRATION_WALLTIME=$OPTARG
;;
v)
REGISTRATION_MEMORY=$OPTARG
;;
w)
JLF_WALLTIME=$OPTARG
;;
z)
JLF_MEMORY=$OPTARG
;;
x)
TARGET_MASK_IMAGE=$OPTARG
;;
y)
TRANSFORM_TYPE=$OPTARG
;;
\?) # getopts issues an error message
echo "$USAGE" >&2
exit 1
;;
esac
done
if [[ $DOQSUB -eq 1 || $DOQSUB -eq 4 ]];
then
qq=`which qsub`
if [[ ${#qq} -lt 1 ]];
then
echo "do you have qsub? if not, then choose another c option ... if so, then check where the qsub alias points ..."
exit 1
fi
fi
if [[ $DOQSUB -eq 5 ]];
then
qq=`which sbatch`
if [[ ${#qq} -lt 1 ]];
then
echo "do you have sbatch? if not, then choose another c option ... if so, then check where the sbatch alias points ..."
exit
fi
fi
if [[ ! -f "$TARGET_IMAGE" ]];
then
echo "Target image '$TARGET_IMAGE' does not exist. See usage: '$0 -h 1'"
exit
fi
if [[ ${#ATLAS_IMAGES[@]} -ne ${#ATLAS_LABELS[@]} ]];
then
echo "The number of atlas images does not equal the number of labels. Ensure that a corresponding set of labels exist for each image."
exit 1
fi
PRECISIONFLAG='f'
if [[ ${PRECISION} -eq 0 ]];
then
PRECISIONFLAG='d'
fi
if [[ ${OUTPUT_PREFIX} == */ ]];
then
OUTPUT_DIR=${OUTPUT_PREFIX%/}
else
OUTPUT_DIR=$(dirname $OUTPUT_PREFIX)
fi
if [[ ! -d $OUTPUT_DIR ]];
then
echo "The output directory \"$OUTPUT_DIR\" does not exist. Making it."
mkdir -p $OUTPUT_DIR
fi
##########################################################################
#
# Perform JLF labeling by
# 1) registering all atlases to target image
# 2) call 'jointfusion'
#
##########################################################################
echo
echo "--------------------------------------------------------------------------------------"
echo " Start JLFization"
echo "--------------------------------------------------------------------------------------"
reportParameters
jobIDs=""
WARPED_ATLAS_IMAGES=()
WARPED_ATLAS_LABELS=()
AFFINE_FILES=()
WARP_FIELDS=()
INVERSE_WARP_FIELDS=()
for (( i = 0; i < ${#ATLAS_IMAGES[@]}; i++ ))
do
IMG_BASE=`basename ${ATLAS_IMAGES[$i]}`
BASENAME=` echo ${IMG_BASE} | cut -d '.' -f 1 `
qscript="${OUTPUT_DIR}/job_${BASENAME}_${i}.sh"
WARPED_ATLAS_IMAGES[${#WARPED_ATLAS_IMAGES[@]}]="${OUTPUT_PREFIX}${BASENAME}_${i}_Warped.nii.gz"
INVERSE_WARPED_ATLAS_IMAGES[${#INVERSE_WARPED_ATLAS_IMAGES[@]}]="${OUTPUT_PREFIX}${BASENAME}_${i}_InverseWarped.nii.gz"
WARPED_ATLAS_LABELS[${#WARPED_ATLAS_LABELS[@]}]="${OUTPUT_PREFIX}${BASENAME}_${i}_WarpedLabels.nii.gz"
WARP_FIELDS[${#WARP_FIELDS[@]}]="${OUTPUT_PREFIX}${BASENAME}_${i}_1Warp.nii.gz"
INVERSE_WARP_FIELDS[${#INVERSE_WARP_FIELDS[@]}]="${OUTPUT_PREFIX}${BASENAME}_${i}_1InverseWarp.nii.gz"
AFFINE_FILES[${#AFFINE_FILES[@]}]="${OUTPUT_PREFIX}${BASENAME}_${i}_0GenericAffine.mat"
if [[ -f "${OUTPUT_PREFIX}${BASENAME}_${i}_WarpedLabels.nii.gz" ]];
then
echo ${OUTPUT_PREFIX}${BASENAME}_${i}_WarpedLabels.nii.gz already exists.
rm -f $qscript
continue
fi
regcall=antsRegistrationSyN.sh
if [[ $RUNQUICK -eq 1 ]];
then
regcall=antsRegistrationSyNQuick.sh
fi
registrationCall="$regcall \
-d ${DIM} \
-p ${PRECISIONFLAG} \
-j 1 \
-t ${TRANSFORM_TYPE} \
-f ${TARGET_IMAGE} \
-m ${ATLAS_IMAGES[$i]} \
-o ${OUTPUT_PREFIX}${BASENAME}_${i}_ > ${OUTPUT_PREFIX}${BASENAME}_${i}_log.txt"
labelXfrmCall="antsApplyTransforms \
-d ${DIM} \
--float 1 \
-i ${ATLAS_LABELS[$i]} \
-r ${TARGET_IMAGE} \
-o ${OUTPUT_PREFIX}${BASENAME}_${i}_WarpedLabels.nii.gz \
-n NearestNeighbor \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_1Warp.nii.gz \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_0GenericAffine.mat >> ${OUTPUT_PREFIX}${BASENAME}_${i}_log.txt"
copyImageHeaderCall="CopyImageHeaderInformation \
${TARGET_IMAGE} \
${OUTPUT_PREFIX}${BASENAME}_${i}_Warped.nii.gz \
${OUTPUT_PREFIX}${BASENAME}_${i}_Warped.nii.gz 1 1 1"
copyLabelsHeaderCall="CopyImageHeaderInformation \
${TARGET_IMAGE} \
${OUTPUT_PREFIX}${BASENAME}_${i}_WarpedLabels.nii.gz \
${OUTPUT_PREFIX}${BASENAME}_${i}_WarpedLabels.nii.gz 1 1 1"
rm -f $qscript
if [[ $DOQSUB -eq 5 ]];
then
# SLURM job scripts must start with a shebang
echo '#!/bin/sh' > $qscript
fi
echo "$registrationCall" >> $qscript
echo "$labelXfrmCall" >> $qscript
echo "$copyImageHeaderCall" >> $qscript
echo "$copyLabelsHeaderCall" >> $qscript
if [[ $DOQSUB -eq 1 ]];
then
id=`qsub -cwd -S /bin/bash -N antsJlfReg $QSUB_OPTS $qscript | awk '{print $3}'`
jobIDs="$jobIDs $id"
sleep 0.5
elif [[ $DOQSUB -eq 4 ]];
then
id=`qsub -N antsJlfReg $QSUB_OPTS -q nopreempt -l nodes=1:ppn=1 -l mem=${REGISTRATION_MEMORY} -l walltime=${REGISTRATION_WALLTIME} $qscript | awk '{print $1}'`
jobIDs="$jobIDs $id"
sleep 0.5
elif [[ $DOQSUB -eq 3 ]];
then
id=`xgrid $XGRID_OPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's: *: :g'`
jobIDs="$jobIDs $id"
elif [[ $DOQSUB -eq 5 ]];
then
id=`sbatch --job-name=antsJlfReg${i} $QSUB_OPTS --nodes=1 --cpus-per-task=1 --time=${REGISTRATION_WALLTIME} --mem=${REGISTRATION_MEMORY} $qscript | rev | cut -f1 -d\ | rev`
jobIDs="$jobIDs $id"
sleep 0.5
elif [[ $DOQSUB -eq 0 ]];
then
echo $qscript
bash $qscript
fi
done
if [[ $DOQSUB -eq 2 ]];
then
echo
echo "--------------------------------------------------------------------------------------"
echo " Starting JLF on max ${CORES} cpucores. "
echo "--------------------------------------------------------------------------------------"
chmod +x ${OUTPUT_DIR}/job_*.sh
$PEXEC -j ${CORES} "sh" ${OUTPUT_DIR}/job_*.sh
fi
jlfCall="antsJointFusion -d ${DIM} -t $TARGET_IMAGE --verbose 1 "
if [[ $DOQSUB -eq 0 ]];
then
# Run job locally
echo
echo "--------------------------------------------------------------------------------------"
echo " Starting JLF"
echo "--------------------------------------------------------------------------------------"
EXISTING_WARPED_ATLAS_IMAGES=()
EXISTING_WARPED_ATLAS_LABELS=()
for (( i = 0; i < ${#WARPED_ATLAS_IMAGES[@]}; i++ ))
do
echo ${WARPED_ATLAS_IMAGES[$i]}
if [[ -f ${WARPED_ATLAS_IMAGES[$i]} ]] && [[ -f ${WARPED_ATLAS_LABELS[$i]} ]];
then
EXISTING_WARPED_ATLAS_IMAGES[${#EXISTING_WARPED_ATLAS_IMAGES[@]}]=${WARPED_ATLAS_IMAGES[$i]}
EXISTING_WARPED_ATLAS_LABELS[${#EXISTING_WARPED_ATLAS_LABELS[@]}]=${WARPED_ATLAS_LABELS[$i]}
fi
done
if [[ ${#EXISTING_WARPED_ATLAS_LABELS[@]} -lt 2 ]];
then
echo "Error: At least 2 warped image/label pairs needs to exist for jointFusion."
exit 1
fi
if [[ ${#EXISTING_WARPED_ATLAS_LABELS[@]} -ne ${#WARPED_ATLAS_LABELS[@]} ]];
then
echo "Warning: One or more registrations failed."
fi
maskCall=''
if [[ $MAJORITYVOTE -eq 1 ]];
then
jlfCall="ImageMath ${DIM} ${OUTPUT_PREFIX}MajorityVotingLabels.nii.gz MajorityVoting ${EXISTING_WARPED_ATLAS_LABELS[@]} "
else
for (( i = 0; i < ${#EXISTING_WARPED_ATLAS_IMAGES[@]}; i++ ))
do
jlfCall="${jlfCall} -g ${EXISTING_WARPED_ATLAS_IMAGES[$i]} -l ${EXISTING_WARPED_ATLAS_LABELS[$i]}"
done
if [[ -z "${OUTPUT_POSTERIORS_FORMAT}" ]];
then
jlfCall="${jlfCall} -o [ ${OUTPUT_PREFIX}Labels.nii.gz,${OUTPUT_PREFIX}Intensity.nii.gz ]"
else
jlfCall="${jlfCall} -o [ ${OUTPUT_PREFIX}Labels.nii.gz,${OUTPUT_PREFIX}Intensity.nii.gz,${OUTPUT_POSTERIORS_FORMAT}]"
fi
if [[ ${TARGET_MASK_IMAGE} == 'otsu' ]];
then
TARGET_MASK_IMAGE="${OUTPUT_PREFIX}TargetMaskImageOtsu.nii.gz"
maskCall="ThresholdImage ${DIM} ${TARGET_IMAGE} ${TARGET_MASK_IMAGE} Otsu 1;"
jlfCall="${jlfCall} -x ${TARGET_MASK_IMAGE}"
elif [[ ${TARGET_MASK_IMAGE} == 'or' ]];
then
TARGET_MASK_IMAGE="${OUTPUT_PREFIX}TargetMaskImageOr.nii.gz"
maskCall="ImageMath ${DIM} ${TARGET_MASK_IMAGE} max ${EXISTING_WARPED_ATLAS_IMAGES[0]} ${EXISTING_WARPED_ATLAS_IMAGES[1]};"
for (( i = 2; i < ${#EXISTING_WARPED_ATLAS_IMAGES[@]}; i++ ))
do
maskCall="${maskCall} ImageMath ${DIM} ${TARGET_MASK_IMAGE} max ${TARGET_MASK_IMAGE} ${EXISTING_WARPED_ATLAS_IMAGES[$i]};"
done
maskCall="${maskCall} ThresholdImage ${DIM} ${TARGET_MASK_IMAGE} ${TARGET_MASK_IMAGE} 0 0 0 1"
jlfCall="${jlfCall} -x ${TARGET_MASK_IMAGE}"
elif [[ -f ${TARGET_MASK_IMAGE} ]];
then
jlfCall="${jlfCall} -x ${TARGET_MASK_IMAGE}"
fi
fi
qscript2="${OUTPUT_PREFIX}JLF.sh"
echo "$maskCall" > $qscript2
echo "$jlfCall" >> $qscript2
if [[ ! -f ${OUTPUT_PREFIX}Labels.nii.gz ]];
then
echo $qscript2
bash $qscript2
else
echo "File ${OUTPUT_PREFIX}Labels.nii.gz already exists"
fi
for (( j = 0; j < ${#TIME_DIRECTORIES[@]}; j++ ))
do
tImg=`ls ${TIME_DIRECTORIES[$j]}/*ExtractedBrain0N4.nii.gz`
tMask=`ls ${TIME_DIRECTORIES[$j]}/*BrainExtractionMask.nii.gz`
# FIXME - inverse of this?
#tMat=`ls ${TIME_DIRECTORIES[$j]}/*SubjectToTemplate0GenericAffine.mat`
#tWarp=`ls ${TIME_DIRECTORIES[$j]}/*SubjectToTemplate1Warp.nii.gz`
tMat=`ls ${TIME_DIRECTORIES[$j]}/*TemplateToSubject1GenericAffine.mat`
tWarp=`ls ${TIME_DIRECTORIES[$j]}/*TemplateToSubject0Warp.nii.gz`
qscript3="${OUTPUT_DIR}/job_timepoint_${j}.sh"
echo '#!/bin/sh' > $qscript3
if [[ ! -f $tImg ]];
then
echo "No target image in ${TIME_DIRECTORIES[$j]}"
exit 1
fi
if [[ ! -f $tMask ]];
then
echo "No mask image in ${TIME_DIRECTORIES[$j]}"
exit 1
fi
if [[ ! -f $tMat ]];
then
echo "No linear transform in ${TIME_DIRECTORIES[$j]}"
exit 1
fi
if [[ ! -f $tWarp ]];
then
echo "No warp in ${TIME_DIRECTORIES[$j]}"
exit 1
fi
jlfTimeCall="antsJointFusion -d ${DIM} -t $tImg -x $tMask -o [ ${OUTPUT_PREFIX}${j}_Labels.nii.gz,${OUTPUT_PREFIX}${j}_Intensity.nii.gz ] --verbose 1 "
for (( i = 0; i < ${#ATLAS_IMAGES[@]}; i++ ))
do
IMG_BASE=`basename ${ATLAS_IMAGES[$i]}`
BASENAME=` echo ${IMG_BASE} | cut -d '.' -f 1 `
labelXfrmCall="antsApplyTransforms \
-d ${DIM} \
--float 1 \
-i ${ATLAS_LABELS[$i]} \
-r ${tImg} \
-o ${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_WarpedLabels.nii.gz \
-n MultiLabel \
-t ${tMat} \
-t ${tWarp} \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_1Warp.nii.gz \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_0GenericAffine.mat >> ${OUTPUT_PREFIX}${BASENAME}_time_${j}_log.txt"
imageXfrmCall="antsApplyTransforms \
-d ${DIM} \
--float 1 \
-i ${ATLAS_IMAGES[$i]} \
-r ${tImg} \
-o ${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_Warped.nii.gz \
-t ${tMat} \
-t ${tWarp} \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_1Warp.nii.gz \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_0GenericAffine.mat >> ${OUTPUT_PREFIX}${BASENAME}_time_${j}_log.txt"
copyImageHeaderCall="CopyImageHeaderInformation \
${tImg} \
${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_Warped.nii.gz \
${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_Warped.nii.gz 1 1 1"
copyLabelsHeaderCall="CopyImageHeaderInformation \
${tImg} \
${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_WarpedLabels.nii.gz \
${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_WarpedLabels.nii.gz 1 1 1"
echo "$imageXfrmCall" >> $qscript3
echo "$labelXfrmCall" >> $qscript3
echo "$copyImageHeaderCall" >> $qscript3
echo "$copyLabelsHeaderCall" >> $qscript3
jlfTimeCall="${jlfTimeCall} -g ${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_Warped.nii.gz -l ${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_WarpedLabels.nii.gz"
done
echo "$jlfTimeCall" >> $qscript3
if [[ ! -f ${OUTPUT_PREFIX}${j}_Labels.nii.gz ]];
then
echo $qscript3
bash $qscript3
else
echo "File ${OUTPUT_PREFIX}${j}_Labels.nii.gz already exists"
fi
done
fi
if [[ $DOQSUB -eq 1 ]];
then
# Run jobs on SGE and wait to finish
echo
echo "--------------------------------------------------------------------------------------"
echo " Starting JLF on SGE cluster. "
echo "--------------------------------------------------------------------------------------"
waitForSGEQJobs.pl 1 600 $jobIDs
# Returns 1 if there are errors
if [[ ! $? -eq 0 ]];
then
echo "qsub submission failed - jobs went into error state"
exit 1;
fi
EXISTING_WARPED_ATLAS_IMAGES=()
EXISTING_WARPED_ATLAS_LABELS=()
for (( i = 0; i < ${#WARPED_ATLAS_IMAGES[@]}; i++ ))
do
echo ${WARPED_ATLAS_IMAGES[$i]}
if [[ -f ${WARPED_ATLAS_IMAGES[$i]} ]] && [[ -f ${WARPED_ATLAS_LABELS[$i]} ]];
then
EXISTING_WARPED_ATLAS_IMAGES[${#EXISTING_WARPED_ATLAS_IMAGES[@]}]=${WARPED_ATLAS_IMAGES[$i]}
EXISTING_WARPED_ATLAS_LABELS[${#EXISTING_WARPED_ATLAS_LABELS[@]}]=${WARPED_ATLAS_LABELS[$i]}
fi
done
if [[ ${#EXISTING_WARPED_ATLAS_LABELS[@]} -lt 2 ]];
then
echo "Error: At least 2 warped image/label pairs needs to exist for jointFusion."
exit 1
fi
if [[ ${#EXISTING_WARPED_ATLAS_LABELS[@]} -ne ${#WARPED_ATLAS_LABELS[@]} ]];
then
echo "Warning: One or more registrations failed."
fi
maskCall=''
if [[ $MAJORITYVOTE -eq 1 ]];
then
jlfCall="ImageMath ${DIM} ${OUTPUT_PREFIX}MajorityVotingLabels.nii.gz MajorityVoting ${EXISTING_WARPED_ATLAS_LABELS[@]} "
else
for (( i = 0; i < ${#EXISTING_WARPED_ATLAS_IMAGES[@]}; i++ ))
do
jlfCall="${jlfCall} -g ${EXISTING_WARPED_ATLAS_IMAGES[$i]} -l ${EXISTING_WARPED_ATLAS_LABELS[$i]}"
done
if [[ -z "${OUTPUT_POSTERIORS_FORMAT}" ]];
then
jlfCall="${jlfCall} -o [ ${OUTPUT_PREFIX}Labels.nii.gz,${OUTPUT_PREFIX}Intensity.nii.gz ]"
else
jlfCall="${jlfCall} -o [ ${OUTPUT_PREFIX}Labels.nii.gz,${OUTPUT_PREFIX}Intensity.nii.gz,${OUTPUT_POSTERIORS_FORMAT}]"
fi
if [[ ${TARGET_MASK_IMAGE} == 'otsu' ]];
then
TARGET_MASK_IMAGE="${OUTPUT_PREFIX}TargetMaskImageOtsu.nii.gz"
maskCall="ThresholdImage ${DIM} ${TARGET_IMAGE} ${TARGET_MASK_IMAGE} Otsu 1;"
jlfCall="${jlfCall} -x ${TARGET_MASK_IMAGE}"
elif [[ ${TARGET_MASK_IMAGE} == 'or' ]];
then
TARGET_MASK_IMAGE="${OUTPUT_PREFIX}TargetMaskImageOr.nii.gz"
maskCall="ImageMath ${DIM} ${TARGET_MASK_IMAGE} max ${EXISTING_WARPED_ATLAS_IMAGES[0]} ${EXISTING_WARPED_ATLAS_IMAGES[1]};"
for (( i = 2; i < ${#EXISTING_WARPED_ATLAS_IMAGES[@]}; i++ ))
do
maskCall="${maskCall} ImageMath ${DIM} ${TARGET_MASK_IMAGE} max ${TARGET_MASK_IMAGE} ${EXISTING_WARPED_ATLAS_IMAGES[$i]};"
done
maskCall="${maskCall} ThresholdImage ${DIM} ${TARGET_MASK_IMAGE} ${TARGET_MASK_IMAGE} 0 0 0 1"
jlfCall="${jlfCall} -x ${TARGET_MASK_IMAGE}"
elif [[ -f ${TARGET_MASK_IMAGE} ]];
then
jlfCall="${jlfCall} -x ${TARGET_MASK_IMAGE}"
fi
fi
qscript2="${OUTPUT_PREFIX}JLF.sh"
echo "$maskCall" > $qscript2
echo "$jlfCall" >> $qscript2
jobIDs=`qsub -cwd -S /bin/bash -N antsJlf $QSUB_OPTS $qscript2 | awk '{print $3}'`
for (( j = 0; j < ${#TIME_DIRECTORIES[@]}; j++ ))
do
tImg=`ls ${TIME_DIRECTORIES[$j]}/*ExtractedBrain0N4.nii.gz`
tMask=`ls ${TIME_DIRECTORIES[$j]}/*BrainExtractionMask.nii.gz`
tMat=`ls ${TIME_DIRECTORIES[$j]}/*SubjectToTemplate0GenericAffine.mat`
tWarp=`ls ${TIME_DIRECTORIES[$j]}/*SubjectToTemplate1Warp.nii.gz`
qscript3="${OUTPUT_DIR}/job_timepoint_${j}.sh"
echo '#!/bin/sh' > $qscript3
if [[ ! -f $tImg ]]; then
echo "No target image in ${TIME_DIRECTORIES[$j]}"
exit 1
fi
if [[ ! -f $tMask ]]; then
echo "No mask image in ${TIME_DIRECTORIES[$j]}"
exit 1
fi
if [[ ! -f $tMat ]]; then
echo "No linear transform in ${TIME_DIRECTORIES[$j]}"
exit 1
fi
if [[ ! -f $tWarp ]]; then
echo "No warp in ${TIME_DIRECTORIES[$j]}"
exit 1
fi
jlfTimeCall="antsJointFusion -d ${DIM} -t $tImg -x $tMask --verbose 1 "
for (( i = 0; i < ${#ATLAS_IMAGES[@]}; i++ ))
do
IMG_BASE=`basename ${ATLAS_IMAGES[$i]}`
BASENAME=` echo ${IMG_BASE} | cut -d '.' -f 1 `
labelXfrmCall="antsApplyTransforms \
-d ${DIM} \
--float 1 \
-i ${ATLAS_LABELS[$i]} \
-r ${tImg} \
-o ${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_WarpedLabels.nii.gz \
-n NearestNeighbor \
-t ${tWarp} \
-t ${tMat} \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_1Warp.nii.gz \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_0GenericAffine.mat >> ${OUTPUT_PREFIX}${BASENAME}_${i}_log.txt"
imageXfrmCall="antsApplyTransforms \
-d ${DIM} \
--float 1 \
-i ${ATLAS_IMAGES[$i]} \
-r ${tImg} \
-o ${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_Warped.nii.gz \
-n NearestNeighbor \
-t ${tWarp} \
-t ${tMat} \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_1Warp.nii.gz \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_0GenericAffine.mat >> ${OUTPUT_PREFIX}${BASENAME}_${i}_log.txt"
copyImageHeaderCall="CopyImageHeaderInformation \
${tImg} \
${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_Warped.nii.gz \
${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_Warped.nii.gz 1 1 1"
copyLabelsHeaderCall="CopyImageHeaderInformation \
${tImg} \
${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_WarpedLabels.nii.gz \
${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_WarpedLabels.nii.gz 1 1 1"
echo "$imageXfrmCall" >> $qscript3
echo "$labelXfrmCall" >> $qscript3
echo "$copyImageHeaderCall" >> $qscript3
echo "$copyLabelsHeaderCall" >> $qscript3
jlfTimeCall="${jlfTimeCall} -g ${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_Warped.nii.gz -l ${OUTPUT_PREFIX}${BASENAME}_${i}_${j}_WarpedLabels.nii.gz"
done
echo "$jlfTimeCall" >> $qscript3
jobTimeIDs=`qsub -cwd -S /bin/bash -N timeJlf $QSUB_OPTS $qscript3 | awk '{print $3}'`
jobIDs="$jobIDs $jobTimeIDs"
done
waitForSGEQJobs.pl 1 600 $jobTimeIDs
fi
if [[ $DOQSUB -eq 4 ]];
then
# Run jobs on PBS and wait to finish
echo
echo "--------------------------------------------------------------------------------------"
echo " Starting JLF on PBS cluster. "
echo "--------------------------------------------------------------------------------------"
waitForPBSQJobs.pl 1 600 $jobIDs
# Returns 1 if there are errors
if [[ ! $? -eq 0 ]];
then
echo "qsub submission failed - jobs went into error state"
exit 1;
fi