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antsJointLabelFusion2.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.
JLF=antsJointFusion
ANTS=antsRegistration
WARP=antsApplyTransforms
SMOOTH=SmoothDisplacementField
PEXEC=ANTSpexec.sh
SGE=waitForSGEQJobs.pl
PBS=waitForPBSQJobs.pl
XGRID=waitForXGridJobs.pl
SLURM=waitForSlurmJobs.pl
fle_error=0
for FLE in $JLF $ANTS $WARP $SMOOTH $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
This adds some additional utilty to the original antsJointLabelFusion.sh script.
Specifically, it adds the parameters '-a', '-b', '-e', and '-s' for performing
multiple piecewise registration steps. For example, suppose one wants to use
joint label fusion to label thoracic CT where the following atlases have been
supplied with the following labels:
label 1: left lung
label 2: right lung
label 3: spinal cord
label 4: heart
This script allows one to perform a piecewise registration where one can register
the two lungs separately and then "stitch" together the resulting transforms. This
is followed up by a registration refinement step where other labeled structures
can be incorporated into driving the registration. An additional benefit is that
one can use the segmentation labels of the atlases to create fixed masks for the
registration. Example usage for the above would be
antsJointLabelFusion2.sh -d 3 ... \
-b 1 -b 2 -b 3 -b 4 \
-e 1 -e 2 \
-a 4 \
-s 10 \
...
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: 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).
-a: isotropic resampling in mm for specifying labels (default = 'NA' = "no resampling").
-b: specify labels to use for dilation and masking for the final registration
-e: subset of labels specified by the '-b' option to be used for the piecewise registration.
If no labels are specified by '-e', it is assumed that all the '-b' labels are to be
used for the initial piecewise registration.
-s: dilation radii for labels specified with option 'b'
-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 = 'majorityvoting')
otsu: use otsu thresholding to define foreground/background
or: 'or' all the warped atlas images to defined foreground/background
majorityvoting: perform a voxelwise label voting. If >= 80% of the warped atlases agree at that
voxel, we keep that voted label at that voxel and *do not* perform JLF. Note that
the 80% threshold is hard-coded but can be easily changed in the script.
<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
--------------------------------------------------------------------------------------
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.
For lung-specific applications, cf https://www.ncbi.nlm.nih.gov/pubmed/26222827
Tustison NJ, Qing K, Wang C, Altes TA, Mugler JP 3rd.
Atlas-based estimation of lung and lobar anatomy in proton MRI.
Magn Reson Med. 2016 Jul;76(1):315-20.
--------------------------------------------------------------------------------------
script by Nick Tustison
--------------------------------------------------------------------------------------
USAGE
exit 1
}
function Help {
cat <<HELP
This adds some additional utilty to the original antsJointLabelFusion.sh script.
Specifically, it adds the parameters '-a', '-b', '-e', and '-s' for performing
multiple piecewise registration steps. For example, suppose one wants to use
joint label fusion to label thoracic CT where the following atlases have been
supplied with the following labels:
label 1: left lung
label 2: right lung
label 3: spinal cord
label 4: heart
This script allows one to perform a piecewise registration where one can register
the two lungs separately and then "stitch" together the resulting transforms. This
is followed up by a registration refinement step where other labeled structures
can be incorporated into driving the registration. An additional benefit is that
one can use the segmentation labels of the atlases to create fixed masks for the
registration. Example usage for the above would be
antsJointLabelFusion2.sh -d 3 ... \
-b 1 -b 2 -b 3 -b 4 \
-e 1 -e 2 \
-a 4 \
-s 10 \
...
`basename $0` will propagate labels from a set of pre-labeled atlases using the JLF
algorithm.
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 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").
-q: Use quick registration parameters: Either 0 or 1 (default = 1).
-b: specify labels to use for dilation and masking for the final registration
-e: subset of labels specified by the '-b' option to be used for the piecewise registration.
If no labels are specified by '-e', it is assumed that all the '-b' labels are to be
used for the initial piecewise registration.
-s: dilation radii (in mm) for labels specified with option 'b'
-a: isotropic resampling in mm for specifying labels (default = 4).
-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 = 'majorityvoting')
otsu: use otsu thresholding to define foreground/background
or: 'or' all the warped atlas images to defined foreground/background
majorityvoting: perform a voxelwise label voting. If >= 80% of the warped atlases agree at that
voxel, we keep that voted label at that voxel and *do not* perform JLF. Note that
the 80% threshold is hard-coded but can be easily changed in the script.
<filename>: a user-specified mask
none: don't use a mask
Requirements:
This scripts relies on the following scripts in your $PATH directory. 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 Nick Tustison
--------------------------------------------------------------------------------------
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'
PIECEWISE_LABELS=()
PIECEWISE_LABELS_SUBSET=()
PIECEWISE_DILATION_RADII=()
ISOTROPIC_RESAMPLING='NA'
KEEP_ALL_IMAGES=0
DOQSUB=0
CORES=1
PRECISION=0
XGRID_OPTS=""
SCRIPT_PREPEND=""
QSUB_OPTS=""
TARGET_MASK_IMAGE="majorityvoting"
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 "a:b:c:d:e:f:g:h:j:k:l:m:o:p:q:r:s: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 $DIM."
exit 1
fi
;;
f)
PRECISION=$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=$OPTARG
;;
a)
ISOTROPIC_RESAMPLING=$OPTARG
;;
b)
PIECEWISE_LABELS[${#PIECEWISE_LABELS[@]}]=$OPTARG
;;
e)
PIECEWISE_LABELS_SUBSET[${#PIECEWISE_LABELS_SUBSET[@]}]=$OPTARG
;;
s)
PIECEWISE_DILATION_RADII[${#PIECEWISE_DILATION_RADII[@]}]=$OPTARG
;;
j) #number of cpu cores to use
CORES=$OPTARG
;;
r)
QSUB_OPTS=$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
if [[ ${#PIECEWISE_LABELS[@]} -gt 0 ]];
then
if [[ ${#PIECEWISE_DILATION_RADII[@]} -eq 1 ]];
then
for (( i = 0; i < ${#PIECEWISE_LABELS[@]}; i++ ))
do
PIECEWISE_DILATION_RADII[${i}]=${PIECEWISE_DILATION_RADII[0]}
done
elif [[ ${#PIECEWISE_LABELS[@]} -ne ${#PIECEWISE_DILATION_RADII[@]} ]];
then
echo "The number of dilation radii does not equal the number of piecewise labels."
exit 1
fi
if [[ ${#PIECEWISE_LABELS_SUBSET[@]} -eq 0 ]];
then
for (( i = 0; i < ${#PIECEWISE_LABELS[@]}; i++ ))
do
PIECEWISE_LABELS_SUBSET[$i]=${PIECEWISE_LABELS[$i]}
done
else
for (( i = 0; i < ${#PIECEWISE_LABELS_SUBSET[@]}; i++ ))
do
LABEL_IS_FOUND=0
for (( j = 0; j < ${#PIECEWISE_LABELS[@]}; j++ ))
do
if [[ ${PIECEWISE_LABELS[$j]} -eq ${PIECEWISE_LABELS_SUBSET[$i]} ]];
then
LABEL_IS_FOUND=1
break
fi
done
if [[ $LABEL_IS_FOUND -eq 0 ]];
then
echo "Subset label ${PIECEWISE_LABELS_SUBSET[$i]} is not found in the labels specified by the -b option."
exit 1
fi
done
fi
fi
ISOTROPIC_RESAMPLING_VECTOR="${ISOTROPIC_RESAMPLING}x${ISOTROPIC_RESAMPLING}"
if [[ $DIM -eq 3 ]];
then
ISOTROPIC_RESAMPLING_VECTOR="${ISOTROPIC_RESAMPLING}x${ISOTROPIC_RESAMPLING}x${ISOTROPIC_RESAMPLING}"
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"
WARPED_ATLAS_LABELS[${#WARPED_ATLAS_LABELS[@]}]="${OUTPUT_PREFIX}${BASENAME}_${i}_WarpedLabels.nii.gz"
if [[ -f ${WARPED_ATLAS_LABELS[${i}]} ]];
then
echo "${WARPED_ATLAS_LABELS[${i}]} already exists."
rm -f $qscript
continue
fi
regcall=antsRegistrationSyN.sh
if [[ $RUNQUICK -eq 1 ]];
then
regcall=antsRegistrationSyNQuick.sh
fi
if [[ ${#PIECEWISE_LABELS[@]} -eq 0 ]];
then
INVERSE_WARPED_ATLAS_IMAGES[${#INVERSE_WARPED_ATLAS_IMAGES[@]}]="${OUTPUT_PREFIX}${BASENAME}_${i}_InverseWarped.nii.gz"
WARP_FIELDS[${#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}_${i}_0GenericAffine.mat"
registrationCall="$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 GenericLabel \
-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" >> $qscript
else
TMP_FILES=()
logFile="${OUTPUT_PREFIX}${BASENAME}_${i}_log.txt"
# Dilate regions and create masks
SUBSET_CONFIDENCE_MASK="${OUTPUT_PREFIX}${BASENAME}_${i}_ConfidenceMask.nii.gz"
CONFIDENCE_DILATED_MASK="${OUTPUT_PREFIX}${BASENAME}_${i}_ConfidenceDilatedMask.nii.gz"
PIECEWISE_MASKS=()
PIECEWISE_DILATED_MASKS=()
PIECEWISE_OUTPUT_PREFIX="${OUTPUT_PREFIX}${BASENAME}_${i}_PiecewiseLabel"
INITIAL_LABEL_IS_SPECIFIED=0
for (( j = 0; j < ${#PIECEWISE_LABELS[@]}; j++ ))
do
PIECEWISE_MASKS[$j]="${PIECEWISE_OUTPUT_PREFIX}${PIECEWISE_LABELS[$j]}.nii.gz"
PIECEWISE_DILATED_MASKS[$j]="${PIECEWISE_OUTPUT_PREFIX}Dilated${PIECEWISE_LABELS[$j]}.nii.gz"
thresholdCall="ThresholdImage ${DIM} ${ATLAS_LABELS[$i]} ${PIECEWISE_MASKS[$j]} ${PIECEWISE_LABELS[$j]} ${PIECEWISE_LABELS[$j]} 1 0"
echo "$thresholdCall" >> $qscript
distanceCall="ImageMath ${DIM} ${PIECEWISE_DILATED_MASKS[$j]} MaurerDistance ${PIECEWISE_MASKS[$j]} 1"
thresholdCall="ThresholdImage ${DIM} ${PIECEWISE_DILATED_MASKS[$j]} ${PIECEWISE_DILATED_MASKS[$j]} -1000000 ${PIECEWISE_DILATION_RADII[$j]} 1 0"
echo "$distanceCall" >> $qscript
echo "$thresholdCall" >> $qscript
if [[ $j -eq 0 ]]
then
echo "cp ${PIECEWISE_DILATED_MASKS[$j]} ${CONFIDENCE_DILATED_MASK}" >> $qscript
else
addCall="ImageMath ${DIM} ${CONFIDENCE_DILATED_MASK} max ${CONFIDENCE_DILATED_MASK} ${PIECEWISE_DILATED_MASKS[$j]}"
echo "$addCall" >> $qscript
fi
SUBSET_LABEL_IS_FOUND=0
for (( k = 0; k < ${#PIECEWISE_LABELS_SUBSET[@]}; k++ ))
do
if [[ ${PIECEWISE_LABELS[$j]} -eq ${PIECEWISE_LABELS_SUBSET[$k]} ]];
then
SUBSET_LABEL_IS_FOUND=1
break
fi
done
if [[ $SUBSET_LABEL_IS_FOUND -eq 0 ]];
then
continue
fi
if [[ $INITIAL_LABEL_IS_SPECIFIED -eq 0 ]]
then
echo "cp ${PIECEWISE_MASKS[$j]} ${SUBSET_CONFIDENCE_MASK}" >> $qscript
INITIAL_LABEL_IS_SPECIFIED=1
else
addCall="ImageMath ${DIM} ${SUBSET_CONFIDENCE_MASK} max ${SUBSET_CONFIDENCE_MASK} ${PIECEWISE_MASKS[$j]}"
echo "$addCall" >> $qscript
fi
done
if [[ ${ISOTROPIC_RESAMPLING} != 'NA' ]];
then
resampleCall="ResampleImage ${DIM} ${SUBSET_CONFIDENCE_MASK} ${SUBSET_CONFIDENCE_MASK} $ISOTROPIC_RESAMPLING_VECTOR 0 1"
echo "$resampleCall" >> $qscript
fi
TMP_FILES=( ${TMP_FILES[@]} ${PIECEWISE_MASKS[@]} ${PIECEWISE_DILATED_MASKS[@]} ${SUBSET_CONFIDENCE_MASK} ${CONFIDENCE_DILATED_MASK} )
# Perform initial linear registration of the whole images
# Note that we're registering the target image to the atlas image since the atlas
# image has the masks (i.e., labels)
INIT_OUTPUT_PREFIX=${OUTPUT_PREFIX}${BASENAME}_${i}_Init
registrationCallInit="antsRegistration -d 3 -v 1 -o $INIT_OUTPUT_PREFIX -r [ ${ATLAS_IMAGES[$i]},${TARGET_IMAGE},0 ]"
registrationCallInit="$registrationCallInit -t Rigid[ 0.15 ] -m MI[ ${ATLAS_IMAGES[$i]},${TARGET_IMAGE},1,32,Regular,0.25 ] -c [ 100x40x10,1e-6,10 ] -f 6x4x3 -s 3x2x1"
registrationCallInit="$registrationCallInit -t Similarity[ 0.15 ] -m MI[ ${ATLAS_IMAGES[$i]},${TARGET_IMAGE},1,32,Regular,0.25 ] -c [ 100x40x10,1e-6,10 ] -f 6x4x3 -s 3x2x1"
registrationCallInit="$registrationCallInit -t Affine[ 0.15 ] -m MI[ ${ATLAS_IMAGES[$i]},${TARGET_IMAGE},1,32,Regular,0.25 ] -c [ 100x40x10,1e-6,10 ] -f 6x4x3 -s 3x2x1 >> $logFile"
echo "$registrationCallInit" >> $qscript
# Register piecewise labels separately
PIECEWISE_TRANSFORM_WARPS=""
for (( j = 0; j < ${#PIECEWISE_LABELS[@]}; j++ ))
do
SUBSET_LABEL_IS_FOUND=0
for (( k = 0; k < ${#PIECEWISE_LABELS_SUBSET[@]}; k++ ))
do
if [[ ${PIECEWISE_LABELS[$j]} -eq ${PIECEWISE_LABELS_SUBSET[$k]} ]];
then
SUBSET_LABEL_IS_FOUND=1
break
fi
done
if [[ $SUBSET_LABEL_IS_FOUND -eq 0 ]];
then
continue
fi
PIECEWISE_OUTPUT_PREFIX=${OUTPUT_PREFIX}${BASENAME}_${i}_PiecewiseLabel${PIECEWISE_LABELS[$j]}_
registrationCallPiecewise="antsRegistration -d 3 -v 1 -z 0 -o $PIECEWISE_OUTPUT_PREFIX -r ${INIT_OUTPUT_PREFIX}0GenericAffine.mat -x ${PIECEWISE_DILATED_MASKS[$j]}"
registrationCallPiecewise="$registrationCallPiecewise -t Rigid[ 0.15 ] -m MI[ ${ATLAS_IMAGES[$i]},${TARGET_IMAGE},1,32,Regular,0.25 ] -c [ 100x100x50,1e-6,10 ] -f 6x4x3 -s 3x2x1"
registrationCallPiecewise="$registrationCallPiecewise -t Similarity[ 0.15 ] -m MI[ ${ATLAS_IMAGES[$i]},${TARGET_IMAGE},1,32,Regular,0.25 ] -c [ 100x100x50,1e-6,10 ] -f 6x4x3 -s 3x2x1"
registrationCallPiecewise="$registrationCallPiecewise -t Affine[ 0.15 ] -m MI[ ${ATLAS_IMAGES[$i]},${TARGET_IMAGE},1,32,Regular,0.25 ] -c [ 100x100x50,1e-6,10 ] -f 6x4x3 -s 3x2x1"
registrationCallPiecewise="$registrationCallPiecewise -t BSplineSyN[ 0.15,40,0 ] -m MI[ ${ATLAS_IMAGES[$i]},${TARGET_IMAGE},1,32,Regular,0.25 ] -c [ 100x40x0,1e-6,10 ] -f 6x4x1 -s 3x2x0 >> $logFile"
echo "$registrationCallPiecewise" >> $qscript
composeCallPiecewise="$WARP \
-d ${DIM} \
-v 1 \
-o [ ${PIECEWISE_OUTPUT_PREFIX}TotalWarp.nii.gz,1 ] \
-r ${ATLAS_IMAGES[$i]} \
-t ${PIECEWISE_OUTPUT_PREFIX}4Warp.nii.gz \
-t ${PIECEWISE_OUTPUT_PREFIX}3Affine.mat \
-t ${PIECEWISE_OUTPUT_PREFIX}2Similarity.mat \
-t ${PIECEWISE_OUTPUT_PREFIX}1Rigid.mat >> $logFile"
echo "$composeCallPiecewise" >> $qscript
TMP_FILES=( ${TMP_FILES[@]} ${PIECEWISE_OUTPUT_PREFIX}1Rigid.mat )
TMP_FILES=( ${TMP_FILES[@]} ${PIECEWISE_OUTPUT_PREFIX}2Similarity.mat )
TMP_FILES=( ${TMP_FILES[@]} ${PIECEWISE_OUTPUT_PREFIX}3Affine.mat )
TMP_FILES=( ${TMP_FILES[@]} ${PIECEWISE_OUTPUT_PREFIX}4Warp.nii.gz )
TMP_FILES=( ${TMP_FILES[@]} ${PIECEWISE_OUTPUT_PREFIX}4InverseWarp.nii.gz )
TMP_FILES=( ${TMP_FILES[@]} ${PIECEWISE_OUTPUT_PREFIX}TotalWarp.nii.gz )
componentCall="ConvertImage ${DIM} ${PIECEWISE_OUTPUT_PREFIX}TotalWarp.nii.gz ${PIECEWISE_OUTPUT_PREFIX}TotalWarp 10"
echo "$componentCall" >> $qscript
components=( 'xvec' 'yvec' 'zvec' )
for (( d = 0; d < ${DIM}; d++ ))
do
maskingCall="ImageMath 3 ${PIECEWISE_OUTPUT_PREFIX}TotalWarp${components[$d]}.nii.gz m ${PIECEWISE_OUTPUT_PREFIX}TotalWarp${components[$d]}.nii.gz ${PIECEWISE_MASKS[$j]}"
echo "$maskingCall" >> $qscript
if [[ ${ISOTROPIC_RESAMPLING} != 'NA' ]];
then
resampleCall="ResampleImage 3 ${PIECEWISE_OUTPUT_PREFIX}TotalWarp${components[$d]}.nii.gz ${PIECEWISE_OUTPUT_PREFIX}TotalWarp${components[$d]}.nii.gz $ISOTROPIC_RESAMPLING_VECTOR 0 0"
echo "$resampleCall" >> $qscript
fi
TMP_FILES=( ${TMP_FILES[@]} ${PIECEWISE_OUTPUT_PREFIX}TotalWarp${components[$d]}.nii.gz )
done
componentCall="ConvertImage ${DIM} ${PIECEWISE_OUTPUT_PREFIX}TotalWarp ${PIECEWISE_OUTPUT_PREFIX}TotalWarp.nii.gz 9"
echo "$componentCall" >> $qscript
PIECEWISE_TRANSFORM_WARPS="${PIECEWISE_TRANSFORM_WARPS} -t ${PIECEWISE_OUTPUT_PREFIX}TotalWarp.nii.gz"
done
# Compose all the piecewise warps
composeCall="${WARP} -d ${DIM} -v 1 \
-o [ ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalWarp.nii.gz,1 ] \
-r ${SUBSET_CONFIDENCE_MASK} \
${PIECEWISE_TRANSFORM_WARPS} >> $logFile"
echo "$composeCall" >> $qscript
# Smooth the displacement field and estimate the inverse
smoothCall="SmoothDisplacementField ${DIM} ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalWarp.nii.gz ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalWarp.nii.gz 4x4x4 5 3 0 ${SUBSET_CONFIDENCE_MASK} >> $logFile"
echo "$smoothCall" >> $qscript
inverseSmoothCall="SmoothDisplacementField ${DIM} ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalWarp.nii.gz ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalInverseWarp.nii.gz 4x4x4 5 3 1 >> $logFile"
echo "$inverseSmoothCall" >> $qscript
# Resample to the full size
xfrmForwardCall="${WARP} -d ${DIM} -v 1 \
-o [ ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalWarp.nii.gz,1 ] \
-r ${ATLAS_IMAGES[$i]} \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalWarp.nii.gz >> $logFile"
echo "$xfrmForwardCall" >> $qscript
xfrmInverseCall="${WARP} -d ${DIM} -v 1 \
-o [ ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalInverseWarp.nii.gz,1 ] \
-r ${ATLAS_IMAGES[$i]} \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalInverseWarp.nii.gz >> $logFile"
echo "$xfrmInverseCall" >> $qscript
# Now do a more refined registration
registrationCallRefined="antsRegistration -d 3 -v 1 -z 0 -o ${OUTPUT_PREFIX}${BASENAME}_${i}_ -r ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalWarp.nii.gz -r ${INIT_OUTPUT_PREFIX}0GenericAffine.mat -x ${CONFIDENCE_DILATED_MASK}"
registrationCallRefined="$registrationCallRefined -t BSplineSyN[ 0.15,40,0 ] -m CC[ ${ATLAS_IMAGES[$i]},${TARGET_IMAGE},1,2 ] -c [ 100x40x0,1e-6,10 ] -f 6x4x1 -s 2x1x0 >> $logFile"
echo "$registrationCallRefined" >> $qscript
atlasXfrmCall="antsApplyTransforms \
-d ${DIM} \
--float 1 \
-i ${ATLAS_IMAGES[$i]} \
-r ${TARGET_IMAGE} \
-o ${OUTPUT_PREFIX}${BASENAME}_${i}_Warped.nii.gz \
-n Linear \
-t [ ${INIT_OUTPUT_PREFIX}0GenericAffine.mat,1 ] \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalInverseWarp.nii.gz \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_2InverseWarp.nii.gz >> ${OUTPUT_PREFIX}${BASENAME}_${i}_log.txt"
echo "$atlasXfrmCall" >> $qscript
labelXfrmCall="antsApplyTransforms \
-d ${DIM} \
--float 1 \
-i ${ATLAS_LABELS[$i]} \
-r ${TARGET_IMAGE} \
-o ${OUTPUT_PREFIX}${BASENAME}_${i}_WarpedLabels.nii.gz \
-n GenericLabel \
-t [ ${INIT_OUTPUT_PREFIX}0GenericAffine.mat,1 ] \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalInverseWarp.nii.gz \
-t ${OUTPUT_PREFIX}${BASENAME}_${i}_2InverseWarp.nii.gz >> ${OUTPUT_PREFIX}${BASENAME}_${i}_log.txt"
echo "$labelXfrmCall" >> $qscript
TMP_FILES=( ${TMP_FILES[@]} ${INIT_OUTPUT_PREFIX}0GenericAffine.mat )
TMP_FILES=( ${TMP_FILES[@]} ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalWarp.nii.gz ${OUTPUT_PREFIX}${BASENAME}_${i}_TotalInverseWarp.nii.gz )
TMP_FILES=( ${TMP_FILES[@]} ${OUTPUT_PREFIX}${BASENAME}_${i}_2Warp.nii.gz ${OUTPUT_PREFIX}${BASENAME}_${i}_2InverseWarp.nii.gz )
copyImageHeaderCall="CopyImageHeaderInformation \
${TARGET_IMAGE} \
${OUTPUT_PREFIX}${BASENAME}_${i}_Warped.nii.gz \
${OUTPUT_PREFIX}${BASENAME}_${i}_Warped.nii.gz 1 1 1"
echo "$copyImageHeaderCall" >> $qscript
copyLabelsHeaderCall="CopyImageHeaderInformation \
${TARGET_IMAGE} \
${OUTPUT_PREFIX}${BASENAME}_${i}_WarpedLabels.nii.gz \
${OUTPUT_PREFIX}${BASENAME}_${i}_WarpedLabels.nii.gz 1 1 1"
echo "$copyLabelsHeaderCall" >> $qscript
if [[ $KEEP_ALL_IMAGES -eq 0 ]];
then
for f in ${TMP_FILES[@]}
do
echo "rm -f $f" >> $qscript
done
fi
fi
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