/usr/lib/ants/antsAtroposN4.sh is in ants 2.1.0-5.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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VERSION="0.0"
if [[ ! -s ${ANTSPATH}/N4BiasFieldCorrection ]]; then
echo we cant find the N4 program -- does not seem to exist. please \(re\)define \$ANTSPATH in your environment.
exit
fi
if [[ ! -s ${ANTSPATH}/Atropos ]]; then
echo we cant find the Atropos program -- does not seem to exist. please \(re\)define \$ANTSPATH in your environment.
exit
fi
function Usage {
cat <<USAGE
`basename $0` iterates between N4 <-> Atropos to improve segmentation results.
Usage:
`basename $0` -d imageDimension
-a inputImage
-x maskImage
-m n4AtroposIterations
-n atroposIterations
-c numberOfClasses
-l posteriorLabelForN4Mask
-o outputPrefix
<OPTARGS>
Example:
bash $0 -d 3 -a t1.nii.gz -x mask.nii.gz -c 4 -p segmentationPriors%d.nii.gz -o output
Required arguments:
-d: image dimension 2 or 3 (for 2- or 3-dimensional image)
-a: input image Anatomical image, typically T1. If more than one
anatomical image is specified, subsequently specified
images are used during the segmentation process.
-x: mask image Binary mask defining the region of interest.
-c: number of segmentation classes Number of classes defining the segmentation
-o: output prefix The following images are created:
* ${OUTPUT_PREFIX}N4Corrected.${OUTPUT_SUFFIX}
* ${OUTPUT_PREFIX}Segmentation.${OUTPUT_SUFFIX}
* ${OUTPUT_PREFIX}SegmentationPosteriors.${OUTPUT_SUFFIX}
Optional arguments:
-m: max. N4 <-> Atropos iterations Maximum number of (outer loop) iterations between N4 <-> Atropos.
-n: max. Atropos iterations Maximum number of (inner loop) iterations in Atropos.
-p: segmentation priors Prior probability images initializing the segmentation.
Specified using c-style formatting, e.g. -p labelsPriors%02d.nii.gz.
-r: mrf Specifies MRF prior (of the form '[weight,neighborhood]', e.g.
'[0.1,1x1x1]' which is default).
-b: posterior formulation Posterior formulation and whether or not to use mixture model proportions.
e.g 'Socrates[1]' (default) or 'Aristotle[1]'. Choose the latter if you
want use the distance priors (see also the -l option for label propagation
control).
-l: label propagation Incorporate a distance prior one the posterior formulation. Should be
of the form 'label[lambda,boundaryProbability]' where label is a value
of 1,2,3,... denoting label ID. The label probability for anything
outside the current label
= boundaryProbability * exp( -lambda * distanceFromBoundary )
Intuitively, smaller lambda values will increase the spatial capture
range of the distance prior. To apply to all label values, simply omit
specifying the label, i.e. -l [lambda,boundaryProbability].
-y: posterior label for N4 weight mask Which posterior probability image should be used to define the
N4 weight mask. Can also specify multiple posteriors in which
case the chosen posteriors are combined.
-s: image file suffix Any of the standard ITK IO formats e.g. nrrd, nii.gz (default), mhd
-k: keep temporary files Keep temporary files on disk (default = 0).
-u: use random seeding Use random number generated from system clock in Atropos (default = 1)
-w: Atropos prior segmentation weight Atropos spatial prior probability weight for the segmentation (default = 0)
-z: Test / debug mode If > 0, attempts to continue after errors.
USAGE
exit 1
}
echoParameters() {
cat <<PARAMETERS
Using antsAtroposN4 with the following arguments:
image dimension = ${DIMENSION}
anatomical image = ${ANATOMICAL_IMAGES[@]}
segmentation priors = ${ATROPOS_SEGMENTATION_PRIORS}
output prefix = ${OUTPUT_PREFIX}
output image suffix = ${OUTPUT_SUFFIX}
N4 parameters (segmentation):
convergence = ${N4_CONVERGENCE}
shrink factor = ${N4_SHRINK_FACTOR}
B-spline parameters = ${N4_BSPLINE_PARAMS}
weight mask post. label = ${N4_WEIGHT_MASK_POSTERIOR_LABELS[@]}
Atropos parameters (segmentation):
convergence = ${ATROPOS_SEGMENTATION_CONVERGENCE}
likelihood = ${ATROPOS_SEGMENTATION_LIKELIHOOD}
prior weight = ${ATROPOS_SEGMENTATION_PRIOR_WEIGHT}
posterior formulation = ${ATROPOS_SEGMENTATION_POSTERIOR_FORMULATION}
mrf = ${ATROPOS_SEGMENTATION_MRF}
Max N4->Atropos iters. = ${ATROPOS_SEGMENTATION_NUMBER_OF_ITERATIONS}
use clock random seed = ${USE_RANDOM_SEEDING}
PARAMETERS
}
# Echos a command to stdout, then runs it
# Will immediately exit on error unless you set debug flag
DEBUG_MODE=0
function logCmd() {
cmd="$*"
echo "BEGIN >>>>>>>>>>>>>>>>>>>>"
echo $cmd
exec 5>&1
logCmdOutput=$( $cmd | tee >(cat - >&5) )
cmdExit=${PIPESTATUS[0]}
if [[ $cmdExit -gt 0 ]];
then
echo "ERROR: command exited with nonzero status $cmdExit"
echo "Command: $cmd"
echo
if [[ ! $DEBUG_MODE -gt 0 ]];
then
exit 1
fi
fi
echo "END <<<<<<<<<<<<<<<<<<<<"
echo
echo
return $cmdExit
}
################################################################################
#
# Main routine
#
################################################################################
HOSTNAME=`hostname`
DATE=`date`
CURRENT_DIR=`pwd`/
OUTPUT_DIR=${CURRENT_DIR}/tmp$RANDOM/
OUTPUT_PREFIX=${OUTPUT_DIR}/tmp
OUTPUT_SUFFIX="nii.gz"
KEEP_TMP_IMAGES=0
USE_RANDOM_SEEDING=1
DIMENSION=3
ANATOMICAL_IMAGES=()
ATROPOS_SEGMENTATION_PRIORS=""
################################################################################
#
# Programs and their parameters
#
################################################################################
N4_ATROPOS_NUMBER_OF_ITERATIONS=15
N4=${ANTSPATH}/N4BiasFieldCorrection
N4_CONVERGENCE="[50x50x50x50,0.0000000001]"
N4_SHRINK_FACTOR=2
N4_BSPLINE_PARAMS="[200]"
N4_WEIGHT_MASK_POSTERIOR_LABELS=()
ATROPOS=${ANTSPATH}/Atropos
ATROPOS_SEGMENTATION_PRIOR_WEIGHT=0.0
ATROPOS_SEGMENTATION_LIKELIHOOD="Gaussian"
ATROPOS_SEGMENTATION_POSTERIOR_FORMULATION="Socrates[1]"
ATROPOS_SEGMENTATION_MASK=''
ATROPOS_SEGMENTATION_NUMBER_OF_ITERATIONS=5
ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES=3
ATROPOS_SEGMENTATION_MRF=''
ATROPOS_SEGMENTATION_LABEL_PROPAGATION=()
if [[ $# -lt 3 ]] ; then
Usage >&2
exit 1
else
while getopts "a:b:c:d:h:k:l:m:n:o:p:r:s:t:u:w:x:y:z:" OPT
do
case $OPT in
c) #number of segmentation classes
ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES=$OPTARG
;;
d) #dimensions
DIMENSION=$OPTARG
if [[ ${DIMENSION} -gt 4 || ${DIMENSION} -lt 2 ]];
then
echo " Error: ImageDimension must be 2, 3, or 4 "
exit 1
fi
;;
h) #help
Usage >&2
exit 0
;;
a) #anatomical t1 image
ANATOMICAL_IMAGES[${#ANATOMICAL_IMAGES[@]}]=$OPTARG
;;
b) #atropos prior weight
ATROPOS_SEGMENTATION_POSTERIOR_FORMULATION=$OPTARG
;;
k) #keep tmp images
KEEP_TMP_IMAGES=$OPTARG
;;
l)
ATROPOS_SEGMENTATION_LABEL_PROPAGATION[${#ATROPOS_SEGMENTATION_LABEL_PROPAGATION[@]}]=$OPTARG
;;
m) #atropos segmentation iterations
N4_ATROPOS_NUMBER_OF_ITERATIONS=$OPTARG
;;
n) #atropos segmentation iterations
ATROPOS_SEGMENTATION_NUMBER_OF_ITERATIONS=$OPTARG
;;
o) #output prefix
OUTPUT_PREFIX=$OPTARG
;;
p) # segmentation label prior image
ATROPOS_SEGMENTATION_PRIORS=$OPTARG
;;
r) #mrf
ATROPOS_SEGMENTATION_MRF=$OPTARG
;;
s) #output suffix
OUTPUT_SUFFIX=$OPTARG
;;
t) #n4 convergence
N4_CONVERGENCE=$OPTARG
;;
u) #use random seeding
USE_RANDOM_SEEDING=$OPTARG
;;
w) #atropos prior weight
ATROPOS_SEGMENTATION_PRIOR_WEIGHT=$OPTARG
;;
x) #atropos segmentation mask
ATROPOS_SEGMENTATION_MASK=$OPTARG
;;
y) #
N4_WEIGHT_MASK_POSTERIOR_LABELS[${#N4_WEIGHT_MASK_POSTERIOR_LABELS[@]}]=$OPTARG
;;
z) #debug mode
DEBUG_MODE=$OPTARG
;;
*) # getopts issues an error message
echo "ERROR: unrecognized option -$OPT $OPTARG"
exit 1
;;
esac
done
fi
if [[ -z "$ATROPOS_SEGMENTATION_MRF" ]];
then
ATROPOS_SEGMENTATION_MRF="[0.1,1x1x1]";
if [[ DIMENSION -eq 2 ]];
then
ATROPOS_SEGMENTATION_MRF="[0.1,1x1]"
fi
fi
ATROPOS_SEGMENTATION_CONVERGENCE="[${ATROPOS_SEGMENTATION_NUMBER_OF_ITERATIONS},0.0]"
################################################################################
#
# Preliminaries:
# 1. Check existence of inputs
# 2. Figure out output directory and mkdir if necessary
#
################################################################################
for (( i = 0; i < ${#ANATOMICAL_IMAGES[@]}; i++ ))
do
if [[ ! -f ${ANATOMICAL_IMAGES[$i]} ]];
then
echo "The specified image \"${ANATOMICAL_IMAGES[$i]}\" does not exist."
exit 1
fi
done
FORMAT=${ATROPOS_SEGMENTATION_PRIORS}
PREFORMAT=${FORMAT%%\%*}
POSTFORMAT=${FORMAT##*d}
FORMAT=${FORMAT#*\%}
FORMAT=${FORMAT%%d*}
REPCHARACTER=''
TOTAL_LENGTH=0
if [ ${#FORMAT} -eq 2 ]
then
REPCHARACTER=${FORMAT:0:1}
TOTAL_LENGTH=${FORMAT:1:1}
fi
# MAXNUMBER=$(( 10 ** $TOTAL_LENGTH ))
MAXNUMBER=1000
PRIOR_IMAGE_FILENAMES=()
POSTERIOR_IMAGE_FILENAMES=()
POSTERIOR_IMAGE_FILENAMES_PREVIOUS_ITERATION=()
for (( i = 1; i <= $ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES; i++ ))
do
NUMBER_OF_REPS=$(( $TOTAL_LENGTH - ${#i} ))
ROOT='';
for(( j=0; j < $NUMBER_OF_REPS; j++ ))
do
ROOT=${ROOT}${REPCHARACTER}
done
PRIOR_FILENAME=${PREFORMAT}${ROOT}${i}${POSTFORMAT}
POSTERIOR_FILENAME=${OUTPUT_PREFIX}SegmentationPosteriors${ROOT}${i}.${OUTPUT_SUFFIX}
POSTERIOR_FILENAME_PREVIOUS_ITERATION=${OUTPUT_PREFIX}SegmentationPosteriorsPreviousIteration${ROOT}${i}.${OUTPUT_SUFFIX}
POSTERIOR_IMAGE_FILENAMES=( ${POSTERIOR_IMAGE_FILENAMES[@]} $POSTERIOR_FILENAME )
POSTERIOR_IMAGE_FILENAMES_PREVIOUS_ITERATION=( ${POSTERIOR_IMAGE_FILENAMES_PREVIOUS_ITERATION[@]} $POSTERIOR_FILENAME_PREVIOUS_ITERATION )
if [[ -f $PRIOR_FILENAME ]];
then
PRIOR_IMAGE_FILENAMES=( ${PRIOR_IMAGE_FILENAMES[@]} $PRIOR_FILENAME )
fi
done
NUMBER_OF_PRIOR_IMAGES=${#PRIOR_IMAGE_FILENAMES[*]}
INITIALIZE_WITH_KMEANS=0
if [[ ${NUMBER_OF_PRIOR_IMAGES} -eq 0 ]];
then
echo "Initializing with kmeans segmentation."
INITIALIZE_WITH_KMEANS=1
elif [[ ${ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES} -ne ${NUMBER_OF_PRIOR_IMAGES} ]];
then
echo "Expected ${ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES} prior images (${NUMBER_OF_PRIOR_IMAGES} are specified). Check the command line specification."
exit 1
fi
for(( j=0; j < $NUMBER_OF_PRIOR_IMAGES; j++ ))
do
if [[ ! -f ${PRIOR_IMAGE_FILENAMES[$j]} ]];
then
echo "Prior image $j ${PRIOR_IMAGE_FILENAMES[$j]} does not exist."
exit 1
fi
done
OUTPUT_DIR=${OUTPUT_PREFIX%\/*}
if [[ ! -d $OUTPUT_DIR ]];
then
echo "The output directory \"$OUTPUT_DIR\" does not exist. Making it."
mkdir -p $OUTPUT_DIR
fi
echoParameters >&2
echo "--------------------- Running `basename $0` on $HOSTNAME ---------------------"
time_start=`date +%s`
################################################################################
#
# Output images
#
################################################################################
ATROPOS_SEGMENTATION_OUTPUT=${OUTPUT_PREFIX}Segmentation
ATROPOS_SEGMENTATION=${ATROPOS_SEGMENTATION_OUTPUT}.${OUTPUT_SUFFIX}
ATROPOS_SEGMENTATION_POSTERIORS=${ATROPOS_SEGMENTATION_OUTPUT}Posteriors%${FORMAT}d.${OUTPUT_SUFFIX}
################################################################################
#
# Segmentation
#
################################################################################
SEGMENTATION_WEIGHT_MASK=${OUTPUT_PREFIX}SegmentationWeightMask.nii.gz
SEGMENTATION_CONVERGENCE_FILE=${OUTPUT_PREFIX}SegmentationConvergence.txt
SEGMENTATION_PREVIOUS_ITERATION=${OUTPUT_PREFIX}SegmentationPreviousIteration.${OUTPUT_SUFFIX}
N4_WEIGHT_MASK_POSTERIOR_IDXS=()
for (( i = 0; i < ${#N4_WEIGHT_MASK_POSTERIOR_LABELS[@]}; i++ ))
do
N4_WEIGHT_MASK_POSTERIOR_IDXS[$i]=$((N4_WEIGHT_MASK_POSTERIOR_LABELS[$i]-1))
done
time_start_segmentation=`date +%s`
if [[ $INITIALIZE_WITH_KMEANS -eq 0 ]]
then
N4_WEIGHT_MASK_IMAGES=()
for (( i = 0; i < ${#N4_WEIGHT_MASK_POSTERIOR_LABELS[@]}; i++ ))
do
N4_WEIGHT_MASK_IMAGES=( ${N4_WEIGHT_MASK_IMAGES[@]} ${PRIOR_IMAGE_FILENAMES[${N4_WEIGHT_MASK_POSTERIOR_IDXS[$i]}]} )
done
if [[ ${#N4_WEIGHT_MASK_IMAGES[@]} -gt 0 ]];
then
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${SEGMENTATION_WEIGHT_MASK} PureTissueN4WeightMask ${N4_WEIGHT_MASK_IMAGES[@]}
fi
fi
if [[ -f ${SEGMENTATION_CONVERGENCE_FILE} ]];
then
logCmd rm -f ${SEGMENTATION_CONVERGENCE_FILE}
fi
POSTERIOR_PROBABILITY_CONVERGED=0
for (( i = 0; i < ${N4_ATROPOS_NUMBER_OF_ITERATIONS}; i++ ))
do
SEGMENTATION_N4_IMAGES=()
for(( j = 0; j < ${#ANATOMICAL_IMAGES[@]}; j++ ))
do
SEGMENTATION_N4_IMAGES=( ${SEGMENTATION_N4_IMAGES[@]} ${ATROPOS_SEGMENTATION_OUTPUT}${j}N4.${OUTPUT_SUFFIX} )
if [[ $j == 0 ]];
then
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${SEGMENTATION_N4_IMAGES[$j]} TruncateImageIntensity ${ANATOMICAL_IMAGES[$j]} 0.025 0.995 256 ${ATROPOS_SEGMENTATION_MASK}
else
cp ${ANATOMICAL_IMAGES[$j]} ${SEGMENTATION_N4_IMAGES[$j]}
fi
exe_n4_correction="${N4} -d ${DIMENSION} -i ${SEGMENTATION_N4_IMAGES[$j]} -x ${ATROPOS_SEGMENTATION_MASK} -s ${N4_SHRINK_FACTOR} -c ${N4_CONVERGENCE} -b ${N4_BSPLINE_PARAMS} -o ${SEGMENTATION_N4_IMAGES[$j]}"
if [[ -f ${SEGMENTATION_WEIGHT_MASK} ]];
then
exe_n4_correction="${exe_n4_correction} -w ${SEGMENTATION_WEIGHT_MASK}"
fi
logCmd $exe_n4_correction
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${SEGMENTATION_N4_IMAGES[$j]} Normalize ${SEGMENTATION_N4_IMAGES[$j]}
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${SEGMENTATION_N4_IMAGES[$j]} m ${SEGMENTATION_N4_IMAGES[$j]} 1000
done
ATROPOS_ANATOMICAL_IMAGES_COMMAND_LINE=''
for (( j = 0; j < ${#ANATOMICAL_IMAGES[@]}; j++ ))
do
ATROPOS_ANATOMICAL_IMAGES_COMMAND_LINE="${ATROPOS_ANATOMICAL_IMAGES_COMMAND_LINE} -a ${SEGMENTATION_N4_IMAGES[$j]}"
done
INITIALIZATION="PriorProbabilityImages[${ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES},${ATROPOS_SEGMENTATION_PRIORS},${ATROPOS_SEGMENTATION_PRIOR_WEIGHT}]"
if [[ INITIALIZE_WITH_KMEANS -eq 1 ]];
then
if [[ $i -eq 0 ]];
then
INITIALIZATION="kmeans[${ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES}]"
else
INITIALIZATION="PriorProbabilityImages[${ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES},${ATROPOS_SEGMENTATION_POSTERIORS},${ATROPOS_SEGMENTATION_PRIOR_WEIGHT}]"
fi
fi
ATROPOS_LABEL_PROPAGATION_COMMAND_LINE=''
for (( j = 0; j < ${#ATROPOS_SEGMENTATION_LABEL_PROPAGATION[@]}; j++ ))
do
ATROPOS_LABEL_PROPAGATION_COMMAND_LINE="${ATROPOS_LABEL_PROPAGATION_COMMAND_LINE} -l ${ATROPOS_SEGMENTATION_LABEL_PROPAGATION[$j]}";
done
exe_segmentation="${ATROPOS} -d ${DIMENSION} -x ${ATROPOS_SEGMENTATION_MASK} -c ${ATROPOS_SEGMENTATION_CONVERGENCE} ${ATROPOS_ANATOMICAL_IMAGES_COMMAND_LINE} ${ATROPOS_LABEL_PROPAGATION_COMMAND_LINE}"
exe_segmentation="${exe_segmentation} -i ${INITIALIZATION} -k ${ATROPOS_SEGMENTATION_LIKELIHOOD} -m ${ATROPOS_SEGMENTATION_MRF} -o [${ATROPOS_SEGMENTATION},${ATROPOS_SEGMENTATION_POSTERIORS}] -r ${USE_RANDOM_SEEDING}"
if [[ $i -eq 0 ]];
then
exe_segmentation="${exe_segmentation} -p Socrates[0]"
else
exe_segmentation="${exe_segmentation} -p ${ATROPOS_SEGMENTATION_POSTERIOR_FORMULATION}"
logCmd cp -f ${ATROPOS_SEGMENTATION} ${SEGMENTATION_PREVIOUS_ITERATION}
for (( j = 0; j < ${#POSTERIOR_IMAGE_FILENAMES[@]}; j++ ))
do
logCmd cp -f ${POSTERIOR_IMAGE_FILENAMES[$j]} ${POSTERIOR_IMAGE_FILENAMES_PREVIOUS_ITERATION[$j]}
done
for (( j = 0; j < ${#ANATOMICAL_IMAGES[@]}; j++ ))
do
ATROPOS_ANATOMICAL_IMAGES_COMMAND_LINE="${ATROPOS_ANATOMICAL_IMAGES_COMMAND_LINE} -a ${SEGMENTATION_N4_IMAGES[$j]}";
done
fi
logCmd $exe_segmentation
if [[ $i -eq 0 ]];
then
if [[ ! -f ${SEGMENTATION_CONVERGENCE_FILE} ]];
then
echo "Iteration,Posterior" > ${SEGMENTATION_CONVERGENCE_FILE}
fi
POSTERIOR_PROBABILITY=0
while read line;
do
tokens=( $line )
if [[ ${tokens[0]} == "Iteration" ]];
then
POSTERIOR_PROBABILITY=${tokens[7]}
fi
done <<< "$logCmdOutput"
echo "${i},${POSTERIOR_PROBABILITY}" >> ${SEGMENTATION_CONVERGENCE_FILE}
fi
if [[ $i -gt 0 && -f ${SEGMENTATION_PREVIOUS_ITERATION} ]];
then
POSTERIOR_PROBABILITY_PREVIOUS_ITERATION=$POSTERIOR_PROBABILITY
POSTERIOR_PROBABILITY=0
while read line;
do
tokens=( $line )
if [[ ${tokens[0]} == "Iteration" ]];
then
POSTERIOR_PROBABILITY=${tokens[7]}
fi
done <<< "$logCmdOutput"
if [[ $( echo "${POSTERIOR_PROBABILITY} < ${POSTERIOR_PROBABILITY_PREVIOUS_ITERATION}"|bc ) -eq 1 ]];
then
POSTERIOR_PROBABILITY_CONVERGED=1
POSTERIOR_PROBABILITY=${POSTERIOR_PROBABILITY_PREVIOUS_ITERATION}
logCmd cp -f ${SEGMENTATION_PREVIOUS_ITERATION} ${ATROPOS_SEGMENTATION}
for (( j = 0; j < ${#POSTERIOR_IMAGE_FILENAMES[@]}; j++ ))
do
logCmd cp -f ${POSTERIOR_IMAGE_FILENAMES_PREVIOUS_ITERATION[$j]} ${POSTERIOR_IMAGE_FILENAMES[$j]}
done
break
else
echo "${i},${POSTERIOR_PROBABILITY}" >> ${SEGMENTATION_CONVERGENCE_FILE}
fi
fi
N4_WEIGHT_MASK_IMAGES=()
for (( j = 0; j < ${#N4_WEIGHT_MASK_POSTERIOR_LABELS[@]}; j++ ))
do
N4_WEIGHT_MASK_IMAGES=( ${N4_WEIGHT_MASK_IMAGES[@]} ${POSTERIOR_IMAGE_FILENAMES[${N4_WEIGHT_MASK_POSTERIOR_IDXS[$j]}]} )
done
if [[ ${#N4_WEIGHT_MASK_IMAGES[@]} -gt 0 ]];
then
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${SEGMENTATION_WEIGHT_MASK} PureTissueN4WeightMask ${N4_WEIGHT_MASK_IMAGES[@]}
fi
done
TMP_FILES=( $SEGMENTATION_WEIGHT_MASK ${POSTERIOR_IMAGE_FILENAMES_PREVIOUS_ITERATION[@]} ${SEGMENTATION_PREVIOUS_ITERATION} )
if [[ $KEEP_TMP_IMAGES -eq 0 ]];
then
for f in ${TMP_FILES[@]}
do
if [[ -e $f ]];
then
logCmd rm $f
else
echo "WARNING: expected temp file doesn't exist: $f"
fi
done
fi
time_end_segmentation=`date +%s`
time_elapsed_segmentation=$((time_end_segmentation - time_start_segmentation))
echo
echo "--------------------------------------------------------------------------------------"
if [[ POSTERIOR_PROBABILITY_CONVERGED -eq 1 ]];
then
echo " Done with segmentation (posterior prob. converged): $(( time_elapsed_segmentation / 3600 ))h $(( time_elapsed_segmentation %3600 / 60 ))m $(( time_elapsed_segmentation % 60 ))s"
else
echo " Done with segmentation (exceeded max. iterations): $(( time_elapsed_segmentation / 3600 ))h $(( time_elapsed_segmentation %3600 / 60 ))m $(( time_elapsed_segmentation % 60 ))s"
fi
echo "--------------------------------------------------------------------------------------"
echo
################################################################################
#
# End of main routine
#
################################################################################
time_end=`date +%s`
time_elapsed=$((time_end - time_start))
echo
echo "--------------------------------------------------------------------------------------"
echo " Done with N4 <-> Atropos processing"
echo " Script executed in $time_elapsed seconds"
echo " $(( time_elapsed / 3600 ))h $(( time_elapsed %3600 / 60 ))m $(( time_elapsed % 60 ))s"
echo "--------------------------------------------------------------------------------------"
SEGMENTATION_CONVERGENCE_SCRIPT=${ATROPOS_SEGMENTATION_OUTPUT}Convergence.R
SEGMENTATION_CONVERGENCE_PLOT=${ATROPOS_SEGMENTATION_OUTPUT}Convergence.pdf
if [[ `type -p RScript` > /dev/null ]];
then
echo "library( ggplot2 )" > $SEGMENTATION_CONVERGENCE_SCRIPT
echo "conv <- read.csv( \"${SEGMENTATION_CONVERGENCE_FILE}\" )" >> $SEGMENTATION_CONVERGENCE_SCRIPT
echo "myPlot <- ggplot( conv, aes( x = Iteration, y = Posterior ) ) +" >> $SEGMENTATION_CONVERGENCE_SCRIPT
echo " geom_point( data = conv, aes( colour = Iteration ), size = 4 ) +" >> $SEGMENTATION_CONVERGENCE_SCRIPT
echo " scale_y_continuous( breaks = seq( 0.8 , 1, by = 0.025 ), labels = seq( 0.8, 1, by = 0.025 ), limits = c( 0.8, 1 ) ) +" >> $SEGMENTATION_CONVERGENCE_SCRIPT
echo " theme( legend.position = \"none\" )" >> $SEGMENTATION_CONVERGENCE_SCRIPT
echo "ggsave( filename = \"$SEGMENTATION_CONVERGENCE_PLOT\", plot = myPlot, width = 4, height = 3, units = 'in' )" >> $SEGMENTATION_CONVERGENCE_SCRIPT
`RScript $SEGMENTATION_CONVERGENCE_SCRIPT`
rm -f $SEGMENTATION_CONVERGENCE_SCRIPT
fi
exit 0
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