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Remove ANTSPATH #1574

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Jul 26, 2023
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Remove ANTSPATH #1574

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3 changes: 1 addition & 2 deletions Dockerfile
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Expand Up @@ -49,8 +49,7 @@ LABEL maintainer="ANTsX team" \
description="ANTs is part of the ANTsX ecosystem (https://github.com/ANTsX). \
ANTs Citation: https://pubmed.ncbi.nlm.nih.gov/24879923"

ENV ANTSPATH="/opt/ants/bin/" \
PATH="/opt/ants/bin:$PATH" \
ENV PATH="/opt/ants/bin:$PATH" \
LD_LIBRARY_PATH="/opt/ants/lib:$LD_LIBRARY_PATH"
RUN apt-get update \
&& apt install -y --no-install-recommends \
Expand Down
52 changes: 18 additions & 34 deletions Scripts/ants.sh
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Expand Up @@ -3,20 +3,17 @@
NUMPARAMS=$#

MAXITERATIONS=30x90x20
if [[ -z ${ANTSPATH} ]] ; then
echo "Environment variable ANTSPATH must be defined"
exit 1
fi
if [[ ! -f "${ANTSPATH}/ANTS" ]] ; then
echo "Cannot find the ANTS program. Please \(re\)define \$ANTSPATH in your environment."

if ! command -v "ANTS" &> /dev/null
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I think you need the square brackets still

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@ghisvail ghisvail Jul 25, 2023 •
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It works without brackets on my machine. I used the pattern in the accepted answer of the SO thread linked above.

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# Make ANTS disappear from PATH.
$ mv $HOME/.local/ants/bin/ANTS{,.bak}

# Run wrapper script.
$ ./Scripts/ants.sh
Cannot find the ANTS program. Please \(re\)define $PATH in your environment.

# Put it back.
$ mv $HOME/.local/ants/bin/ANTS{.bak,}

# Run wrapper script again.
$ ./Scripts/ants.sh
 USAGE ::  
  sh   ants.sh  ImageDimension  fixed.ext  moving.ext  OPTIONAL-OUTPREFIX   OPTIONAL-max-iterations  OPTIONAL-Labels-In-Fixed-Image-Space-To-Deform-To-Moving-

then
echo "Cannot find the ANTS program. Please \(re\)define \$PATH in your environment."
exit 1
fi

if [ $NUMPARAMS -lt 3 ]
then
echo " USAGE :: "
echo " sh ants.sh ImageDimension fixed.ext moving.ext OPTIONAL-OUTPREFIX OPTIONAL-max-iterations OPTIONAL-Labels-In-Fixed-Image-Space-To-Deform-To-Moving-Image Option-DoANTSQC "
echo " be sure to set ANTSPATH environment variable "
echo " Max-Iterations in form : JxKxL where "
echo " J = max iterations at coarsest resolution (here, reduce by power of 2^2) "
echo " K = middle resolution iterations ( here, reduce by power of 2 ) "
Expand All @@ -27,18 +24,6 @@ echo " Other parameters are updates of the defaults used in the A. Klein evaluat
exit
fi

#ANTSPATH=YOURANTSPATH
if [ ${#ANTSPATH} -le 0 ]
then
echo " Please set ANTSPATH=LocationOfYourAntsBinaries "
echo " Either set this in your profile or directly, here in the script. "
echo " For example : "
echo " ANTSPATH=/home/yourname/bin/ants/ "
exit
else
echo " ANTSPATH is $ANTSPATH "
fi

#initialization, here, is unbiased
DIM=$1

Expand Down Expand Up @@ -101,7 +86,6 @@ fi
# exit


echo " ANTSPATH is $ANTSPATH "
echo " Mapping Parameters :: "
echo " Transformation is: $TRANSFORMATION "
echo " MaxIterations : $MAXITERATIONS "
Expand All @@ -116,10 +100,10 @@ echo " "


if [[ ! -s ${OUTPUTNAME}repaired.nii.gz ]] ; then
${ANTSPATH}/N4BiasFieldCorrection -d $DIM -i $MOVING -o ${OUTPUTNAME}repaired.nii.gz -s 2 -c [ 50x50x50x50,0.000001 ] -b [ 200 ]
# ${ANTSPATH}/N3BiasFieldCorrection $DIM $MOVING ${OUTPUTNAME}repaired.nii.gz 4
N4BiasFieldCorrection -d $DIM -i $MOVING -o ${OUTPUTNAME}repaired.nii.gz -s 2 -c [ 50x50x50x50,0.000001 ] -b [ 200 ]
# N3BiasFieldCorrection $DIM $MOVING ${OUTPUTNAME}repaired.nii.gz 4
fi
exe=" ${ANTSPATH}/ANTS $DIM -m ${METRIC}${FIXED},${OUTPUTNAME}repaired.nii.gz,${METRICPARAMS} -t $TRANSFORMATION -r $REGULARIZATION -o ${OUTPUTNAME} -i $MAXITERATIONS --use-Histogram-Matching --number-of-affine-iterations 10000x10000x10000x10000x10000 --MI-option 32x16000 "
exe=" ANTS $DIM -m ${METRIC}${FIXED},${OUTPUTNAME}repaired.nii.gz,${METRICPARAMS} -t $TRANSFORMATION -r $REGULARIZATION -o ${OUTPUTNAME} -i $MAXITERATIONS --use-Histogram-Matching --number-of-affine-iterations 10000x10000x10000x10000x10000 --MI-option 32x16000 "

echo " $exe "

Expand All @@ -128,31 +112,31 @@ exe=" ${ANTSPATH}/ANTS $DIM -m ${METRIC}${FIXED},${OUTPUTNAME}repaired.nii.gz,$
#below, some affine options
#--MI-option 16x8000 #-a InitAffine.txt --continue-affine 0

${ANTSPATH}/WarpImageMultiTransform $DIM ${OUTPUTNAME}repaired.nii.gz ${OUTPUTNAME}deformed.nii.gz ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED}
WarpImageMultiTransform $DIM ${OUTPUTNAME}repaired.nii.gz ${OUTPUTNAME}deformed.nii.gz ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED}

if [ ${#LABELIMAGE} -gt 3 ]
then
${ANTSPATH}/WarpImageMultiTransform $DIM $LABELIMAGE ${OUTPUTNAME}labeled.nii.gz -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz -R ${MOVING} --use-NN
WarpImageMultiTransform $DIM $LABELIMAGE ${OUTPUTNAME}labeled.nii.gz -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz -R ${MOVING} --use-NN
fi

exit

if [ $DoANTSQC -eq 1 ] ; then
# measure image similarity
for SIM in 0 1 2 ; do
${ANTSPATH}/MeasureImageSimilarity $DIM $SIM $FIXED ${OUTPUTNAME}deformed.nii.gz
MeasureImageSimilarity $DIM $SIM $FIXED ${OUTPUTNAME}deformed.nii.gz
done
# measure dice overlap and mds
${ANTSPATH}/ThresholdImage $DIM $FIXED ${OUTPUTNAME}fixthresh.nii.gz Otsu 4
${ANTSPATH}/ThresholdImage $DIM $MOVING ${OUTPUTNAME}movthresh.nii.gz Otsu 4
${ANTSPATH}/WarpImageMultiTransform $DIM ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}defthresh.nii.gz ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED} --use-NN
${ANTSPATH}/ImageMath $DIM ${OUTPUTNAME}dicestats.txt DiceAndMinDistSum ${OUTPUTNAME}fixthresh.nii.gz ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}mindistsum.nii.gz
ThresholdImage $DIM $FIXED ${OUTPUTNAME}fixthresh.nii.gz Otsu 4
ThresholdImage $DIM $MOVING ${OUTPUTNAME}movthresh.nii.gz Otsu 4
WarpImageMultiTransform $DIM ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}defthresh.nii.gz ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED} --use-NN
ImageMath $DIM ${OUTPUTNAME}dicestats.txt DiceAndMinDistSum ${OUTPUTNAME}fixthresh.nii.gz ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}mindistsum.nii.gz
# labelstats for jacobian wrt segmenation
# below, to compose
# ${ANTSPATH}ComposeMultiTransform $DIM ${OUTPUTNAME}CompWarp.nii.gz -R $FIXED ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt
# ${ANTSPATH}CreateJacobianDeterminantImage $DIM ${OUTPUTNAME}CompWarp.nii.gz ${OUTPUTNAME}jacobian.nii.gz 0
# ${ANTSPATH}ImageMath $DIM ${OUTPUTNAME}movlabstat.txt LabelStats ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}movthresh.nii.gz
# ${ANTSPATH}ImageMath $DIM ${OUTPUTNAME}jaclabstat.txt LabelStats ${OUTPUTNAME}defthresh.nii.gz ${OUTPUTNAME}jacobian.nii.gz
# ComposeMultiTransform $DIM ${OUTPUTNAME}CompWarp.nii.gz -R $FIXED ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt
# CreateJacobianDeterminantImage $DIM ${OUTPUTNAME}CompWarp.nii.gz ${OUTPUTNAME}jacobian.nii.gz 0
# ImageMath $DIM ${OUTPUTNAME}movlabstat.txt LabelStats ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}movthresh.nii.gz
# ImageMath $DIM ${OUTPUTNAME}jaclabstat.txt LabelStats ${OUTPUTNAME}defthresh.nii.gz ${OUTPUTNAME}jacobian.nii.gz
# we compare the output of these last two lines:
# the Volume of the movlabstat computation vs. the mass of the jaclabstat
fi
54 changes: 27 additions & 27 deletions Scripts/antsASLProcessing.sh
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@@ -1,16 +1,16 @@
#!/bin/bash

if [[ ! -s ${ANTSPATH}/antsRegistration ]]
if ! command -v antsRegistration &> /dev/null
then
echo "Cannot find antsRegistration. Please \(re\)define \$ANTSPATH in your environment."
echo "Cannot find antsRegistration. Please \(re\)define \$PATH in your environment."
fi
if [[ ! -s ${ANTSPATH}/antsApplyTransforms ]]
if ! command -v antsApplyTransforms &> /dev/null
then
echo "Cannot find antsApplyTransforms. Please \(re\)define \$ANTSPATH in your environment."
echo "Cannot find antsApplyTransforms. Please \(re\)define \$PATH in your environment."
fi
if [[ ! -s ${ANTSPATH}/antsIntermodalityIntrasubject.sh ]]
if ! command -v antsIntermodalityIntrasubject.sh &> /dev/null
then
echo "Cannot find antsIntermodalityIntrasubject.sh script. Please \(re\)define \$ANTSPATH in your environemnt."
echo "Cannot find antsIntermodalityIntrasubject.sh script. Please \(re\)define \$PATH in your environemnt."
fi

function Usage {
Expand Down Expand Up @@ -258,33 +258,33 @@ then
mkdir -p `dirname $OUTNAME`
fi
if [[ ! -s ${OUTNAME}/AveragePCASL.nii.gz ]] ; then
logCmd ${ANTSPATH}/antsMotionCorr -d 3 -a $PCASL -o ${OUTNAME}AveragePCASL.nii.gz
logCmd antsMotionCorr -d 3 -a $PCASL -o ${OUTNAME}AveragePCASL.nii.gz
fi
logCmd ${ANTSPATH}/ThresholdImage 3 ${OUTNAME}AveragePCASL.nii.gz ${OUTNAME}tmp.nii.gz 600 999999
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}tmp.nii.gz ME ${OUTNAME}tmp.nii.gz 2
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}tmp.nii.gz GetLargestComponent ${OUTNAME}tmp.nii.gz
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}tmp.nii.gz MD ${OUTNAME}tmp.nii.gz 3
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}pCASLBrain.nii.gz m ${OUTNAME}AveragePCASL.nii.gz ${OUTNAME}tmp.nii.gz
logCmd ThresholdImage 3 ${OUTNAME}AveragePCASL.nii.gz ${OUTNAME}tmp.nii.gz 600 999999
logCmd ImageMath 3 ${OUTNAME}tmp.nii.gz ME ${OUTNAME}tmp.nii.gz 2
logCmd ImageMath 3 ${OUTNAME}tmp.nii.gz GetLargestComponent ${OUTNAME}tmp.nii.gz
logCmd ImageMath 3 ${OUTNAME}tmp.nii.gz MD ${OUTNAME}tmp.nii.gz 3
logCmd ImageMath 3 ${OUTNAME}pCASLBrain.nii.gz m ${OUTNAME}AveragePCASL.nii.gz ${OUTNAME}tmp.nii.gz

INTERSUBJECT_PARAMS=" -d 3 -i ${OUTNAME}pCASLBrain.nii.gz -r $ANATOMICAL_IMAGE -x $BRAINMASK -w ${TRANSFORM_PREFIX}SubjectToTemplate -t 2 -o $OUTNAME "
if [[ -n $LABELS ]]
then
INTERSUBJECT_PARAMS=" ${INTERSUBJECT_PARAMS} -l $LABELS "
fi

logCmd ${ANTSPATH}/antsIntermodalityIntrasubject.sh $INTERSUBJECT_PARAMS
logCmd ${ANTSPATH}/N4BiasFieldCorrection -d 3 -i ${OUTNAME}AveragePCASL.nii.gz -o ${OUTNAME}AveragePCASL.nii.gz -r 1 -s 4
logCmd ${ANTSPATH}/N4BiasFieldCorrection -d 3 -i ${OUTNAME}AveragePCASL.nii.gz -o ${OUTNAME}AveragePCASL.nii.gz -r 1 -s 2
logCmd ${ANTSPATH}/N4BiasFieldCorrection -d 3 -i ${OUTNAME}AveragePCASL.nii.gz -o ${OUTNAME}AveragePCASL.nii.gz -r 1 -s 1
logCmd ${ANTSPATH}/ThresholdImage 3 ${OUTNAME}AveragePCASL.nii.gz ${OUTNAME}OtsuMask.nii.gz Otsu 4
logCmd ${ANTSPATH}/ThresholdImage 3 ${OUTNAME}OtsuMask.nii.gz ${OUTNAME}OtsuMask.nii.gz 2 4
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}OtsuMask.nii.gz ME ${OUTNAME}OtsuMask.nii.gz 1
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}OtsuMask.nii.gz MD ${OUTNAME}OtsuMask.nii.gz 1
logCmd ${ANTSPATH}/ThresholdImage 3 ${OUTNAME}brainmask.nii.gz ${OUTNAME}BrainThresh.nii.gz 1 999
logCmd ${ANTSPATH}/MultiplyImages 3 ${OUTNAME}OtsuMask.nii.gz ${OUTNAME}BrainThresh.nii.gz ${OUTNAME}OtsuMask.nii.gz
logCmd antsIntermodalityIntrasubject.sh $INTERSUBJECT_PARAMS
logCmd N4BiasFieldCorrection -d 3 -i ${OUTNAME}AveragePCASL.nii.gz -o ${OUTNAME}AveragePCASL.nii.gz -r 1 -s 4
logCmd N4BiasFieldCorrection -d 3 -i ${OUTNAME}AveragePCASL.nii.gz -o ${OUTNAME}AveragePCASL.nii.gz -r 1 -s 2
logCmd N4BiasFieldCorrection -d 3 -i ${OUTNAME}AveragePCASL.nii.gz -o ${OUTNAME}AveragePCASL.nii.gz -r 1 -s 1
logCmd ThresholdImage 3 ${OUTNAME}AveragePCASL.nii.gz ${OUTNAME}OtsuMask.nii.gz Otsu 4
logCmd ThresholdImage 3 ${OUTNAME}OtsuMask.nii.gz ${OUTNAME}OtsuMask.nii.gz 2 4
logCmd ImageMath 3 ${OUTNAME}OtsuMask.nii.gz ME ${OUTNAME}OtsuMask.nii.gz 1
logCmd ImageMath 3 ${OUTNAME}OtsuMask.nii.gz MD ${OUTNAME}OtsuMask.nii.gz 1
logCmd ThresholdImage 3 ${OUTNAME}brainmask.nii.gz ${OUTNAME}BrainThresh.nii.gz 1 999
logCmd MultiplyImages 3 ${OUTNAME}OtsuMask.nii.gz ${OUTNAME}BrainThresh.nii.gz ${OUTNAME}OtsuMask.nii.gz

if [ ! -f ${OUTNAME}_kcbf.nii.gz ]; then
logCmd ${ANTSPATH}/antsNetworkAnalysis.R \
logCmd antsNetworkAnalysis.R \
-o $OUTNAME \
--freq 0.01x0.1 \
--mask ${OUTNAME}OtsuMask.nii.gz \
Expand All @@ -298,7 +298,7 @@ if [ ! -f ${OUTNAME}_kcbf.nii.gz ]; then
--replace $SAMPLE_WITH_REPLACEMENT
fi

logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
logCmd antsApplyTransforms -d 3 \
-i ${OUTNAME}_kcbf.nii.gz \
-r $TEMPLATE \
-o ${OUTNAME}MeanCBFWarpedToTemplate.nii.gz \
Expand All @@ -308,7 +308,7 @@ logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
-t ${OUTNAME}1Warp.nii.gz \
-t ${OUTNAME}0GenericAffine.mat

logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
logCmd antsApplyTransforms -d 3 \
-i $LABELS \
-r ${OUTNAME}AveragePCASL.nii.gz \
-o ${OUTNAME}LabelsWarpedToPCASL.nii.gz \
Expand All @@ -318,15 +318,15 @@ logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
-t [ ${OUTNAME}0GenericAffine.mat,1 ] \
-t ${OUTNAME}1InverseWarp.nii.gz

logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
logCmd antsApplyTransforms -d 3 \
-i ${OUTNAME}_kcbf.nii.gz \
-r $ANATOMICAL_IMAGE \
-o ${OUTNAME}MeanCBFWarpedToT1.nii.gz \
-n Linear \
-t ${OUTNAME}1Warp.nii.gz \
-t ${OUTNAME}0GenericAffine.mat \

logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
logCmd antsApplyTransforms -d 3 \
-i $SEGMENTATION \
-r ${OUTNAME}AveragePCASL.nii.gz \
-o ${OUTNAME}SegmentationWarpedToPCASL.nii.gz \
Expand Down
30 changes: 16 additions & 14 deletions Scripts/antsAtroposN4.sh
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Expand Up @@ -2,12 +2,14 @@

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.
if ! command -v N4BiasFieldCorrection &> /dev/null
then
echo we cant find the N4 program -- does not seem to exist. please \(re\)define \$PATH 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.
if ! command -v Atropos &> /dev/null
then
echo we cant find the Atropos program -- does not seem to exist. please \(re\)define \$PATH in your environment.
exit
fi

Expand Down Expand Up @@ -46,13 +48,13 @@ DEBUG_MODE=0

N4_ATROPOS_NUMBER_OF_ITERATIONS=15

N4=${ANTSPATH}/N4BiasFieldCorrection
N4=N4BiasFieldCorrection
N4_CONVERGENCE="[ 50x50x50x50,0.0000000001 ]"
N4_SHRINK_FACTOR=2
N4_BSPLINE_PARAMS="[ 200 ]"
N4_WEIGHT_MASK_POSTERIOR_LABELS=()

ATROPOS=${ANTSPATH}/Atropos
ATROPOS=Atropos
ATROPOS_SEGMENTATION_PRIOR_WEIGHT=0.0
ATROPOS_SEGMENTATION_LIKELIHOOD="Gaussian"
ATROPOS_SEGMENTATION_POSTERIOR_FORMULATION="Socrates[ 1 ]"
Expand Down Expand Up @@ -457,10 +459,10 @@ ATROPOS_SEGMENTATION_POSTERIORS=${ATROPOS_SEGMENTATION_OUTPUT}Posteriors%${FORMA

if [[ ${DENOISE_ANATOMICAL_IMAGES} -ne 0 ]];
then
if [[ ! -s ${ANTSPATH}/DenoiseImage ]];
if [[ ! -s DenoiseImage ]];
then
echo "Error: we can't find the DenoiseImage program."
echo "Perhaps you need to \(re\)define \$ANTSPATH in your environment or update your repository."
echo "Perhaps you need to \(re\)define \$PATH in your environment or update your repository."
exit
fi
fi
Expand All @@ -472,10 +474,10 @@ for (( j = 0; j < ${#ANATOMICAL_IMAGES[@]}; j++ ))
do
SEGMENTATION_PREPROCESSED_IMAGES=( ${SEGMENTATION_PREPROCESSED_IMAGES[@]} ${ATROPOS_SEGMENTATION_OUTPUT}PreprocessedAnatomical${j}.${OUTPUT_SUFFIX} )
# Truncate on the whole head to get outliers over the whole volume, without losing contrast in the brain
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${SEGMENTATION_PREPROCESSED_IMAGES[$j]} TruncateImageIntensity ${ANATOMICAL_IMAGES[$j]} 0 0.995 256
logCmd ImageMath ${DIMENSION} ${SEGMENTATION_PREPROCESSED_IMAGES[$j]} TruncateImageIntensity ${ANATOMICAL_IMAGES[$j]} 0 0.995 256
if [[ ${DENOISE_ANATOMICAL_IMAGES} -ne 0 ]];
then
logCmd ${ANTSPATH}/DenoiseImage -d ${DIMENSION} -i ${SEGMENTATION_PREPROCESSED_IMAGES[$j]} -o ${SEGMENTATION_PREPROCESSED_IMAGES[$j]} --verbose 1
logCmd DenoiseImage -d ${DIMENSION} -i ${SEGMENTATION_PREPROCESSED_IMAGES[$j]} -o ${SEGMENTATION_PREPROCESSED_IMAGES[$j]} --verbose 1
fi
done

Expand Down Expand Up @@ -508,7 +510,7 @@ if [[ $INITIALIZE_WITH_KMEANS -eq 0 ]]

if [[ ${#N4_WEIGHT_MASK_IMAGES[@]} -gt 0 ]];
then
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${SEGMENTATION_WEIGHT_MASK} PureTissueN4WeightMask ${N4_WEIGHT_MASK_IMAGES[@]}
logCmd ImageMath ${DIMENSION} ${SEGMENTATION_WEIGHT_MASK} PureTissueN4WeightMask ${N4_WEIGHT_MASK_IMAGES[@]}
fi
fi

Expand All @@ -530,8 +532,8 @@ for (( i = 0; i < ${N4_ATROPOS_NUMBER_OF_ITERATIONS}; i++ ))
exe_n4_correction="${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
logCmd ImageMath ${DIMENSION} ${SEGMENTATION_N4_IMAGES[$j]} Normalize ${SEGMENTATION_N4_IMAGES[$j]}
logCmd ImageMath ${DIMENSION} ${SEGMENTATION_N4_IMAGES[$j]} m ${SEGMENTATION_N4_IMAGES[$j]} 1000
done

ATROPOS_ANATOMICAL_IMAGES_COMMAND_LINE=''
Expand Down Expand Up @@ -642,7 +644,7 @@ for (( i = 0; i < ${N4_ATROPOS_NUMBER_OF_ITERATIONS}; i++ ))

if [[ ${#N4_WEIGHT_MASK_IMAGES[@]} -gt 0 ]];
then
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${SEGMENTATION_WEIGHT_MASK} PureTissueN4WeightMask ${N4_WEIGHT_MASK_IMAGES[@]}
logCmd ImageMath ${DIMENSION} ${SEGMENTATION_WEIGHT_MASK} PureTissueN4WeightMask ${N4_WEIGHT_MASK_IMAGES[@]}
fi

done
Expand Down
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