Merge pull request #1574 from ghisvail/rm-antspath

Remove ANTSPATH
ANTsX · Jul 26, 2023 · f3c720e · f3c720e
2 parents 3cecf99 + 2afb0cd
commit f3c720e
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Showing 34 changed files with 878 additions and 1,313 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -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 \

diff --git a/Scripts/ants.sh b/Scripts/ants.sh
@@ -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
+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 ) "
@@ -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
 
@@ -101,7 +86,6 @@ fi
 # exit
 
 
-echo  " ANTSPATH  is $ANTSPATH     "
 echo " Mapping Parameters  :: "
 echo  " Transformation is:  $TRANSFORMATION "
 echo " MaxIterations :   $MAXITERATIONS "
@@ -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 "
 
@@ -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
diff --git a/Scripts/antsASLProcessing.sh b/Scripts/antsASLProcessing.sh
@@ -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 {
@@ -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 \
@@ -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 \
@@ -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 \
@@ -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 \

diff --git a/Scripts/antsAtroposN4.sh b/Scripts/antsAtroposN4.sh
@@ -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
 
@@ -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=${ANTSPATH}/Atropos
+ATROPOS=Atropos
 ATROPOS_SEGMENTATION_PRIOR_WEIGHT=0.0
 ATROPOS_SEGMENTATION_LIKELIHOOD="Gaussian"
 ATROPOS_SEGMENTATION_POSTERIOR_FORMULATION="Socrates[ 1 ]"
@@ -457,10 +459,10 @@ ATROPOS_SEGMENTATION_POSTERIORS=${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
@@ -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
 
@@ -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
 
@@ -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=''
@@ -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