===========================================================
                                      .___ __  __   
          _________________  __ __  __| _/|__|/  |_ 
         / ___\_` __ \__  \ |  |  \/ __ | | \\_  __\
        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
        \___  /|__|  (____  /____/\____ | |__||__|  
       /_____/            \/           \/           
              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
ants-2.1.0/ANTS.cmake-1-
ants-2.1.0/ANTS.cmake:2:include(${CMAKE_CURRENT_LIST_DIR}/Common.cmake)
ants-2.1.0/ANTS.cmake-3-
##############################################
ants-2.1.0/ANTS.cmake-45-find_package(ITK 4 REQUIRED)
ants-2.1.0/ANTS.cmake:46:include(${ITK_USE_FILE})
ants-2.1.0/ANTS.cmake-47-
##############################################
ants-2.1.0/ANTS.cmake-52-  if(VTK_FOUND)
ants-2.1.0/ANTS.cmake:53:    include(${VTK_USE_FILE})
ants-2.1.0/ANTS.cmake-54-  else(VTK_FOUND)
##############################################
ants-2.1.0/ANTSnightly.sh-10-# make the testing directory, based on current user name
ants-2.1.0/ANTSnightly.sh:11:#user=`who -m | sed -e 's/ .*$//'`
ants-2.1.0/ANTSnightly.sh-12-user=${LOGNAME}
##############################################
ants-2.1.0/ANTSnightly.sh-89-if [ "${OsName}" = "Darwin" ] ; then
ants-2.1.0/ANTSnightly.sh:90:    Compiler=clang-`clang -v 2>&1 | head -1 | awk '{print $4}'`
ants-2.1.0/ANTSnightly.sh:91:    Compiler=${Compiler}-`clang -v 2>&1 | tail -2 | head -1 | awk '{print $2}'`
ants-2.1.0/ANTSnightly.sh-92-    export CC=`which clang`
##############################################
ants-2.1.0/ANTSnightly.sh-133-    echo "Building in `pwd`"
ants-2.1.0/ANTSnightly.sh:134:    scriptname=`basename $0`
ants-2.1.0/ANTSnightly.sh-135-    make -j ${NPROCS}
##############################################
ants-2.1.0/CMake/ExternalData.cmake-607-if(ExternalData_CONFIG)
ants-2.1.0/CMake/ExternalData.cmake:608:  include(${ExternalData_CONFIG})
ants-2.1.0/CMake/ExternalData.cmake-609-endif()
##############################################
ants-2.1.0/CMake/ProjectSourceVersion.cmake-37-if(_GIT_VERSION_HASH STREQUAL "GITDIR-NOTFOUND")
ants-2.1.0/CMake/ProjectSourceVersion.cmake:38:  include( "${CMAKE_CURRENT_SOURCE_DIR}/CMake/ProjectSourceVersionVars.cmake" )
ants-2.1.0/CMake/ProjectSourceVersion.cmake-39-  return()
##############################################
ants-2.1.0/CMake/SlicerMacroCheckExternalProjectDependency.cmake-68-      if(EXISTS "${EXTERNAL_PROJECT_DIR}/External_${dep}.cmake")
ants-2.1.0/CMake/SlicerMacroCheckExternalProjectDependency.cmake:69:        include(${EXTERNAL_PROJECT_DIR}/External_${dep}.cmake)
ants-2.1.0/CMake/SlicerMacroCheckExternalProjectDependency.cmake-70-      elseif(EXISTS "${Slicer_ADDITIONAL_EXTERNAL_PROJECT_DIR}/External_${dep}.cmake")
ants-2.1.0/CMake/SlicerMacroCheckExternalProjectDependency.cmake:71:        include(${Slicer_ADDITIONAL_EXTERNAL_PROJECT_DIR}/External_${dep}.cmake)
ants-2.1.0/CMake/SlicerMacroCheckExternalProjectDependency.cmake-72-      else()
##############################################
ants-2.1.0/CMake/ANTSExternalData.cmake-1-get_filename_component(_ITKExternalData_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
ants-2.1.0/CMake/ANTSExternalData.cmake:2:include(${_ITKExternalData_DIR}/ExternalData.cmake)
ants-2.1.0/CMake/ANTSExternalData.cmake-3-
##############################################
ants-2.1.0/CMakeLists.txt-51-  project(SuperBuild_${LOCAL_PROJECT_NAME})
ants-2.1.0/CMakeLists.txt:52:  include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
ants-2.1.0/CMakeLists.txt-53-  include(CPack)   # This must always be last!
##############################################
ants-2.1.0/CMakeLists.txt-56-  project(${LOCAL_PROJECT_NAME})
ants-2.1.0/CMakeLists.txt:57:  include("${CMAKE_CURRENT_SOURCE_DIR}/${LOCAL_PROJECT_NAME}.cmake")
ants-2.1.0/CMakeLists.txt-58-  include(CPack)   # This must always be last!
##############################################
ants-2.1.0/Examples/CMakeLists.txt-175-   )
ants-2.1.0/Examples/CMakeLists.txt:176:include(${VTK_USE_FILE})
ants-2.1.0/Examples/CMakeLists.txt-177-include_directories(${VTK_INCLUDE_DIRS})
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh-4-ROOT=/home/hwang3/MA2012 
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh:5:labels=`cat $ROOT/labels`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh:6:labels1=`cat $ROOT/labels1`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh-7-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh:8:rates=`cat $ROOT/samplerates1`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh-9-DR=1
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh:10:IDs=`cat $ROOT/Testing/Test`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh:11:TrainIDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl.sh-12-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh-8-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh:9:LABELS=`cat $ROOT/labels`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh-10-L=$1
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh-14-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh:15:IDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/bl_qsub.sh-16-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion.sh-7-lambda=0.1
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion.sh:8:IDs=`cat $ROOT/Testing/Test`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion.sh:9:TrainIDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion.sh-10-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub.sh-13-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub.sh:14:IDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub.sh-15-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub_train.sh-12-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub_train.sh:13:IDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/label_fusion_qsub_train.sh-14-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/sa.sh-3-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/sa.sh:4:IDs=`cat $ROOT/Testing/Test`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/sa.sh:5:TrainIDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/sa.sh-6-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-3-
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh:4:IDs0=`cat $ROOT/Testing/Test`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh:5:IDs=`cat $ROOT/Training/Train`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-6-
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-8-    for ref in $IDs0;do 
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh:9:        check=`ls $ROOT/warped/${id}_to_${ref}_image.nii.gz`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-10-        if [[ $check != '' ]]; then
##############################################
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-20-    for ref in $IDs;do
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh:21:        check=`ls $ROOT/warped/${id}_to_${ref}_image.nii.gz`
ants-2.1.0/ExternalApplications/MALF/CaseStudy/warpAtlas.sh-22-        if [[ $check != '' ]]; then
##############################################
ants-2.1.0/ProjectSourceVersion.cmake-37-if(_GIT_VERSION_HASH STREQUAL "GITDIR-NOTFOUND")
ants-2.1.0/ProjectSourceVersion.cmake:38:  include( "${CMAKE_CURRENT_SOURCE_DIR}/CMake/ProjectSourceVersionVars.cmake" )
ants-2.1.0/ProjectSourceVersion.cmake-39-  return()
##############################################
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-20-PARAM8=0
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:21:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 2  `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:22:for x in $LL ; do  PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ;  let NFILES=$NFILES+1  ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:23:PARAM1=` awk -v a=$PARAM1 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-24-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:25:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 3  `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:26:for x in $LL ; do PARAM2=` awk -v a=$PARAM2 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:27:PARAM2=` awk -v a=$PARAM2 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-28-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:29:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 4  `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:30:for x in $LL ; do PARAM3=` awk -v a=$PARAM3 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:31:PARAM3=` awk -v a=$PARAM3 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-32-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:33:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 5  `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:34:for x in $LL ; do PARAM4=` awk -v a=$PARAM4 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:35:PARAM4=` awk -v a=$PARAM4 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-36-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:37:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 6  `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:38:for x in $LL ; do PARAM5=` awk -v a=$PARAM5 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:39:PARAM5=` awk -v a=$PARAM5 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-40-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:41:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 7  `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:42:for x in $LL ; do PARAM6=` awk -v a=$PARAM6 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:43:PARAM6=` awk -v a=$PARAM6 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-44-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:45:LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 2  `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:46:for x in $LL ; do PARAM7=` awk -v a=$PARAM7 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:47:PARAM7=` awk -v a=$PARAM7 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-48-
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:49:LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 3  `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:50:for x in $LL ; do PARAM8=` awk -v a=$PARAM8 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh:51:PARAM8=` awk -v a=$PARAM8 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage2DAffine.sh-52-
##############################################
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-27-PARAM15=0
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:28:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 2  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:29:for x in $LL ; do  PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ;  let NFILES=$NFILES+1  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:30:PARAM1=` awk -v a=$PARAM1 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-31-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:32:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 3  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:33:for x in $LL ; do PARAM2=` awk -v a=$PARAM2 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:34:PARAM2=` awk -v a=$PARAM2 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-35-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:36:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 4  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:37:for x in $LL ; do PARAM3=` awk -v a=$PARAM3 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:38:PARAM3=` awk -v a=$PARAM3 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-39-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:40:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 5  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:41:for x in $LL ; do PARAM4=` awk -v a=$PARAM4 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:42:PARAM4=` awk -v a=$PARAM4 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-43-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:44:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 6  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:45:for x in $LL ; do PARAM5=` awk -v a=$PARAM5 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:46:PARAM5=` awk -v a=$PARAM5 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-47-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:48:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 7  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:49:for x in $LL ; do PARAM6=` awk -v a=$PARAM6 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:50:PARAM6=` awk -v a=$PARAM6 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-51-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:52:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 8  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:53:for x in $LL ; do PARAM7=` awk -v a=$PARAM7 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:54:PARAM7=` awk -v a=$PARAM7 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-55-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:56:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 9  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:57:for x in $LL ; do PARAM8=` awk -v a=$PARAM8 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:58:PARAM8=` awk -v a=$PARAM8 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-59-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:60:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 10  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:61:for x in $LL ; do PARAM9=` awk -v a=$PARAM9 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:62:PARAM9=` awk -v a=$PARAM9 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-63-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:64:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 11  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:65:for x in $LL ; do PARAM10=` awk -v a=$PARAM10 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:66:PARAM10=` awk -v a=$PARAM10 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-67-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:68:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 12  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:69:for x in $LL ; do PARAM11=` awk -v a=$PARAM11 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:70:PARAM11=` awk -v a=$PARAM11 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-71-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:72:LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 13  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:73:for x in $LL ; do PARAM12=` awk -v a=$PARAM12 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:74:PARAM12=` awk -v a=$PARAM12 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-75-
##############################################
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-78-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:79:LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 2  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:80:for x in $LL ; do  PARAM13=` awk -v a=$PARAM13 -v b=$x 'BEGIN{print (a + b)}' ` ;  done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:81:PARAM13=` awk -v a=$PARAM13 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-82-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:83:LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 3  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:84:for x in $LL ; do PARAM14=` awk -v a=$PARAM14 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:85:PARAM14=` awk -v a=$PARAM14 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-86-
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:87:LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 4  `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:88:for x in $LL ; do PARAM15=` awk -v a=$PARAM15 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh:89:PARAM15=` awk -v a=$PARAM15 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/ANTSAverage3DAffine.sh-90-
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-9-
ants-2.1.0/Scripts/ANTSpexec.sh:10:`basename $0` [-h] [-r] [-j nb_jobs] command arg_list
ants-2.1.0/Scripts/ANTSpexec.sh-11-
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-21-
ants-2.1.0/Scripts/ANTSpexec.sh:22:    `basename $0` somecommand arg1 arg2 arg3
ants-2.1.0/Scripts/ANTSpexec.sh-23-
ants-2.1.0/Scripts/ANTSpexec.sh:24:    `basename $0` -j 3 \"somecommand -r -p\" arg1 arg2 arg3
ants-2.1.0/Scripts/ANTSpexec.sh-25-
ants-2.1.0/Scripts/ANTSpexec.sh:26:    `basename $0` -j 6 -r \"convert -scale 50% * small/small_*\" *.jpg"
ants-2.1.0/Scripts/ANTSpexec.sh-27-
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-42-
ants-2.1.0/Scripts/ANTSpexec.sh:43:`basename $0` [-h] [-r] [-j nb_jobs] command arg_list
ants-2.1.0/Scripts/ANTSpexec.sh-44-
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-54-
ants-2.1.0/Scripts/ANTSpexec.sh:55:    `basename $0` somecommand arg1 arg2 arg3
ants-2.1.0/Scripts/ANTSpexec.sh-56-
ants-2.1.0/Scripts/ANTSpexec.sh:57:    `basename $0` -j 3 \"somecommand -r -p\" arg1 arg2 arg3
ants-2.1.0/Scripts/ANTSpexec.sh-58-
ants-2.1.0/Scripts/ANTSpexec.sh:59:    `basename $0` -j 6 -r \"convert -scale 50% * small/small_*\" *.jpg"
ants-2.1.0/Scripts/ANTSpexec.sh-60-
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-112-	whm=` whoami `
ants-2.1.0/Scripts/ANTSpexec.sh:113:	num=` ps U $whm | grep -i "${PID} "  | wc -l `
ants-2.1.0/Scripts/ANTSpexec.sh-114-        if [ $num = 2 ]    ;  then
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-126-	whm=` whoami `
ants-2.1.0/Scripts/ANTSpexec.sh:127:	num=` ps U $whm | grep -i "${PID} "  | wc -l `
ants-2.1.0/Scripts/ANTSpexec.sh-128-        if [ $num = 1 ]  ; then
##############################################
ants-2.1.0/Scripts/ANTSpexec.sh-163-
ants-2.1.0/Scripts/ANTSpexec.sh:164:shift `expr $OPTIND - 1` # shift input args, ignore processed args
ants-2.1.0/Scripts/ANTSpexec.sh-165-COMMAND=$1
##############################################
ants-2.1.0/Scripts/ants.sh-66-
ants-2.1.0/Scripts/ants.sh:67:OUTPUTNAME=` echo $MOVING | cut -d '.' -f 1 `
ants-2.1.0/Scripts/ants.sh-68-
##############################################
ants-2.1.0/Scripts/ants.sh-93-  TRANSFORMATION=SyN[0.25]
ants-2.1.0/Scripts/ants.sh:94:  ITERATLEVEL=(`echo $MAXITERATIONS | tr 'x' ' '`)
ants-2.1.0/Scripts/ants.sh-95-  NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/antsASLProcessing.sh-17-  cat <<USAGE
ants-2.1.0/Scripts/antsASLProcessing.sh:18:`basename $0` performs ASL processing based on ANTs tools.  Preprocessing of T1 images using antsCorticalThickness.sh is assumed.  The following steps are performed:
ants-2.1.0/Scripts/antsASLProcessing.sh-19-  1) Calculation of average pCASL image.
##############################################
ants-2.1.0/Scripts/antsASLProcessing.sh-27-Required arguments:
ants-2.1.0/Scripts/antsASLProcessing.sh:28:`basename $0` -a anatomical image (skull stripped)
ants-2.1.0/Scripts/antsASLProcessing.sh-29-              -p brain segmentation priors (C-style, e.g. priors%d.nii.gz)
##############################################
ants-2.1.0/Scripts/antsASLProcessing.sh-53-  cat <<PARAMETERS
ants-2.1.0/Scripts/antsASLProcessing.sh:54:  Using `basename $0` with the following parameters:
ants-2.1.0/Scripts/antsASLProcessing.sh-55-
##############################################
ants-2.1.0/Scripts/antsASLProcessing.sh-255-# Do processing.
ants-2.1.0/Scripts/antsASLProcessing.sh:256:if [[ ! -d `dirname $OUTNAME` ]]
ants-2.1.0/Scripts/antsASLProcessing.sh-257-then
ants-2.1.0/Scripts/antsASLProcessing.sh:258:  mkdir -p `dirname $OUTNAME`
ants-2.1.0/Scripts/antsASLProcessing.sh-259-fi
##############################################
ants-2.1.0/Scripts/antsAtroposN4.sh-16-
ants-2.1.0/Scripts/antsAtroposN4.sh:17:`basename $0` iterates between N4 <-> Atropos to improve segmentation results.
ants-2.1.0/Scripts/antsAtroposN4.sh-18-
##############################################
ants-2.1.0/Scripts/antsAtroposN4.sh-20-
ants-2.1.0/Scripts/antsAtroposN4.sh:21:`basename $0` -d imageDimension
ants-2.1.0/Scripts/antsAtroposN4.sh-22-              -a inputImage
##############################################
ants-2.1.0/Scripts/antsAtroposN4.sh-369-
ants-2.1.0/Scripts/antsAtroposN4.sh:370:echo "---------------------  Running `basename $0` on $HOSTNAME  ---------------------"
ants-2.1.0/Scripts/antsAtroposN4.sh-371-
##############################################
ants-2.1.0/Scripts/antsAtroposN4.sh-616-
ants-2.1.0/Scripts/antsAtroposN4.sh:617:    `RScript $SEGMENTATION_CONVERGENCE_SCRIPT`
ants-2.1.0/Scripts/antsAtroposN4.sh-618-    rm -f $SEGMENTATION_CONVERGENCE_SCRIPT
##############################################
ants-2.1.0/Scripts/antsBrainExtraction.sh-24-
ants-2.1.0/Scripts/antsBrainExtraction.sh:25:`basename $0` performs template-based brain extraction.
ants-2.1.0/Scripts/antsBrainExtraction.sh-26-
##############################################
ants-2.1.0/Scripts/antsBrainExtraction.sh-28-
ants-2.1.0/Scripts/antsBrainExtraction.sh:29:`basename $0` -d imageDimension
ants-2.1.0/Scripts/antsBrainExtraction.sh-30-              -a anatomicalImage
##############################################
ants-2.1.0/Scripts/antsBrainExtraction.sh-299-
ants-2.1.0/Scripts/antsBrainExtraction.sh:300:echo "---------------------  Running `basename $0` on $HOSTNAME  ---------------------"
ants-2.1.0/Scripts/antsBrainExtraction.sh-301-
##############################################
ants-2.1.0/Scripts/antsCorticalThickness.sh-32-
ants-2.1.0/Scripts/antsCorticalThickness.sh:33:`basename $0` performs T1 anatomical brain processing where the following steps are currently applied:
ants-2.1.0/Scripts/antsCorticalThickness.sh-34-
##############################################
ants-2.1.0/Scripts/antsCorticalThickness.sh-41-
ants-2.1.0/Scripts/antsCorticalThickness.sh:42:`basename $0` -d imageDimension
ants-2.1.0/Scripts/antsCorticalThickness.sh-43-              -a anatomicalImage
##############################################
ants-2.1.0/Scripts/antsCorticalThickness.sh-649-
ants-2.1.0/Scripts/antsCorticalThickness.sh:650:echo "---------------------  Running `basename $0` on $HOSTNAME  ---------------------"
ants-2.1.0/Scripts/antsCorticalThickness.sh-651-
##############################################
ants-2.1.0/Scripts/antsCorticalThickness.sh-1220-
ants-2.1.0/Scripts/antsCorticalThickness.sh:1221:ccmetric=`${ANTSPATH}/ImageMath ${DIMENSION} a PearsonCorrelation ${REGISTRATION_TEMPLATE} ${EXTRACTED_SEGMENTATION_BRAIN_DEFORMED} ${REGISTRATION_TEMPLATE_BRAIN_MASK}`
ants-2.1.0/Scripts/antsCorticalThickness.sh:1222:bvol=`${ANTSPATH}/ImageMath ${DIMENSION} a total ${BRAIN_EXTRACTION_MASK}  | cut -d ':' -f 2 | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/antsCorticalThickness.sh:1223:gvol=`${ANTSPATH}/ImageMath ${DIMENSION} a total ${BRAIN_SEGMENTATION_GM}  | cut -d ':' -f 2 | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/antsCorticalThickness.sh:1224:wvol=`${ANTSPATH}/ImageMath ${DIMENSION} a total ${BRAIN_SEGMENTATION_WM}  | cut -d ':' -f 2 | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/antsCorticalThickness.sh:1225:thks=`${ANTSPATH}/ImageMath ${DIMENSION} a total $CORTICAL_THICKNESS_IMAGE | cut -d ':' -f 2 | cut -d ' ' -f 2 `
ants-2.1.0/Scripts/antsCorticalThickness.sh-1226-echo "PearsonCorrelation,BVOL,GVol,WVol,ThicknessSum" >   ${OUTPUT_PREFIX}brainvols.csv
##############################################
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-16-
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh:17:`basename $0` performs restration between a scalar image and a T1 image:
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-18-
##############################################
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-20-
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh:21:`basename $0` -d imageDimension
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-22-              -r anatomicalT1image (brain or whole-head, depending on modality) to align to
##############################################
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-260-
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh:261:echo "---------------------  Running `basename $0` on $HOSTNAME  ---------------------"
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-262-
##############################################
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-317-    # FIXME - how to name these reasonably
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh:318:    AUXO=`basename ${AUX_IMAGES[$i]} .nii.gz`
ants-2.1.0/Scripts/antsIntermodalityIntrasubject.sh-319-    #AUXO=${OUTPUT_PREFIX}_aux_${i}_warped.nii.gz
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-21-
ants-2.1.0/Scripts/antsIntroduction.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsIntroduction.sh-23-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-46-
ants-2.1.0/Scripts/antsIntroduction.sh:47:`basename $0` -d ImageDimension -r fixed.ext -i moving.ext
ants-2.1.0/Scripts/antsIntroduction.sh-48-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-76-
ants-2.1.0/Scripts/antsIntroduction.sh:77: Use `basename $0` -h for extended help.
ants-2.1.0/Scripts/antsIntroduction.sh-78---------------------------------------------------------------------------------------
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-93-
ants-2.1.0/Scripts/antsIntroduction.sh:94: `basename $0` will perform an elastic or diffeomorphic transformation of the moving image
ants-2.1.0/Scripts/antsIntroduction.sh-95- into the fixed image space.
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-103-
ants-2.1.0/Scripts/antsIntroduction.sh:104: `basename $0` -d ImageDimension -r fixed.ext -i moving.ext
ants-2.1.0/Scripts/antsIntroduction.sh-105-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-288-# put all related processes in array
ants-2.1.0/Scripts/antsIntroduction.sh:289:  runningANTSpids=( `ps -C ANTS -C N4BiasFieldCorrection -C antsIntroduction.sh | awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsIntroduction.sh-290-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-349-        MOVING=$OPTARG
ants-2.1.0/Scripts/antsIntroduction.sh:350:        OUTPUTNAME=` echo basename $MOVING | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsIntroduction.sh-351-        ;;
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-391-
ants-2.1.0/Scripts/antsIntroduction.sh:392:FIXED=`basename ${FIXED}`
ants-2.1.0/Scripts/antsIntroduction.sh:393:MOVING=`basename ${MOVING}`
ants-2.1.0/Scripts/antsIntroduction.sh-394-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-415-echo "input files: checking"
ants-2.1.0/Scripts/antsIntroduction.sh:416:compareheaders=`${ANTSPATH}/ImageMath $DIM ${OUTPUTNAME}repaired.nii.gz CompareHeadersAndImages $FIXED $MOVING  | grep FailureState | cut -d ' ' -f 4 `
ants-2.1.0/Scripts/antsIntroduction.sh-417-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-426-
ants-2.1.0/Scripts/antsIntroduction.sh:427:ITERATLEVEL=(`echo $MAXITERATIONS | tr 'x' ' '`)
ants-2.1.0/Scripts/antsIntroduction.sh-428-NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-504-else
ants-2.1.0/Scripts/antsIntroduction.sh:505:echo "Invalid transformation metric. Use RI, RA, EL, SY, S2, GR , DD or EX or type bash `basename $0` -h."
ants-2.1.0/Scripts/antsIntroduction.sh-506-exit 1
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-534-else
ants-2.1.0/Scripts/antsIntroduction.sh:535:echo "Invalid similarity metric. Use CC, MI, MSQ or PR or type bash`basename $0` -h."
ants-2.1.0/Scripts/antsIntroduction.sh-536-exit 1
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-542-
ants-2.1.0/Scripts/antsIntroduction.sh:543:MOVINGBASE=` echo ${MOVING} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsIntroduction.sh-544-
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-602-echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/antsIntroduction.sh:603:FIXEDBASE=` echo ${FIXED} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsIntroduction.sh-604-${ANTSPATH}/WarpImageMultiTransform $DIM ${FIXED} ${FIXEDBASE}_InverseWarp.nii.gz -R ${MOVING} -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-651-echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/antsIntroduction.sh:652:FIXEDBASE=` echo ${FIXED} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsIntroduction.sh-653-${ANTSPATH}/WarpImageMultiTransform $DIM ${FIXED} ${FIXEDBASE}_InverseWarp.nii.gz -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz -R ${OUTPUTNAME}.nii.gz
##############################################
ants-2.1.0/Scripts/antsIntroduction.sh-739-# save output in starting dir - remove inputs, then remove tempdir
ants-2.1.0/Scripts/antsIntroduction.sh:740:rm `basename ${FIXED}`
ants-2.1.0/Scripts/antsIntroduction.sh:741:rm `basename ${MOVING}`
ants-2.1.0/Scripts/antsIntroduction.sh-742-cp * ../
##############################################
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-32-
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh:33:`basename $0` performs a longitudinal cortical thickness estimation.  The following steps
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-34-are performed:
##############################################
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-47-
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh:48:`basename $0` -d imageDimension
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-49-              -e brainTemplate
##############################################
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-537-
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh:538:echo "---------------------  Running `basename $0` on $HOSTNAME  ---------------------"
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-539-
##############################################
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-854-
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh:855:    BASENAME_ID=`basename ${ANATOMICAL_IMAGES[$i]}`
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-856-    BASENAME_ID=${BASENAME_ID/\.nii\.gz/}
##############################################
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-888-          do
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh:889:            BASENAME_LOCAL_ID=`basename ${ANATOMICAL_IMAGES[$j]}`
ants-2.1.0/Scripts/antsLongitudinalCorticalThickness.sh-890-            BASENAME_LOCAL_ID=${BASENAME_LOCAL_ID/\.nii\.gz/}
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-21-
ants-2.1.0/Scripts/antsMalfLabeling.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsMalfLabeling.sh-23-
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-74-
ants-2.1.0/Scripts/antsMalfLabeling.sh:75:`basename $0` -d ImageDimension -o OutputPrefix <other options> <images>
ants-2.1.0/Scripts/antsMalfLabeling.sh-76-
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-112-
ants-2.1.0/Scripts/antsMalfLabeling.sh:113:`basename $0` -d 3 -t target.nii.gz -o malf \
ants-2.1.0/Scripts/antsMalfLabeling.sh-114-              -p malfPosteriors%04d.nii.gz \
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-142-
ants-2.1.0/Scripts/antsMalfLabeling.sh:143:`basename $0` will propagate labels from a set of pre-labeled atlases using the MALF
ants-2.1.0/Scripts/antsMalfLabeling.sh-144-algorithm.
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-147-
ants-2.1.0/Scripts/antsMalfLabeling.sh:148:`basename $0` -d ImageDimension -o OutputPrefix <other options> <images>
ants-2.1.0/Scripts/antsMalfLabeling.sh-149-
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-151-
ants-2.1.0/Scripts/antsMalfLabeling.sh:152:`basename $0` -d 3 -t target.nii.gz -o malf \
ants-2.1.0/Scripts/antsMalfLabeling.sh-153-              -p malfPosteriors%04d.nii.gz \
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-262-# put all related processes in array
ants-2.1.0/Scripts/antsMalfLabeling.sh:263:runningANTSpids=( `ps -C antsRegistration -C ImageMath| awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-264-
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-310-##Getting system info from linux can be done with these variables.
ants-2.1.0/Scripts/antsMalfLabeling.sh:311:# RAM=`cat /proc/meminfo | sed -n -e '/MemTotal/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMalfLabeling.sh:312:# RAMfree=`cat /proc/meminfo | sed -n -e '/MemFree/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMalfLabeling.sh-313-# cpu_free_ram=$((${RAMfree}/${cpu_count}))
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-378-   OUTPUT_PREFIX=$OPTARG
ants-2.1.0/Scripts/antsMalfLabeling.sh:379:   OUTPUT_DIR=`dirname ${OUTPUT_PREFIX}`
ants-2.1.0/Scripts/antsMalfLabeling.sh-380-   ;;
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-450-  do
ants-2.1.0/Scripts/antsMalfLabeling.sh:451:    IMG_BASE=`basename ${ATLAS_IMAGES[$i]}`
ants-2.1.0/Scripts/antsMalfLabeling.sh:452:    BASENAME=` echo ${IMG_BASE} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMalfLabeling.sh-453-
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-497-      then
ants-2.1.0/Scripts/antsMalfLabeling.sh:498:        id=`qsub -cwd -S /bin/bash -N antsMalfReg -v ANTSPATH=$ANTSPATH $QSUB_OPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/antsMalfLabeling.sh-499-        jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-502-      then
ants-2.1.0/Scripts/antsMalfLabeling.sh:503:        id=`qsub -N antsMalfReg -v ANTSPATH=$ANTSPATH $QSUB_OPTS -q nopreempt -l nodes=1:ppn=1 -l mem=8gb -l walltime=20:00:00 $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/antsMalfLabeling.sh-504-        jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-507-      then
ants-2.1.0/Scripts/antsMalfLabeling.sh:508:        id=`xgrid $XGRID_OPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's:  *: :g'`
ants-2.1.0/Scripts/antsMalfLabeling.sh-509-        jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-552-
ants-2.1.0/Scripts/antsMalfLabeling.sh:553:                OVERLAP_MEASURES=( `${ANTSPATH}/LabelOverlapMeasures ${DIM} ${TMP_WARPED_ATLAS_LABEL_MASK} ${TARGET_MASK_IMAGE} 1` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-554-                TOKENS=( ${OVERLAP_MEASURES[1]//,/\ } )
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-624-
ants-2.1.0/Scripts/antsMalfLabeling.sh:625:                OVERLAP_MEASURES=( `${ANTSPATH}/LabelOverlapMeasures ${DIM} ${TMP_WARPED_ATLAS_LABEL_MASK} ${TARGET_MASK_IMAGE} 1` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-626-                TOKENS=( ${OVERLAP_MEASURES[1]//,/\ } )
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-664-
ants-2.1.0/Scripts/antsMalfLabeling.sh:665:    jobIDs=`qsub -cwd -S /bin/bash -N antsMalf -v ANTSPATH=$ANTSPATH $QSUB_OPTS $qscript2 | awk '{print $3}'`
ants-2.1.0/Scripts/antsMalfLabeling.sh-666-    ${ANTSPATH}/waitForSGEQJobs.pl 1 600 $jobIDs
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-695-
ants-2.1.0/Scripts/antsMalfLabeling.sh:696:                OVERLAP_MEASURES=( `${ANTSPATH}/LabelOverlapMeasures ${DIM} ${TMP_WARPED_ATLAS_LABEL_MASK} ${TARGET_MASK_IMAGE} 1` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-697-                TOKENS=( ${OVERLAP_MEASURES[1]//,/\ } )
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-735-
ants-2.1.0/Scripts/antsMalfLabeling.sh:736:    jobIDs=`qsub -N antsMalf -v ANTSPATH=$ANTSPATH $QSUB_OPTS -q nopreempt -l nodes=1:ppn=1 -l mem=8gb -l walltime=30:00:00 $qscript2 | awk '{print $1}'`
ants-2.1.0/Scripts/antsMalfLabeling.sh-737-    ${ANTSPATH}/waitForPBSQJobs.pl 1 600 $jobIDs
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-754-
ants-2.1.0/Scripts/antsMalfLabeling.sh:755:                OVERLAP_MEASURES=( `${ANTSPATH}/LabelOverlapMeasures ${DIM} ${TMP_WARPED_ATLAS_LABEL_MASK} ${TARGET_MASK_IMAGE} 1` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-756-                TOKENS=( ${OVERLAP_MEASURES[1]//,/\ } )
##############################################
ants-2.1.0/Scripts/antsMalfLabeling.sh-824-
ants-2.1.0/Scripts/antsMalfLabeling.sh:825:                OVERLAP_MEASURES=( `${ANTSPATH}/LabelOverlapMeasures ${DIM} ${TMP_WARPED_ATLAS_LABEL_MASK} ${TARGET_MASK_IMAGE} 1` )
ants-2.1.0/Scripts/antsMalfLabeling.sh-826-                TOKENS=( ${OVERLAP_MEASURES[1]//,/\ } )
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-21-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-23-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-70-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:71:`basename $0` -d ImageDimension -o OUTPREFIX <other options> <images>
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-72-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-130-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:131:`basename $0` -d 3 -m 30x50x20 -t GR -s CC -c 1 -o MY -z InitialTemplate.nii.gz  *RF*T1x.nii.gz
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-132-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-227-        echo " shapeupdatetotemplate---voxel-wise averaging of the inverse warp fields (from subject to template)"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:228:        echo "   ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-229-        echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-230-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:231:        ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-232-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-263-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:264:    outdir=`dirname ${TEMPLATES[0]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-265-    if [[ ${#outdir} -eq 0 ]]
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-269-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:270:    files=`ls ${outdir}/job*.sh`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:271:    BASENAME1=`echo $files[1] | cut -d 'b' -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-272-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-277-       then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:278:         BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-279-         mv "$file" "${BASENAME1}b_000${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-282-        then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:283:          BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-284-          mv "$file" "${BASENAME1}b_00${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-287-        then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:288:          BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-289-          mv "$file" "${BASENAME1}b_0${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-317-# put all related processes in array
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:318:  runningANTSpids=( `ps -C ANTS -C N4BiasFieldCorrection -C ImageMath| awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-319-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-380-##Getting system info from linux can be done with these variables.
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:381:# RAM=`cat /proc/meminfo | sed -n -e '/MemTotal/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:382:# RAMfree=`cat /proc/meminfo | sed -n -e '/MemFree/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-383-# cpu_free_ram=$((${RAMfree}/${cpu_count}))
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-537-else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:538:  MODALITYWEIGHTS=(`echo $MODALITYWEIGHTSTRING | tr 'x' "\n"`)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-539-  if [[ ${#MODALITYWEIGHTS[@]} -ne $NUMBEROFMODALITIES ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-574-    echo "Please provide at least 2 filenames for the template."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:575:    echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-576-    exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-578-    then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:579:    extension=`echo ${IMAGESETVARIABLE#*.}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-580-    if [[ $extension = 'csv' || $extension = 'txt' ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-585-            do
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:586:            files=(`echo $line | tr ',' ' '`)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-587-            if [[ ${#files[@]} -ne $NUMBEROFMODALITIES ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-599-    else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:600:        range=`${ANTSPATH}/ImageMath $TDIM abs nvols ${IMAGESETVARIABLE} | tail -1 | cut -d "," -f 4 | cut -d " " -f 2 | cut -d "]" -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-601-        if [[ ${range} -eq 1 && ${TDIM} -ne 4 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-603-            echo "Please provide at least 2 filenames for the template."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:604:            echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-605-            exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-608-            echo "This is a multivolume file. Use -d 4"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:609:            echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-610-            exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-769-# remove old job bash scripts
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:770:outdir=`dirname ${TEMPLATES[0]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-771-if [[ ${#outdir} -eq 0 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-798-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:799:        IMGbase=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:800:        BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-801-        RIGID="${outdir}/rigid${i}_0_${IMGbase}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-813-            let k=$i+$j
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:814:            IMGbase=`basename ${IMAGESETARRAY[$k]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:815:            BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-816-            RIGID="${outdir}/rigid${i}_${j}_${IMGbase}"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:817:            IMGbaseBASE=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:818:            BASENAMEBASE=` echo ${IMGbaseBASE} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-819-            exe2="$exe2 ${WARP} $DIM ${IMAGESETARRAY[$k]} $RIGID ${outdir}/rigid${i}_0_${BASENAMEBASE}Affine.txt -R ${TEMPLATES[$j]}\n"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-826-            then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:827:            id=`qsub -cwd -S /bin/bash -N antsBuildTemplate_rigid -v ANTSPATH=$ANTSPATH $QSUBOPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-828-            jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-831-            then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:832:            id=`qsub -N antsrigid -v ANTSPATH=$ANTSPATH $QSUBOPTS -q nopreempt -l nodes=1:ppn=1 -l walltime=20:00:00 -l mem=8gb $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-833-            jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-841-            then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:842:            id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's:  *: :g'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-843-            #echo "xgrid $XGRIDOPTS -job submit /bin/bash $qscript"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-919-            let k=$i-$j
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:920:            IMGbase=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:921:            BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-922-            RIGID="${outdir}/rigid${k}_${j}_${IMGbase}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-971-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:972:ITERATLEVEL=(` echo $MAXITERATIONS | tr 'x' ' ' `)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-973-NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1045-else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1046:    echo "Invalid transformation metric. Use EL, SY, S2, GR , DD or EX or type bash `basename $0` -h."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1047-    exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1114-            else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1115:                echo "Invalid similarity metric. Use CC, MI, MSQ or PR or type bash `basename $0` -h."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1116-                exit 1
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1117-            fi
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1118:            TEMPLATEbase=`basename ${TEMPLATES[$k]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1119:            indir=`dirname ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1120-            if [[ ${#indir} -eq 0 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1123-            fi
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1124:            IMGbase=`basename ${IMAGESETARRAY[$l]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1125-            POO=${OUTPUTNAME}template${k}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1126-            OUTFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1127:            OUTFN=`basename ${OUTFN}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1128-            DEFORMED="${outdir}/${OUTFN}${l}WarpedToTemplate.nii.gz"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1129-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1130:            IMGbase=`basename ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1131-            POO=${OUTPUTNAME}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1132-            OUTWARPFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1133:            OUTWARPFN=`basename ${OUTWARPFN}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1134-            OUTWARPFN="${OUTWARPFN}${j}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1151-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1152:        IMGbase=`basename ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1153-        POO=${OUTPUTNAME}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1154-        OUTWARPFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1155:        OUTWARPFN=`basename ${OUTWARPFN}${j}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1156-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1171-            echo -e "$exe" > $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1172:            id=`qsub -cwd -N antsBuildTemplate_deformable_${i} -S /bin/bash -v ANTSPATH=$ANTSPATH $QSUBOPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1173-            jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1178-            echo -e "$exe" >> $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1179:            id=`qsub -N antsdef${i} -v ANTSPATH=$ANTSPATH -q nopreempt -l nodes=1:ppn=1 -l walltime=20:00:00 -l mem=8gb $QSUBOPTS $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1180-            jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1188-            echo -e "$exe" >> $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1189:            id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's:  *: :g'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1190-            jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1197-        # counter updated, but not directly used in this loop
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh:1198:        count=`expr $count + 1`;
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction.sh-1199-    #  echo " submitting job number $count " # for debugging only
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-21-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-23-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-70-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:71:`basename $0` -d ImageDimension -o OutputPrefix <other options> <images>
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-72-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-182-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:183:`basename $0` -d 3 -i 3 -k 1 -f 4x2x1 -s 2x1x0vox -q 30x20x4 -t SyN  -m CC -c 0 -o MY sub*avg.nii.gz
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-184-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-301-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:302:    imagelist=(`ls ${outputname}template${whichtemplate}*WarpedToTemplate.nii.gz`)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-303-    if [[ ${#imagelist[@]} -eq 0  ]] ; then
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-309-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:310:    WARPLIST=( `ls ${outputname}*[0-9]Warp.nii.gz 2> /dev/null` )
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-311-    NWARPS=${#WARPLIST[*]}
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-322-          echo " shapeupdatetotemplate---voxel-wise averaging of the inverse warp fields (from subject to template)"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:323:          echo "   ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-324-          date
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-325-          echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:326:          ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-327-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-369-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:370:    outdir=`dirname ${TEMPLATES[0]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-371-    if [[ ${#outdir} -eq 0 ]]
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-375-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:376:    files=`ls ${outdir}/job*.sh`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:377:    BASENAME1=`echo $files[1] | cut -d 'b' -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-378-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-383-       then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:384:         BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-385-         mv "$file" "${BASENAME1}b_000${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-388-        then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:389:          BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-390-          mv "$file" "${BASENAME1}b_00${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-393-        then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:394:          BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-395-          mv "$file" "${BASENAME1}b_0${BASENAME2}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-423-# put all related processes in array
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:424:runningANTSpids=( `ps -C antsRegistration -C N4BiasFieldCorrection -C ImageMath| awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-425-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-486-##Getting system info from linux can be done with these variables.
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:487:# RAM=`cat /proc/meminfo | sed -n -e '/MemTotal/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:488:# RAMfree=`cat /proc/meminfo | sed -n -e '/MemFree/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-489-# cpu_free_ram=$((${RAMfree}/${cpu_count}))
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-665-  else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:666:    MODALITYWEIGHTS=(`echo $MODALITYWEIGHTSTRING | tr 'x' "\n"`)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-667-    if [[ ${#MODALITYWEIGHTS[@]} -ne $NUMBEROFMODALITIES ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-719-else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:720:  echo "Invalid transformation. See `basename $0` -h for help menu."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-721-  exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-752-    echo "Please provide at least 2 filenames for the template inputs."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:753:    echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-754-    exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-756-    then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:757:    extension=`echo ${IMAGESETVARIABLE#*.}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-758-    if [[ $extension = 'csv' || $extension = 'txt' ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-763-            do
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:764:            files=(`echo $line | tr ',' ' '`)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-765-            if [[ ${#files[@]} -ne $NUMBEROFMODALITIES ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-777-    else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:778:        range=`${ANTSPATH}/ImageMath $TDIM abs nvols ${IMAGESETVARIABLE} | tail -1 | cut -d "," -f 4 | cut -d " " -f 2 | cut -d "]" -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-779-        if [[ ${range} -eq 1 && ${TDIM} -ne 4 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-781-            echo "Please provide at least 2 filenames for the template."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:782:            echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-783-            exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-786-            echo "This is a multivolume file. Use -d 4"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:787:            echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-788-            exit 1
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-949-# remove old job bash scripts
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:950:outdir=`dirname ${TEMPLATES[0]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-951-if [[ ${#outdir} -eq 0 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-986-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:987:        IMGbase=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:988:        BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-989-        RIGID="${outdir}/rigid${i}_0_${IMGbase}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-999-            let k=$i+$j
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1000:            IMGbase=`basename ${IMAGESETARRAY[$k]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1001:            BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1002-            RIGID="${outdir}/rigid${i}_${j}_${IMGbase}"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1003:            IMGbaseBASE=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1004:            BASENAMEBASE=` echo ${IMGbaseBASE} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1005-            exe2="$exe2 ${WARP} -d $DIM --float $USEFLOAT -i ${IMAGESETARRAY[$k]} -o $RIGID -t ${outdir}/rigid${i}_0GenericAffine.mat -r ${TEMPLATES[$j]}\n"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1012-          then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1013:            id=`qsub -cwd -S /bin/bash -N antsBuildTemplate_rigid -v ANTSPATH=$ANTSPATH $QSUBOPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1014-            jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1017-          then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1018:            id=`qsub -N antsrigid -v ANTSPATH=$ANTSPATH $QSUBOPTS -q nopreempt -l nodes=1:ppn=1 -l mem=${PBSMEMORY} -l walltime=${PBSWALLTIME} $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1019-            jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1027-          then
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1028:            id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's:  *: :g'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1029-            #echo "xgrid $XGRIDOPTS -job submit /bin/bash $qscript"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1106-            let k=$i-$j
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1107:            IMGbase=`basename ${IMAGESETARRAY[$i]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1108:            BASENAME=` echo ${IMGbase} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1109-            RIGID="${outdir}/rigid${k}_${j}_${IMGbase}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1156-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1157:ITERATLEVEL=(` echo $MAXITERATIONS | tr 'x' ' ' `)
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1158-NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1244-            else
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1245:              echo "Invalid similarity metric. Use CC, MI, MSQ, DEMONS or type bash `basename $0` -h."
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1246-              exit 1
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1247-            fi
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1248:            TEMPLATEbase=`basename ${TEMPLATES[$k]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1249:            indir=`dirname ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1250-            if [[ ${#indir} -eq 0 ]];
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1253-              fi
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1254:            IMGbase=`basename ${IMAGESETARRAY[$l]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1255-            POO=${OUTPUTNAME}template${k}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1256-            OUTFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1257:            OUTFN=`basename ${OUTFN}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1258-            DEFORMED="${outdir}/${OUTFN}${l}WarpedToTemplate.nii.gz"
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1259-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1260:            IMGbase=`basename ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1261-            POO=${OUTPUTNAME}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1262-            OUTWARPFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1263:            OUTWARPFN=`basename ${OUTWARPFN}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1264-            OUTWARPFN="${OUTWARPFN}${j}"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1293-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1294:        IMGbase=`basename ${IMAGESETARRAY[$j]}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1295-        POO=${OUTPUTNAME}${IMGbase}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1296-        OUTWARPFN=${POO%.*.*}
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1297:        OUTWARPFN=`basename ${OUTWARPFN}${j}`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1298-
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1333-            echo -e "$exe" > $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1334:            id=`qsub -cwd -N antsBuildTemplate_deformable_${i} -S /bin/bash -v ANTSPATH=$ANTSPATH $QSUBOPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1335-            jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1340-            echo -e "$exe" >> $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1341:            id=`qsub -N antsdef${i} -v ANTSPATH=$ANTSPATH -q nopreempt -l nodes=1:ppn=1 -l mem=${PBSMEMORY} -l walltime=${PBSWALLTIME} $QSUBOPTS $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1342-            jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1350-            echo -e "$exe" >> $qscript
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1351:            id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's:  *: :g'`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1352-            jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1359-        # counter updated, but not directly used in this loop
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1360:        count=`expr $count + 1`;
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1361-    # echo " submitting job number $count " # for debugging only
##############################################
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1420-
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1421:    WARPFILES=`ls ${OUTPUTNAME}*Warp.nii.gz | grep -v "InverseWarp"`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh:1422:    AFFINEFILES=`ls ${OUTPUTNAME}*GenericAffine.mat`
ants-2.1.0/Scripts/antsMultivariateTemplateConstruction2.sh-1423-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-218-    if ( ! -d "${outdir}${dirname}") {
ants-2.1.0/Scripts/antsNeuroimagingBattery:219:      `mkdir -p ${outdir}${dirname}`;
ants-2.1.0/Scripts/antsNeuroimagingBattery-220-      }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-223-    my $ref = "${obase}ref.nii.gz";
ants-2.1.0/Scripts/antsNeuroimagingBattery:224:    system("${ANTSPATH}/ImageMath 3 $ref m $anat $mask" );
ants-2.1.0/Scripts/antsNeuroimagingBattery-225-    my $res = "${ANTSPATH}/ResampleImageBySpacing 3 $ref $ref 2.0 2.0 2.0";
ants-2.1.0/Scripts/antsNeuroimagingBattery-226-    print("$res\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:227:    system($res);
ants-2.1.0/Scripts/antsNeuroimagingBattery-228-  
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-230-    print( "$dtiexe\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:231:    system( $dtiexe );
ants-2.1.0/Scripts/antsNeuroimagingBattery-232-  
ants-2.1.0/Scripts/antsNeuroimagingBattery:233:    system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}fa_anatomical.nii.gz TensorFA ${outdir}${dirname}${outname}${outid}dt_anatomical.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery:234:    system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}fa_anatomical.nii.gz m ${outdir}${dirname}${outname}${outid}fa_anatomical.nii.gz $mask");
ants-2.1.0/Scripts/antsNeuroimagingBattery-235-    
ants-2.1.0/Scripts/antsNeuroimagingBattery:236:     system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}md_anatomical.nii.gz TensorMeanDiffusion ${outdir}${dirname}${outname}${outid}dt_anatomical.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery:237:    system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}md_anatomical.nii.gz m ${outdir}${dirname}${outname}${outid}md_anatomical.nii.gz $mask");
ants-2.1.0/Scripts/antsNeuroimagingBattery-238-    
ants-2.1.0/Scripts/antsNeuroimagingBattery:239:    system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}rd_anatomical.nii.gz TensorRadialDiffusion ${outdir}${dirname}${outname}${outid}dt_anatomical.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery:240:    system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}rd_anatomical.nii.gz m ${outdir}${dirname}${outname}${outid}rd_anatomical.nii.gz $mask");
ants-2.1.0/Scripts/antsNeuroimagingBattery-241-    
ants-2.1.0/Scripts/antsNeuroimagingBattery-242-    # Remove for space reasons
ants-2.1.0/Scripts/antsNeuroimagingBattery:243:    system("rm ${outdir}${dirname}${outname}${outid}dt_anatomical.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery-244-       
ants-2.1.0/Scripts/antsNeuroimagingBattery-245-    if ( -s "${outdir}${dirname}${outname}${outid}dt_template.nii.gz") {
ants-2.1.0/Scripts/antsNeuroimagingBattery:246:      system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}fa_template.nii.gz TensorFA ${outdir}${dirname}${outname}${outid}dt_template.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery-247-    
ants-2.1.0/Scripts/antsNeuroimagingBattery:248:       system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}md_template.nii.gz TensorMeanDiffusion ${outdir}${dirname}${outname}${outid}dt_template.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery-249-    
ants-2.1.0/Scripts/antsNeuroimagingBattery:250:      system("${ANTSPATH}/ImageMath 3 ${outdir}${dirname}${outname}${outid}rd_template.nii.gz TensorRadialDiffusion ${outdir}${dirname}${outname}${outid}dt_template.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery-251-
ants-2.1.0/Scripts/antsNeuroimagingBattery:252:      system("rm ${outdir}${dirname}${outname}${outid}dt_template.nii.gz");
ants-2.1.0/Scripts/antsNeuroimagingBattery-253-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-273-    if ( ! -d "${outdir}${dirname}") {
ants-2.1.0/Scripts/antsNeuroimagingBattery:274:      `mkdir -p ${outdir}${dirname}`;
ants-2.1.0/Scripts/antsNeuroimagingBattery-275-      }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-284-      # Create anatomical reference to align to      
ants-2.1.0/Scripts/antsNeuroimagingBattery:285:      system("${ANTSPATH}/ImageMath 3 $ref m $anat $mask" );
ants-2.1.0/Scripts/antsNeuroimagingBattery:286:      system("${ANTSPATH}/ResampleImageBySpacing 3 $ref $ref 2.0 2.0 2.0");
ants-2.1.0/Scripts/antsNeuroimagingBattery-287-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-289-      my $m0Moco1 = "${ANTSPATH}/antsMotionCorr -d 3 -a $pcaslfile -o $meanpcasl";
ants-2.1.0/Scripts/antsNeuroimagingBattery:290:      system($m0Moco1);
ants-2.1.0/Scripts/antsNeuroimagingBattery-291-    
ants-2.1.0/Scripts/antsNeuroimagingBattery-292-      my $m0Moco2 = "${ANTSPATH}/antsMotionCorr -d 3 -o [ ${outdir}${dirname}${outname}${outid}, $meanpcasl, $meanpcasl ] -u 1 -m mi[ $meanpcasl, $pcaslfile, 1, 32, Regular, 0.1 ] -t Affine[0.2] -i 25 -e 1 -f 1 -s 0 -l 0";
ants-2.1.0/Scripts/antsNeuroimagingBattery:293:      system( $m0Moco2 );
ants-2.1.0/Scripts/antsNeuroimagingBattery-294-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-296-      print( "\n\n\n$makecbf\n\n\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:297:      system( $makecbf );      
ants-2.1.0/Scripts/antsNeuroimagingBattery-298-    }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-301-    
ants-2.1.0/Scripts/antsNeuroimagingBattery:302:    system( $alignexe );
ants-2.1.0/Scripts/antsNeuroimagingBattery-303-
ants-2.1.0/Scripts/antsNeuroimagingBattery:304:    system("${ANTSPATH}/antsMotionCorrStats -x ${outdir}${dirname}${outname}${outid}brainmask.nii.gz -m ${outdir}${dirname}${outname}${outid}MOCOparams.csv -o ${outdir}${dirname}${outname}${outid}MOCOStatsFramewise.csv -f 1");
ants-2.1.0/Scripts/antsNeuroimagingBattery-305-
ants-2.1.0/Scripts/antsNeuroimagingBattery:306:    system("${ANTSPATH}/antsMotionCorrStats -x ${outdir}${dirname}${outname}${outid}brainmask.nii.gz -m ${outdir}${dirname}${outname}${outid}MOCOparams.csv -o ${outdir}${dirname}${outname}${outid}MOCOStatsReference.csv -f 0");
ants-2.1.0/Scripts/antsNeuroimagingBattery-307-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-330-    if ( ! -d "${outdir}${dirname}") {
ants-2.1.0/Scripts/antsNeuroimagingBattery:331:      `mkdir -p ${outdir}${dirname}`;
ants-2.1.0/Scripts/antsNeuroimagingBattery-332-      }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-343-
ants-2.1.0/Scripts/antsNeuroimagingBattery:344:      system("${ANTSPATH}/ImageMath 3 $ref m $anat $mask" );
ants-2.1.0/Scripts/antsNeuroimagingBattery-345-      my $res = "${ANTSPATH}/ResampleImageBySpacing 3 $ref $ref 2.0 2.0 2.0";
ants-2.1.0/Scripts/antsNeuroimagingBattery:346:      system($res);
ants-2.1.0/Scripts/antsNeuroimagingBattery-347-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-349-      my $m0Moco1 = "${ANTSPATH}/antsMotionCorr -d 3 -a $m0file -o $meanM0";
ants-2.1.0/Scripts/antsNeuroimagingBattery:350:      system($m0Moco1);
ants-2.1.0/Scripts/antsNeuroimagingBattery-351-    
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-353-      print( "$m0Moco2\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:354:      system( $m0Moco2 );
ants-2.1.0/Scripts/antsNeuroimagingBattery-355-    
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-359-    #print("$paslMoco\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:360:    #system($paslMoco);  
ants-2.1.0/Scripts/antsNeuroimagingBattery-361-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-363-      print( "\n\n\n$makecbf\n\n\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:364:      system( $makecbf );
ants-2.1.0/Scripts/antsNeuroimagingBattery-365-    }  
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-369-    
ants-2.1.0/Scripts/antsNeuroimagingBattery:370:    system( $alignexe );
ants-2.1.0/Scripts/antsNeuroimagingBattery-371-    
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-389-    print( "Create diretory\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:390:    `mkdir -p ${outdir}${dirname}`;
ants-2.1.0/Scripts/antsNeuroimagingBattery-391-    }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-405-  my $stc = "${ANTSPATH}/ImageMath 4 $bold SliceTimingCorrection $boldfile 0 bspline";
ants-2.1.0/Scripts/antsNeuroimagingBattery:406:  system($stc);
ants-2.1.0/Scripts/antsNeuroimagingBattery-407-  
ants-2.1.0/Scripts/antsNeuroimagingBattery-408-  # Motion correction
ants-2.1.0/Scripts/antsNeuroimagingBattery:409:  system("${ANTSPATH}/antsMotionCorr -d 3 -a $bold -o $meanbold");
ants-2.1.0/Scripts/antsNeuroimagingBattery:410:  system("${ANTSPATH}/antsMotionCorr -d 3 -o [ ${obase}, $bold, $meanbold ] -u 1 -m mi[ $meanbold, $bold, 1, 32, Regular, 0.1 ] -t Affine[0.2] -i 25 -e 1 -f 1 -s 0 -l 0 -u 1");
ants-2.1.0/Scripts/antsNeuroimagingBattery-411-       
ants-2.1.0/Scripts/antsNeuroimagingBattery-412-
ants-2.1.0/Scripts/antsNeuroimagingBattery:413:  system("${ANTSPATH}/ImageMath 3 $ref m $anat $mask" );
ants-2.1.0/Scripts/antsNeuroimagingBattery-414-  my $res = "${ANTSPATH}/ResampleImageBySpacing 3 $ref $ref 2.0 2.0 2.0";
ants-2.1.0/Scripts/antsNeuroimagingBattery:415:  system($res);
ants-2.1.0/Scripts/antsNeuroimagingBattery-416-  }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-418-  my $alignexe = "sh ${ANTSPATH}/antsIntermodalityIntrasubject.sh -d 3 -t 2 -i $meanbold -r $ref -R $anat -x $mask $warpflag -o ${outdir}${dirname}${outname}${outid} -T $template";
ants-2.1.0/Scripts/antsNeuroimagingBattery:419:  system( $alignexe );
ants-2.1.0/Scripts/antsNeuroimagingBattery-420-
ants-2.1.0/Scripts/antsNeuroimagingBattery:421:  system("${ANTSPATH}/antsMotionCorrStats -x ${outdir}${dirname}${outname}${outid}_brainmask.nii.gz -m ${outdir}${dirname}${outname}${outid}_MOCOparams.csv -0 ${outdir}${dirname}${outname}${outid}_MOCOstats.csv -f 1");
ants-2.1.0/Scripts/antsNeuroimagingBattery-422-
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-435-    print( "Create diretory\n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:436:    `mkdir -p ${outdir}${dirname}`;
ants-2.1.0/Scripts/antsNeuroimagingBattery-437-    }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-451-  # Motion correction
ants-2.1.0/Scripts/antsNeuroimagingBattery:452:  system("${ANTSPATH}/antsMotionCorr -d 3 -a $rsboldfile -o $meanbold");
ants-2.1.0/Scripts/antsNeuroimagingBattery-453-  print("${ANTSPATH}/antsMotionCorr -d 3 -o [ ${obase}, $bold, $meanbold ] -u 1 -m mi[ $meanbold, $rsboldfile, 1, 32, Regular, 0.1 ] -t Affine[0.2] -i 25 -e 1 -f 1 -s 0 -l 0 -u 1 \n");
ants-2.1.0/Scripts/antsNeuroimagingBattery:454:  system("${ANTSPATH}/antsMotionCorr -d 3 -o [ ${obase}, $bold, $meanbold ] -m mi[ $meanbold, $rsboldfile, 1, 32, Regular, 0.1 ] -t Affine[0.2] -i 25 -e 1 -f 1 -s 0 -l 0 -u 1");
ants-2.1.0/Scripts/antsNeuroimagingBattery-455-       
ants-2.1.0/Scripts/antsNeuroimagingBattery-456-
ants-2.1.0/Scripts/antsNeuroimagingBattery:457:  system("${ANTSPATH}/ImageMath 3 $ref m $anat $mask" );
ants-2.1.0/Scripts/antsNeuroimagingBattery-458-  my $res = "${ANTSPATH}/ResampleImageBySpacing 3 $ref $ref 2.0 2.0 2.0";
ants-2.1.0/Scripts/antsNeuroimagingBattery:459:  system($res);
ants-2.1.0/Scripts/antsNeuroimagingBattery-460-  }
##############################################
ants-2.1.0/Scripts/antsNeuroimagingBattery-462-  my $alignexe = "sh ${ANTSPATH}/antsIntermodalityIntrasubject.sh -d 3 -t 2 -i $meanbold -r $ref -R $anat -x $mask $warpflag -o ${outdir}${dirname}${outname}${outid} -T $template";
ants-2.1.0/Scripts/antsNeuroimagingBattery:463:  system( $alignexe );
ants-2.1.0/Scripts/antsNeuroimagingBattery-464-
ants-2.1.0/Scripts/antsNeuroimagingBattery:465:  system("${ANTSPATH}/antsMotionCorrStats -x ${outdir}${dirname}${outname}${outid}brainmask.nii.gz -m ${outdir}${dirname}${outname}${outid}MOCOparams.csv -o ${outdir}${dirname}${outname}${outid}MOCOStatsFramewise.csv -f 1");
ants-2.1.0/Scripts/antsNeuroimagingBattery-466-
ants-2.1.0/Scripts/antsNeuroimagingBattery:467:  system("${ANTSPATH}/antsMotionCorrStats -x ${outdir}${dirname}${outname}${outid}brainmask.nii.gz -m ${outdir}${dirname}${outname}${outid}MOCOparams.csv -o ${outdir}${dirname}${outname}${outid}MOCOStatsReference.csv -f 0");
ants-2.1.0/Scripts/antsNeuroimagingBattery-468-  }
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-21-
ants-2.1.0/Scripts/antsRegistrationSyN.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsRegistrationSyN.sh-23-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-49-
ants-2.1.0/Scripts/antsRegistrationSyN.sh:50:`basename $0` -d ImageDimension -f FixedImage -m MovingImage -o OutputPrefix
ants-2.1.0/Scripts/antsRegistrationSyN.sh-51-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-91-
ants-2.1.0/Scripts/antsRegistrationSyN.sh:92:`basename $0` -d 3 -f fixedImage.nii.gz -m movingImage.nii.gz -o output
ants-2.1.0/Scripts/antsRegistrationSyN.sh-93-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-111-
ants-2.1.0/Scripts/antsRegistrationSyN.sh:112:`basename $0` -d ImageDimension -f FixedImage -m MovingImage -o OutputPrefix
ants-2.1.0/Scripts/antsRegistrationSyN.sh-113-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-115-
ants-2.1.0/Scripts/antsRegistrationSyN.sh:116:`basename $0` -d 3 -f fixedImage.nii.gz -m movingImage.nii.gz -o output
ants-2.1.0/Scripts/antsRegistrationSyN.sh-117-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-215-# put all related processes in array
ants-2.1.0/Scripts/antsRegistrationSyN.sh:216:runningANTSpids=( `ps -C antsRegistration | awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsRegistrationSyN.sh-217-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyN.sh-362-SIZESTRING="${SIZESTRING%\\n}"
ants-2.1.0/Scripts/antsRegistrationSyN.sh:363:SIZE=( `echo $SIZESTRING | tr 'x' ' '` )
ants-2.1.0/Scripts/antsRegistrationSyN.sh-364-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-21-
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-23-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-49-
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:50:`basename $0` -d ImageDimension -f FixedImage -m MovingImage -o OutputPrefix
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-51-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-90-
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:91:`basename $0` -d 3 -f fixedImage.nii.gz -m movingImage.nii.gz -o output
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-92-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-110-
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:111:`basename $0` -d ImageDimension -f FixedImage -m MovingImage -o OutputPrefix
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-112-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-114-
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:115:`basename $0` -d 3 -f fixedImage.nii.gz -m movingImage.nii.gz -o output
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-116-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-214-# put all related processes in array
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:215:runningANTSpids=( `ps -C antsRegistration | awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-216-
##############################################
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-361-SIZESTRING="${SIZESTRING%\\n}"
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh:362:SIZE=( `echo $SIZESTRING | tr 'x' ' '` )
ants-2.1.0/Scripts/antsRegistrationSyNQuick.sh-363-
##############################################
ants-2.1.0/Scripts/antsaffine.sh-59-
ants-2.1.0/Scripts/antsaffine.sh:60:OUTPUTNAME=` echo $MOVING | cut -d '.' -f 1 `
ants-2.1.0/Scripts/antsaffine.sh-61-
##############################################
ants-2.1.0/Scripts/antsbashstats.sh-93-stat_median() {
ants-2.1.0/Scripts/antsbashstats.sh:94:  NUMS=(`sort -n $1`)
ants-2.1.0/Scripts/antsbashstats.sh-95-  TOTALNUMS=${#NUMS[*]}
##############################################
ants-2.1.0/Scripts/antsdeformationmag.sh-16-ANTSPATH=$4
ants-2.1.0/Scripts/antsdeformationmag.sh:17:dimarr=(`${ANTSPATH}/PrintHeader ${inwarp}xvec.nii.gz  | grep Spacing | grep , | wc `)
ants-2.1.0/Scripts/antsdeformationmag.sh-18-DIM=${dimarr[0]}
##############################################
ants-2.1.0/Scripts/antswithdt.sh-100-  TRANSFORMATION=SyN[0.25]
ants-2.1.0/Scripts/antswithdt.sh:101:  ITERATLEVEL=(`echo $MAXITERATIONS | tr 'x' ' '`)
ants-2.1.0/Scripts/antswithdt.sh-102-  NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/basic_ants_example.sh-134-TEM=${OUTPUTNAME}BTPtemplate.nii.gz
ants-2.1.0/Scripts/basic_ants_example.sh:135:NM1=` echo $JJ | cut -d '.' -f 1 `
ants-2.1.0/Scripts/basic_ants_example.sh-136-INVW=" -i ${OUTPUTNAME}BTP${NM1}Affine.txt ${OUTPUTNAME}BTP${NM1}InverseWarp.nii.gz "
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-21-
ants-2.1.0/Scripts/buildtemplateparallel.sh:22:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/buildtemplateparallel.sh-23-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-74-
ants-2.1.0/Scripts/buildtemplateparallel.sh:75:`basename $0` -d ImageDimension -o OUTPREFIX <other options> <images>
ants-2.1.0/Scripts/buildtemplateparallel.sh-76-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-126-
ants-2.1.0/Scripts/buildtemplateparallel.sh:127:`basename $0` -d 3 -m 30x50x20 -t GR -s CC -c 1 -o MY -z InitialTemplate.nii.gz  *RF*T1x.nii.gz
ants-2.1.0/Scripts/buildtemplateparallel.sh-128-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-164-
ants-2.1.0/Scripts/buildtemplateparallel.sh:165:`basename $0` will make a template out of the input files using an elastic
ants-2.1.0/Scripts/buildtemplateparallel.sh-166-or diffeomorphic transformation. This script builds a template iteratively from the input
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-171-
ants-2.1.0/Scripts/buildtemplateparallel.sh:172:`basename $0` -d ImageDimension -o OUTPREFIX <other options> <images>
ants-2.1.0/Scripts/buildtemplateparallel.sh-173-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-175-
ants-2.1.0/Scripts/buildtemplateparallel.sh:176: bash `basename $0` -d 3 -m 30x50x20 -t GR  -s CC -c 1 -o MY -z InitialTemplate.nii.gz  *RF*T1x.nii.gz
ants-2.1.0/Scripts/buildtemplateparallel.sh-177-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-377-
ants-2.1.0/Scripts/buildtemplateparallel.sh:378:	${ANTSPATH}/AverageImages $dim ${templatename}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`
ants-2.1.0/Scripts/buildtemplateparallel.sh-379-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-433-    PARAM8=0
ants-2.1.0/Scripts/buildtemplateparallel.sh:434:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 2  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:435:    for x in $LL ; do  PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ;  let NFILES=$NFILES+1  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:436:    PARAM1=` awk -v a=$PARAM1 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-437-
ants-2.1.0/Scripts/buildtemplateparallel.sh:438:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 3  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:439:    for x in $LL ; do PARAM2=` awk -v a=$PARAM2 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:440:    PARAM2=` awk -v a=$PARAM2 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-441-
ants-2.1.0/Scripts/buildtemplateparallel.sh:442:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 4  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:443:    for x in $LL ; do PARAM3=` awk -v a=$PARAM3 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:444:    PARAM3=` awk -v a=$PARAM3 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-445-
ants-2.1.0/Scripts/buildtemplateparallel.sh:446:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 5  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:447:    for x in $LL ; do PARAM4=` awk -v a=$PARAM4 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:448:    PARAM4=` awk -v a=$PARAM4 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-449-
ants-2.1.0/Scripts/buildtemplateparallel.sh:450:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 6  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:451:    for x in $LL ; do PARAM5=` awk -v a=$PARAM5 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:452:    PARAM5=0 # ` awk -v a=$PARAM5 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-453-
ants-2.1.0/Scripts/buildtemplateparallel.sh:454:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 7  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:455:    for x in $LL ; do PARAM6=` awk -v a=$PARAM6 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:456:    PARAM6=0 # ` awk -v a=$PARAM6 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-457-
ants-2.1.0/Scripts/buildtemplateparallel.sh:458:    LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 2  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:459:    for x in $LL ; do PARAM7=` awk -v a=$PARAM7 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:460:    PARAM7=` awk -v a=$PARAM7 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-461-
ants-2.1.0/Scripts/buildtemplateparallel.sh:462:    LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 3  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:463:    for x in $LL ; do PARAM8=` awk -v a=$PARAM8 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:464:    PARAM8=` awk -v a=$PARAM8 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-465-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-492-    PARAM15=0
ants-2.1.0/Scripts/buildtemplateparallel.sh:493:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 2  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:494:    for x in $LL ; do  PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ;  let NFILES=$NFILES+1  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:495:    PARAM1=` awk -v a=$PARAM1 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-496-
ants-2.1.0/Scripts/buildtemplateparallel.sh:497:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 3  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:498:    for x in $LL ; do PARAM2=` awk -v a=$PARAM2 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:499:    PARAM2=` awk -v a=$PARAM2 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-500-
ants-2.1.0/Scripts/buildtemplateparallel.sh:501:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 4  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:502:    for x in $LL ; do PARAM3=` awk -v a=$PARAM3 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:503:    PARAM3=` awk -v a=$PARAM3 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-504-
ants-2.1.0/Scripts/buildtemplateparallel.sh:505:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 5  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:506:    for x in $LL ; do PARAM4=` awk -v a=$PARAM4 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:507:    PARAM4=` awk -v a=$PARAM4 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-508-
ants-2.1.0/Scripts/buildtemplateparallel.sh:509:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 6  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:510:    for x in $LL ; do PARAM5=` awk -v a=$PARAM5 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:511:    PARAM5=` awk -v a=$PARAM5 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-512-
ants-2.1.0/Scripts/buildtemplateparallel.sh:513:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 7  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:514:    for x in $LL ; do PARAM6=` awk -v a=$PARAM6 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:515:    PARAM6=` awk -v a=$PARAM6 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-516-
ants-2.1.0/Scripts/buildtemplateparallel.sh:517:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 8  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:518:    for x in $LL ; do PARAM7=` awk -v a=$PARAM7 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:519:    PARAM7=` awk -v a=$PARAM7 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-520-
ants-2.1.0/Scripts/buildtemplateparallel.sh:521:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 9  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:522:    for x in $LL ; do PARAM8=` awk -v a=$PARAM8 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:523:    PARAM8=` awk -v a=$PARAM8 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-524-
ants-2.1.0/Scripts/buildtemplateparallel.sh:525:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 10  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:526:    for x in $LL ; do PARAM9=` awk -v a=$PARAM9 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:527:    PARAM9=` awk -v a=$PARAM9 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-528-
ants-2.1.0/Scripts/buildtemplateparallel.sh:529:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 11  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:530:    for x in $LL ; do PARAM10=` awk -v a=$PARAM10 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:531:    PARAM10=0 # ` awk -v a=$PARAM10 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-532-
ants-2.1.0/Scripts/buildtemplateparallel.sh:533:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 12  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:534:    for x in $LL ; do PARAM11=` awk -v a=$PARAM11 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:535:    PARAM11=0 # ` awk -v a=$PARAM11 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-536-
ants-2.1.0/Scripts/buildtemplateparallel.sh:537:    LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 13  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:538:    for x in $LL ; do PARAM12=` awk -v a=$PARAM12 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:539:    PARAM12=0 # ` awk -v a=$PARAM12 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-540-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-542-
ants-2.1.0/Scripts/buildtemplateparallel.sh:543:    LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 2  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:544:    for x in $LL ; do  PARAM13=` awk -v a=$PARAM13 -v b=$x 'BEGIN{print (a + b)}' ` ;  done
ants-2.1.0/Scripts/buildtemplateparallel.sh:545:    PARAM13=` awk -v a=$PARAM13 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-546-
ants-2.1.0/Scripts/buildtemplateparallel.sh:547:    LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 3  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:548:    for x in $LL ; do PARAM14=` awk -v a=$PARAM14 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:549:    PARAM14=` awk -v a=$PARAM14 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-550-
ants-2.1.0/Scripts/buildtemplateparallel.sh:551:    LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 4  `
ants-2.1.0/Scripts/buildtemplateparallel.sh:552:    for x in $LL ; do PARAM15=` awk -v a=$PARAM15 -v b=$x 'BEGIN{print (a + b)}' `  ; done
ants-2.1.0/Scripts/buildtemplateparallel.sh:553:    PARAM15=` awk -v a=$PARAM15 -v b=$NFILES 'BEGIN{print (a / b)}' `
ants-2.1.0/Scripts/buildtemplateparallel.sh-554-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-565-    files=`ls job*.sh`
ants-2.1.0/Scripts/buildtemplateparallel.sh:566:    BASENAME1=`echo $files[1] | cut -d 'b' -f 1`
ants-2.1.0/Scripts/buildtemplateparallel.sh-567-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-572-	  then
ants-2.1.0/Scripts/buildtemplateparallel.sh:573:	  BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/buildtemplateparallel.sh-574-	  mv "$file" "${BASENAME1}b_000${BASENAME2}"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-577-	  then
ants-2.1.0/Scripts/buildtemplateparallel.sh:578:	  BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/buildtemplateparallel.sh-579-	  mv "$file" "${BASENAME1}b_00${BASENAME2}"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-582-	  then
ants-2.1.0/Scripts/buildtemplateparallel.sh:583:	  BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/buildtemplateparallel.sh-584-	  mv "$file" "${BASENAME1}b_0${BASENAME2}"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-599-# put all related processes in array
ants-2.1.0/Scripts/buildtemplateparallel.sh:600:  runningANTSpids=( `ps -C ANTS -C N4BiasFieldCorrection -C ImageMath| awk '{ printf "%s\n", $1 ; }'` )
ants-2.1.0/Scripts/buildtemplateparallel.sh-601-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-659-##Getting system info from linux can be done with these variables.
ants-2.1.0/Scripts/buildtemplateparallel.sh:660:# RAM=`cat /proc/meminfo | sed -n -e '/MemTotal/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/buildtemplateparallel.sh:661:# RAMfree=`cat /proc/meminfo | sed -n -e '/MemFree/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
ants-2.1.0/Scripts/buildtemplateparallel.sh-662-# cpu_free_ram=$((${RAMfree}/${cpu_count}))
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-785-    echo "Please provide at least 2 filenames for the template."
ants-2.1.0/Scripts/buildtemplateparallel.sh:786:    echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/buildtemplateparallel.sh-787-    exit 1
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-790-
ants-2.1.0/Scripts/buildtemplateparallel.sh:791:    range=`${ANTSPATH}/ImageMath $TDIM abs nvols ${IMAGESETVARIABLE} | tail -1 | cut -d "," -f 4 | cut -d " " -f 2 | cut -d "]" -f 1 `
ants-2.1.0/Scripts/buildtemplateparallel.sh-792-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-795-	echo "Please provide at least 2 filenames for the template."
ants-2.1.0/Scripts/buildtemplateparallel.sh:796:	echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/buildtemplateparallel.sh-797-	exit 1
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-800-	echo "This is a multivolume file. Use -d 4"
ants-2.1.0/Scripts/buildtemplateparallel.sh:801:	echo "Use `basename $0` -h for help"
ants-2.1.0/Scripts/buildtemplateparallel.sh-802-	exit 1
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-949-
ants-2.1.0/Scripts/buildtemplateparallel.sh:950:      BASENAME=` echo ${IMG} | cut -d '.' -f 1 `
ants-2.1.0/Scripts/buildtemplateparallel.sh-951-
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-964-      if [ $DOQSUB -eq 1 ] ; then
ants-2.1.0/Scripts/buildtemplateparallel.sh:965:		id=`qsub -cwd -S /bin/bash -N antsBuildTemplate_rigid -v ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1,LD_LIBRARY_PATH=$LD_LIBRARY_PATH,ANTSPATH=$ANTSPATH $QSUBOPTS $qscript | awk '{print $3}'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-966-		jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-969-        echo "cp -R /jobtmp/pbstmp.\$PBS_JOBID/* ${currentdir}" >> $qscript;
ants-2.1.0/Scripts/buildtemplateparallel.sh:970:		id=`qsub -N antsrigid -v ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1,LD_LIBRARY_PATH=$LD_LIBRARY_PATH,ANTSPATH=$ANTSPATH $QSUBOPTS -q nopreempt -l nodes=1:ppn=1 -l walltime=4:00:00 $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-971-		jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-977-      elif  [ $DOQSUB -eq 3 ] ; then
ants-2.1.0/Scripts/buildtemplateparallel.sh:978:	id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's:  *: :g'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-979-	#echo "xgrid $XGRIDOPTS -job submit /bin/bash $qscript"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-1090-# Begin Main Loop
ants-2.1.0/Scripts/buildtemplateparallel.sh:1091:ITERATLEVEL=(` echo $MAXITERATIONS | tr 'x' ' ' `)
ants-2.1.0/Scripts/buildtemplateparallel.sh-1092-NUMLEVELS=${#ITERATLEVEL[@]}
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-1164-    if [ $DOQSUB -eq 1 ]; then
ants-2.1.0/Scripts/buildtemplateparallel.sh:1165:	id=`qsub -cwd -N antsBuildTemplate_deformable_${i} -S /bin/bash -v ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1,LD_LIBRARY_PATH=$LD_LIBRARY_PATH,ANTSPATH=$ANTSPATH $QSUBOPTS $exe | awk '{print $3}'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-1166-	     jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-1172-      echo "cp -R /jobtmp/pbstmp.\$PBS_JOBID/* ${currentdir}" >> $qscript;
ants-2.1.0/Scripts/buildtemplateparallel.sh:1173:	     id=`qsub -N antsdef${i} -v ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1,LD_LIBRARY_PATH=$LD_LIBRARY_PATH,ANTSPATH=$ANTSPATH -q nopreempt -l nodes=1:ppn=1 -l walltime=4:00:00 $QSUBOPTS $qscript | awk '{print $1}'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-1174-	     jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-1183-	     echo "$exe" >> $qscript
ants-2.1.0/Scripts/buildtemplateparallel.sh:1184:      id=`xgrid $XGRIDOPTS -job submit /bin/bash $qscript | awk '{sub(/;/,"");print $3}' | tr '\n' ' ' | sed 's:  *: :g'`
ants-2.1.0/Scripts/buildtemplateparallel.sh-1185-	     jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/buildtemplateparallel.sh-1190-    # counter updated, but not directly used in this loop
ants-2.1.0/Scripts/buildtemplateparallel.sh:1191:    count=`expr $count + 1`;
ants-2.1.0/Scripts/buildtemplateparallel.sh-1192-
##############################################
ants-2.1.0/Scripts/directlabels.sh-25-
ants-2.1.0/Scripts/directlabels.sh:26:`basename $0` -d ImageDimension -s InputSegmentationImage -l CorticalLabelImage <OPTARGS> -o OutputImage
ants-2.1.0/Scripts/directlabels.sh-27-
##############################################
ants-2.1.0/Scripts/directlabels.sh-84-
ants-2.1.0/Scripts/directlabels.sh:85:  OUTPUT=(`${ANTSPATH}/LabelGeometryMeasures $DIMENSION $LABEL_IMAGE`);
ants-2.1.0/Scripts/directlabels.sh-86-
##############################################
ants-2.1.0/Scripts/directlabels.sh-89-  begin=10
ants-2.1.0/Scripts/directlabels.sh:90:  increment=`expr 5 + $DIMENSION + $DIMENSION + $DIMENSION + $DIMENSION`
ants-2.1.0/Scripts/directlabels.sh-91-
##############################################
ants-2.1.0/Scripts/directlabels.sh-94-    LABELS[$count]=${OUTPUT[$i]}
ants-2.1.0/Scripts/directlabels.sh:95:    count=`expr $count + 1`
ants-2.1.0/Scripts/directlabels.sh-96-  done
##############################################
ants-2.1.0/Scripts/directlabels.sh-98-  ## Get bounding boxes
ants-2.1.0/Scripts/directlabels.sh:99:  begin=`expr 15 + $DIMENSION + $DIMENSION`
ants-2.1.0/Scripts/directlabels.sh:100:  increment=`expr 5 + $DIMENSION + $DIMENSION + $DIMENSION + $DIMENSION`
ants-2.1.0/Scripts/directlabels.sh-101-
##############################################
ants-2.1.0/Scripts/directlabels.sh-103-  for (( i=begin; i<=${#OUTPUT[@]}; i+=$increment )); do
ants-2.1.0/Scripts/directlabels.sh:104:    for (( j=0; j<`expr $DIMENSION + $DIMENSION`; j++ )); do
ants-2.1.0/Scripts/directlabels.sh:105:      BOUNDING_BOXES[$count]=${BOUNDING_BOXES[$count]}${OUTPUT[`expr $i+$j`]}
ants-2.1.0/Scripts/directlabels.sh-106-    done
ants-2.1.0/Scripts/directlabels.sh:107:    count=`expr $count + 1`;
ants-2.1.0/Scripts/directlabels.sh-108-  done
##############################################
ants-2.1.0/Scripts/directlabels.sh-110-  ## read thickness .csv file if it exists
ants-2.1.0/Scripts/directlabels.sh:111:  extension=`echo ${THICKNESS_PRIOR_ESTIMATE#*.}`
ants-2.1.0/Scripts/directlabels.sh-112-
##############################################
ants-2.1.0/Scripts/directlabels.sh-117-      do
ants-2.1.0/Scripts/directlabels.sh:118:      bar=(`echo $line | tr ',' ' '`)
ants-2.1.0/Scripts/directlabels.sh-119-
##############################################
ants-2.1.0/Scripts/directlabels.sh-158-
ants-2.1.0/Scripts/directlabels.sh:159:      jp1=`expr $j + 1`
ants-2.1.0/Scripts/directlabels.sh-160-      maxValue=${elements[$jp1]}
##############################################
ants-2.1.0/Scripts/directlabels.sh-164-
ants-2.1.0/Scripts/directlabels.sh:165:      count=`expr $count + 1`
ants-2.1.0/Scripts/directlabels.sh-166-    done
##############################################
ants-2.1.0/Scripts/directlabels.sh-180-   #
ants-2.1.0/Scripts/directlabels.sh:181:   OUTPUT=(`${ANTSPATH}/ThresholdImage $DIMENSION $LABEL_IMAGE $grayMatterMask ${LABELS[$i]} ${LABELS[$i]} 1 0`)
ants-2.1.0/Scripts/directlabels.sh:182:   OUTPUT=(`${ANTSPATH}/ThresholdImage $DIMENSION $SEG_IMAGE $whiteMatterMask 3 3 3 0`)
ants-2.1.0/Scripts/directlabels.sh:183:   OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION $grayMatterMask m $grayMatterMask $SEG_IMAGE`)
ants-2.1.0/Scripts/directlabels.sh:184:   OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION $gmWmMask + $grayMatterMask $whiteMatterMask`)
ants-2.1.0/Scripts/directlabels.sh:185:   OUTPUT=(`${ANTSPATH}/ExtractRegionFromImage $DIMENSION $gmWmMask ${TMPDIR}seg_${LABELS[$i]}.nii.gz $minIndex $maxIndex`)
ants-2.1.0/Scripts/directlabels.sh:186:   OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION ${TMPDIR}seg_${LABELS[$i]}.nii.gz PadImage ${TMPDIR}seg_${LABELS[$i]}.nii.gz $PADDING`)
ants-2.1.0/Scripts/directlabels.sh-187-   if [ -f $WMPROB_IMAGE ]; then
ants-2.1.0/Scripts/directlabels.sh:188:     OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION $whiteMatterMask m $whiteMatterMask $WMPROB_IMAGE`)
ants-2.1.0/Scripts/directlabels.sh:189:     OUTPUT=(`${ANTSPATH}/ExtractRegionFromImage $DIMENSION $whiteMatterMask ${TMPDIR}wm_${LABELS[$i]}.nii.gz $minIndex $maxIndex`);
ants-2.1.0/Scripts/directlabels.sh:190:     OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION ${TMPDIR}wm_${LABELS[$i]}.nii.gz PadImage ${TMPDIR}wm_${LABELS[$i]}.nii.gz $PADDING`);
ants-2.1.0/Scripts/directlabels.sh-191-   fi
ants-2.1.0/Scripts/directlabels.sh-192-   if [ -f $GMPROB_IMAGE ]; then
ants-2.1.0/Scripts/directlabels.sh:193:     OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION $grayMatterMask m $grayMatterMask $GMPROB_IMAGE`)
ants-2.1.0/Scripts/directlabels.sh:194:     OUTPUT=(`${ANTSPATH}/ExtractRegionFromImage $DIMENSION $grayMatterMask ${TMPDIR}gm_${LABELS[$i]}.nii.gz $minIndex $maxIndex`);
ants-2.1.0/Scripts/directlabels.sh:195:     OUTPUT=(`${ANTSPATH}/ImageMath $DIMENSION ${TMPDIR}gm_${LABELS[$i]}.nii.gz PadImage ${TMPDIR}gm_${LABELS[$i]}.nii.gz $PADDING`);
ants-2.1.0/Scripts/directlabels.sh-196-   fi
##############################################
ants-2.1.0/Scripts/directlabels.sh-206-
ants-2.1.0/Scripts/directlabels.sh:207:    files=`ls ${TMPDIR}job*.sh`
ants-2.1.0/Scripts/directlabels.sh:208:    BASENAME1=`echo $files[1] | cut -d 'b' -f 1`
ants-2.1.0/Scripts/directlabels.sh-209-
##############################################
ants-2.1.0/Scripts/directlabels.sh-214-	  then
ants-2.1.0/Scripts/directlabels.sh:215:	  BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/directlabels.sh-216-	  mv "$file" "${BASENAME1}b_000${BASENAME2}"
##############################################
ants-2.1.0/Scripts/directlabels.sh-219-	  then
ants-2.1.0/Scripts/directlabels.sh:220:	  BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/directlabels.sh-221-	  mv "$file" "${BASENAME1}b_00${BASENAME2}"
##############################################
ants-2.1.0/Scripts/directlabels.sh-224-	  then
ants-2.1.0/Scripts/directlabels.sh:225:	  BASENAME2=`echo $file | cut -d 'b' -f 2 `
ants-2.1.0/Scripts/directlabels.sh-226-	  mv "$file" "${BASENAME1}b_0${BASENAME2}"
##############################################
ants-2.1.0/Scripts/directlabels.sh-232-
ants-2.1.0/Scripts/directlabels.sh:233:  output=( `${ANTSPATH}/CreateImage $DIMENSION $SEG_IMAGE $OUTPUT_IMAGE 0` );
ants-2.1.0/Scripts/directlabels.sh-234-
##############################################
ants-2.1.0/Scripts/directlabels.sh-246-      minValue=${elements[$j]}
ants-2.1.0/Scripts/directlabels.sh:247:      minValue=`expr $minValue - $PADDING`;
ants-2.1.0/Scripts/directlabels.sh-248-
##############################################
ants-2.1.0/Scripts/directlabels.sh-250-
ants-2.1.0/Scripts/directlabels.sh:251:      count=`expr $count + 1`
ants-2.1.0/Scripts/directlabels.sh-252-    done
##############################################
ants-2.1.0/Scripts/directlabels.sh-255-
ants-2.1.0/Scripts/directlabels.sh:256:    output=(`${ANTSPATH}/PasteImageIntoImage $DIMENSION $OUTPUT_IMAGE $TMPDIR/direct_${LABELS[$i]}.nii.gz $OUTPUT_IMAGE $minIndex 0 2 -1`);
ants-2.1.0/Scripts/directlabels.sh-257-  done
##############################################
ants-2.1.0/Scripts/directlabels.sh-409-  if [ $DOQSUB -eq 1 ]; then
ants-2.1.0/Scripts/directlabels.sh:410:    id=`qsub -cwd -N DiReCT_${LABEL} -S /bin/bash -v ANTSPATH=$ANTSPATH $QSUBOPTS $exe | awk '{print $3}'`
ants-2.1.0/Scripts/directlabels.sh-411-    jobIDs="$jobIDs $id"
##############################################
ants-2.1.0/Scripts/directlabels.sh-417-    echo "  Performing DiReCT for label ${LABEL}."
ants-2.1.0/Scripts/directlabels.sh:418:    output=(`$exe`)
ants-2.1.0/Scripts/directlabels.sh-419-  fi
##############################################
ants-2.1.0/Scripts/directlabels.sh-436-  fi
ants-2.1.0/Scripts/directlabels.sh:437:  count=`expr $count + 1`
ants-2.1.0/Scripts/directlabels.sh-438-done
##############################################
ants-2.1.0/Scripts/lohmann.sh-42-
ants-2.1.0/Scripts/lohmann.sh:43:OUTPUTNAME=` echo $FIXED | cut -d '.' -f 1 `
ants-2.1.0/Scripts/lohmann.sh-44-
##############################################
ants-2.1.0/Scripts/newAntsExample.sh-16-fi
ants-2.1.0/Scripts/newAntsExample.sh:17:nm1=` basename $f | cut -d '.' -f 1 `
ants-2.1.0/Scripts/newAntsExample.sh:18:nm2=` basename $m | cut -d '.' -f 1 `
ants-2.1.0/Scripts/newAntsExample.sh-19-reg=${AP}antsRegistration           # path to antsRegistration
##############################################
ants-2.1.0/Scripts/phantomstudy.sh-8-do
ants-2.1.0/Scripts/phantomstudy.sh:9:    count=`expr $count + 1`					# Increment the counter
ants-2.1.0/Scripts/phantomstudy.sh-10-   echo " count is $count  and file is $x "
##############################################
ants-2.1.0/Scripts/phantomstudy.sh-24-do
ants-2.1.0/Scripts/phantomstudy.sh:25:    count=`expr $count + 1`					# Increment the counter
ants-2.1.0/Scripts/phantomstudy.sh-26-   echo " count is $count  and file is $x "
##############################################
ants-2.1.0/Scripts/registerimages.pl-47-	system $waitcmd;
ants-2.1.0/Scripts/registerimages.pl:48:	$output = `$waitcmd`;
ants-2.1.0/Scripts/registerimages.pl-49-
##############################################
ants-2.1.0/Scripts/sccan_tests-21-params=" -e 0 -n 2 -i 20 -r 0 -p 0  " # most common parameters
ants-2.1.0/Scripts/sccan_tests:22:t1=`${PATHTOSCCAN}/sccan --scca two-view[ ${PATHTODATA}myview1.csv , ${PATHTODATA}myview_mismatch.csv , na , na , 0.5 , 0.5 ] -o ${OUT}.nii.gz $params `
ants-2.1.0/Scripts/sccan_tests-23-test1=$?
ants-2.1.0/Scripts/sccan_tests:24:t2=`${PATHTOSCCAN}/sccan --svd sparse[ ${PATHTODATA}myview3.csv , na , -0.15 ] -o ${OUT}.nii.gz -n 15 -i 500 `
ants-2.1.0/Scripts/sccan_tests-25-# ${PATHTOSCCAN}/sccan --svd  sparse[ ${PATHTODATA}myview3.csv , na , -0.15 ] -o ${OUT}.nii.gz -n 15 -i 500
##############################################
ants-2.1.0/Scripts/sccan_tests-27-paramsb=" -e 0 -n 2 -i 50 -r 0 -p 0  --partial-scca-option PQminusR " # most common parameters
ants-2.1.0/Scripts/sccan_tests:28:t3=`${PATHTOSCCAN}/sccan --scca partial[ ${PATHTODATA}myview2.csv , ${PATHTODATA}myview3.csv , ${PATHTODATA}myview4.csv , na , na , na , -0.4 , -0.9 , 1] -o ${OUT}.nii.gz $paramsb `
ants-2.1.0/Scripts/sccan_tests-29-test3=$?
ants-2.1.0/Scripts/sccan_tests:30:t4=`${PATHTOSCCAN}/sccan --svd sparse[ ${PATHTODATA}myview1.csv , na , 0.5 ] -o ${OUT}.nii.gz `
ants-2.1.0/Scripts/sccan_tests-31-# ${PATHTOSCCAN}/sccan --sparse-svd [ ${PATHTODATA}myview1.csv , na , -1] -o ${OUT}.nii.gz -n 25 -i 1000
##############################################
ants-2.1.0/Scripts/sccan_tests-33-test4=$?
ants-2.1.0/Scripts/sccan_tests:34:t5a=`${PATHTOSCCAN}/sccan --scca partial[ ${PATHTODATA}myview2.csv , ${PATHTODATA}myview3.csv , ${PATHTODATA}myview4.csv , na , na , na , -0.05 , 0.1 , 1] -o ${OUT}.nii.gz $paramsb`
ants-2.1.0/Scripts/sccan_tests:35:t5b=`${PATHTOSCCAN}/sccan --scca partial[ ${PATHTODATA}myview2.csv , ${PATHTODATA}myview3.csv , ${PATHTODATA}myview4.csv , na , na , na , -0.05 ,  0.1 , 1] -o ${OUT}.nii.gz $paramsb`
ants-2.1.0/Scripts/sccan_tests-36-echo $t5a > tempa.txt
##############################################
ants-2.1.0/Scripts/sccan_tests-43-rm tempa.txt tempb.txt
ants-2.1.0/Scripts/sccan_tests:44:t5a=`${PATHTOSCCAN}/sccan --scca partial[ ${PATHTODATA}myview2.csv , ${PATHTODATA}myview3.csv , ${PATHTODATA}myview4.csv , na , na , na ,  0.05 , 0.1 , 1] -o ${OUT}.nii.gz $paramsb`
ants-2.1.0/Scripts/sccan_tests:45:t5b=`${PATHTOSCCAN}/sccan --scca partial[ ${PATHTODATA}myview2.csv , ${PATHTODATA}myview3.csv , ${PATHTODATA}myview4.csv , na , na , na , -0.05 ,  0.1 , 1] -o ${OUT}.nii.gz $paramsb`
ants-2.1.0/Scripts/sccan_tests-46-echo $t5a > tempa.txt
##############################################
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-19-
ants-2.1.0/Scripts/shapeupdatetotemplate.sh:20:Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-21-
##############################################
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-172-    echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/shapeupdatetotemplate.sh:173:    imagelist=(`ls ${outputname}template${whichtemplate}*WarpedToTemplate.nii.gz`)
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-174-    if [[ ${#imagelist[@]} -eq 0  ]] ; then
##############################################
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-180-
ants-2.1.0/Scripts/shapeupdatetotemplate.sh:181:    WARPLIST=( `ls ${outputname}*[0-9]Warp.nii.gz 2> /dev/null` )
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-182-    NWARPS=${#WARPLIST[*]}
##############################################
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-193-          echo " shapeupdatetotemplate---voxel-wise averaging of the inverse warp fields (from subject to template)"
ants-2.1.0/Scripts/shapeupdatetotemplate.sh:194:          echo "   ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`"
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-195-          date
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-196-          echo "--------------------------------------------------------------------------------------"
ants-2.1.0/Scripts/shapeupdatetotemplate.sh:197:          ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`
ants-2.1.0/Scripts/shapeupdatetotemplate.sh-198-
##############################################
ants-2.1.0/Scripts/thickstudy.sh-5-do
ants-2.1.0/Scripts/thickstudy.sh:6:    count=`expr $count + 1`					# Increment the counter
ants-2.1.0/Scripts/thickstudy.sh-7-    echo " $x "
##############################################
ants-2.1.0/Scripts/waitForPBSQJobs.pl-37-
ants-2.1.0/Scripts/waitForPBSQJobs.pl:38:my $qstatOutput = `qstat -u $user`;
ants-2.1.0/Scripts/waitForPBSQJobs.pl-39-
##############################################
ants-2.1.0/Scripts/waitForPBSQJobs.pl-132-    # Use of backticks rather than system permits a ctrl+c to work
ants-2.1.0/Scripts/waitForPBSQJobs.pl:133:    `sleep $delay`;
ants-2.1.0/Scripts/waitForPBSQJobs.pl:134:    $qstatOutput = `qstat -u $user`;
ants-2.1.0/Scripts/waitForPBSQJobs.pl-135-    @qstatLines = split("\n", $qstatOutput);
##############################################
ants-2.1.0/Scripts/waitForSGEQJobs.pl-35-
ants-2.1.0/Scripts/waitForSGEQJobs.pl:36:my $qstatOutput = `qstat -u $user`;
ants-2.1.0/Scripts/waitForSGEQJobs.pl-37-
##############################################
ants-2.1.0/Scripts/waitForSGEQJobs.pl-114-	# Use of backticks rather than system permits a ctrl+c to work
ants-2.1.0/Scripts/waitForSGEQJobs.pl:115:	`sleep $delay`;
ants-2.1.0/Scripts/waitForSGEQJobs.pl:116:	$qstatOutput = `qstat -u $user`;
ants-2.1.0/Scripts/waitForSGEQJobs.pl-117-	@qstatLines = split("\n", $qstatOutput);
##############################################
ants-2.1.0/Scripts/waitForXGridJobs.pl-57-#$statline = 0;
ants-2.1.0/Scripts/waitForXGridJobs.pl:58:#@result = `xgrid $xgridflags -job attributes -id $jobIDs[i]`;
ants-2.1.0/Scripts/waitForXGridJobs.pl-59-#for ($i=0; $i<scalar(@result); $i++) {
##############################################
ants-2.1.0/Scripts/waitForXGridJobs.pl-80-	# Get the status of this ID
ants-2.1.0/Scripts/waitForXGridJobs.pl:81:	@result = `xgrid $xgridflags -job attributes -id $job`;
ants-2.1.0/Scripts/waitForXGridJobs.pl-82-	$statline=0;
##############################################
ants-2.1.0/Scripts/waitForXGridJobs.pl-117-	    print "  ($timestamp) Still waiting for $jobsIncomplete jobs - sleeping $delay\n\n";
ants-2.1.0/Scripts/waitForXGridJobs.pl:118:		`sleep $delay`;
ants-2.1.0/Scripts/waitForXGridJobs.pl-119-	}
##############################################
ants-2.1.0/Scripts/warpimages.pl-44-	system $waitcmd;
ants-2.1.0/Scripts/warpimages.pl:45:	$output = `$waitcmd`;
ants-2.1.0/Scripts/warpimages.pl-46-
##############################################
ants-2.1.0/Scripts/weightedaverage.sh-5-count=9
ants-2.1.0/Scripts/weightedaverage.sh:6:for x in `ls -tr  $1 `
ants-2.1.0/Scripts/weightedaverage.sh-7-do
ants-2.1.0/Scripts/weightedaverage.sh:8:    count=`expr $count + 1`					# Increment the counter
ants-2.1.0/Scripts/weightedaverage.sh-9-   echo " count is $count  and file is $x at it $i "
##############################################
ants-2.1.0/SuperBuild.cmake-14-#-----------------------------------------------------------------------------
ants-2.1.0/SuperBuild.cmake:15:include(${CMAKE_CURRENT_SOURCE_DIR}/Common.cmake)
ants-2.1.0/SuperBuild.cmake-16-
##############################################
ants-2.1.0/antsRegistrationCLP/CMakeLists.txt-2-find_package(SlicerExecutionModel REQUIRED GenerateCLP)
ants-2.1.0/antsRegistrationCLP/CMakeLists.txt:3:include(${GenerateCLP_USE_FILE})
ants-2.1.0/antsRegistrationCLP/CMakeLists.txt-4-
##############################################
ants-2.1.0/.pc/deb_local-data.patch/CMake/ANTSExternalData.cmake-1-get_filename_component(_ITKExternalData_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
ants-2.1.0/.pc/deb_local-data.patch/CMake/ANTSExternalData.cmake:2:include(${_ITKExternalData_DIR}/ExternalData.cmake)
ants-2.1.0/.pc/deb_local-data.patch/CMake/ANTSExternalData.cmake-3-