Merge pull request #727 from ANTsX/fixGlob

Fix glob problems by spacing square brackets in ANTs command lines
ANTsX · Mar 4, 2019 · f154285 · f154285
2 parents b40ace7 + 1818057
commit f154285
Show file tree

Hide file tree

Showing 37 changed files with 516 additions and 512 deletions.
diff --git a/Scripts/ANTSpexec.sh b/Scripts/ANTSpexec.sh
@@ -7,7 +7,7 @@ function Usage {
 
 Usage:
 
-`basename $0` [-h] [-r] [-j nb_jobs] command arg_list
+`basename $0` [-h ] [-r ] [-j nb_jobs ] command arg_list
 
 Optional arguments:
 
@@ -40,7 +40,7 @@ Mac (Darwin) and Linux (CentOS 5).
 
 Usage:
 
-`basename $0` [-h] [-r] [-j nb_jobs] command arg_list
+`basename $0` [-h ] [-r ] [-j nb_jobs ] command arg_list
 
 Optional arguments:
 
@@ -85,7 +85,7 @@ function regeneratequeuelinux {
     NUM=0
     for PID in $OLDREQUEUE
     do
-        if [ -d /proc/$PID  ] ; then
+        if [ -d /proc/$PID ] ; then
             QUEUE="$QUEUE $PID"
             NUM=$(($NUM+1))
         fi

diff --git a/Scripts/ants.sh b/Scripts/ants.sh
@@ -3,16 +3,16 @@
 NUMPARAMS=$#
 
 MAXITERATIONS=30x90x20
-if [ ${#ANTSPATH} -le 3 ] ; then
-  echo we guess at your ants path
-  export ANTSPATH=${ANTSPATH:="/ipldev/scratch/aghayoor/ANTS/release/bin"} # EDIT THIS
+if [[ -z ${ANTSPATH} ]] ; then
+  echo "Environment variable ANTSPATH must be defined"
+  exit 1
 fi
-if [ ! -s ${ANTSPATH}/ANTS ] ; then
-  echo we cant find the ANTS program -- does not seem to exist.  please \(re\)define \$ANTSPATH in your environment.
-  exit
+if [[ ! -f "${ANTSPATH}/ANTS" ]] ; then
+  echo "Cannot find the ANTS program. Please \(re\)define \$ANTSPATH in your environment."
+  exit 1
 fi
 
-if [ $NUMPARAMS -lt 3  ]
+if [ $NUMPARAMS -lt 3 ]
 then
 echo " USAGE ::  "
 echo "  sh   ants.sh  ImageDimension  fixed.ext  moving.ext  OPTIONAL-OUTPREFIX   OPTIONAL-max-iterations  OPTIONAL-Labels-In-Fixed-Image-Space-To-Deform-To-Moving-Image     Option-DoANTSQC "
@@ -22,7 +22,7 @@ echo "  J = max iterations at coarsest resolution (here, reduce by power of 2^2)
 echo " K = middle resolution iterations ( here, reduce by power of 2 ) "
 echo " L = fine resolution iterations ( here, full resolution ) -- this level takes much more time per iteration "
 echo " an extra  Ix before JxKxL would add another level "
-echo " Default ierations is  $MAXITERATIONS  -- you can often get away with fewer for many apps "
+echo " Default iterations is $MAXITERATIONS  -- you can often get away with fewer for many apps "
 echo " Other parameters are updates of the defaults used in the A. Klein evaluation paper in Neuroimage, 2009 "
 exit
 fi
@@ -67,36 +67,36 @@ fi
 OUTPUTNAME=` echo $MOVING | cut -d '.' -f 1 `
 
 
-if [ $NUMPARAMS -gt 4  ]
+if [ $NUMPARAMS -gt 4 ]
 then
  MAXITERATIONS=$5
 fi
 
 LABELIMAGE=0
-if [ $NUMPARAMS -gt 5  ]
+if [ $NUMPARAMS -gt 5 ]
 then
  LABELIMAGE=$6
 fi
 
 DoANTSQC=0
-if [ $NUMPARAMS -gt 6  ]
+if [ $NUMPARAMS -gt 6 ]
 then
  DoANTSQC=$7
 fi
 
-if [ $NUMPARAMS -gt 3  ]
+if [ $NUMPARAMS -gt 3 ]
 then
   OUTPUTNAME=${4}
 fi
 
 # Mapping Parameters
-  TRANSFORMATION=SyN[0.25]
+  TRANSFORMATION="SyN[ 0.25 ]"
   ITERATLEVEL=(`echo $MAXITERATIONS | tr 'x' ' '`)
   NUMLEVELS=${#ITERATLEVEL[@]}
   echo $NUMLEVELS
-  REGULARIZATION=Gauss[3,0]
-  METRIC=CC[
-    METRICPARAMS=1,4]
+  REGULARIZATION="Gauss[ 3,0 ]"
+  METRIC="CC[ "
+    METRICPARAMS="1,4 ]"
 # echo " $METRICPARAMS  &  $METRIC "
 # exit
 
@@ -116,7 +116,7 @@ echo " "
 
 
 if [[ ! -s ${OUTPUTNAME}repaired.nii.gz ]] ; then
-${ANTSPATH}/N4BiasFieldCorrection -d $DIM -i $MOVING -o ${OUTPUTNAME}repaired.nii.gz -s 2 -c [50x50x50x50,0.000001] -b [200]
+${ANTSPATH}/N4BiasFieldCorrection -d $DIM -i $MOVING -o ${OUTPUTNAME}repaired.nii.gz -s 2 -c [ 50x50x50x50,0.000001 ] -b [ 200 ]
 # ${ANTSPATH}/N3BiasFieldCorrection $DIM $MOVING   ${OUTPUTNAME}repaired.nii.gz  4
 fi
 exe=" ${ANTSPATH}/ANTS $DIM -m  ${METRIC}${FIXED},${OUTPUTNAME}repaired.nii.gz,${METRICPARAMS}  -t $TRANSFORMATION  -r $REGULARIZATION -o ${OUTPUTNAME}   -i $MAXITERATIONS   --use-Histogram-Matching  --number-of-affine-iterations 10000x10000x10000x10000x10000 --MI-option 32x16000  "

diff --git a/Scripts/antsASLProcessing.sh b/Scripts/antsASLProcessing.sh
@@ -315,7 +315,7 @@ logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
     -n MultiLabel \
     -t ${TRANSFORM_PREFIX}TemplateToSubject0Warp.nii.gz \
     -t ${TRANSFORM_PREFIX}TemplateToSubject1GenericAffine.mat \
-    -t [${OUTNAME}0GenericAffine.mat,1] \
+    -t [ ${OUTNAME}0GenericAffine.mat,1 ] \
     -t ${OUTNAME}1InverseWarp.nii.gz
 
 logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
@@ -331,7 +331,7 @@ logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
   -r ${OUTNAME}AveragePCASL.nii.gz \
   -o ${OUTNAME}SegmentationWarpedToPCASL.nii.gz \
   -n MultiLabel \
-  -t [${OUTNAME}0GenericAffine.mat,1] \
+  -t [ ${OUTNAME}0GenericAffine.mat,1 ] \
   -t ${OUTNAME}1InverseWarp.nii.gz \
 
 if ! $KEEP_TMP_FILES

diff --git a/Scripts/antsAtroposN4.sh b/Scripts/antsAtroposN4.sh
@@ -51,23 +51,23 @@ Optional arguments:
      -n:  max. Atropos iterations               Maximum number of (inner loop) iterations in Atropos.
      -p:  segmentation priors                   Prior probability images initializing the segmentation.
                                                 Specified using c-style formatting, e.g. -p labelsPriors%02d.nii.gz.
-     -r:  mrf                                   Specifies MRF prior (of the form '[weight,neighborhood]', e.g.
-                                                '[0.1,1x1x1]' which is default).
+     -r:  mrf                                   Specifies MRF prior (of the form '[ weight,neighborhood ]', e.g.
+                                                '[ 0.1,1x1x1 ]' which is default).
      -g:  denoise anatomical images             Denoise anatomical images (default = 0).
      -b:  posterior formulation                 Posterior formulation and whether or not to use mixture model proportions.
-                                                e.g 'Socrates[1]' (default) or 'Aristotle[1]'.  Choose the latter if you
+                                                e.g 'Socrates[ 1 ]' (default) or 'Aristotle[ 1 ]'.  Choose the latter if you
                                                 want use the distance priors (see also the -l option for label propagation
                                                 control).
      -l:  label propagation                     Incorporate a distance prior one the posterior formulation.  Should be
-                                                of the form 'label[lambda,boundaryProbability]' where label is a value
+                                                of the form 'label[ lambda,boundaryProbability ]' where label is a value
                                                 of 1,2,3,... denoting label ID.  The label probability for anything
                                                 outside the current label
 
                                                   = boundaryProbability * exp( -lambda * distanceFromBoundary )
 
                                                 Intuitively, smaller lambda values will increase the spatial capture
                                                 range of the distance prior.  To apply to all label values, simply omit
-                                                specifying the label, i.e. -l [lambda,boundaryProbability].
+                                                specifying the label, i.e. -l [ lambda,boundaryProbability ].
      -y:  posterior label for N4 weight mask    Which posterior probability image should be used to define the
                                                 N4 weight mask.  Can also specify multiple posteriors in which
                                                 case the chosen posteriors are combined.
@@ -117,12 +117,12 @@ PARAMETERS
 DEBUG_MODE=0
 
 function logCmd() {
-  cmd="$*"
+  cmd="$@"
   echo "BEGIN >>>>>>>>>>>>>>>>>>>>"
   echo $cmd
 
   exec 5>&1
-  logCmdOutput=$( $cmd | tee >(cat - >&5) )
+  logCmdOutput=$( "$@" | tee >(cat - >&5) )
 
   cmdExit=${PIPESTATUS[0]}
 
@@ -179,15 +179,15 @@ ATROPOS_SEGMENTATION_PRIORS=""
 N4_ATROPOS_NUMBER_OF_ITERATIONS=15
 
 N4=${ANTSPATH}/N4BiasFieldCorrection
-N4_CONVERGENCE="[50x50x50x50,0.0000000001]"
+N4_CONVERGENCE="[ 50x50x50x50,0.0000000001 ]"
 N4_SHRINK_FACTOR=2
-N4_BSPLINE_PARAMS="[200]"
+N4_BSPLINE_PARAMS="[ 200 ]"
 N4_WEIGHT_MASK_POSTERIOR_LABELS=()
 
 ATROPOS=${ANTSPATH}/Atropos
 ATROPOS_SEGMENTATION_PRIOR_WEIGHT=0.0
 ATROPOS_SEGMENTATION_LIKELIHOOD="Gaussian"
-ATROPOS_SEGMENTATION_POSTERIOR_FORMULATION="Socrates[1]"
+ATROPOS_SEGMENTATION_POSTERIOR_FORMULATION="Socrates[ 1 ]"
 ATROPOS_SEGMENTATION_MASK=''
 ATROPOS_SEGMENTATION_NUMBER_OF_ITERATIONS=5
 ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES=3
@@ -277,14 +277,14 @@ fi
 
 if [[ -z "$ATROPOS_SEGMENTATION_MRF" ]];
   then
-    ATROPOS_SEGMENTATION_MRF="[0.1,1x1x1]";
+    ATROPOS_SEGMENTATION_MRF="[ 0.1,1x1x1 ]";
     if [[ DIMENSION -eq 2 ]];
       then
-        ATROPOS_SEGMENTATION_MRF="[0.1,1x1]"
+        ATROPOS_SEGMENTATION_MRF="[ 0.1,1x1 ]"
       fi
   fi
 
-ATROPOS_SEGMENTATION_CONVERGENCE="[${ATROPOS_SEGMENTATION_NUMBER_OF_ITERATIONS},0.0]"
+ATROPOS_SEGMENTATION_CONVERGENCE="[ ${ATROPOS_SEGMENTATION_NUMBER_OF_ITERATIONS},0.0 ]"
 
 ################################################################################
 #
@@ -311,7 +311,7 @@ FORMAT=${FORMAT%%d*}
 
 REPCHARACTER=''
 TOTAL_LENGTH=0
-if [ ${#FORMAT} -eq 2 ]
+if [[ ${#FORMAT} -eq 2 ]]
   then
     REPCHARACTER=${FORMAT:0:1}
     TOTAL_LENGTH=${FORMAT:1:1}
@@ -478,14 +478,14 @@ for (( i = 0; i < ${N4_ATROPOS_NUMBER_OF_ITERATIONS}; i++ ))
         ATROPOS_ANATOMICAL_IMAGES_COMMAND_LINE="${ATROPOS_ANATOMICAL_IMAGES_COMMAND_LINE} -a ${SEGMENTATION_N4_IMAGES[$j]}"
       done
 
-    INITIALIZATION="PriorProbabilityImages[${ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES},${ATROPOS_SEGMENTATION_PRIORS},${ATROPOS_SEGMENTATION_PRIOR_WEIGHT}]"
+    INITIALIZATION="PriorProbabilityImages[ ${ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES},${ATROPOS_SEGMENTATION_PRIORS},${ATROPOS_SEGMENTATION_PRIOR_WEIGHT}]"
     if [[ INITIALIZE_WITH_KMEANS -eq 1 ]];
       then
         if [[ $i -eq 0 ]];
           then
-            INITIALIZATION="kmeans[${ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES}]"
+            INITIALIZATION="kmeans[ ${ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES} ]"
           else
-            INITIALIZATION="PriorProbabilityImages[${ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES},${ATROPOS_SEGMENTATION_POSTERIORS},${ATROPOS_SEGMENTATION_PRIOR_WEIGHT}]"
+            INITIALIZATION="PriorProbabilityImages[ ${ATROPOS_SEGMENTATION_NUMBER_OF_CLASSES},${ATROPOS_SEGMENTATION_POSTERIORS},${ATROPOS_SEGMENTATION_PRIOR_WEIGHT} ]"
           fi
       fi
 
@@ -496,11 +496,11 @@ for (( i = 0; i < ${N4_ATROPOS_NUMBER_OF_ITERATIONS}; i++ ))
       done
 
     exe_segmentation="${ATROPOS} -d ${DIMENSION} -x ${ATROPOS_SEGMENTATION_MASK} -c ${ATROPOS_SEGMENTATION_CONVERGENCE} ${ATROPOS_ANATOMICAL_IMAGES_COMMAND_LINE} ${ATROPOS_LABEL_PROPAGATION_COMMAND_LINE} --verbose 1"
-    exe_segmentation="${exe_segmentation} -i ${INITIALIZATION} -k ${ATROPOS_SEGMENTATION_LIKELIHOOD} -m ${ATROPOS_SEGMENTATION_MRF} -o [${ATROPOS_SEGMENTATION},${ATROPOS_SEGMENTATION_POSTERIORS}] -r ${USE_RANDOM_SEEDING}"
+    exe_segmentation="${exe_segmentation} -i ${INITIALIZATION} -k ${ATROPOS_SEGMENTATION_LIKELIHOOD} -m ${ATROPOS_SEGMENTATION_MRF} -o [ ${ATROPOS_SEGMENTATION},${ATROPOS_SEGMENTATION_POSTERIORS} ] -r ${USE_RANDOM_SEEDING}"
 
     if [[ $i -eq 0 ]];
       then
-        exe_segmentation="${exe_segmentation} -p Socrates[0]"
+        exe_segmentation="${exe_segmentation} -p Socrates[ 0 ]"
       else
         exe_segmentation="${exe_segmentation} -p ${ATROPOS_SEGMENTATION_POSTERIOR_FORMULATION}"
 

diff --git a/Scripts/antsBrainExtraction.sh b/Scripts/antsBrainExtraction.sh
@@ -115,10 +115,10 @@ PARAMETERS
 DEBUG_MODE=0
 
 function logCmd() {
-  cmd="$*"
+  cmd="$@"
   echo "BEGIN >>>>>>>>>>>>>>>>>>>>"
   echo $cmd
-  $cmd
+  ( "$@" )
 
   cmdExit=$?
 
@@ -178,26 +178,26 @@ ATROPOS_CSF_CLASS_LABEL=1
 ATROPOS_GM_CLASS_LABEL=2
 ATROPOS_WM_CLASS_LABEL=3
 
-ATROPOS_BRAIN_EXTRACTION_INITIALIZATION="kmeans[${ATROPOS_NUM_CLASSES}]"
+ATROPOS_BRAIN_EXTRACTION_INITIALIZATION="kmeans[ ${ATROPOS_NUM_CLASSES} ]"
 ATROPOS_BRAIN_EXTRACTION_LIKELIHOOD="Gaussian"
-ATROPOS_BRAIN_EXTRACTION_CONVERGENCE="[3,0.0]"
+ATROPOS_BRAIN_EXTRACTION_CONVERGENCE="[ 3,0.0 ]"
 
 ANTS=${ANTSPATH}/antsRegistration
 ANTS_MAX_ITERATIONS="100x100x70x20"
-ANTS_TRANSFORMATION="SyN[0.1,3,0]"
+ANTS_TRANSFORMATION="SyN[ 0.1,3,0 ]"
 ANTS_LINEAR_METRIC_PARAMS="1,32,Regular,0.25"
-ANTS_LINEAR_CONVERGENCE="[1000x500x250x100,1e-8,10]"
+ANTS_LINEAR_CONVERGENCE="[ 1000x500x250x100,1e-8,10 ]"
 ANTS_METRIC="CC"
 ANTS_METRIC_PARAMS="1,4"
 
 WARP=${ANTSPATH}/antsApplyTransforms
 
 N4=${ANTSPATH}/N4BiasFieldCorrection
-N4_CONVERGENCE_1="[50x50x50x50,0.0000001]"
-N4_CONVERGENCE_2="[50x50x50x50,0.0000001]"
+N4_CONVERGENCE_1="[ 50x50x50x50,0.0000001 ]"
+N4_CONVERGENCE_2="[ 50x50x50x50,0.0000001 ]"
 N4_SHRINK_FACTOR_1=4
 N4_SHRINK_FACTOR_2=2
-N4_BSPLINE_PARAMS="[200]"
+N4_BSPLINE_PARAMS="[ 200 ]"
 
 USE_FLOAT_PRECISION=0
 
@@ -226,18 +226,18 @@ else
           c) #k-means segmentation params
        # Check conventional ANTs vector designation (i.e.,  'x')
        kmeansParamsArr=(${OPTARG//x/ })  
-       if [ ${#kmeansParamsArr[@]} -ne 4 ];
+       if [[ ${#kmeansParamsArr[@]} -ne 4 ]];
          then
            # Check alternative form
            kmeansParamsArr=(${OPTARG//,/ })  
-           if [ ${#kmeansParamsArr[@]} -ne 4 ];
+           if [[ ${#kmeansParamsArr[@]} -ne 4 ]];
              then
                echo "ERROR:  unrecognized kmeans option (-c)."
                exit 1
              fi
          fi
        ATROPOS_NUM_CLASSES=${kmeansParamsArr[0]}
-       ATROPOS_BRAIN_EXTRACTION_INITIALIZATION="kmeans[${ATROPOS_NUM_CLASSES}]"
+       ATROPOS_BRAIN_EXTRACTION_INITIALIZATION="kmeans[ ${ATROPOS_NUM_CLASSES} ]"
        ATROPOS_CSF_CLASS_LABEL=${kmeansParamsArr[1]}
        ATROPOS_GM_CLASS_LABEL=${kmeansParamsArr[2]} 
        ATROPOS_WM_CLASS_LABEL=${kmeansParamsArr[3]}
@@ -277,18 +277,18 @@ else
   done
 fi
 
-ATROPOS_BRAIN_EXTRACTION_MRF="[0.1,1x1x1]"
+ATROPOS_BRAIN_EXTRACTION_MRF="[ 0.1,1x1x1 ]"
 if [[ $DIMENSION -eq 2 ]];
   then
-    ATROPOS_BRAIN_EXTRACTION_MRF="[0.1,1x1]"
+    ATROPOS_BRAIN_EXTRACTION_MRF="[ 0.1,1x1 ]"
   fi
 
 if [[ -z "$ATROPOS_SEGMENTATION_MRF" ]];
   then
-    ATROPOS_SEGMENTATION_MRF="[0.1,1x1x1]";
+    ATROPOS_SEGMENTATION_MRF="[ 0.1,1x1x1 ]";
     if [[ $DIMENSION -eq 2 ]];
       then
-        ATROPOS_SEGMENTATION_MRF="[0.1,1x1]"
+        ATROPOS_SEGMENTATION_MRF="[ 0.1,1x1 ]"
       fi
   fi
 
@@ -329,7 +329,7 @@ if [[ $DEBUG_MODE -gt 0 ]];
    # certain things are hard coded elsewhere, eg number of levels
 
    ANTS_MAX_ITERATIONS="40x40x20x0"
-   ANTS_LINEAR_CONVERGENCE="[100x100x50x10,1e-8,10]"
+   ANTS_LINEAR_CONVERGENCE="[ 100x100x50x10,1e-8,10 ]"
 
    # Leave N4 / Atropos alone because they're pretty fast
 
@@ -462,10 +462,10 @@ if [[ ! -f ${EXTRACTION_MASK} || ! -f ${EXTRACTION_WM} ]];
 
 #             exe_initial_align="${ANTSPATH}/antsAffineInitializer ${DIMENSION} ${EXTRACTION_INITIAL_AFFINE_FIXED} ${EXTRACTION_INITIAL_AFFINE_MOVING} ${EXTRACTION_INITIAL_AFFINE} 15 0.1 0 10"
           exe_initial_align="${ANTSPATH}/antsAI -d ${DIMENSION} -v 1"
-          exe_initial_align="${exe_initial_align} -m Mattes[${EXTRACTION_INITIAL_AFFINE_FIXED},${EXTRACTION_INITIAL_AFFINE_MOVING},32,Regular,0.2]"
-          exe_initial_align="${exe_initial_align} -t Affine[0.1]"
-          exe_initial_align="${exe_initial_align} -s [20,0.12]"
-          exe_initial_align="${exe_initial_align} -g [40,0x40x40]"
+          exe_initial_align="${exe_initial_align} -m Mattes[ ${EXTRACTION_INITIAL_AFFINE_FIXED},${EXTRACTION_INITIAL_AFFINE_MOVING},32,Regular,0.2 ]"
+          exe_initial_align="${exe_initial_align} -t Affine[ 0.1 ]"
+          exe_initial_align="${exe_initial_align} -s [ 20,0.12 ]"
+          exe_initial_align="${exe_initial_align} -g [ 40,0x40x40 ]"
           exe_initial_align="${exe_initial_align} -p 0"
           exe_initial_align="${exe_initial_align} -c 10"
           exe_initial_align="${exe_initial_align} -o ${EXTRACTION_INITIAL_AFFINE}"
@@ -478,14 +478,14 @@ if [[ ! -f ${EXTRACTION_MASK} || ! -f ${EXTRACTION_WM} ]];
 
           logCmd $exe_initial_align
 
-          basecall="${ANTS} -d ${DIMENSION} -u 1 -w [0.025,0.975] -o ${EXTRACTION_WARP_OUTPUT_PREFIX} -r ${EXTRACTION_INITIAL_AFFINE} -z 1 --float ${USE_FLOAT_PRECISION} --verbose 1"
+          basecall="${ANTS} -d ${DIMENSION} -u 1 -w [ 0.025,0.975 ] -o ${EXTRACTION_WARP_OUTPUT_PREFIX} -r ${EXTRACTION_INITIAL_AFFINE} -z 1 --float ${USE_FLOAT_PRECISION} --verbose 1"
           if [[ -f ${EXTRACTION_REGISTRATION_MASK} ]];
             then
-              basecall="${basecall} -x [${EXTRACTION_REGISTRATION_MASK}]"
+              basecall="${basecall} -x [ ${EXTRACTION_REGISTRATION_MASK} ]"
             fi
-          stage1="-m MI[${EXTRACTION_TEMPLATE},${N4_CORRECTED_IMAGES[0]},${ANTS_LINEAR_METRIC_PARAMS}] -c ${ANTS_LINEAR_CONVERGENCE} -t Rigid[0.1] -f 8x4x2x1 -s 4x2x1x0"
-          stage2="-m MI[${EXTRACTION_TEMPLATE},${N4_CORRECTED_IMAGES[0]},${ANTS_LINEAR_METRIC_PARAMS}] -c ${ANTS_LINEAR_CONVERGENCE} -t Affine[0.1] -f 8x4x2x1 -s 4x2x1x0"
-          stage3="-m CC[${EXTRACTION_TEMPLATE},${N4_CORRECTED_IMAGES[0]},0.5,4] -m CC[${EXTRACTION_TEMPLATE_LAPLACIAN},${EXTRACTION_LAPLACIAN},0.5,4] -c [50x10x0,1e-9,15] -t ${ANTS_TRANSFORMATION} -f 4x2x1 -s 2x1x0"
+          stage1="-m MI[ ${EXTRACTION_TEMPLATE},${N4_CORRECTED_IMAGES[0]},${ANTS_LINEAR_METRIC_PARAMS} ] -c ${ANTS_LINEAR_CONVERGENCE} -t Rigid[ 0.1 ] -f 8x4x2x1 -s 4x2x1x0"
+          stage2="-m MI[ ${EXTRACTION_TEMPLATE},${N4_CORRECTED_IMAGES[0]},${ANTS_LINEAR_METRIC_PARAMS} ] -c ${ANTS_LINEAR_CONVERGENCE} -t Affine[ 0.1 ] -f 8x4x2x1 -s 4x2x1x0"
+          stage3="-m CC[ ${EXTRACTION_TEMPLATE},${N4_CORRECTED_IMAGES[0]},0.5,4 ] -m CC[ ${EXTRACTION_TEMPLATE_LAPLACIAN},${EXTRACTION_LAPLACIAN},0.5,4 ] -c [ 50x10x0,1e-9,15 ] -t ${ANTS_TRANSFORMATION} -f 4x2x1 -s 2x1x0"
 
           exe_brain_extraction_1="${basecall} ${stage1} ${stage2} ${stage3}"
 
@@ -513,7 +513,7 @@ if [[ ! -f ${EXTRACTION_MASK} || ! -f ${EXTRACTION_WM} ]];
 
         ## Step 2 ##
 
-        exe_brain_extraction_2="${WARP} -d ${DIMENSION} -i ${EXTRACTION_PRIOR} -o ${EXTRACTION_MASK_PRIOR_WARPED} -r ${ANATOMICAL_IMAGES[0]} -n Gaussian -t [${EXTRACTION_GENERIC_AFFINE},1] -t ${EXTRACTION_INVERSE_WARP} --float ${USE_FLOAT_PRECISION} --verbose 1"
+        exe_brain_extraction_2="${WARP} -d ${DIMENSION} -i ${EXTRACTION_PRIOR} -o ${EXTRACTION_MASK_PRIOR_WARPED} -r ${ANATOMICAL_IMAGES[0]} -n Gaussian -t [ ${EXTRACTION_GENERIC_AFFINE},1 ] -t ${EXTRACTION_INVERSE_WARP} --float ${USE_FLOAT_PRECISION} --verbose 1"
         logCmd $exe_brain_extraction_2
 
         ## superstep 1b ##