ENH: Fix output dir logic in scripts, check dim in template construction

CONTRIBUTING.md

@@ -14,7 +14,7 @@ Once your code compiles without error and runs satisfactorily, you can open a pu
 
 ### 3. Open a pull request
 
-All contributions must be made via pull request on a fork of the ANTs repository. The developers will review and give feedback. 
+All contributions must be made via pull request on a fork of the ANTs repository. The developers will review and give feedback.
 
 Write your commit messages using the standard prefixes for ITK commit messages:
 
@@ -31,4 +31,4 @@ A Github continuous integration test will be run on the PR, confirming that it c
 
 ### Licensing of contributions
 
-All accepted contributions will be incorporated into the ANTs source code and distributed according to the terms of the ANTs license. 
+All accepted contributions will be incorporated into the ANTs source code and distributed according to the terms of the ANTs license.

Scripts/antsBrainExtraction.sh

@@ -339,7 +339,13 @@ for (( i = 0; i < ${#ANATOMICAL_IMAGES[@]}; i++ ))
     fi
   done
 
-OUTPUT_DIR=${OUTPUT_PREFIX%\/*}
+if [[ ${OUTPUT_PREFIX} == */ ]];
+  then
+    OUTPUT_DIR=${OUTPUT_PREFIX%/}
+  else
+    OUTPUT_DIR=$(dirname $OUTPUT_PREFIX)
+  fi
+
 if [[ ! -d $OUTPUT_DIR ]];
   then
     echo "The output directory \"$OUTPUT_DIR\" does not exist. Making it."

Scripts/antsCorticalThickness.sh

@@ -9,7 +9,7 @@ SCRIPTS_DEPENDENCIES=( 'antsBrainExtraction.sh' 'antsAtroposN4.sh' )
 
 for D in ${PROGRAM_DEPENDENCIES[@]};
   do
-    if ! command -v ${D} &> /dev/null 
+    if ! command -v ${D} &> /dev/null
       then
         echo "Error:  we can't find the $D program."
         echo "Perhaps you need to \(re\)define \$PATH in your environment."
@@ -19,7 +19,7 @@ for D in ${PROGRAM_DEPENDENCIES[@]};
 
 for D in ${SCRIPT_DEPENDENCIES[@]};
   do
-    if ! command -v ${D} &> /dev/null 
+    if ! command -v ${D} &> /dev/null
       then
         echo "We can't find the $D script."
         echo "Perhaps you need to \(re\)define \$PATH in your environment."
@@ -703,7 +703,13 @@ if [[ $DO_REGISTRATION_TO_TEMPLATE -eq 1 ]];
       fi
   fi
 
-OUTPUT_DIR=${OUTPUT_PREFIX%\/*}
+if [[ ${OUTPUT_PREFIX} == */ ]];
+  then
+    OUTPUT_DIR=${OUTPUT_PREFIX%/}
+  else
+    OUTPUT_DIR=$(dirname $OUTPUT_PREFIX)
+  fi
+
 if [[ ! -d $OUTPUT_DIR ]];
   then
     echo "The output directory \"$OUTPUT_DIR\" does not exist. Making it."

Scripts/antsIntermodalityIntrasubject.sh

@@ -222,7 +222,13 @@ if [[ ${#ANATOMICAL_SPACE} -lt 1 ]];
     ANATOMICAL_SPACE=$ANATOMICAL_BRAIN
   fi
 
-OUTPUT_DIR=${OUTPUT_PREFIX%\/*}
+if [[ ${OUTPUT_PREFIX} == */ ]];
+  then
+    OUTPUT_DIR=${OUTPUT_PREFIX%/}
+  else
+    OUTPUT_DIR=$(dirname $OUTPUT_PREFIX)
+  fi
+
 if [[ ! -d $OUTPUT_DIR ]];
   then
     echo "The output directory \"$OUTPUT_DIR\" does not exist. Making it."

Scripts/antsJointLabelFusion.sh

@@ -193,7 +193,7 @@ Compulsory arguments (minimal command line requires SGE cluster, otherwise use -
      -l:  Labels:         Labels corresponding to atlas (cf -g).
 
 Optional arguments:
-  
+
      -m:  Majority vote:  Use majority vote instead of joint label fusion (default = ${MAJORITYVOTE}).
 
      -k:  Keep files:     Keep warped atlas and label files (default = ${KEEP_ALL_IMAGES}).
@@ -492,7 +492,19 @@ if [[ ${PRECISION} -eq 0 ]];
     PRECISIONFLAG='d'
   fi
 
-mkdir ${OUTPUT_DIR}
+if [[ ${OUTPUT_PREFIX} == */ ]];
+  then
+    OUTPUT_DIR=${OUTPUT_PREFIX%/}
+  else
+    OUTPUT_DIR=$(dirname $OUTPUT_PREFIX)
+  fi
+
+if [[ ! -d $OUTPUT_DIR ]];
+  then
+    echo "The output directory \"$OUTPUT_DIR\" does not exist. Making it."
+    mkdir -p $OUTPUT_DIR
+  fi
+
 
 ##########################################################################
 #

Scripts/antsLongitudinalCorticalThickness.sh

@@ -614,7 +614,13 @@ if [[ $DO_REGISTRATION_TO_TEMPLATE -eq 1 ]];
       fi
   fi
 
-OUTPUT_DIR=${OUTPUT_PREFIX%\/*}
+if [[ ${OUTPUT_PREFIX} == */ ]];
+  then
+    OUTPUT_DIR=${OUTPUT_PREFIX%/}
+  else
+    OUTPUT_DIR=$(dirname $OUTPUT_PREFIX)
+  fi
+
 if [[ ! -d $OUTPUT_DIR ]];
   then
     echo "The output directory \"$OUTPUT_DIR\" does not exist. Making it."

Scripts/antsLongitudinalJointLabelFusion.sh

@@ -484,7 +484,18 @@ if [[ ${PRECISION} -eq 0 ]];
     PRECISIONFLAG='d'
   fi
 
-mkdir ${OUTPUT_DIR}
+if [[ ${OUTPUT_PREFIX} == */ ]];
+  then
+    OUTPUT_DIR=${OUTPUT_PREFIX%/}
+  else
+    OUTPUT_DIR=$(dirname $OUTPUT_PREFIX)
+  fi
+
+if [[ ! -d $OUTPUT_DIR ]];
+  then
+    echo "The output directory \"$OUTPUT_DIR\" does not exist. Making it."
+    mkdir -p $OUTPUT_DIR
+  fi
 
 ##########################################################################
 #

Scripts/antsMultivariateTemplateConstruction.sh

@@ -600,7 +600,19 @@ elif [[ $nargs -lt 6 ]]
     Usage >&2
 fi
 
-OUTPUT_DIR=`dirname ${OUTPUTNAME}`
+if [[ -z ${DIM} ]]
+  then
+    echo "Image dimension (-d) is required"
+    exit 1
+  fi
+
+if [[ ${OUTPUTNAME} == */ ]];
+  then
+    OUTPUT_DIR=${OUTPUTNAME%/}
+  else
+    OUTPUT_DIR=$(dirname $OUTPUTNAME)
+  fi
+
 if [[ ! -d $OUTPUT_DIR ]];
   then
     echo "The output directory \"$OUTPUT_DIR\" does not exist. Making it."

Scripts/antsMultivariateTemplateConstruction2.sh

@@ -699,7 +699,18 @@ elif [[ $nargs -lt 6 ]]
     Usage >&2
 fi
 
-OUTPUT_DIR=`dirname ${OUTPUTNAME}`
+if [[ -z ${DIM} ]]
+  then
+    echo "Image dimension (-d) is required"
+    exit 1
+  fi
+
+if [[ ${OUTPUTNAME} == */ ]];
+  then
+    OUTPUT_DIR=${OUTPUTNAME%/}
+  else
+    OUTPUT_DIR=$(dirname $OUTPUTNAME)
+  fi
 
 if [[ ! -d $OUTPUT_DIR ]];
   then