WIP: Couple more fixes. antsLongitudinalCorticalThickness.sh working

Scripts/antsIntroduction.sh

@@ -444,8 +444,8 @@ then
 # Mapping Parameters for the LDDMM style SyN --- the params are SyN[ GradientStepLength,NTimeDiscretizationPoints,IntegrationTimeStep]
 # increasing IntegrationTimeStep increases accuracy in the diffeomorphism integration and takes more computation time.
 # NTimeDiscretizationPoints is set to 2 here
-TRANSFORMATION=SyN[ 1,2,0.05]
-REGULARIZATION=Gauss[ 3,0.]
+TRANSFORMATION="SyN[ 1,2,0.05 ]"
+REGULARIZATION="Gauss[ 3,0. ]"
 
 elif [ "${TRANSFORMATIONTYPE}" == "SY" ]
 then
@@ -454,7 +454,7 @@ then
 # NTimeDiscretizationPoints is the number of spatial indices in the time dimension (the 4th dim when doing 3D registration)
 # increasing NTimeDiscretizationPoints increases flexibility and takes more computation time.
 # the --geodesic option enables either 1 asymmetric gradient estimation or 2 symmetric gradient estimation (the default here )
-TRANSFORMATION=" SyN[1,2,0.05 ] --geodesic 2 "
+TRANSFORMATION=" SyN[ 1,2,0.05 ] --geodesic 2 "
 REGULARIZATION="Gauss[ 3,0. ]"
 
 elif [ "${TRANSFORMATIONTYPE}" == "LDDMM" ]

Scripts/buildtemplateparallel.sh

@@ -29,7 +29,7 @@ SETPATH
 # export ANTSPATH=${ANTSPATH:="$HOME/bin/ants/"} # EDIT THIS
 
 #ANTSPATH=YOURANTSPATH
-if [  ${#ANTSPATH} -le 3 ]
+if [ ${#ANTSPATH} -le 3 ]
     then
     setPath >&2
 fi
@@ -568,7 +568,7 @@ function ANTSAverage3DAffine {
 function jobfnamepadding {
 
     files=`ls job*.sh`
-    BASENAME1=`echo $files[1 ] | cut -d 'b' -f 1`
+    BASENAME1=`echo $files[1] | cut -d 'b' -f 1`
 
     for file in ${files}
       do
@@ -759,7 +759,7 @@ fi
 
 if [[ $DOQSUB -eq 1 || $DOQSUB -eq 4 ]] ; then
   qq=`which  qsub`
-  if [  ${#qq} -lt 1 ] ; then
+  if [ ${#qq} -lt 1 ] ; then
     echo do you have qsub?  if not, then choose another c option ... if so, then check where the qsub alias points ...
     exit
   fi