full path of scripts

Author: Antonios Makropoulos

dhcp-pipeline.sh

@@ -60,8 +60,6 @@ threads=1
 minimal=1
 noreorient=0
 cleanup=1
-codedir=$(dirname "$BASH_SOURCE")
-scriptdir=$codedir/scripts
 
 shift; shift; shift;
 while [ $# -gt 0 ]; do
@@ -85,8 +83,11 @@ done
 [ "$T2" != "-" -a "$T2" != "" ] || { echo "T2 image not provided!" >&2; exit 1; }
 
 # check whether the different tools are set and load parameters
+codedir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 . $codedir/parameters/configuration.sh
 
+scriptdir=$codedir/scripts
+
 roundedAge=`printf "%.*f\n" 0 $age` #round
 [ $roundedAge -lt $template_max_age ] || { roundedAge=$template_max_age; }
 [ $roundedAge -gt $template_min_age ] || { roundedAge=$template_min_age; }

parameters/configuration.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # local directories
-export parameters_dir=$(dirname "$BASH_SOURCE")
+export parameters_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 export code_dir=$parameters_dir/..
 
 # setup path from installation

scripts/misc/pipeline.sh

@@ -51,7 +51,10 @@ age=$2
 
 datadir=`pwd`
 threads=1
-scriptdir=$(dirname "$BASH_SOURCE")
+
+# check whether the different tools are set and load parameters
+codedir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+. $codedir/parameters/configuration.sh
 
 shift; shift
 while [ $# -gt 0 ]; do

scripts/segmentation/pipeline.sh

@@ -28,7 +28,10 @@ age=$3
 
 datadir=`pwd`
 threads=1
-scriptdir=$(dirname "$BASH_SOURCE")
+
+# check whether the different tools are set and load parameters
+codedir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+. $codedir/parameters/configuration.sh
 
 shift; shift; shift
 while [ $# -gt 0 ]; do

scripts/surface/pipeline.sh

@@ -38,7 +38,10 @@ subj=$1
 
 datadir=`pwd`
 threads=1
-scriptdir=$(dirname "$BASH_SOURCE")
+
+# check whether the different tools are set and load parameters
+codedir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+. $codedir/parameters/configuration.sh
 
 shift
 while [ $# -gt 0 ]; do
@@ -97,7 +100,7 @@ fi
 # create files of each hemisphere
 for hi in {0..1}; do
     h=${Hemi[$hi]}
-    runhemisphere $scriptdir/process-surfaces-hemisphere.sh $subj $h $segdir $outvtk $outwb $outtmp &
+    runhemisphere $codedir/process-surfaces-hemisphere.sh $subj $h $segdir $outvtk $outwb $outtmp &
     if [ $threads -eq 1 ];then wait;fi
 done
 if [ $threads -gt 1 ];then wait;fi
@@ -140,7 +143,7 @@ fi
 
 # create myelin map etc.
 if [ -f restore/T1/$subj.nii.gz ];then 
-  run $scriptdir/create-myelin-map.sh $subj
+  run $codedir/create-myelin-map.sh $subj
 
   for STRINGII in MyelinMap@func SmoothedMyelinMap@func; do
     Map=`echo $STRINGII | cut -d "@" -f 1`