Commit 93778863 authored by Saad Jbabdi's avatar Saad Jbabdi
Browse files

fixed a small bug in parsing

parent f802968e
...@@ -13,7 +13,10 @@ ...@@ -13,7 +13,10 @@
#export LD_LIBRARY_PATH #export LD_LIBRARY_PATH
ptxbin_gpu=$FSLDIR/bin/probtrackx2_gpu ptxbin_gpu=$FSLDIR/bin/probtrackx2_gpu
# Location of xtract data
datadir=$FSLDIR/etc/xtract_data
# tmp dir for testing
datadir=/vols/Scratch/saad/xtract_data
Usage() { Usage() {
cat << EOF cat << EOF
...@@ -68,7 +71,7 @@ while [ ! -z "$1" ];do ...@@ -68,7 +71,7 @@ while [ ! -z "$1" ];do
-out) out=$2;shift;; -out) out=$2;shift;;
-str) str=$2;shift;; -str) str=$2;shift;;
-p) p=$2;shift;; -p) p=$2;shift;;
-species) spec={$2^^};shift;; # converts to uppercase -species) spec=$2;shift;; # converts to uppercase
-stdwarp) std2diff=$2;diff2std=$3;shift;shift;; -stdwarp) std2diff=$2;diff2std=$3;shift;shift;;
-gpu) gpu=1;; -gpu) gpu=1;;
-native) nat=1;; -native) nat=1;;
...@@ -91,6 +94,7 @@ if [ "$std2diff" == "" ];then ...@@ -91,6 +94,7 @@ if [ "$std2diff" == "" ];then
fi fi
fi fi
echo SPECIES $spec
# GPU stuff # GPU stuff
...@@ -116,7 +120,7 @@ if [ "$out" == "" ];then ...@@ -116,7 +120,7 @@ if [ "$out" == "" ];then
errflag=1 errflag=1
fi fi
if [ "$xspec" == "" ];then if [ "$spec" == "" ];then
if [ "$str" == "" ];then if [ "$str" == "" ];then
echo "Must set compulsory argument '-str'" echo "Must set compulsory argument '-str'"
errflag=1 errflag=1
...@@ -133,11 +137,11 @@ if [ "$xspec" == "" ];then ...@@ -133,11 +137,11 @@ if [ "$xspec" == "" ];then
fi fi
else else
if [ "$spec" == "HUMAN" ];then if [ "$spec" == "HUMAN" ];then
p=$FSLDIR/etc/fsl_autoPtx/protocols/Human p=$datadir/Human
str=$FSLDIR/etc/fsl_autoPtx/protocols/structList str=$p/structureList
elif [ "$spec" == "MACAQUE" ];then elif [ "$spec" == "MACAQUE" ];then
p=$FSLDIR/etc/fsl_autoPtx/protocols/Macaque p=$datadir/Macaque
str=$FSLDIR/etc/fsl_autoPtx/protocols/structList str=$p/structureList
else else
echo "Species must be one of HUMAN or MACAQUE" echo "Species must be one of HUMAN or MACAQUE"
errflag=1 errflag=1
......
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