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

fixed a small bug in parsing

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