Commit 363101ee authored by Shaun Warrington's avatar Shaun Warrington
Browse files

Updated default xtract_data path

parent adb812bf
......@@ -9,14 +9,14 @@ if [ "$2" == "" ];then
echo ""
echo " <brain> : FA or T1 image or similar contrast"
echo " <outputBase> : Prefix for output image and warps"
echo " [F99Dir] : Default is $FSLDIR/etc/xtract_data/standard/F99"
echo " [F99Dir] : Default is $FSLDIR/data/xtract_data/standard/F99"
echo ""
exit 1
fi
f99dir=$3
if [ "$atl" == "" ];then
f99dir=$FSLDIR/etc/xtract_data/standard/F99
f99dir=$FSLDIR/data/xtract_data/standard/F99
fi
# Parse args
......@@ -26,12 +26,12 @@ conf=$f99dir/config
out=$2
# REGISTRATION TO F99 ATLAS
# REGISTRATION TO F99 ATLAS
echo ""
echo " ---> Remove Bias Field"
fast -n 1 -b -B -l 10 -o ${out}_struct_brain $anat
fast -n 1 -b -B -l 10 -o ${out}_struct_brain $anat
echo ""
echo " ---> Initial affine registration"
......
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