/usr/lib/ants/landmarkmatch.sh is in ants 1.9.2+svn680.dfsg-4.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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if [ $# -lt 6 ]
then
echo " USAGE \n sh $0 fixed.nii fixedhipp.nii moving.nii movinghipp.nii ITERATIONS LandmarkWeight "
echo " you should set LandmarkWeight yourself --- the intensity weight is 1. so the landmark weight should be in that range (e.g. 0.5 => 1 ) "
echo " the usage indicates .nii but you can use whatever image type you like (as long as itk can read it).
also, the fixedhipp.nii can contain either the full hippocampus or the landmarks for the hippocampus --- this would be your template.
the moving.nii can contain either one as well. if the moving contains the landmarks and the fixed contains the full
hippocampus, then this is known as "partial matching" as in Pluta, et al Hippocampus 2009. "
exit
fi
#ANTSPATH="/mnt/aibs1/avants/bin/ants/"
ITS=$5
LMWT=$6
INTWT=1
FIX=$1
FIXH=$2
MOV=$3
MOVH=$4
OUT=${MOV%.*}
NN=${#OUT}
MM=${#MOV}
let DD=MM-NN
if [ $DD -eq 3 ]
then
OUT=${MOV%.*.*}
fi
OUT2=${FIX%.*}
NN=${#OUT2}
MM=${#FIX}
let DD=MM-NN
if [ $DD -eq 3 ]
then
OUT2=${FIX%.*.*}
fi
dothis=0
if [ $dothis -eq 1 ]
then
# here, we select a subset of the labeled regions
FIXHMOD=${OUT2}locmod.nii.gz
MOVHMOD=${OUT}locmod.nii.gz
for i in $MOVH
do
PRE=$OUT
TOUT=${PRE}locmod.nii.gz
echo " DOING $TOUT "
${ANTSPATH}ThresholdImage 3 $i ${PRE}tempb.nii.gz 30.5 32.5
${ANTSPATH}MultiplyImages 3 $i ${PRE}tempb.nii.gz $TOUT
${ANTSPATH}ThresholdImage 3 $i ${PRE}tempb.nii.gz 20.5 22.5
${ANTSPATH}MultiplyImages 3 $i ${PRE}tempb.nii.gz ${PRE}tempb.nii
${ANTSPATH}ImageMath 3 $TOUT + $TOUT ${PRE}tempb.nii.gz
${ANTSPATH}ThresholdImage 3 $i ${PRE}tempb.nii.gz 8.5 10.5
${ANTSPATH}MultiplyImages 3 $i ${PRE}tempb.nii.gz ${PRE}tempb.nii.gz
${ANTSPATH}ImageMath 3 $TOUT + $TOUT ${PRE}tempb.nii.gz
done
else
FIXHMOD=$FIXH
MOVHMOD=$MOVH
fi
KNN=10
PERCENTtoUSE=0.5
PARZSIG=10
LM=PSE[${FIX},${MOV},${FIXHMOD},${MOVHMOD},${LMWT},${PERCENTtoUSE},${PARZSIG},0,${KNN}]
echo $LM
if [ $# -gt 6 ]
then
OUT=$7
fi
STEPL=0.25
INTENSITY=PR[$FIX,${MOV},${INTWT},4]
if [ $LMWT -le 0 ]
then
exe="${ANTSPATH}ANTS 3 -o $OUT -i $ITS -t SyN[${STEPL}] -r Gauss[3,0] -m $INTENSITY "
else
exe="${ANTSPATH}ANTS 3 -o $OUT -i $ITS -t SyN[${STEPL}] -r Gauss[3,0] -m $LM -m $INTENSITY "
fi
echo " $exe "
$exe
${ANTSPATH}WarpImageMultiTransform 3 $MOV ${OUT}deformed.nii.gz ${OUT}Warp.nii.gz ${OUT}Affine.txt -R $FIX
${ANTSPATH}WarpImageMultiTransform 3 $MOVH ${OUT}label.nii.gz ${OUT}Warp.nii.gz ${OUT}Affine.txt -R $FIX --use-NN
${ANTSPATH}WarpImageMultiTransform 3 $FIXH ${OUT}labelinv.nii.gz -i ${OUT}Affine.txt ${OUT}InverseWarp.nii.gz -R $MOV --use-NN
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