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#!/bin/bash
if [ $# -lt 7 ]
then
echo " USAGE \n sh command.sh fixed.nii fixedhipp.nii moving.nii movinghipp.nii outputname iterations DIM "
echo " the template = fixed.nii , the individual = moving.nii "
echo " iterations should be of the form 100x100x10 "
exit
fi
if ! command -v ANTS &> /dev/null
then
echo we cant find the ANTS program -- does not seem to exist. please \(re\)define \$PATH in your environment.
exit
fi
FIX=$1
FIXH=$2
MOV=$3
MOVH=$4
OUT=$5
ITS=$6
DIM=$7
if [ ${#FIX} -lt 1 -o ! -f $FIX ]
then
echo " Problem with specified Fixed Image => User Specified Value = $FIX "
exit
fi
if [ ${#MOV} -lt 1 -o ! -f $MOV ]
then
echo " Problem with specified Moving Image => User Specified Value = $MOV "
exit
fi
if [ ${#FIXH} -lt 1 -o ! -f $FIXH ]
then
echo " Problem with specified Fixed Label Image => User Specified Value = $FIXH "
exit
fi
if [ ${#MOVH} -lt 1 -o ! -f $MOVH ]
then
echo " Problem with specified Moving Label Image => User Specified Value = $MOVH "
exit
fi
# == Important Parameters Begin ==
LMWT=$9 # weight on landmarks
INTWT=$8 # weight on intensity -- twice the landmarks
# PSE/point-set-expectation/PointSetExpectation[fixedImage,movingImage,fixedPoints,movingPoints,weight,pointSetPercentage,pointSetSigma,boundaryPointsOnly,kNeighborhood, PartialMatchingIterations=100000]
# the partial matching option assumes the complete labeling is in the first set of label parameters ...
# more iterations leads to more symmetry in the matching - 0 iterations means full asymmetry
PCT=0.1 # percent of labeled voxels to use
PARZ=100 # PARZEN sigma
LM=PSE[ ${FIX},${MOV},$FIXH,$MOVH,${LMWT},${PCT},${PARZ},0,25,100]
INTENSITY=CC[ $FIX,${MOV},${INTWT},4]
# == Important Parameters end? ==
ANTS $DIM -o $OUT -i $ITS -t SyN[ 0.25 ] -r Gauss[ 3,0 ] -m $INTENSITY -m $LM
WarpImageMultiTransform $DIM $MOV ${OUT}toTemplate.nii.gz ${OUT}Warp.nii.gz ${OUT}Affine.txt -R $FIX
WarpImageMultiTransform $DIM $FIX ${OUT}toMov.nii.gz -i ${OUT}Affine.txt ${OUT}InverseWarp.nii.gz -R $MOV
WarpImageMultiTransform $DIM $FIXH ${OUT}hipp.nii.gz -i ${OUT}Affine.txt ${OUT}InverseWarp.nii.gz -R $MOV --UseNN
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