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- #! /bin/bash
- if [ $# -eq 3 ];then
- src=$1
- trg=$2
- outp=$3
- elif [ $# -eq 5 ];then
- src=$1
- trg=$2
- src_mask=$3
- trg_mask=$4
- outp=$5
- else
- echo "Usage $0 <source> <target> [source mask] [target mask] <output_prefix>"
- echo "Output will be <output_prefix>0_NL.xfm and <output_prefix>0NL_inverse.xfm with corresponding grid files"
- exit 1
- fi
- if [ ! -z $trg_mask ];then
- mask="-x [${src_mask},${trg_mask}] "
- fi
- antsRegistration -v -d 3 --float 1 \
- --output "[${outp}]" \
- --use-histogram-matching 0 --winsorize-image-intensities "[0.005,0.995]" \
- --transform "SyN[0.7,3,0]" \
- --metric "CC[${src},${trg},1,4]" \
- --convergence "[50x50x30,1e-6,10]" \
- --shrink-factors 4x2x1 --smoothing-sigmas 2x1x0vox \
- ${mask} --minc
|
