Registration example

registration.sh

#!/usr/bin/env bash

fixedfile=$1
movingfile=$2
output=$3

antsRegistration --dimensionality 3 --float 0 --verbose 1 \
                 --output [$output,${output}.nii.gz] \
                 --interpolation LanczosWindowedSinc \
                 --winsorize-image-intensities [0.005,0.995] \
                 --use-histogram-matching 1 \
                 --transform Translation[ 0.075 ] \
                 --metric Mattes[ ${fixedfile},${movingfile},1,32,None ] \
                 --convergence [ 500x500x500x500x500x500,1e-7,10 ] \
                 --shrink-factors 5x5x5x5x4x3 \
                 --smoothing-sigmas 5.078205771322212x4.651927085986457x4.225322606736783x3.798282560433022x3.370641399941647x2.942137020149432mm \
                 --masks [ NOMASK,NOMASK ] \
                 --transform Rigid[ 0.1 ] \
                 --metric Mattes[ ${fixedfile},${movingfile},1,32,None ] \
                 --convergence [ 500x500x500x500x500x500,1e-7,10 ] \
                 --shrink-factors 5x5x4x3x2x1 \
                 --smoothing-sigmas 3.798282560433022x3.370641399941647x2.942137020149432x2.5123277660148595x2.0804050381276458x1.6447045940431997mm \
                 --masks [ NOMASK,NOMASK ]

if [ -f ${output}0GenericAffine.mat ] ; then
    mv ${output}0GenericAffine.mat ${output}.mat
fi