commandSyN.sh

#! /bin/sh

baseDirectory=${PWD}

fixedImage=${baseDirectory}/Data/nap_rest_deobl_desp_volreg_1.nii.gz
movingImage=${baseDirectory}/Data/anat_skullstripBrainExtractionBrain.nii.gz
maskImage=${baseDirectory}/fixedMask.nii.gz

# make mask of slab image

ThresholdImage 3 ${fixedImage} ${maskImage} 1100 Inf

# Register T1 to EPI slab with mask
outputPrefix=${baseDirectory}/epiSlabxT1

antsRegistration --verbose 1 \
                 --dimensionality 3 \
                 --float 0 \
                 --interpolation Linear \
                 --use-histogram-matching 0 \
                 --winsorize-image-intensities [0.005,0.995] \
                 --output [${outputPrefix},${outputPrefix}Warped.nii.gz,${outputPrefix}InverseWarped.nii.gz] \
                 --initial-moving-transform [${fixedImage},${movingImage},1] \
                 --transform translation[0.1] \
                   --metric MI[${fixedImage},${movingImage},1,32,Random,0.25] \
                   --convergence [50,1e-6,10] \
                   --shrink-factors 1 \
                   --smoothing-sigmas 0vox \
                   --masks [${maskImage},NULL] \
                 --transform Rigid[0.1] \
                   --metric MI[${fixedImage},${movingImage},1,32,Random,0.25] \
                   --convergence [500x250x50,1e-6,10] \
                   --shrink-factors 2x2x1 \
                   --smoothing-sigmas 2x1x0vox \
                   --masks [${maskImage},NULL] \
                 --transform SyN[0.1,3,0] \
                   --metric MI[${fixedImage},${movingImage},1,32] \
                   --convergence [50x10,1e-6,10] \
                   --shrink-factors 2x1 \
                   --smoothing-sigmas 1x0vox \
                   --masks [${maskImage},NULL]