abi2dsurqec_40micron.sh

#!/bin/sh

#Resize to same size as dsurqec atlases
ResampleImage 3 abi_10micron_average.nii abi_15micron_average.nii 0.015x0.015x0.015 size=1 spacing=0 4
fslorient -copyqform2sform abi_15micron_average.nii
ResampleImage 3 abi_10micron_average.nii abi_40micron_average.nii 0.04x0.04x0.04 size=1 spacing=0 4
fslorient -copyqform2sform abi_40micron_average.nii
ResampleImage 3 abi_10micron_average.nii abi_200micron_average.nii 0.2x0.2x0.2 size=1 spacing=0 4
fslorient -copyqform2sform abi_200micron_average.nii

#Correct resamoling of the annotation files: Use antsAppyTransform with Identity matrix. Multilabel interpolation can be used which is not possible in ResampleImage
antsApplyTransforms -d 3 -e 0 -i abi_10micron_annotation.nii -r abi_15micron_average.nii -o abi_15micron_annotation.nii -n MultiLabel -t Identity
fslorient -copyqform2sform abi_15micron_annotation.nii
antsApplyTransforms -d 3 -e 0 -i abi_10micron_annotation.nii -r abi_40micron_average.nii -o abi_40micron_annotation.nii -n MultiLabel -t Identity
fslorient -copyqform2sform abi_40micron_annotation.nii

# Registration call
antsRegistration \
	--float 1 \
	--collapse-output-transforms 1 \
	--dimensionality 3 \
	--initial-moving-transform [dsurqec_40micron_masked.nii,abi_40micron_average.nii, 1 ] \
	--initialize-transforms-per-stage 0 --interpolation Linear --output [ abi2dsurqec_, abi2dsurqec_40micron_masked.nii ] \
	--interpolation Linear \
	\
	--transform Rigid[ 0.5 ] \
	--metric MI[dsurqec_40micron_masked.nii,abi_40micron_average.nii, 1, 64, Random, 0.3 ] \
	--convergence [ 400x400x400x200, 1e-9, 10 ] \
	--smoothing-sigmas 3.0x2.0x1.0x0.0vox \
	--shrink-factors 10x4x2x1 \
	--use-estimate-learning-rate-once 0 \
	--use-histogram-matching 1 \
	\
	--transform Affine[ 0.1 ] \
	--metric MI[dsurqec_40micron_masked.nii,abi_40micron_average.nii, 1, 64, Regular, 0.3 ] \
	--convergence [ 400x200, 1e-10, 10 ] \
	--smoothing-sigmas 1.0x0.0vox \
	--shrink-factors 2x1 \
	--use-estimate-learning-rate-once 0 \
	--use-histogram-matching 1 \
	\
	--transform SyN[0.1,3,0] \
	--metric CC[dsurqec_40micron_masked.nii,abi_40micron_average.nii,1,4] \
	--convergence [100x70x50x20,1e-6,10] \
	--shrink-factors 8x4x2x1 \
	--smoothing-sigmas 3x2x1x0vox \
	\
	--winsorize-image-intensities [ 0.05, 0.95 ] \
	--write-composite-transform 1 \
	--verbose

fslorient -copyqform2sform abi2dsurqec_40micron_masked.nii

#Use the composite to transform annotation file

antsApplyTransforms -d 3 -i abi_10micron_annotation.nii -r dsurqec_40micron_masked.nii -o abi2dsurqec_40_annotation.nii -t abi2dsurqec_Composite.h5 -n MultiLabel
fslorient -copyqform2sform abi2dsurqec_40_annotation.nii

# Cleanup

rm abi2dsurqec_InverseComposite.h5