mirror_warp_calc.sh

#!/bin/bash
# Calculate the diffeomorphic warp required to map one hemisphere onto the other.
# Requires an initial reflection of images about the midsagittal plane followed by the
# diffeomorphic warping of the reflected to the unreflected image.
#
# This implementation requires both T1 and T2 contrasts for a multivariate optimization.
#
# AUTHOR : Mike Tyszka
# PLACE  : Caltech
# DATES  : 2015-07-30 JMT From scratch
#          2016-03-25 JMT Separate calc and apply components of mirror warp

if [ $# -lt 3 ]
then
  echo "USAGE : mirror_warp_calc.sh <T1> <T2> <Output Directory>"
  exit
fi

T1_orig=$1
T2_orig=$2
out_dir=$3

echo "Original T1w image : ${T1_orig}"
echo "Original T2w image : ${T2_orig}"
echo "Output Directory   : ${out_dir}"

# Create output directory safely
echo "Safely creating output directory"
mkdir -p $out_dir

# Copies of original T1 and T2 in output directory
T1=${out_dir}/T1.nii.gz
T2=${out_dir}/T2.nii.gz

# LR mirrored versions of original images
T1_mirror=${out_dir}/T1_mirror.nii.gz
T2_mirror=${out_dir}/T2_mirror.nii.gz

# Final mirror warped versions of original images
T1_mirror_warp=${out_dir}/T1_mirror_warp.nii.gz
T2_mirror_warp=${out_dir}/T2_mirror_warp.nii.gz

# ANTs output prefix
ANTS_prefix=${out_dir}/Mirror
ANTS_warp=WarpImageMultiTransform
mirror_affine=${ANTS_prefix}Affine.txt
mirror_warp=${ANTS_prefix}Warp.nii.gz

# Bivariate ANTs registration options
ANTS_OPTS="-i 30x90x20 -t SyN[0.25] -r Gauss[3,0] --use-Histogram-Matching --number-of-affine-iterations 10000x10000x1000 --MI-option 32x16000"

# Copy T1 and T2 images into output directory
echo "  Copying original images to output directory"
cp $T1_orig $T1
cp $T2_orig $T2
chmod +w $T1 $T2

# L-R flip master T1 and T2 templates
echo "  Reflecting images about the mid-sagittal plane"
mirror.py -i $T1 -o $T1_mirror
mirror.py -i $T2 -o $T2_mirror

if [ ! -s ${mirror_warp} ]
then

  # Warp L-R flipped T1 and T2 onto their unflipped versions
  echo "  Warping L-R reflected images onto their unreflected versions"
  ${ANTSPATH}/ANTS 3 -m CC[${T1},${T1_mirror},1,5] -m CC[${T2},${T2_mirror},1,5] ${ANTS_OPTS} -o ${ANTS_prefix}

	# Apply mirror warp to L-R flipped T1 and T2
	echo "  Applying mirror warp"
	${ANTSPATH}/WarpImageMultiTransform 3 ${T1_mirror} ${T1_mirror_warp} $mirror_warp $mirror_affine
	${ANTSPATH}/WarpImageMultiTransform 3 ${T2_mirror} ${T2_mirror_warp} $mirror_warp $mirror_affine

else

  echo "  Previous version of warp exists - exiting"

fi