automatic_registration_US_to_MRI.sh

#!/bin/sh

# Input arguments

case_num=${1-"1"}
image_folder=${2:-"bucket/RESECT/RESECT/NIFTI/Case${case_num}"}
us_image=${3:-"US/Case${case_num}-US-before.nii.gz"}
mri_image=${4:-"MRI/Case${case_num}-FLAIR.nii.gz"}
tag_file=${5:-"Landmarks/Case${case_num}-MRI-beforeUS.tag"}

# Create directory to store the outputs
mkdir -p $image_folder/output

# Resample images into a common reference frame and isotropic voxel size of 0.5x0.5x0.5 mm
c3d $image_folder/$us_image $image_folder/$mri_image -reslice-identity -resample-mm 0.5x0.5x0.5mm \
-o $image_folder/output/Case${case_num}-MRI_in_US.nii.gz

c3d $image_folder/$us_image -resample-mm 0.5x0.5x0.5mm -o $image_folder/output/Case${case_num}-US.nii.gz

# Apply linear rigid pre-registration
./linearBCV -F $image_folder/output/Case${case_num}-MRI_in_US.nii.gz -M $image_folder/output/Case${case_num}-US.nii.gz \
-R 1 -O $image_folder/output/affine${case_num}

# Generate 2 text files containing landmarks
python3 ./landmarks_split_txt.py --inputtag $image_folder/$tag_file --savetxt $image_folder/output/Case${case_num}_lm

# Generate landmark segmentations as a NIFTI file
c3d $image_folder/output/Case${case_num}-MRI_in_US.nii.gz -scale 0 \
-landmarks-to-spheres $image_folder/output/Case${case_num}_lm_mri.txt 1 \
-o $image_folder/output/Case${case_num}-MRI-landmarks.nii.gz

c3d $image_folder/output/Case${case_num}-US.nii.gz -scale 0 \
-landmarks-to-spheres $image_folder/output/Case${case_num}_lm_us.txt 1 \
-o $image_folder/output/Case${case_num}-US-landmarks.nii.gz

# Perform non linear registration
./deedsBCV -F $image_folder/output/Case${case_num}-MRI_in_US.nii.gz -M $image_folder/output/Case${case_num}-US.nii.gz \
-O $image_folder/output/Case${case_num}-deeds -S $image_folder/output/Case${case_num}-US-landmarks.nii.gz -A $image_folder/output/affine${case_num}_matrix.txt

# Calculate mTRE
python3 ./landmarks_centre_mass.py --inputnii $image_folder/output/Case${case_num}-MRI-landmarks.nii.gz \
--movingnii $image_folder/output/Case${case_num}-deeds_deformed_seg.nii.gz --savetxt $image_folder/output/Case${case_num}-results