To register the proton mask (H1Mask.nii.gz) to the CT mask (CTtMask.nii.gz) run the following command after installing ANTs:
antsRegistrationSyN.sh -d 3 -o H1xCT -f H1Mask.nii.gz -m CtMask.nii.gz -t b
Compare the result (H1xCTWarped.nii.gz) with the correct result (H1xCTWarpedNickResults.nii.gz) to ensure they're the same.
Here's a screenshot of the CT warped mask in the space of the H1 mask.
