Glad you are pleased with the results. The amount of time it takes is subject to quite a few factors, and you may be able to reduce it. See, for example, https://github.com/HolyLab/RegisterQD.jl/issues/21#issuecomment-537295913.
You can use JLD, JLD2, or Julia’s own serializer to save the transformation arrays. Or you can convert them to affine transformations and just store the matrices using CSV, HDF5, MAT, or some other format.