adding affine registration

[camilolaiton]

Hello @yonibrowning, @galenlynch,

I have included the following changes to the registration process:

1. Optional moving mask, this will be used once we have a good ventricle segmentation network.
2. Affine registration step. We were computing the rigid and then relying on the deformable to do the scaling and shearing which is not great.
3. I included more iterations in the multi-resolution deformable registration. This means that we increase the compute time (it is about 20 mins increase).

[yonibrowning]

Looks good to me!