Support for a slightly more flexible use of masks

[azylbertal]

• Added two optional inputs to ants.registration:

  • moving_mask - a mask that applies to the moving image (default: None)
  • mask_all_stages - if True, mask(s) are applied during all stages of registration (eg Affine and SyN). Otherwise (default) they are only applied at the last stage (usually SyN) as was the original behaviour.

• Slightly simplified the code for providing masks (or "NA" if none is provided) as arguments,

[ntustison]

I was away for the weekend and so am just looking at this. We should probably look at porting similar functionality to ANTsR.

[cookpa]

I think this is good to merge. I ran some tests and the command lines look correct with the various options.