oesteban
commented
1 year ago @effigies - this requires nitransforms to open ITK's h5 files with only affines (it did before with nonlinear, not with just affines). So, if time permits, it would be nice to make sure nipy/nitransforms#174 gets through with a sound implementation. After so much time without working on nitransforms, your feedback will definitely be critical to ensure I don't merge a half-baked thing.
This PR modifies the code to follow more closely (Mortamet et al., 2009). Now, the "hat" mask cuts through the through-plane axis (Z), which is more theoretically sound than the previous solution.
cc/ @eilidhmacnicol because this will need some translation to rodents