Ok, I pitched this problem in a forum where people were discussing using large documentation and code data bases for priming AI for working in slicer, which includes debugging! Claude spotted the bug and fixed it. Interestingly, in my hands GPT 5.2 was suggesting a similar fix with zero documentation priming, but I didn’t completely trust it.
It appears that what was happening is that if the user selected only one mask (either fixed or moving) it didn’t load it and ran with no warning.
A new slicer ants released a couple of days ago with this fixed (see link). You can either replace the suspect .py file in your existing ANTs or install the absolute latest Slicer and then find the new extension from within the GUI
@mikebind is an expert user, so he might add some comments about how well it’s working. The masks seem to change the registration in fairly sensible ways, but I haven’t probed it rigorously.
Things I plan to check:
1.) can different masks be mixed at matched at different stages (confirm at least in the CLI)?
2.) Why was I getting a funny result in the old version when adding a fixed AND moving mask (since this shouldn’t trigger this bug)? Test if this is still happening, i.e., not a separate bug to address.