I am currently working on a project of within subject registration of T1 and T2 images on human brains, and I want to add a brain mask to the registration. Does ITK have a class for automated brain extraction? Any suggestions? Thanks!
You may want to look into the Skull Stripping remote module:
You can give this filter a try in 3D Slicer (it comes with a GUI, so you don’t need to do any scripting or compilation): https://www.slicer.org/wiki/Documentation/Nightly/Modules/SwissSkullStripper