As has been discussed on the ANTs issue tracker https://github.com/ANTsX/ANTs/issues/543, the existing heuristics for the MI overlap are not very good.
Right now, its based on a ratio of points at https://github.com/hinerm/ITK/blob/master/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.hxx#L218
This really a good heuristic as it makes the success/failure depend on things like having an uncropped image with lots of background (where the background is unimportant). It also causes failures where you want to use a mask to do some finer adjustments to an affine registration to match specific anatomy, but the mask is “too small” according to the fraction.
The idea as a replacement is something based on the size/number of samples for the joint histogram.
I’d like to open this up for discussion as to how to implement.