If holes are the main problem, we could move the correct_minor_errors from dipy.nn.utils to segment utils and use that. The function is intended to exactly do that and remove any non connected masks

Thanks @pjsjongsung, we might need to rename this function correct_minor_errors. Hard to guess, it is not very explicit. is this function correcting only this "minor errors" or there are other errors ?

It only corrects for the two mentioned errors: holes and non connected masks. We could change it to something like correct_mask?

We could change it to something like correct_mask?

fill_holes() ?

But it does also remove non connected masks. fill_holes_select_largest sounds too long though.

You could also split it into fill_holes and remove_islands or some such since those don't necessarily need to be paired.

That does sound reasonable. I'll go ahead and do that.

Just realized the current implementation is not separable. Will go with remove_holes_and_islands. I guess the name can be long since it will mostly be an internal function.