What's the purpose of masking / VOI in registration?

Problem: What does the masking option in some of the registration modules accomplish ?
Explanation: The masking option is a very effective tool to focus the registration onto the image content that is most important. It is often the case that the alignment of the two images is more important in some areas than others. Masking provides the opportunity to specify those regions and make the algorithm ignore the image content outside the mask. This does not mean that the rest is not registered, but rather that it moves along passively, i.e. areas outside the mask do not actively contribute to the cost function that determines the quality of the match. Note the mask defines the areas to include, i.e. to exclude a particular region, build a mask that contains the entire object/image except that region.
Note: masking within the registration is different from feeding a masked/stripped image as input, where areas of no interest have been erased. Such masking can still produce valuable results and is a viable option if the module in question does not provide a direct masking option. But direct masking by erasing portions of the image content can produce sharp edges that registration methods can lock onto. If the edge becomes dominant then the resulting registration will be only as good as the accuracy of the masking. That problem does not occur when using masking option within the module.
The following modules provide masking:

Projects:SlicerFAQ:RegistrationMasking