Many patients that survive stroke have to face serious functional disabilities for the rest of their lives, which is a personal drama for themselves and their relatives, and an elevated charge for society. Thus, functional recovery after stroke must be a key aspect of the development of new therapeutic approaches. This is the second of a series of two works on which we review the strategies and tools available nowadays for the assessment of multiple aspects related to brain function (both in humans and research animals) and that are helping neuroscientist to better understand the processes of functional restoration and reorganization of the brain, that are triggered following stroke. We have assumed that a multidisciplinary approach is able to provide us with a wider perspective of the underlying mechanisms behind tissue repair, plastic reorganization of the brain and compensatory mechanisms, that can be triggered after stroke. In the second of the works of this series we are focusing in a series of techniques, complementary to the already discussed in the first work, and that are based on MR. These techniques are discussed separately from those ones, because they tackle with aspects not directly related to brain function, although they somehow do in indirect ways, or because they are based on physicochemical or physiological principles different from those discussed on the first work of this series.