Patients, who survive focal brain injury for example stroke, undergo complete or more commonly partial recovery of function. There is a growing interest in designing therapeutic strategies to promote cerebral reorganisation as a way of reducing rather than compensating for impairment. Positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) rely on the assumption that neuronal activity is closely coupled to a local increase in cerebral blood flow (CBF) secondary to an increase in metabolism. Functional MRI comprises different methods, but the studies described in this chapter use blood oxygen level-dependent (BOLD) imaging techniques. The interpretation of functional imaging data from patients with brain lesions will be influenced by the site and extent of lesions. Voxel-based morphometry (VBM) and diffusion tensor imaging (DTI) techniques provide accurate objective anatomical data that can be used to address hypotheses about the structure-function relationships of surviving brain regions.