Stroke survivors improve their motor functions through two main mechanisms: reduction of the impairments and development of compensatory strategies. To disentangle these mechanisms and to tailor assistance to individual needs, detailed descriptions of the patients are crucial. Here we describe an experimental apparatus that includes a set of inertial measurement units (IMUs) and a planar manipulandum, to be used as assessment and rehabilitation tool. We propose a pipeline for generating personalized musculoskeletal models to reconstruct whole-body movements, with the specific aim of distinguishing between compensation and true recovery for tailored rehabilitation interventions.