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This paper explores patient-centered design (PCD) as a methodology for personalization of software used in rehabilitation of cognitive disabilities. This methodology serves scenarios where clinical priorities, expertise, and services can be factored into socio-technical software design decisions and clinicians explicitly included in the process. The clinical context anticipates the patient's progress toward at least partial recovery and justifies clinical services. PCD builds on and integrates user-centered design (UCD) and participatory design (PD). Case studies come from work in traumatic brain injury rehabilitation.