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Computer aided diagnosis (CAD) system is an effective system of systems engineering (SoSE) in the medical field. The CAD system using medical images is constructed by integrating medical image acquisition system, medical image processing system, and clinical data analysis system, and it presents both of quantitative and qualitative data for physicians. This article proposes a CAD system for diagnosing neonatal and infantile brain disorders. The CAD system acquires intracranial images using MR scanner system, and segments the cerebral volume and surface using medical image processing systems, and produces cerebral volume and area, and 3-D rendering of cerebral surface. Especially, this article proposes medical image processing systems based on expert knowledge systems for neonatal/infantile brain MR images. To validate the proposed CAD system, it has been applied to three neonatal and five infantile MR images.