Abstract: Functional medical image scans are currently assessed by comparison with reference data but a number of problems arise from the fact that the reference data is not acquired from the same source as the scan. Complicated processes are required to compensate for variations in e.g. patient anatomy, data acquisition systems and inherent variance in the acquisition process. The invention avoids these problems by using known techniques to generate a virtual function scan from a structural scan (e.g. MRI) for comparison with the acquired medical image scan. Since both scans are derived from the same source, there is no need for e.g. registration of the patient anatomy and the reference data.