Systems and methods for generating biomarkers associated with neuropsychiatric disorders, neurodevelopmental disorders, neurobehavioral disorders, or other neurological disorders are described. In general, the biomarkers are generated based on correlations between functional imaging data and clinical acquired from a subject, as computed using a multivariate classifier. Functional imaging data may include functional magnetic resonance images, or activation maps generated from such images. Clinical data generally includes data associated with a clinical or behavioral characterization of the subject. The biomarkers can be used to monitor or otherwise assess a treatment response; to provide diagnostic information, such as subtyping or classifying a disorder; to provide prognostic information, such as a prediction of treatment response or outcome; or to indicate functional or anatomical targets for treatments.