1. A method of generating a report to help decide among a plurality of treatment options for a patient with a given medical condition for use with a computer system, the method comprising: receiving patient information related to the patient and the medical condition; querying a treatment option database to generate a plurality of potential treatment options for the medical condition; receiving preference information indicative of the patient's preference for potential treatment outcomes of the treatment options to produce a preference value; analyzing indexed study data relating to the plurality of treatment options; producing, at least in part in a computer process, a study score for each of the treatment options based on the analysis of the indexed data; determining, for each treatment option, a treatment score as a function of at least the preference value and the study score; generating a report listing the treatment options and a) the treatment scores or b) the information derived from the treatment scores.