1. A computer-based system for determining patient-specific vascular information, the system comprising at least one computer configured to: store template data containing names of a principal vascular element and other vascular elements in a vascular portion of a patient, which defines relative positional relationships among the principal vascular element and the other vascular elements; receive first three dimensional data representing a shape of the vascular portion of the patient, the three dimensional data being suitable for simulations using computational fluid dynamics (CFD); determine, from the first three dimensional data, a cross-sectional area of each of vascular elements in the vascular portion of the patient, and identify a vascular element with a largest median value of the area as the principal vascular element; and label names to the vascular elements in the first three dimensional data, by applying the template data, based on the relative positional relationships with the principal vascular element.