Highlights • Introduction of a framework for quantitative and observer-independent validation of vessel segmentation in the MRA images • Demonstration of a practical application of a custom-designed magnetic resonance angiography simulator as a reliable tool for quantitative validation of vessel segmentation algorithms that provides objective and reproducible results. • Development of a realistic digital phantom of an intracranial arterial tree based on a real Time-of-Flight data set. • Performing thorough validation of a level-set vessel segmentation algorithm implemented in the Vascular Modeling Toolkit (VMTK), an open-source software library. • A comparison study of three vessel segmentation algorithms: 1) the VMTK's level-set method, 2) the Chan-Vese formulation of level-set method and 3) the multi-scale Hessian-based vessel enhancement funciton.