Purpose: To propose an atlas-based method that uses both phase and magnitude images to integrate anatomical information in order to improve the segmentation of blood vessels in cerebral phase-contrast magnetic resonance angiography (PC-MRA). Material and Methods: An atlas of the whole head was developed to store the anatomical information. The atlas divides a magnitude image into several vascular areas, each of which has specific vessel properties. It can be applied to any magnitude image of an entire or nearly entire head by deformable matching, which helps to segment blood vessels from the associated phase image. The segmentation method used afterwards consists of a topology-preserving, region-growing algorithm that uses adaptive threshold values depending on the current region of the atlas. This algorithm builds the arterial and venous trees by iteratively adding voxels that are selected according to their grayscale value and the variation of values in their neighborhood. The topology preservation is guaranteed because only simple points are selected during the growing process. Results: The method was performed on 40 PC-MRA images of the brain. The results were validated using maximum intensity projection (MIP) and three-dimensional surface rendering visualization, and compared with results obtained with two non-atlas-based methods. Conclusion: The results show that the proposed method significantly improves the segmentation of cerebral vascular structures from PC-MRA. These experiments tend to prove that the use of vascular atlases is an effective way to optimize vessel segmentation of cerebral images.