Mouse models are an important way for exploring relationships between blood hemodynamics and eventual plaque formation. We have developed a mouse model of aortic regurgitation (AR) that produces large changes in plaque burden with charges in hemodynamics [Zhou et al., 2010, "Aortic Regurgitation Dramatically Alters the Distribution of Atherosclerotic Lesions and Enhances Atherogenesis in Mice," Arterioscler. Thromb. Vasc. Biol., 30(6), pp. 1181–1188]. In this paper, we explore the amount of detail needed for realistic computational fluid dynamics (CFD) calculations in this experimental model. The CFD calculations use inputs based on experimental measurements from ultrasound (US), micro computed tomography (CT), and both anatomical magnetic resonance imaging (MRI) and phase contrast MRI (PC-MRI). The adequacy of five different levels of model complexity (a) subject-specific CT data from a single mouse; (b) subject-specific CT centerlines with radii from US; (c) same as (b) but with MRI derived centerlines; (d) average CT centerlines and averaged vessel radius and branching vessels; and (e) same as (d) but with averaged MRI centerlines) is evaluated by demonstrating their impact on relative residence time (RRT) outputs. The paper concludes by demonstrating the necessity of subject-specific geometry and recommends for inputs the use of CT or anatomical MRI for establishing the aortic centerlines, M-mode US for scaling the aortic diameters, and a combination of PC-MRI and Doppler US for estimating the spatial and temporal characteristics of the input wave forms.