We present a fully automatic approach to recover boundary conditions and locations of the
vessel wall, given a crude initial guess and some velocity cross-sections, which can be
corrupted by noise. This paper contributes to the body of work regarding patient-specific
numerical simulations of blood flow, where the computational domain and boundary
conditions have an implicit uncertainty and error, that derives from acquiring and
processing clinical data in the form of medical images. The tools described in this paper
fit well in the current approach of performing patient-specific simulations, where a
reasonable segmentation of the medical images is used to form the computational domain,
and boundary conditions are obtained as velocity cross-sections from phase-contrast
magnetic resonance imaging. The only additional requirement in the proposed methods is to
obtain additional velocity cross-section measurements throughout the domain. The tools
developed around optimal control theory, would then minimize a user defined cost function
to fit the observations, while solving the incompressible Navier-Stokes equations.
Examples include two-dimensional idealized geometries and an anatomically realistic
saccular geometry description.