An intensity inhomogeneity correction system includes a log operator which performs a log operation on the intensity values of the original MR image. A regular grid generator partitions the image domain and then a compute and select establishes reliable orientation constraints at grid locations. A bias field surface reconstructor reconstructs a bias field surface from selected orientation constraints with a thin-plate spline by using a preconditioned conjugate gradient. An intensity inhomogeneities remover subtracts an estimated bias function from the original log image and an exponential operation on the bias-field corrected log image provides a corrected image.