Systems and methods for generating a three-dimensional image of an object from multiple two-dimensional images acquired using a magnetic resonance imaging (“MRI”) system are provided. The three-dimensional image has high spatial resolution in all three spatial dimensions. The multiple two-dimensional images can be acquired in one or more orientations (e.g., axial, coronal, sagittal, oblique). The in-plane resolution of these images can be several times finer than the through-plane resolution (i.e., the slice thickness). The images are Fourier transformed along their respective slice orientation direction and processed using the slice profile to generate a Fourier representation of the three-dimensional image with the target spatial resolution. Inverse Fourier transforming this Fourier representation generates the desired three-dimensional image.