The present invention provides a system and method for parallel imaging that performs auto-calibrating reconstructions with a 2D (for 2D imaging) or 3D kernel (for 3D imaging) that exploits the computational efficiencies available when operating in certain data “domains” or “spaces”. The reconstruction process of multi-coil data is separated into a “training phase” and an “application phase” in which reconstruction weights are applied to acquired data to synthesize (replace) missing data. The choice of data space, i.e., k-space, hybrid space, or image space, in which each step occurs is independently optimized to reduce total reconstruction time for a given imaging application. As such, the invention retains the image quality benefits of using a 2D k-space kernel without the computational burden of applying a 2D k-space convolution kernel.