MEDICAL IMAGING WITH DISTORTION CORRECTION

Methods, systems, and apparatus, including computer programs encoded on computer storage media, for medical imaging with distortion correction. One example includes obtaining distorted image data of a subject brain, the distorted image data comprising a time series of three-dimensional image tensors generated at least in part from an echo planar imaging session of the subject brain. A derived three-dimensional tensor is derived from the distorted image data. A non-rigid alignment function to non-rigidly align the derived three-dimensional tensor to a reference tensor is determined, producing a non-rigidly aligned derived 3D tensor. A rigid alignment function to rigidly align the non-rigidly aligned derived 3D tensor to the reference tensor is determined. Distortion-corrected image data is created by applying the rigid alignment function and the non-rigid alignment function to the time series of three-dimensional image tensors.