A method of detecting whether or not a body chamber has an abnormal structure or function including: (a) providing a stack of images as input to a system comprising one or more hardware processors configured to obtain a stack of medical images comprising at least a representation of the body chamber inside the patient; to obtain a region of interest using a convolutional network trained to locate the body chamber, wherein the region of interest corresponds to the body chamber from each of the medical images; and to infer a shape of the body chamber using a stacked auto-encoder (AE) network trained to delineate the body chamber, wherein the AE network segments the body chamber; (b) operating the system to detect the body chamber in the images using deep convolutional networks trained to locate the body chamber, to infer a shape of the body chamber using a stacked auto-encoder trained to delineate the body chamber, and to incorporate the inferred shape into a deformable model for segmentation; and (c) detecting whether or not the body chamber has an abnormal structure, wherein an abnormal structure is indicated by a body chamber clinical indicia that is different from a corresponding known standard clinical indicia for the body chamber.