1. A system for detecting pulmonary embolisms in a subject's vasculature, the system comprising: an input configured to receive images acquired from a subject; a processor configured to process the images with steps comprising: i. receiving, using the input, a set of images representing a vasculature of the subject; ii. analyzing the set of images to identify pulmonary embolism candidates associated with the vasculature; iii. generating, for identified pulmonary embolism candidates, image patches based on a vessel-aligned image representation; iii. applying a set of convolutional neural networks to the generated image patches to identify pulmonary embolisms; vi. generating a report indicating identified pulmonary embolisms; and an output for displaying the report.