Methods and systems for analyzing images are disclosed. An example method may comprise inputting one or more of a first image or a second image into a fully convolutional network, and determining an updated fully convolutional network by optimizing a similarity metric associated with spatially transforming the first image to match the second image. The one or more values of the fully convolutional network may be adjusted to optimize the similarity metric. The method may comprise registering one or more of the first image or the second image based on the updated fully convolutional network.