Medical image registration is a common technique that involves overlaying two images, such as MRI scans, to compare and analyze anatomical differences in great detail. If a patient has a brain tumor, for instance, doctors can overlap a brain scan from several months ago onto a more recent scan to analyze small changes in the tumor’s progress.

This process, however, can often take two hours or more, as traditional systems meticulously align each of potentially a million pixels in the combined scans. MIT researchers describe a machine-learning algorithm that can register brain scans and other 3-D images more than 1,000 times more quickly using novel learning techniques.

The algorithm works by “learning” while registering thousands of pairs of images. In doing so, it acquires information about how to align images and estimates some optimal alignment parameters. After training, it uses those parameters to map all pixels of one image to another, all at once. This reduces registration time to a minute or two using a normal computer, or less than a second using a GPU with comparable accuracy to state-of-the-art systems.

“The tasks of aligning a brain MRI shouldn’t be that different when you’re aligning one pair of brain MRIs or another,” says Guha Balakrishnan, a graduate student in MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) and Department of Engineering and Computer Science (EECS). “There is information you should be able to carry over in how you do the alignment. If you’re able to learn something from previous image registration, you can do a new task much faster and with the same accuracy.”

Retaining information

The researchers’ algorithm, called “VoxelMorph,” is powered by a convolutional neural network (CNN), a machine-learning approach commonly used for image processing. These networks consist of many nodes that process image and other information across several layers of computation.

The researchers trained their algorithm on 7,000 publicly available MRI brain scans and then tested it on 250 additional scans. During training, brain scans were fed into the algorithm in pairs. Using a CNN and modified computation layer called a spatial transformer, the method captures similarities of voxels in one MRI scan with voxels in the other scan. In doing so, the algorithm learns information about groups of voxels — such as anatomical shapes common to both scans — which it uses to calculate optimized parameters that can be applied to any scan pair.

When fed two new scans, a simple mathematical “function” uses those optimized parameters to rapidly calculate the exact alignment of every voxel in both scans. In short, the algorithm’s CNN component gains all necessary information during training so that, during each new registration, the entire registration can be executed using one, easily computable function evaluation.

The researchers found their algorithm could accurately register all of their 250 test brain scans — those registered after the training set — within two minutes using a traditional central processing unit, and in under one second using a graphics processing unit.

Importantly, the algorithm is “unsupervised,” meaning it doesn’t require additional information beyond image data. Some registration algorithms incorporate CNN models but require a “ground truth,” meaning another traditional algorithm is first run to compute accurate registrations. The researchers’ algorithm maintains its accuracy without that data.

Source: Massachusetts Institute of Technology