Quicksilver: Fast Predictive Image Registration - a Deep Learning Approach

This paper introduces Quicksilver, a fast deformable image registration method. Quicksilver registration for image-pairs works by patch-wise prediction of a deformation model based directly on image appearance. A deep encoder-decoder network is used as the prediction model. While the prediction strategy is general, we focus on predictions for the Large Deformation Diffeomorphic Metric Mapping (LDDMM) model. Specifically, we predict the momentum-parameterization of LDDMM, which facilitates a patch-wise prediction strategy while maintaining the theoretical properties of LDDMM, such as guaranteed diffeomorphic mappings for sufficiently strong regularization. We also provide a probabilistic version of our prediction network which can be sampled during the testing time to calculate uncertainties in the predicted deformations. Finally, we introduce a new correction network which greatly increases the prediction accuracy of an already existing prediction network. We show experimental results for uni-modal atlas-to-image as well as uni- / multi- modal image-to-image registrations. These experiments demonstrate that our method accurately predicts registrations obtained by numerical optimization, is very fast, achieves state-of-the-art registration results on four standard validation datasets, and can jointly learn an image similarity measure. Quicksilver is freely available as an open-source software.Comment: Add new discussion

Towards an efficient segmentation of small rodents brain: a short critical review

One of the most common tasks in small rodents MRI pipelines is the voxel-wise segmentation of the volume in multiple classes. While many segmentation schemes have been developed for the human brain, fewer are available for rodent MRI, often by adaptation from human neuroimaging. Common methods include atlas-based and clustering schemes. The former labels the target volume by registering one or more pre-labeled atlases using a deformable registration method, in which case the result depends on the quality of the reference volumes, the registration algorithm and the label fusion approach, if more than one atlas is employed. The latter is based on an expectation maximization procedure to maximize the variance between voxel categories, and is often combined with Markov Random Fields and the atlas based approach to include spatial information, priors, and improve the classification accuracy. Our primary goal is to critically review the state of the art of rat and mouse segmentation of neuro MRI volumes and compare the available literature on popular, readily and freely available MRI toolsets, including SPM, FSL and ANTs, when applied to this task in the context of common pre-processing steps. Furthermore, we will briefly address the emerging Deep Learning methods for the segmentation of medical imaging, and the perspectives for applications to small rodents