NimbleReg: A light-weight deep-learning framework for diffeomorphic image registration

This paper presents NimbleReg, a light-weight deep-learning (DL) framework for diffeomorphic image registration leveraging surface representation of multiple segmented anatomical regions. Deep learning has revolutionized image registration but most methods typically rely on cumbersome gridded representations, leading to hardware-intensive models. Reliable fine-grained segmentations, that are now accessible at low cost, are often used to guide the alignment. Light-weight methods representing segmentations in terms of boundary surfaces have been proposed, but they lack mechanism to support the fusion of multiple regional mappings into an overall diffeomorphic transformation. Building on these advances, we propose a DL registration method capable of aligning surfaces from multiple segmented regions to generate an overall diffeomorphic transformation for the whole ambient space. The proposed model is light-weight thanks to a PointNet backbone. Diffeomoprhic properties are guaranteed by taking advantage of the stationary velocity field parametrization of diffeomorphisms. We demonstrate that this approach achieves alignment comparable to state-of-the-art DL-based registration techniques that consume images.

POLAFFINI: Efficient feature-based polyaffine initialization for improved non-linear image registration

This paper presents an efficient feature-based approach to initialize non-linear image registration. Today, nonlinear image registration is dominated by methods relying on intensity-based similarity measures. A good estimate of the initial transformation is essential, both for traditional iterative algorithms and for recent one-shot deep learning (DL)-based alternatives. The established approach to estimate this starting point is to perform affine registration, but this may be insufficient due to its parsimonious, global, and non-bending nature. We propose an improved initialization method that takes advantage of recent advances in DL-based segmentation techniques able to instantly estimate fine-grained regional delineations with state-of-the-art accuracies. Those segmentations are used to produce local, anatomically grounded, feature-based affine matchings using iteration-free closed-form expressions. Estimated local affine transformations are then fused, with the log-Euclidean polyaffine framework, into an overall dense diffeomorphic transformation. We show that, compared to its affine counterpart, the proposed initialization leads to significantly better alignment for both traditional and DL-based non-linear registration algorithms. The proposed approach is also more robust and significantly faster than commonly used affine registration algorithms such as FSL FLIRT.

Eddeep: Fast eddy-current distortion correction for diffusion MRI with deep learning

Modern diffusion MRI sequences commonly acquire a large number of volumes with diffusion sensitization gradients of differing strengths or directions. Such sequences rely on echo-planar imaging (EPI) to achieve reasonable scan duration. However, EPI is vulnerable to off-resonance effects, leading to tissue susceptibility and eddy-current induced distortions. The latter is particularly problematic because it causes misalignment between volumes, disrupting downstream modelling and analysis. The essential correction of eddy distortions is typically done post-acquisition, with image registration. However, this is non-trivial because correspondence between volumes can be severely disrupted due to volume-specific signal attenuations induced by varying directions and strengths of the applied gradients. This challenge has been successfully addressed by the popular FSL~Eddy tool but at considerable computational cost. We propose an alternative approach, leveraging recent advances in image processing enabled by deep learning (DL). It consists of two convolutional neural networks: 1) An image translator to restore correspondence between images; 2) A registration model to align the translated images. Results demonstrate comparable distortion estimates to FSL~Eddy, while requiring only modest training sample sizes. This work, to the best of our knowledge, is the first to tackle this problem with deep learning. Together with recently developed DL-based susceptibility correction techniques, they pave the way for real-time preprocessing of diffusion MRI, facilitating its wider uptake in the clinic.

Resolving quantitative MRI model degeneracy with machine learning via training data distribution design

Quantitative MRI (qMRI) aims to map tissue properties non-invasively via models that relate these unknown quantities to measured MRI signals. Estimating these unknowns, which has traditionally required model fitting - an often iterative procedure, can now be done with one-shot machine learning (ML) approaches. Such parameter estimation may be complicated by intrinsic qMRI signal model degeneracy: different combinations of tissue properties produce the same signal. Despite their many advantages, it remains unclear whether ML approaches can resolve this issue. Growing empirical evidence appears to suggest ML approaches remain susceptible to model degeneracy. Here we demonstrate under the right circumstances ML can address this issue. Inspired by recent works on the impact of training data distributions on ML-based parameter estimation, we propose to resolve model degeneracy by designing training data distributions. We put forward a classification of model degeneracies and identify one particular kind of degeneracies amenable to the proposed attack. The strategy is demonstrated successfully using the Revised NODDI model with standard multi-shell diffusion MRI data as an exemplar. Our results illustrate the importance of training set design which has the potential to allow accurate estimation of tissue properties with ML.