Hojjat Azadbakht

Antoine Legouhy, Cosimo Campo, Ross Callaghan et al.

In this work we present Polaffini, a robust and versatile framework for anatomically grounded registration. Medical image registration is dominated by intensity-based registration methods that rely on surrogate measures of alignment quality. In contrast, feature-based approaches that operate by identifying explicit anatomical correspondences, while more desirable in theory, have largely fallen out of favor due to the challenges of reliably extracting features. However, such challenges are now significantly overcome thanks to recent advances in deep learning, which provide pre-trained segmentation models capable of instantly delivering reliable, fine-grained anatomical delineations. We aim to demonstrate that these advances can be leveraged to create new anatomically-grounded image registration algorithms. To this end, we propose Polaffini, which obtains, from these segmented regions, anatomically grounded feature points with 1-to-1 correspondence in a particularly simple way: extracting their centroids. These enable efficient global and local affine matching via closed-form solutions. Those are used to produce an overall transformation ranging from affine to polyaffine with tunable smoothness. Polyaffine transformations can have many more degrees of freedom than affine ones allowing for finer alignment, and their embedding in the log-Euclidean framework ensures diffeomorphic properties. Polaffini has applications both for standalone registration and as pre-alignment for subsequent non-linear registration, and we evaluate it against popular intensity-based registration techniques. Results demonstrate that Polaffini outperforms competing methods in terms of structural alignment and provides improved initialisation for downstream non-linear registration. Polaffini is fast, robust, and accurate, making it particularly well-suited for integration into medical image processing pipelines.

Louise E. G. Baron, Ross Callaghan, David M. Cash et al.

Structural MRI-to-amyloid PET synthesis has been proposed as a non-invasive alternative for amyloid assessment in Alzheimer's disease (AD). However, reported performance of identical models varies widely across studies, and increasingly complex architectures have not led to consistent gains. This inconsistency is thought to be caused by a fundamental biological ambiguity: MRI captures neurodegeneration, while PET measures amyloid pathology - two processes that are often temporally decoupled in AD. As a result, similar MRI patterns may correspond to different amyloid states, creating ambiguous one-to-many mappings. MRI-to-amyloid PET synthesis may therefore be intrinsically ill-posed; however, this idea has yet to be tested scientifically. The aim of this work is to test this hypothesis through two controlled experiments. We first control the training distribution by stratifying paired MRI-PET data by amyloid and neurodegeneration status. Using two standard synthesis models under a controlled design, we show that biologically unambiguous mappings are learnable in isolation, but performance collapses when data ambiguity is introduced. This demonstrates that ambiguity in the data distribution, rather than architectural capacity, constrains performance. Second, we show that introducing orthogonal biological information in the form of plasma biomarkers resolves this ambiguity. When multimodal inputs are incorporated, performance improves and stability is restored. Together, these findings suggest that limited and inconsistent performance in MRI-to-amyloid PET synthesis is explained by intrinsic biological ambiguity, and that stable, meaningful progress requires multimodal integration rather than architectural complexity.

Antoine Legouhy, Ross Callaghan, Whitney Stee et al.

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.