Beyond the LUMIR challenge: The pathway to foundational registration models

Medical image challenges have played a transformative role in advancing the field, catalyzing algorithmic innovation and establishing new performance standards across diverse clinical applications. Image registration, a foundational task in neuroimaging pipelines, has similarly benefited from the Learn2Reg initiative. Building on this foundation, we introduce the Large-scale Unsupervised Brain MRI Image Registration (LUMIR) challenge, a next-generation benchmark designed to assess and advance unsupervised brain MRI registration. Distinct from prior challenges that leveraged anatomical label maps for supervision, LUMIR removes this dependency by providing over 4,000 preprocessed T1-weighted brain MRIs for training without any label maps, encouraging biologically plausible deformation modeling through self-supervision. In addition to evaluating performance on 590 held-out test subjects, LUMIR introduces a rigorous suite of zero-shot generalization tasks, spanning out-of-domain imaging modalities (e.g., FLAIR, T2-weighted, T2*-weighted), disease populations (e.g., Alzheimer's disease), acquisition protocols (e.g., 9.4T MRI), and species (e.g., macaque brains). A total of 1,158 subjects and over 4,000 image pairs were included for evaluation. Performance was assessed using both segmentation-based metrics (Dice coefficient, 95th percentile Hausdorff distance) and landmark-based registration accuracy (target registration error). Across both in-domain and zero-shot tasks, deep learning-based methods consistently achieved state-of-the-art accuracy while producing anatomically plausible deformation fields. The top-performing deep learning-based models demonstrated diffeomorphic properties and inverse consistency, outperforming several leading optimization-based methods, and showing strong robustness to most domain shifts, the exception being a drop in performance on out-of-domain contrasts.

Fine-Tuning TransMorph with Gradient Correlation for Anatomical Alignment

Unsupervised deep learning is a promising method in brain MRI registration to reduce the reliance on anatomical labels, while still achieving anatomically accurate transformations. For the Learn2Reg2024 LUMIR challenge, we propose fine-tuning of the pre-trained TransMorph model to improve the convergence stability as well as the deformation smoothness. The former is achieved through the FAdam optimizer, and consistency in structural changes is incorporated through the addition of gradient correlation in the similarity measure, improving anatomical alignment. The results show slight improvements in the Dice and HdDist95 scores, and a notable reduction in the NDV compared to the baseline TransMorph model. These are also confirmed by inspecting the boundaries of the tissue. Our proposed method highlights the effectiveness of including Gradient Correlation to achieve smoother and structurally consistent deformations for interpatient brain MRI registration.