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 Hd-Dist95 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.

Diffeomorphic deformable image registration ensures smooth invertible transformations across inspiratory and expiratory chest CT scans. Yet, in practice, deep learning-based diffeomorphic methods struggle to capture large deformations between inspiratory and expiratory volumes, and therefore lack inverse consistency. Existing methods also fail to account for model uncertainty, which can be useful for improving performance. We propose an uncertainty-aware test-time adaptation framework for inverse consistent diffeomorphic lung registration. Our method uses Monte Carlo (MC) dropout to estimate spatial uncertainty that is used to improve model performance. We train and evaluate our method for inspiratory-to-expiratory CT registration on a large cohort of 675 subjects from the COPDGene study, achieving a higher Dice similarity coefficient (DSC) between the lung boundaries (0.966) compared to both VoxelMorph (0.953) and TransMorph (0.953). Our method demonstrates consistent improvements in the inverse registration direction as well with an overall DSC of 0.966, higher than VoxelMorph (0.958) and TransMorph (0.956). Paired t-tests indicate statistically significant improvements.

In the last decade, convolutional neural networks (ConvNets) have been a major focus of research in medical image analysis. However, the performances of ConvNets may be limited by a lack of explicit consideration of the long-range spatial relationships in an image. Recently Vision Transformer architectures have been proposed to address the shortcomings of ConvNets and have produced state-of-the-art performances in many medical imaging applications. Transformers may be a strong candidate for image registration because their unlimited receptive field enables a more precise comprehension of the spatial correspondence between moving and fixed images. Here, we present TransMorph, a hybrid Transformer-ConvNet model for volumetric medical image registration. This paper also presents diffeomorphic and Bayesian variants of TransMorph: the diffeomorphic variants ensure the topology-preserving deformations, and the Bayesian variant produces a well-calibrated registration uncertainty estimate. We extensively validated the proposed models using 3D medical images from three applications: inter-patient and atlas-to-patient brain MRI registration and phantom-to-CT registration. The proposed models are evaluated in comparison to a variety of existing registration methods and Transformer architectures. Qualitative and quantitative results demonstrate that the proposed Transformer-based model leads to a substantial performance improvement over the baseline methods, confirming the effectiveness of Transformers for medical image registration.