LUMINR: Intensity-conditioned Meta-learned INRs for Accelerated Medical Image Registration

Deformable image registration models implicitly encode deformation priors through their parametrization and optimization. In this work, we conduct a validation study on continuous registration methods to examine how these implicit priors affect performance across different registration tasks. Classic B-Spline transformations impose locality, smoothness, and scale through their control-point structure, whereas recent INR-based methods impose different priors through neural parameterization and optimization. We compare INR-Dense (IDIR), which directly models a dense displacement field using a SIREN-based INR; INR-BSCP (SINR), which predicts B-Spline control points with an INR; D-BSCP, which directly optimizes single-scale B-Spline control points; and MR-D-BSCP, which adds a multiresolution coarse-to-fine scheme. Experiments on inter-subject brain MR registration (OASIS) and intra-subject exhale-to-inhale lung CT registration (DIR-LAB 4DCT) reveal different behavior across deformation regimes. On OASIS, where deformations are moderate but locally complex, D-BSCP matches or slightly outperforms INR-BSCP, suggesting that the B-Spline parameterization accounts for much of INR-BSCP's effectiveness. On DIR-LAB 4DCT, where respiratory motion is larger and more coherent, single-scale B-Spline methods (D-BSCP and INR-BSCP) are less suitable, while INR-Dense and MR-D-BSCP are more effective. Across both tasks, MR-D-BSCP achieves the best performance among the tested continuous parameterizations. These findings highlight that registration accuracy depends strongly on matching the induced deformation prior to the target motion pattern, and support prior-deformation matching as a practical design principle for medical image registration. Our code will be available at https://github.com/HengjieLiu/RightPriorDIR.

Implicit Neural Representations (INRs) have recently gained popularity for their ability to model functions using simple and lightweight networks. These methods have also proven effective in deformable image registration. In this work, we extend INRs for deformable image registration to the domain of temporal image registration, focusing on periodic temporal image sequences. Our approach, Temporal-IDIR, optimizes a single INR to model deformations across all frames in a temporal image sequence simultaneously, allowing for self-regularization through its own deformation predictions. To achieve this, we introduce a temporal consistency loss that penalizes discrepancies between direct source-to-target transformations and those traversing intermediate frames. We evaluate our framework on the DIR-LAB dataset, using the target registration error (TRE) between annotated and moved landmarks as the metric. Here, we achieve a TRE of 1.03 mm, outperforming other INR-based registration methods. Additionally, our framework supports smooth interpolation between time frames by estimating deformations between the given input frames. Code is publicly available at https://github.com/MMLowes/Temporal_INR.

Deep learning registration methods routinely stack two kinds of enhancement on a base network: architectural additions such as affine pre-alignment stages, and training-objective additions such as regularization losses. Papers tend to adopt both at once, so it is unclear which is doing the work. I ran a controlled ablation to separate them. Using the OASIS brain MRI dataset (394 training subjects, 20 test subjects), I trained four variants of the same registration pipeline: a baseline 3D U-Net with basic similarity losses, the same U-Net with a full regularization suite, an affine-plus-deformable architecture with basic losses, and the affine architecture with the full suite. I evaluated registration accuracy (MSE, NCC, SSIM), deformation quality (Jacobian determinant preservation, displacement statistics, an anatomical plausibility score), and computational cost. Regularization alone accounted for most of the gain: a 21.3% relative gain on the MSE-improvement metric (1.78% to 2.16%, P<.001) and a 21.8% relative gain in NCC improvement, while cutting maximum deformation from 53.1 to 0.51 units, a 99.0% reduction, at essentially no computational cost (-0.06% inference time). The combined model produced the largest accuracy gain, 25.8% (1.78% to 2.24%), and raised anatomical plausibility from 0.596 to 0.930, at a moderate +9.8% inference-time cost. Gradient correlation rose from 0.742 at baseline to 0.980 for the fully enhanced model. All enhanced variants reached sub-voxel accuracy under plausible deformation constraints. Regularization losses are the primary driver in this setting, delivering the accuracy gains and almost all of the deformation control for free at inference time, while the affine architecture adds a smaller complementary benefit at acceptable cost. The 99% reduction in unrealistic deformations addresses a known barrier to clinical deployment.