Medical Image Registration

Correspondence is fundamentally relational: it seeks the unknown transformation between two observations of a common scene, not the content of either. Yet the dominant learning-based methods do not represent the transformation as a first-class object in the architecture. They encode each image independently and let a learned similarity function or a deep decoder discover the mapping implicitly. Phase correlation is the canonical exception, measuring the inter-image relationship directly in the Fourier domain, but the rigidity of its fixed basis confines it to global translation. We introduce a learned generalization of phase correlation that lifts this restriction by learning the basis on which the transformation decomposes. The same algebraic primitive extends to dense non-rigid deformations and to unitary dynamics. On the ACDC cardiac-MRI benchmark the framework matches or exceeds prior published baselines on both registration directions. On CAMUS echocardiography it matches state-of-the-art without auxiliary scoring or adaptive-smoothness mechanisms. Applied to time-evolved wavefunction pairs of the 1-D quantum harmonic oscillator, the same framework recovers the Hermite-function eigenstates and the quantized energy levels of the unknown Hamiltonian from observation pairs alone.

Accurate intraoperative liver registration is challenging due to substantial soft-tissue deformation yet sparse intraoperative measurements. Biomechanical models regularize this ill-posedness with prior knowledge but exhibit persistent prediction bias due to simplifying assumptions, while data-driven learning solutions struggle with data efficiency, generalization, and physical plausibility. We propose a hybrid registration framework that adapts a biomechanical prior using sparse intraoperative correspondences. Rather than learning a full deformation field, we learn a residual deformation function that corrects linear biomechanical predictions, modeled as a graph neural diffusion function with geometry-aware attention over the 3D liver mesh. To enable long-range information transfer of sparse observations, we take a novel perspective of sparse intraoperative measurements as \textit{context} samples where input-output pairs of the residual deformation function are fully observed, casting the problem into learning-to-learn this residual function from intraoperative context samples with feedforward meta-learners. Experiments on a deformable liver phantom dataset demonstrate improved registration accuracy and generalization compared to rigid, biomechanical, and data-driven baselines, particularly for out-of-distribution geometries and deformations.

Hyperspectral Imaging (HSI) is a promising modality for intraoperative assessment of resection margins in Breast-Conserving Surgery (BCS), but its clinical translation requires aligning the inherently 2D spectral information onto the 3D shape of the excised tissue so that suspicious regions can be precisely localized for targeted follow-up. We present a fully automated, calibration-free pipeline that produces a 3D hyperspectral point cloud of an ex-vivo lumpectomy specimen from a set of consumer-camera RGB images and a single top-down HSI acquisition. The 3D geometry is reconstructed with a deep-learning Structure-from-Motion backbone, stabilized in a metric reference frame by a custom bundle adjustment that enforces consistency on the corners of four ArUco markers placed around the specimen. The HSI cube is then registered to the reconstruction without recovering the HSI camera pose: the markers, visible in both modalities, define 16 corner correspondences that drive a planar homography, and 3D coordinates are recovered by lookup on an orthographically rendered depth map. Evaluated on two ex-vivo lumpectomy specimens, the pipeline achieves a median 3D registration error below 1~mm and a 2D reprojection error below 0.02 mm, with a total per-specimen processing time under 4 minutes on accelerated hardware. These results support the feasibility of integrating HSI-guided spatial localization into intraoperative margin assessment workflows for breast-conserving surgery.

Accurate execution of preoperative plans in corrective femoral osteotomies remains challenging. Current techniques are limited by variable accuracy, invasiveness, and radiation exposure, with free-hand methods and patient-specific instrumentation (PSI) often requiring >30 and >6 fluoroscopic images, respectively. We present an integrated, electromagnetic tracking (EMT)-based navigation system for femoral osteotomies that minimizes dissection and intraoperative fluoroscopy. The system couples CT-based preoperative planning with one-time intraoperative C-arm calibration and accurate X-ray-to-CT registration from two fluoroscopic images acquired at initialization. This enables real-time, fluoroscopy-free EMT navigation of the saw blade and bone fragments relative to the preoperative plan, and is compatible with uniplanar and biplanar osteotomies. In a feasibility study using 18 synthetic femora, EMT guidance significantly outperformed free-hand execution in total angular error ($(3.05 \pm 0.75)^\circ$ vs.\ $(6.32 \pm 2.36)^\circ$, $p=0.031$), assuming the same minimal surgical exposure for both. No EMT-guided trials exceeded the >5° clinical threshold, whereas free-hand produced 4 outliers of 6 trials. The system achieved statistical equivalence ($\pm 2^\circ$, $\pm 2,\text{mm}$) to PSI for total angular ($p \le 0.02$) and total translational ($p=0.048$) errors, with no significant differences in user questionnaire scores. By transferring preoperative plans using only two fluoroscopic images while matching PSI accuracy without additional surgical exposure, the proposed system motivates subsequent cadaveric and clinical validation.

Accurate registration of CAD models to CT scans is essential for establishing ground truth geometry in volumetric imaging. Obtaining reliable object masks is of growing importance in machine learning settings; as recent architectures grow more capable, huge datasets are required to fully utilise their capabilities. Traditional intensity-based methods fail when CT grayscale values lack calibration references, while point-based algorithms (e.g., ICP, RANSAC) require feature correspondence unavailable between idealized CAD geometry and noisy volumetric CT data. We propose a two-stage geometric registration method for cylindrical objects (ionization chambers) that takes advantage of the distinctive geometric features of the objects. First, we estimate the 3D rotation axis by detecting elliptical cross-sections across CT slices, fitting ellipses to edge-detected contours, and performing PCA on the fitted ellipse centers after RANSAC outlier removal. Second, we voxelize the CAD model, orient it along the detected axis, and maximize volumetric overlap with the CT scan through translational adjustment. This approach achieves robust registration with tilt and orientation errors below $0.1^\circ$ without intensity calibration or feature matching. Once registered, the aligned CAD model provides ground truth geometry for applications including machine learning-based object localization and automated analysis in industrial CT workflows.

Ultrasound is the most widely used real-time imaging modality in clinical practice, yet per-frame video annotation remains a major bottleneck: expert labels are scarce and costly, and image appearance varies with speckle, shadowing, attenuation, and operator-dependent probe pose. This is especially limiting because clinically relevant information is often dynamic, from left-ventricular motion in echocardiography to muscle and bone kinematics in musculoskeletal imaging. Population atlases can amortize annotation cost by registering observations to a shared canonical coordinate system, but existing neural atlas methods mainly target single videos, small test-time image sets, or object-centric image collections. We introduce a cohort-scale neural atlas for ultrasound video: a single canonical chart with per-video Generative Latent Optimization embeddings, trained jointly over thousands of frames in DINOv3 feature space. Across five cardiac and musculoskeletal datasets with point landmarks and segmentation masks, our method learns coherent canonical templates and enables accurate atlas-space annotation transfer. On EchoNet-Dynamic and MSK-Bone, it supports single- and few-shot transfer with accuracy competitive with strong dense-correspondence baselines, while training in minutes on a single consumer GPU. The learned embeddings are interpretable: linear projections reveal structured cohort variation, image-decoder interpolation produces anatomically plausible intermediate frames, and test-time latent inversion reconstructs held-out frames through the atlas. These results suggest that cohort-scale neural atlases offer a practical, interpretable representation for reducing expert annotation burden in ultrasound video analysis.

Deformable medical image registration aligns anatomical structures across images but remains computationally dense at 3D resolution. Spiking neural networks (SNNs) offer sparse event-driven computation, yet have not been systematically studied for deformable medical image registration. We introduce SpikeReg, a spiking U-Net for 3D brain MRI registration. SpikeReg is initialized from an analog ANN registration teacher, converted by layer-wise weight transfer and activation-percentile threshold calibration, and fine-tuned with a surrogate-gradient objective combining local cross-correlation, diffusion regularization, and spike-rate sparsity. On the OASIS Learn2Reg validation split ($19$ image pairs), SpikeReg reaches Dice $0.7474 \pm 0.032$, with no significant paired Dice difference from the ANN teacher ($0.7480 \pm 0.037$, $p = 0.67$), at a $12.8\%$ mean spike rate and a $55.5\times$ projected arithmetic-energy reduction under an event-sparse SynOps/MAC proxy relative to the dense-ANN baseline. We additionally report two negative findings: displacement distillation from the ANN teacher hurts performance, and ANN teachers trained with a label-Dice loss fail to transfer through rate-code conversion. Together these results show that dense geometric prediction can be performed under sparse event-driven computation, opening a path toward neuromorphic medical image registration.

Cortical surface registration is often driven by local geometric descriptors (e.g., sulcal depth and curvature). While this approach achieves geometric correspondence, it neglects the long-range wiring constraints imposed by white-matter anatomy. Diffusion MRI tractography offers these crucial constraints; however, prior connectivity-informed pipelines typically align precomputed connectivity matrices, making the optimization highly sensitive to connectivity estimation and its resolution. In this paper, we introduce a novel connectivity-based surface registration method that aligns cortical surfaces by operating directly on white-matter fiber-tract endpoints. We model tract endpoints as a point cloud on the product manifold $Ω\times Ω$, where $Ω$ represents the spherical domain of the inflated cortical hemispheres. Our alignment method iteratively (i) computes a small diffeomorphic warp for $Ω$ by minimizing connectivity mismatch, and (ii) updates the endpoints based on this warp. The method relies on a geometric framework that ensures output warps are diffeomorphisms and has a final goal that optimizes the matching of well-known fiber bundles. Experiments on Human Connectome Project (HCP) data demonstrate improved tract-level correspondence, achieving higher connectivity-level overlap coefficients on major fiber bundles and stronger robustness across grid resolutions for $Ω$ compared to state-of-the-art methods such as ENCORE and MSMAll.

Cross-modal 3D medical image analysis requires voxelwise representations that remain anatomically consistent across imaging contrasts, scanners, and acquisition protocols. Recent work has shown that frozen 2D Vision Transformer (ViT) foundation models can support such representations, but typical pipelines extract features along a single anatomical axis and adapt those features inside a registration solver for one image pair at a time, leaving complementary viewing directions unused and producing representations that do not transfer to new volumes. We introduce VoxCor, a training-free fit--transform method for reusable volumetric feature representations from frozen 2D ViT foundation models. During an offline fitting phase, VoxCor combines triplanar ViT inference with a compact closed-form weighted partial least squares (WPLS) projection that uses fitting-time voxel correspondences to select modality-stable anatomical directions in the triplanar feature space. At transform time, new volumes are mapped by triplanar ViT inference and linear projection alone, without fine-tuning or registration. Voxel correspondences can then be queried directly by nearest-neighbor search. We evaluate VoxCor on intra-subject Abdomen MR--CT and inter-subject HCP T2w--T1w tasks using deformable registration, voxelwise k-nearest-neighbor segmentation, and segmentation-center landmark localization. VoxCor improves the hardest cross-subject, cross-modality transfer settings, reduces encoder sensitivity for dense correspondence transfer, and yields registration performance competitive with handcrafted descriptors and learned 3D features. This positions VoxCor as a reusable feature layer for downstream multimodal analysis beyond pairwise registration. Code, configuration files, and implementation details are publicly available on GitHub at guneytombak/VoxCor.

Quantitative cardiac magnetic resonance imaging (MRI) enables non-invasive myocardial tissue characterization but relies on robust motion correction within these variable-length, variable-contrast image sequences. Groupwise registration, which simultaneously aligns all images, has shown greater robustness than pairwise registration for motion correction. However, current deep-learning-based groupwise registration methods cannot generalize across MRI sequences: the architecture typically encodes input data as a fixed-length channel stack, which rigidly couples network design to protocol-specific sequence length, input ordering, and contrast dynamics. At inference time, any change in imaging protocols will render the network unusable. In this work, we introduce \emph{\AnyTwoReg}, a new set-based groupwise registration framework that takes a quantitative MRI sequence as an unordered set. This set formulation fundamentally decouples network design from sequence length and input ordering. By utilizing a shared encoder and correlation-guided feature aggregation, \emph{\AnyTwoReg} constructs a permutation-invariant canonical reference for registration, and learns a permutation-equivariant mapping from images to deformation fields. Additionally, we extract contrast-insensitive image features from an existing foundation model to handle extreme contrast variations. Trained exclusively on a single public $T_1$ mapping dataset (STONE, sequence length $L=11$), \AnyTwoReg generalizes to two unseen quantitative MRI datasets (MOLLI, ASL) with variable lengths ($L \in [11, 60]$) and different contrast dynamics. It achieves strong cross-protocol generalization in a zero-shot manner, and consistently improves downstream quantitative mapping quality. Notably, while designed for quantitative MRI sequences, our framework is directly applicable to Cine MRI sequences for inter-cardiac-phase registration.

Accurate CT-MRI registration of the cervical spine is essential for preoperative planning because this region is anatomically complex,highly variable,and vulnerable to injury of the vertebral arteries and spinal cord. However,cervical CT-MRI registration remains underexplored,particularly for rigid-deformable hybrid modeling,and the lack of high-quality annotated multimodal data further limits progress. To address these challenges, we construct and release a comprehensively annotated CT-MRI dataset, R-D-Reg, and propose MSR, a rigid-deformable hybrid registration framework for complex joint structures. Specifically, MSR includes a rigid registration module for independent local rigid alignment of individual vertebrae and a deformable registration module with an MSL block that combines Mamba-based global modeling and Swin Transformer-based local modeling through adaptive gating. The rigid and deformable deformation fields are then fused to generate a hybrid field that better preserves local anatomical consistency. The code and dataset are publicly available at https://github.com/ssc1230609-spec/MSR-registration.

Clinical fusion of Single Photon Emission Computed Tomography Myocardial Perfusion Imaging (SPECT MPI) and Computed Tomography Angiography (CTA) remains limited by cross-modality misregistration and reliance on manual landmarks, which can hinder accurate ischemia localization and lesion-level functional assessment. To address this issue, we propose a registration and fusion framework for SPECT MPI and CTA that integrates functional and structural information for comprehensive cardiac evaluation. The proposed pipeline performs U-Net-based segmentation on both modalities. On SPECT MPI, only the left ventricle (LV) is extracted, and anatomical landmarks are automatically derived from characteristic LV structures. On CTA, both ventricles are segmented, and their spatial relationship is used to automatically define landmarks at the interventricular septal junction. Scale-space consistency preprocessing and landmark-driven coarse registration are applied to mitigate initial misalignment. Based on this initialization, multiple fine registration methods are evaluated on LV epicardial surface point clouds, including ICP, SICP, CPD, CluReg, FFD, and BCPD-plus-plus. The resulting transformations are then propagated to voxel-level resampling for high-precision SPECT-CTA fusion. In a retrospective cohort of 60 patients, the proposed framework preserved sub-millimeter coronary detail from CTA while accurately overlaying quantitative SPECT perfusion. Among the evaluated methods, BCPD-plus-plus achieved the highest accuracy with a mean point cloud distance of 1.7 mm. By combining robust initialization, comparative fine registration, and voxel-level fusion, the proposed approach provides a practical solution for myocardial ischemia localization and functional evaluation of coronary lesions, while remaining independent of any specific fine registration algorithm.

Whole-body Positron Emission Tomography (PET) registration is essential for multi-parametric tumor characterization and assessment of metastatic disease progression. In deep learning-based deformable registration, the dense displacement field (DDF) regularizer is crucial for stabilizing optimization and preventing unrealistic deformations in large 3D volumes. A key challenge in whole-body deformable registration is anatomical heterogeneity, rigid structures (e.g., bones) should undergo stronger regularization, whereas soft tissues require more flexible deformation and weaker constraints. In this work, we propose a simple yet effective CT-guided spatially-varying regularization strategy for whole-body cross-tracer deformable PET registration. The key idea is to use the paired CT volume from the PET/CT acquisition to construct a voxel-wise regularization map for the DDF, replacing the conventional single global regularization weight. This yields anatomy-adaptive regularization strength across rigid and soft tissues. The proposed method is evaluated on a real clinical cross-tracer PET/CT dataset of 296 patients involving 18F-PSMA and 18F-FDG, showing that the proposed method achieves statistically significant improvements over weakly-supervised registration baseline in both whole-body registration performance and organ-wise alignment.

Soft-tissue deformation remains a major limitation in image-guided neurosurgery, where intra-operative anatomy can deviate substantially from pre-operative imaging due to brain shift, compromising navigation accuracy and surgical safety. Existing compensation methods often rely on intra-operative MRI, CT, or ultrasound, which are disruptive and difficult to integrate repeatedly into the surgical workflow. In contrast, partial 3D cortical surfaces can be reconstructed as point clouds from stereoscopic microscopes or laser range scanners (LRS), capturing only a limited portion of the exposed cortex. This makes point cloud registration a practical alternative without interrupting surgery; however, such partial and noisy observations make deformation estimation highly challenging. In this study, we propose a deep learning-based framework for non-rigid volume-to-surface registration, enabling dense displacement field estimation from sparse intra-operative surface observations without explicit point correspondences or volumetric intra-operative imaging. The network leverages multi-scale point-based feature extraction and a hierarchical deformation decoder to capture both global and local deformations. The key contribution lies in integrating partial intra-operative surface information into the full pre-operative point cloud domain, enabling implicit correspondence learning and dense deformation recovery under limited visibility. Quantitative results demonstrate accurate recovery of fine-scale deformations, achieving an Endpoint Error (EPE) of 1.13 +/- 0.75 mm and RMSE of 1.33 +/- 0.81 mm under challenging partial-surface conditions. The proposed approach supports automatic, workflow-compatible brain-shift compensation from sparse surface observations.

Image registration is an ill-posed dense vision task, where multiple solutions achieve similar loss values, motivating probabilistic inference. Variational inference has previously been employed to capture these distributions, however restrictive assumptions about the posterior form can lead to poor characterisation, overconfidence and low-quality samples. More flexible posteriors are typically bottlenecked by the complexity of high-dimensional covariance matrices required for dense 3D image registration. In this work, we present a memory and computationally efficient inference method, Structured SIR, that enables expressive, multi-modal, characterisation of uncertainty with high quality samples. We propose the use of a Sampled Importance Resampling (SIR) algorithm with a novel memory-efficient high-dimensional covariance parameterisation as the sum of a low-rank covariance and a sparse, spatially structured Cholesky precision factor. This structure enables capturing complex spatial correlations while remaining computationally tractable. We evaluate the efficacy of this approach in 3D dense image registration of brain MRI data, which is a very high-dimensional problem. We demonstrate that our proposed method produces uncertainty estimates that are significantly better calibrated than those produced by variational methods, achieving equivalent or better accuracy. Crucially, we show that the model yields highly structured multi-modal posterior distributions, enable effective and efficient uncertainty quantification.

Acquiring per-frame annotations for ultrasound videos is costly and requires clinical expertise, limiting learning-based analysis. We study cross-video annotation transfer: propagating user-specified annotations from a labeled ultrasound video to an independently acquired target video with no target-side labels or manual initialization. Video trackers and segmentation propagators rely on temporal continuity and require a prompt in every new sequence, whereas cross-image feature matching and one-shot segmentation estimate correspondences independently, without enforcing coherent deformations or supporting both point and mask annotations. We present Match4Annotate, a test-time framework with three stages. A spatiotemporal implicit feature representation lifts frozen vision foundation-model features into a continuous field over space and time, enabling queries beyond the backbone resolution. A continuous implicit feature flow then aligns the source and target fields under a smooth-deformation prior, estimating correspondence in feature space rather than relying on intensity consistency, which is often violated in ultrasound by speckle and acquisition-dependent appearance. Finally, flow-guided annotation transfer uses the estimated flow as a spatial prior over feature similarity. This formulation unifies sparse point and dense mask transfer and includes unconstrained feature matching and direct flow warping as limiting cases. On four clinical ultrasound datasets spanning echocardiography and musculoskeletal imaging, Match4Annotate achieves state-of-the-art annotation transfer, outperforming dense feature-matching baselines across PCK thresholds and one-shot segmentation methods in Dice score. It also demonstrates bidirectional transfer of left-ventricular annotations across datasets. It requires no task-specific training and adapts to each video in minutes on a single consumer GPU.

In computer- and robot-assisted orthopedic surgery (CAOS), patient-specific surgical plans derived from preoperative imaging define target locations and implant trajectories. During surgery, these plans must be accurately transferred, relying on precise cross-registration between preoperative and intraoperative data. However, substantial modality heterogeneity across imaging modalities makes this registration challenging and error-prone. Robust, automatic, and modality-agnostic bone surface registration is therefore clinically important. We propose NeuralBoneReg, a self-supervised, surface-based framework that registers bone surfaces using 3D point clouds as a modality-agnostic representation. NeuralBoneReg includes two modules: an implicit neural unsigned distance field (UDF) that learns the preoperative bone model, and an MLP-based registration module that performs global initialization and local refinement by generating transformation hypotheses to align the intraoperative point cloud with the neural UDF. Unlike SOTA supervised methods, NeuralBoneReg operates in a self-supervised manner, without requiring inter-subject training data. We evaluated NeuralBoneReg against baseline methods on two publicly available multi-modal datasets: a CT-ultrasound dataset of the fibula and tibia (UltraBones100k) and a CT-RGB-D dataset of spinal vertebrae (SpineDepth). The evaluation also includes a newly introduced CT-ultrasound dataset of cadaveric subjects containing femur and pelvis (UltraBones-Hip), which will be made publicly available. NeuralBoneReg matches or surpasses existing methods across all datasets, achieving mean RRE/RTE of 1.83°/2.02 mm on UltraBones100k, 1.90°/1.56 mm on UltraBones-Hip, and 3.78°/2.80 mm on SpineDepth. These results demonstrate strong generalizability across anatomies and modalities, providing robust and accurate cross-modal alignment for CAOS.

Encoder-Decoder architectures are widely used in deep learning-based Deformable Image Registration (DIR), where the encoder extracts multi-scale features and the decoder predicts deformation fields by recovering spatial locations. However, current methods lack specialized extraction of features (that are useful for registration) and predict deformation jointly and homogeneously in all three directions. In this paper, we propose a novel expert-guided DIR network with Mixture of Experts (MoE) mechanism applied in both encoder and decoder, named SHMoAReg. Specifically, we incorporate Mixture of Attention heads (MoA) into encoder layers, while Spatial Heterogeneous Mixture of Experts (SHMoE) into the decoder layers. The MoA enhances the specialization of feature extraction by dynamically selecting the optimal combination of attention heads for each image token. Meanwhile, the SHMoE predicts deformation fields heterogeneously in three directions for each voxel using experts with varying kernel sizes. Extensive experiments conducted on two publicly available datasets show consistent improvements over various methods, with a notable increase from 60.58% to 65.58% in Dice score for the abdominal CT dataset. Furthermore, SHMoAReg enhances model interpretability by differentiating experts' utilities across/within different resolution layers. To the best of our knowledge, we are the first to introduce MoE mechanism into DIR tasks.

Learning-based medical image registration has matched the accuracy of conventional methods while offering superior computational efficiency. However, existing approaches suffer from poor generalization across diverse clinical scenarios, requiring the laborious development of multiple isolated networks for specific registration tasks, \emph{e.g.}, inter-/intra-subject registration or anatomical region-specific alignment, leading to cumbersome development pipelines. To overcome this limitation, we propose \textbf{UniReg}, the first conditional unified model for multi-scenario medical image registration, which combines the precision advantages of task-specific learning methods with the generalization of traditional optimization methods. Our key innovation is a unified registration framework that adaptively estimates deformation fields conditioned on: (1) anatomical structure priors, (2) registration type constraints (inter/intra-subject), and (3) instance-specific features, enabling effective alignment across heterogeneous CT and MR registration scenarios within a single model. Through comprehensive experiments on multiple CT/MR registration datasets, UniReg achieves superior average registration accuracy compared with current state-of-the-art learning-based methods while exhibiting strong cross-scenario generalization. Moreover, by replacing multiple isolated task-specific models with a compact unified model, UniReg substantially reduces the overall training burden in terms of total training cost and model redundancy.

This paper describes a new spatial correspondence representation based on paired regions-of-interest (ROIs), for medical image registration. The distinct properties of the proposed ROI-based correspondence are discussed, in the context of potential benefits in clinical applications following image registration, compared with alternative correspondence-representing approaches, such as those based on sampled displacements and spatial transformation functions. These benefits include a clear connection between learning-based image registration and segmentation, which in turn motivates two cases of image registration approaches using (pre-)trained segmentation networks. Based on the segment anything model (SAM), a vision foundation model for segmentation, we develop a new registration algorithm SAMReg, which does not require any training (or training data), gradient-based fine-tuning or prompt engineering. The proposed SAMReg models are evaluated across five real-world applications, including intra-subject registration tasks with cardiac MR and lung CT, challenging inter-subject registration scenarios with prostate MR and retinal imaging, and an additional evaluation with a non-clinical example with aerial image registration. The proposed methods outperform both intensity-based iterative algorithms and DDF-predicting learning-based networks across tested metrics including Dice and target registration errors on anatomical structures, and further demonstrates competitive performance compared to weakly-supervised registration approaches that rely on fully-segmented training data. Open source code and examples are available at: https://github.com/sqhuang0103/SAMReg.git.

Deep learning has shown significant value in medical image registration for motion correction; however, current techniques are either limited by the type and range of motion they can handle or require iterative inference and/or retraining for new imaging data. To address these limitations, we introduce UniMo, a Unified Motion Correction framework that uses deep neural networks to correct various types of motion in medical imaging. UniMo uses an alternating optimization scheme with a unified loss function to train an integrated model of 1) an equivariant neural network for global rigid motion correction and 2) an encoder-decoder network for local deformations. It features a geometric deformation augmenter that 1) enhances the robustness of global motion correction by addressing local deformations, whether caused by non-rigid motion or geometric distortions, and 2) generates augmented data to improve training. As a hybrid model that uses both image intensities and shapes, UniMo is robust to appearance variations and generalizes to various imaging modalities without retraining. We trained and tested UniMo for motion tracking in fetal magnetic resonance imaging, which is challenging due to 1) both large rigid and non-rigid motion and 2) large variations in image appearance. We then tested the trained model, without retraining, on three public datasets: MedMNIST, lung CT, and BraTS. UniMo surpassed existing motion correction methods in accuracy and, notably, enabled one-time training on a single modality while maintaining high stability and adaptability across multiple unseen imaging datasets. By offering a unified solution to motion correction, UniMo marks a significant advance in challenging applications with a mixture of bulk motion and local deformations. Code is available at https://github.com/IntelligentImaging/UNIMO

Dense prediction is a fundamental requirement for many medical vision tasks such as medical image restoration, registration, and segmentation. The most popular vision model, Convolutional Neural Networks (CNNs), has reached bottlenecks due to the intrinsic locality of convolution operations. Recently, transformers have been widely adopted for dense prediction for their capability to capture long-range visual dependence. However, due to the high computational complexity and large memory consumption of self-attention operations, transformers are usually used at downsampled feature resolutions. Such usage cannot effectively leverage the tissue-level textural information available only at the full image resolution. This textural information is crucial for medical dense prediction as it can differentiate the subtle human anatomy in medical images. In this study, we hypothesize that Multi-layer Perceptrons (MLPs) are superior alternatives to transformers in medical dense prediction where tissue-level details dominate the performance, as MLPs enable long-range dependence at the full image resolution. To validate our hypothesis, we develop a full-resolution hierarchical MLP framework that uses MLPs beginning from the full image resolution. We evaluate this framework with various MLP blocks on a wide range of medical dense prediction tasks including restoration, registration, and segmentation. Extensive experiments on six public well-benchmarked datasets show that, by simply using MLPs at full resolution, our framework outperforms its CNN and transformer counterparts and achieves state-of-the-art performance on various medical dense prediction tasks.