Automatic LV Localization and Short-Axis Plane Estimation from Arbitrary CMR Slice

Reconstructing a three-dimensional left-ventricular (LV) endocardial surface from cardiac magnetic resonance (CMR) data is challenging when supervision is available on only a small number of axial slices. Through-plane geometry is weakly constrained, and automatically generated two-dimensional masks can propagate segmentation errors into the recovered shape. We present MR-RS-SDFR, a per-case implicit signed distance field (SDF) framework that reconstructs a continuous LV surface from a CMR volume and sparse axial weak masks. The method first builds a cross-slice SDF initialization from axial and longitudinal geometric cues and then refines the field using two complementary signals: MRI edge-field normal alignment, which provides an image-derived boundary cue independent of the weak masks, and differentiable reslice Dice and contour consistency, which preserve agreement with the observed planes. We evaluate three weak-mask generators -- LOO TransUNet, LOO nnU-Net, and an off-the-shelf Medical SAM3 model used without MM-WHS-specific training or fine-tuning -- and five sparsity levels from 4 to 64 axial planes. In the sparse-16 setting, final MR-RS-SDFR reconstruction reaches 0.928 Dice and 3.80mm HD95 with Medical SAM3 masks. The upstream generators do not exhibit a single common ranking across 2D and dense 3D segmentation, and nnU-Net- and Medical-SAM3-driven sparse reconstruction achieve the same mean final Dice despite different upstream error profiles. Across all three sparse-16 mask sources, MR-RS-SDFR is numerically better than protocol-matched full GHD+DVS in both Dice and HD95. Final Dice improves markedly from sparse-4 to sparse-16 and then saturates at the reported precision through sparse-64. These results support MRI-guided per-case SDF refinement as a reconstruction strategy that remains effective across weak-mask generators and supervision densities.

Clinical acquisition in cardiac magnetic resonance (CMR) imaging involves obtaining cross-sectional planes of the heart along the radial and longitudinal directions. Despite these planes being 2D cross-sectional images of the heart, radiologists understand the 3D spatial and continuous temporal nature of the organ being imaged. The same can not be said about the conventional deep learning architectures used to process CMR images, which rely on in-plane and grid-based operations, and are hence unable to organically integrate information from all imaging planes. This paper builds upon previous work on neural implicit segmentation functions (NISF) to overcome unaddressed challenges in cardiac function modeling in the CMR domain. For a given subject, our architecture builds a shared 3D+time representations from all available acquisition planes regardless of orientation. By design, predictions along any imaging plane orientation are cross-sections of the same 3D representation, leading to spatio-temporal consistency across all slices. Moreover, our architecture makes the rotation and translation parameters of imaging planes learnable, allowing us to correct for the commonplace respiratory and patient motion between slice acquisitions under a rigid assumption. Furthermore, interpolation of intensities and segmentation can be performed in 4D at any desired resolution. We perform our study on a 120 subject sub-cohort of CMR imaging data from the UK-Biobank. Our in-plane segmentation performance is on-par with existing CMR segmentation methods and explore how the majority of failure cases arise from limitations in the ground-truth segmentation, for which our representations make predictions with better anatomical accuracy than its original training data. We also evaluate our motion-correction capabilities, displaying quantitative and qualitative improvements in slice alignment.

Cardiac magnetic resonance (CMR) imaging provides complementary information on cardiac anatomy, function, and tissue characterization across multiple sequences and views. In this work, we investigate foundation model pretraining for 2D CMR and introduce CMRVision, a CMR-specific foundation model trained using DINOv3-style self-supervised learning on a multi-center, multi-sequence cohort of 36 million CMR images. We systematically evaluate architectural and training design choices for domain-specific pretraining. CMRVision is evaluated on two downstream tasks: multi-task segmentation across cine, late gadolinium enhancement (LGE), and mapping sequences, and cine view classification. Our experiments show that CMR-specific pretraining, smaller patch sizes, and patch-level objectives consistently improve downstream performance. Across a multi-task segmentation benchmark, CMRVision achieved the strongest overall performance, outperforming prior natural-image (NI), medical-image, supervised, and CMR foundation model baselines. Improvements were modest but consistent across structures and sequences, with Dice scores ranging from 0.940-0.967 for LV and 0.855-0.905 for myocardium, and reaching 0.929 for RV, 0.920 for LA, and 0.931 for RA. The largest gains were observed for myocardium segmentation in LGE and mapping images. In a zero-shot segmentation task on unseen LGE long-axis views, the model achieved an average Dice score of 0.692, demonstrating cross-view generalization. For cine view classification, CMRVision achieved the highest average accuracy (0.906), compared to prior methods reported in the literature. These results highlight the potential of CMRVision to support robust and generalizable cardiac MRI analysis across multiple sequences and views.