Point Cloud Registration for Fusion between SPECT MPI and CTA Images

We propose Bi-PT, a pipeline for reconstructing 3D four-chamber human heart meshes from clinical sparsely sampled cardiac magnetic resonance imaging (CMR) data. This work addresses the error-prone generation of 3D cardiac shape from a sparse point cloud (SPC) extracted from 2D long-axis and short-axis views used in routine clinical CMR protocols. Bi-PT enables accurate inference of the four-chamber heart mesh from the SPC by learning robust point features via bidirectional point cross-attention between an atlas and the SPC, together with per-point semantic labels that improve correspondence estimation. We formulate the deformation field as a Neural Ordinary Differential Equation (NODE) parameterized by a per-point affine transformation and translation to deform the atlas toward the target heart shape. By learning such a NODE, we can guarantee the deformation field to be a locally affine diffeomorphic deformation. We also integrate a semantic label loss into the Chamfer distance to encourage label-consistent correspondences and add a smoothness regularization to stabilize and improve the learning of the deformation field. Extensive experiments demonstrate that Bi-PT achieves accurate and robust performance compared to baselines.

Computational models of the human heart are widely used to study electromechanical and fluid-dynamical cardiac function and to support applications such as in silico clinical trials. However, most studies remain limited to single or patient-specific anatomies, restricting the inclusion of population-level variability required for uncertainty quantification. A key challenge is translating medical-image segmentations, which may contain artifacts, mesh defects or disjoint domains, into topologically coherent geometries suitable for multiphysics simulations. In this work, we present a semi-automatic pipeline that converts CT-based segmentations into simulation-ready cardiac meshes within a few minutes while preserving anatomical and topological consistency. Building on modern deep learning segmentation methods, the framework incorporates a template-based registration stage to regularize artifacts and enforce mesh-quality constraints. A Chamfer-distance morphing strategy deforms a high-quality template toward each segmented heart, matching individual chambers while preserving topology. The resulting meshes are watertight, isotopological, and endowed with consistent point-to-point correspondence. The pipeline is validated on 58 healthy cardiac CT scans, including all cardiac chambers and proximal vessel segments. The resulting meshes can be represented in a unified shape space, enabling the construction of a statistical shape model of the heart and major vessels. Principal Component Analysis shows that a low-dimensional latent space efficiently captures population variability, while Gaussian Mixture Modeling enables synthetic anatomy generation. Overall, the proposed framework (released open-source) provides a pathway from raw segmentations to simulation-ready cardiac geometries, enabling anatomically consistent virtual cohorts for large-scale in silico studies.

Single Ventricle Physiology (SVP) is a rare subtype of congenital heart disease characterized by the presence of a single functional cardiac ventricle with atypical anatomic configurations that challenge conventional image segmentation approaches. The scarcity of clinical data and the morphological diversity across SVP subtypes make the development of robust segmentation methods particularly difficult. To address these limitations, we propose a cardiac MRI segmentation framework focused on ventricular chambers and myocardium segmentation tailored for SVP. First, we introduce a data augmentation pipeline that generates synthetic 3D cardiac meshes using SDF4CHD and corresponding synthetic cardiac MRI through generative modeling. Second, we introduce SV-Cine, a diagnosis-conditioned adaptation of the foundation model CineMA that incorporates patient-level diagnostic information through Feature-wise Linear Modulation layers, enabling diagnosis-aware feature adaptation during segmentation. We evaluated the framework on an internal cohort with varying SVP subtypes. SV-Cine achieved median Dice scores of 0.89 (IQR: 0.80--0.91) for the left ventricle and 0.72 (IQR: 0.54--0.84) for the right ventricle, outperforming the strongest baseline, nnU-Net, by 0.39 Dice points on right ventricle segmentation. It also yields a median ejection fraction error of 5.55 percentage points (IQR: 3.41--7.69) for the dominant ventricle. Compared with the internal cohort, LV and myocardium segmentation performance was lower for the external cohort; whereas RV Dice scores were comparable for both cohorts. Our findings suggest that a pretrained foundation model can be adapted for highly specialized downstream tasks through usage of diagnosis priors while leveraging anatomic knowledge learned from large-scale MRI datasets during pretraining.