Patient-specific cardiac modeling combines geometries of the heart derived from medical images and biophysical simulations to predict various aspects of cardiac function. However, generating simulation-suitable models of the heart from patient image data often requires complicated procedures and significant human effort. We present a fast and automated deep-learning method to construct simulation-suitable models of the heart from medical images. The approach constructs meshes from 3D patient images by learning to deform a small set of deformation handles on a whole heart template. For both 3D CT and MR data, this method achieves promising accuracy for whole heart reconstruction, consistently outperforming prior methods in constructing simulation-suitable meshes of the heart. When evaluated on time-series CT data, this method produced more anatomically and temporally consistent geometries than prior methods, and was able to produce geometries that better satisfy modeling requirements for cardiac flow simulations. Our source code and pretrained networks are available at https://github.com/fkong7/HeartDeformNets.

The emergence of deep learning has considerably advanced the state-of-the-art in cardiac magnetic resonance (CMR) segmentation. Many techniques have been proposed over the last few years, bringing the accuracy of automated segmentation close to human performance. However, these models have been all too often trained and validated using cardiac imaging samples from single clinical centres or homogeneous imaging protocols. This has prevented the development and validation of models that are generalizable across different clinical centres, imaging conditions or scanner vendors. To promote further research and scientific benchmarking in the field of generalizable deep learning for cardiac segmentation, this paper presents the results of the Multi-Centre, Multi-Vendor and Multi-Disease Cardiac Segmentation (M&Ms) Challenge, which was recently organized as part of the MICCAI 2020 Conference. A total of 14 teams submitted different solutions to the problem, combining various baseline models, data augmentation strategies, and domain adaptation techniques. The obtained results indicate the importance of intensity-driven data augmentation, as well as the need for further research to improve generalizability towards unseen scanner vendors or new imaging protocols. Furthermore, we present a new resource of 375 heterogeneous CMR datasets acquired by using four different scanner vendors in six hospitals and three different countries (Spain, Canada and Germany), which we provide as open-access for the community to enable future research in the field.

Using observation data to estimate unknown parameters in computational models is broadly important. This task is often challenging because solutions are non-unique due to the complexity of the model and limited observation data. However, the parameters or states of the model are often known to satisfy additional constraints beyond the model. Thus, we propose an approach to improve parameter estimation in such inverse problems by incorporating constraints in a Bayesian inference framework. Constraints are imposed by constructing a likelihood function based on fitness of the solution to the constraints. The posterior distribution of the parameters conditioned on (1) the observed data and (2) satisfaction of the constraints is obtained, and the estimate of the parameters is given by the maximum a posteriori estimation or posterior mean. Both equality and inequality constraints can be considered by this framework, and the strictness of the constraints can be controlled by constraint uncertainty denoting a confidence on its correctness. Furthermore, we extend this framework to an approximate Bayesian inference framework in terms of the ensemble Kalman filter method, where the constraint is imposed by re-weighing the ensemble members based on the likelihood function. A synthetic model is presented to demonstrate the effectiveness of the proposed method and in both the exact Bayesian inference and ensemble Kalman filter scenarios, numerical simulations show that imposing constraints using the method presented improves identification of the true parameter solution among multiple local minima.

SimVascular is an open source software platform for cardiovascular simulation, providing a complete pipeline from medical image data to volumetric model construction, meshing, and blood flow simulation. Previous workshops and educational programs have utilized SimVascular, but learning assessments have not been used to rigorously quantify gains in conceptual understanding. Goal: The purpose of this study is to assess the learning of students enrolled in graduate engineering courses at two different institutions (Purdue University and Stanford University) who used SimVascular to perform image-based blood flow modeling projects as part of a course. Methods: Twenty-two engineering and medical students were given both pre- and post-assessments to quantify their initial familiarity and eventual progress learning computational techniques for biomedical blood flow simulations. The students rated their agreement with eleven different statements. Results: Initial responses were relatively low, suggesting that there was substantial room for student learning. Students then utilized the SimVascular platform to run multiple hemodynamic blood flow simulations. The post-assessment showed a significant increase in agreement with all 11 statements (p<;0.05). Conclusion: These initial efforts demonstrate the effectiveness of SimVascular as a teaching tool in a classroom setting.

Tracing the paths of collections of particles through a flow field is a key step for many flow visualization and analysis methods. When a flow field is interpolated from the nodes of an unstructured mesh, the process of advecting a particle must first find which cell in the unstructured mesh contains the particle. Since the paths of nearby particles often diverge, the parallelization of particle advection quickly leads to incoherent memory accesses of the unstructured mesh. We have developed a new block advection GPU approach that reorganizes particles into spatially coherent bundles as they follow their advection paths, which greatly improves memory coherence and thus shared-memory GPU performance. This approach works best for flows that meet the CFL criterion on unstructured meshes of uniformly sized elements, small enough to fit at least two timesteps in GPU memory.