The heart adapts to physiological and pathological changes in loading. This can cause the heart to change size and shape. These changes can in turn have significant impact on cardiac function. However, it is not clear if large changes in function are caused by large changes in shape or can smaller changes also be important. Biophysical computational models of the heart provide a quantitative framework for mapping changes in anatomy to whole heart function. We created a publicly available healthy four-chamber heart virtual cohort from clinical images. Each patient's heart anatomy in the virtual cohorts was described by the contribution of different components of heart shape. The shape components are ranked by the amount of shape variance that they explain. Simulations of cardiac electrical activation and mechanical pump function in hearts with shapes describe by different combinations of shape components were performed. This allowed us to show that some shape components that explain a large amount of electrical and mechanical function variance only explain a small amount of anatomical variance. This highlights the need to have high fidelity anatomical models in cardiac simulations and demonstrates that subtle changes in cardiac anatomy can have a large impact on cardiac function.
The codebase provides a set of methods for mesh generation, 3D alignment for atlas generation, tetrahedralisation of the surface meshes with gmsh, rigid mesh manipulation, deformation and file management.
The project is an element of the framework used for statistical shape analysis of tetrahedral meshes, which allows for studies of cardiac shape, function and statistical reasoning.
Briefly, we segmented four-chamber hearts from CT images using an automatic segmentation step with post-processing using Seg3D. The final segmentation consisted of 31 different labels for the blood pools, myocardium and the outflow tracts of the main vessels as well as the papillary muscles. The cardiac valves were modelled as surfaces between the blood pools of the chambers. Similar surfaces were also added to the vessel locations to close the endocardial surfaces. We built unstructured tetrahedral meshes of all elements except the blood pools and papillary muscles using the Computational Geometry Algorithm Library (CGAL) with average edge length of 1 mm. One of the main differences of our meshes with respect to other whole-heart meshes, is the addition of auxiliary anatomical components needed to add mechanics boundary conditions.
We have made all the meshes from the CT and synthetic cohort available for the community in .vtk format. We have added 1000 more meshes modifying the PCA weights randomly withing 2 SD range. The same anatomical structures are present in all the meshes described, but fibres and UVC were not included in the extra 1000 batch. A VTK file for each mesh was included (in ASCII) as an UNSTRUCTURED GRID. In all the cases the following fields were included: POINTS, with the coordinates of the points in mm; CELL TYPES, having all of the points the value 10 since they are tetrahedra; CELLS, with the indices of the vertices of every element; and CELL DATA corresponding to the meshing tags.
Please quote the following publication: Cristobal Rodero, Maciej Marciniak, Marina Strocchi, Stefano Longobardi, John Whitaker, Mark D. O'Neill, Karli Gillette, Christoph Augustin, Gernot Plank, Ed Vigmond, Pablo Lamata, Steven A. Niederer. (2021) Linking statistical shape models and simulated function in the healthy adult human heart. DOI: https://doi.org/10.1371/journal.pcbi.1008851
The code is openly available. If this tool has been useful in your research, please reference this site: https://github.com/MaciejPMarciniak/CardiacShapeModel