DOI: 10.5281/zenodo.5573921
title: Four-Chamber Human Heart Model for the Simulation of Cardiac Electrophysiology and Cardiac Mechanics

description: This repository contains a four-chamber model of the human heart which is ready to use for simulations of cardiac electrophysiology and cardiac mechanics problems. When using this dataset, please also cite the accompanying paper Gerach, T.; Schuler, S.; Fröhlich, J.; Lindner, L.; Kovacheva, E.; Moss, R.; Wülfers, E.M.; Seemann, G.; Wieners, C.; Loewe, A. Electro-Mechanical Whole-Heart Digital Twins: A Fully Coupled Multi-Physics Approach. <em>Mathematics</em> <strong>2021</strong>, <em>9</em>, 1247. https://doi.org/10.3390/math9111247 The cardiac anatomy was manually segmented from magnetic resonance imaging (MRI) data of a 33 year old male volunteer. The volunteer provided informed consent and the study was approved by the IRB of Heidelberg University Hospital (Fritz et al., 2014).<br> The MRI data were acquired using a 1.5 T MR tomography system and consist of a static whole heart image stack taken during diastasis as well as time-resolved images in several long and short axis slices. Based on the segmentation, we first labeled the atria and the ventricles. The geometry was extended by a representation of the mitral valve, the tricuspid valve, the aortic valve and the pulmonary valve. Additionally, we closed the endo- and epicardial surfaces of the atria and added truncated pulmonary veins, vena cavae as well as the ascending aorta and pulmonary artery. Furthermore, we added a concentric layer of tissue around the entire heart which phenomenologically represents the influence of the pericardium and the surrounding tissue. Two tetrahedral meshes were created using Gmsh (Geuzaine et al., 2009): (1) the mechanical reference domain (<strong>M.vtu</strong>) with 128,976 elements (on average 3.17 mm edge length) and (2) the electrophysiological reference domain (<strong>EP.vtu</strong>) as a subset of M with 50,058,295 elements (on average 0.4 mm edge length).<br> We used rule-based methods to assign the myofiber orientation on EP: Wachter et al. (2015) was used for the atria and Bayer et al. (2012) for the ventricles. The fiber angle in the ventricles was chosen as +60° and -60° on the endocardial and epicardial surface, respectively. The sheet angle was set to -65° on the endocardium and 25° on the epicardium. Github repositories to these fiber generation tools are given in the sidebar. All geometry files are given in millimeter (mm). <strong>Data:</strong><br> We provide time resolved data evaluated from cine MRI data, which can be used for model calibration. Wall thickening (<strong>17AHA_WT.txt</strong>) / fractional wall thickening (<strong>17AHA_fractionalWT.txt</strong>) in the 17 AHA segments of the left ventricle Atrioventricular plane displacement (<strong>AVPD.txt</strong>) and velocity (<strong>AVPV.txt</strong>) as well as the displacement of all tracked points used for AVPD calculation (<strong>AVPD_trackedPoints.txt</strong>) Left and right ventricular volume (<strong>Volume_LV_RV.txt</strong>). RV volume is only available for end-diastole and end systole. <strong>Surfaces:</strong><br> This directory contains *.stl files with triangulated surfaces on which boundary conditions can be applied. <strong>cavityXX.stl</strong>: blood volume of the LV, RV, LA, RA <strong>epicard.stl</strong>: the whole epicardium <strong>outerPeri.stl</strong> and <strong>outerTrunks.stl</strong>: surfaces for Dirichlet boundary conditions <strong>master.stl </strong>and <strong>slave.stl</strong>: surfaces used for the frictionless contact problem described in Fritz et al. (2014) <strong>TetGen:</strong><br> Contains the geometry <strong>M.vtu</strong> in the TetGen file format. .bases: fiber, sheet, and normal orientation at quadrature points of all elements .node: vertex coordinates .ele: list of tetrahedra .sur: list of triangles T4: mesh with 4 node tetrahedrons and 3 node triangles T10: mesh with 10 node tetrahedrons and 3 node triangles (refined once, compared to T4 version) <strong>EP.vtu:</strong><br> Contains the cell arrays Fiber and Material. <strong>M.vtu:</strong><br> Contains the cell arrays Fiber, Sheet, Sheetnormal, Material, and Label. <strong>LabelIDs.txt:</strong><br> List of Label and Material identification numbers and corresponding anatomical structures.
description: {"references": ["Fritz, T. et al., (2014) Simulation of the contraction of the ventricles in a human heart model including atria and pericardium: Finite element analysis of a frictionless contact problem. Biomechanics and Modeling in Mechanobiology 13(3):627\u2013641", "Geuzaine, C. et al. (2009). Gmsh: A 3-d finite element mesh generator with built-in pre- and post-processing facilities. Int J Numer Methods Eng, 79:1309\u20131331.", "Bayer, JD. et al., (2012) A novel rule-based algorithm for assigning myocardial fiber orientation to computational heart models. Annals of Biomedical Engineering 40(10):2243\u20132254", "Wachter, A. et al., (2015) Mesh structure-independent modeling of patient-specific atrial fiber orientation. Current Directions in Biomedical Engineering 1(1):409\u2013412"]}