Repository Overview

This repository accompanies the paper “An efficient end-to-end computational framework for the generation of ECG-calibrated volumetric models of human atrial electrophysiology”, published in Medical Image Analysis.

It provides four volumetric meshes of biatrial models together with a reference torso built around each model. These were derived from clinical data and are distributed along with the necessary parameters and data files to reproduce the results presented in Section 3.8 of the study.

Data Description

For each patient Si, i = 1,…,4, the following data are included:

• Volumetric biatrial meshes: Si/mshdata/Si_atria.elem
  Meshes have an average resolution of 0.9 mm and are suitable for Eikonal-based cardiac electrophysiology (CEP) simulations.

• Torso and biatrial meshes: Si/mshdata/Si_atria_torso.vtk

• Lead field solutions: Si/leadfield/Si_electrode.dat
  Contain data for the nine electrodes {R, L, F, V1, …, V6} extracted from the volumetric biatrial meshes.

• Calibrated activation sites: Si/activation_sites/activation_site.vtx
  Lists of vertices in the volumetric biatrial meshes that reproduce the study results.

• Parameter files: Si/simdata/Si_parameters.par
  Define simulation parameters for reproducing the study using the openCARP software. These files link the meshes and activation sites for CEP simulations.

• Activation sequences: Si/simdata/vm.igb
  Represent the evolution of the transmembrane potential over time.

• Activation maps: Si/simdata/vm_activation_seq.dat
  Provide the activation sequences obtained in the study.

• Position of the electrodes on the torso: electrode_nodes.json
  Lists of vertices in the volumetric biatrial-torso mesh corresponding to the electrodes position used to compute the lead field.

Prerequisites for Reproducing the Study

• Software compatibility: All data formats are compatible with openCARP (release v18.1).

• Running simulations: The Eikonal - solver can be executed to reproduced the distributed results using:
  openCARP +F Si_parameters.par

• Electrocardiogram (ECG) reconstruction: Unfiltered ECGs for each patient can be obtained by combining the activation sequence (vm.igb) with the corresponding lead field, and integrating over the atrial domain [1].

• Visualization: Meshes and results can be visualized using the meshalyzer software.

• Format conversion: Meshes can be converted to .vtk, .stl, or openCARP-compatible formats using meshtool.

How to Cite

When using the data provided in this repository, please cite the paper “An efficient end-to-end computational framework for the generation of ECG-calibrated volumetric models of human atrial electrophysiology.”

References

[1] Potse, M., 2018. Scalable and accurate ECG simulation for reaction-diffusion models of the human heart. Frontiers in physiology 9, 370.