Getting started

The Vascular Model Repository is a library of cardiovascular models. Model projects can be downloaded in .zip format from the Repository. Each archive contains a project compatible with SimVascular, an open-source software for patient-specific cardiovascular modeling and simulation. We refer to the SimVascular website and Getting started page for an in-depth discussion of the software capabilities and its usage. In this documentation, we limit ourselves to recall that a SimVascular project can be opened by clicking File > Open SV Project... in the graphical user interface and by selecting the desired project folder.

Although the models are compatible with SimVascular by design, some components (in particular, image data and computational meshes) can be easily opened in other pieces of software too. Here is a brief description of the subfolders contained in each project:

Images: directory containing medical image data in .vti format, which can be opened, for example, using Paraview.

Paths: directory containing path files in *.pth format, where * is usually one of the vessels making up the current model. Path files store path points (in .xml format) manually identified during the centerline identification stage of SimVascular.

Segmentations: directory containing contour files in *.ctgr format, where * is usually one of the vessels making up the current model. Contour files store contour points (in .xml format) manually identified during the segmentation stage of SimVascular.

Models: directory containing the surface model of the geometry.

Meshes: directory containing the meshes of the model. Surface meshes are stored in .vtp, while volumetric meshes are stored in .msh and .vtu formats; .vtp and .vtu files can be opened, for example, using Paraview.

flow-files: directory containing inflow boundary conditions. These as stored in files called inflow_3d.flow, i.e., as raw text files in which each row corresponds to a particular timestep and flowrate value. Note that, in SimVascular, a positive inflow requires a negative sign (as the normal to the inlet surface and the velocity field have opposite orientations).

Simulations: directory containing simulation files compatible with SimVascular. Please note that simulation results are currently not included in the repository.

History

The Vascular Model Repository was originally created by Nathan Wilson and the Open Source Medical Software Corporation (OSMSC) under contract HHSN268201100035C with the National Institues of Health (NIH). The repository has then been migrated into its current form in a joint effort between the Cardiovascular Biomechanics Computation Lab at Stanford University, the Shadden Lab at Berkeley University, and Nathan Wilson. The project is currently supported by the NIH National Library of Medicine (grant 5R01LM013120).

References

We refer to the following publications for additional details on the Vascular Model Repository. If you find the repository useful, please consider citing these references.

N.M. Wilson, A.K. Ortiz, and A.B. Johnson, The Vascular Model Repository: A Public Resource of Medical Imaging Data and Blood Flow Simulation Results, J. Med. Devices 7(4), 040923 (Dec 05, 2013) doi:10.1115/1.4025983.

M.R. Pfaller, J. Pham, A. Verma, N.M. Wilson, D.W. Parker, W. Yang, and A.L. Marsden, Automated generation of 0D and 1D reduced-order models of patient-specific blood flow, arXiv:2111.04878.

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