Laplace-Dirichlet Rule-Based (LDRB) algorithm for assigning myocardial fiber orientations

A software for assigning myocardial fiber orientations based on the Laplace Dirichlet Ruled-Based algorithm based on FEniCSx.

Bayer, J.D., Blake, R.C., Plank, G. and Trayanova, N.A., 2012. A novel rule-based algorithm for assigning myocardial fiber orientation to computational heart models. Annals of biomedical engineering, 40(10), pp.2243-2254.(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518842/)

Getting started

For example if you have a bi-ventricular geometry (e.g from cardiac-geometries), you can generate fibers as follows

import cardiac_geometries
import ldrb
import dolfinx

# Generate an idealized BiV geometry
geo = cardiac_geometries.mesh.biv_ellipsoid(outdir=geodir)
# Generate fibers with 60/-60 fibers angles on the endo- and epicardium
system = ldrb.dolfinx_ldrb(mesh=geo.mesh, ffun=geo.ffun, markers=geo.markers, alpha_endo_lv=60, alpha_epi_lv=-60, beta_endo_lv=0, beta_epi_lv=0, fiber_space="P_2")
# Visualize fibers in Paraview
with dolfinx.io.VTXWriter(
    geo.mesh.comm, outdir / f"microstructure-viz.bp", [system.f0, system.s0, system.n0], engine="BP4"
) as vtx:
    vtx.write(0.0)

If you now open the file microstructure-viz.bp in Paraview (using the ADIOS2VTXReader), select Glyph and choose f0 as orientation array you can see the fiber orientations similar to the following figure (here I have also added a Calculator to compute the fiber angle)

Note that you can achieve the the same results using the command line interface

ldrb mesh.xdmf --markers-file markers.json --fiber-space P_2 --alpha-endo-lv 60 --alpha-epi-lv -60 --beta-endo-lv 0 --beta-epi-lv 0

Note that if you don't specify a different angle for the RV or Septum, then the same angle as the LV will be used.

Installation

pip

python3 -m pip install fenicsx-ldrb

Docker

To pull the latest docker image you can do

docker pull ghcr.io/finsberg/fenicsx-ldrb:main

or choose a specific version e.g

docker pull ghcr.io/finsberg/fenicsx-ldrb:v0.1.4

Note that you can also run the cli directly using docker e.g

docker run --rm -v $PWD:/home/shared -w /home/shared -it ghcr.io/finsberg/fenicsx-ldrb ldrb --help

Documentation

See https://finsberg.github.io/fenicsx-ldrb

License

MIT

Contributors

Henrik Finsberg (henriknf@simula.no)

finsberg / fenicsx-ldrb