UK Biobank atlas - mesh generation

UK Biobank atlas - mesh generation#

Generate meshes using the UK Biobank atlas (https://www.cardiacatlas.org/biventricular-modes/)

Install#

Install with pip

python3 -m pip install ukb-atlas

or (latest version)

python3 -m pip install git+https://github.com/ComputationalPhysiology/ukb-atlas

or similarly with pipx

pipx install ukb-atlas

or (latest version)

pipx install git+https://github.com/ComputationalPhysiology/ukb-atlas.git

Quick start#

To generate surfaces from the UK Biobank atlas, run the following command

$ ukb-atlas surf data --mode -1 --std 1.5 --case ED
INFO:ukb.atlas:Generating points from /root/.ukb/UKBRVLV.h5
INFO:ukb.atlas:Using mode -1 and std 1.5
INFO:ukb.surface:Saved data/LV_ENDO_ED.stl
INFO:ukb.surface:Saved data/RV_SEPTUM_ED.stl
INFO:ukb.surface:Saved data/RV_FREEWALL_ED.stl
INFO:ukb.surface:Saved data/LV_EPI_ED.stl
INFO:ukb.surface:Saved data/RV_EPI_ED.stl
INFO:ukb.surface:Saved data/MV_ED.stl
INFO:ukb.surface:Saved data/AV_ED.stl
INFO:ukb.surface:Saved data/TV_ED.stl
INFO:ukb.surface:Saved data/PV_ED.stl

Each STL file is one region of the biventricular template. The file data/surfaces.json records which files make up each surface of the mesh: LV_ENDO, RV_ENDO (RV septum and free wall), EPI (LV and RV epicardium), and the valve rims MV, AV, TV and PV. Now we can generate a mesh from these surfaces

$ ukb-atlas mesh data
INFO:ukb.mesh:Creating mesh for ED with char_length_max=5.0, char_length_min=5.0
INFO:ukb.mesh:Created mesh data/ED.msh

The mesh has the physical surfaces LV_ENDO, RV_ENDO, EPI, MV, AV, TV and PV, and the physical volume Wall.

Now we can also create a mesh without the outflow tracts using the cilp command

$ ukb-atlas clip data
ukb-atlas clip data
INFO:ukb.clip:Folder: data
INFO:ukb.clip:Case: ED
INFO:ukb.clip:Origin: [-13.612554383622273, 18.55767189380559, 15.135103714006394]
INFO:ukb.clip:Normal: [-0.7160843664428893, 0.544394641424108, 0.4368725838557541]
INFO:ukb.clip:Reading data/LV_ENDO_ED.stl
Warning: PLY writer doesn't support multidimensional point data yet. Skipping Normals.
Warning: PLY doesn't support 64-bit integers. Casting down to 32-bit.
INFO:ukb.clip:Saved data/lv_clipped.ply
INFO:ukb.clip:Reading data/RV_SEPTUM_ED.stl, data/RV_FREEWALL_ED.stl
INFO:ukb.clip:Saving data/rv_clipped.ply
Warning: PLY writer doesn't support multidimensional point data yet. Skipping Normals.
Warning: PLY doesn't support 64-bit integers. Casting down to 32-bit.
INFO:ukb.clip:Reading data/LV_EPI_ED.stl, data/RV_EPI_ED.stl
INFO:ukb.clip:Saving data/epi_clipped.ply
Warning: PLY writer doesn't support multidimensional point data yet. Skipping Normals.
Warning: PLY doesn't support 64-bit integers. Casting down to 32-bit.

and then create a mesh from the clipped surfaces

$ ukb-atlas mesh data --clipped
INFO:ukb.mesh:Creating clipped mesh for ED with char_length_max=5.0, char_length_min=5.0
INFO:ukb.mesh:Created mesh data/ED_clipped.msh

The clipped mesh has the physical surfaces LV_ENDO, RV_ENDO, EPI and BASE, and the physical volume Wall.

Geometries#

surf takes a --geometry (-g) option, and mesh builds whichever geometry surf wrote:

Geometry	Physical surfaces	Physical volumes
`biv` (default)	`LV_ENDO`, `RV_ENDO`, `EPI`, `MV`, `AV`, `TV`, `PV`	`Wall`
`biv-closed`	as `biv`, plus `MV_CAP`, `AV_CAP`, `TV_CAP`, `PV_CAP`	`Wall`, `LV_CAVITY`, `RV_CAVITY`
`lv`	`LV_ENDO`, `EPI`, `RV_SEPTUM`, `SEPTAL_BRIDGE`, `MV`, `AV`	`Wall`
`lv-closed`	as `lv`, plus `MV_CAP`, `AV_CAP`	`Wall`, `LV_CAVITY`

MV, AV, TV and PV are the rims where the endocardium and epicardium meet at each valve. In the closed geometries each valve opening is also closed by a cap (*_CAP), so the LV (LV_ENDO + MV_CAP + AV_CAP) and RV (RV_ENDO + TV_CAP + PV_CAP) cavities are closed surfaces. The cavities are meshed as their own volumes, sharing nodes with the wall at the endocardium. The LV-only geometries keep the outflow tract; the LV wall is closed on the RV side by the RV septal surface (RV_SEPTUM) and a surface through the wall along the RV insertion (SEPTAL_BRIDGE), and its EPI is the LV epicardium only.

$ ukb-atlas surf data -g biv-closed
$ ukb-atlas mesh data

clip only supports the biv geometries.

We can also export labelled point clouds directly from the atlas using the points command

$ ukb-atlas points data --mode -1 --std 1.5 --case both
INFO:ukb.atlas:Generating points from /root/.ukb/UKBRVLV.h5
INFO:ukb.atlas:Using mode -1 and std 1.5
INFO:ukb.pointcloud:Saved data/ED_pointcloud.tsv
INFO:ukb.pointcloud:Saved data/ES_pointcloud.tsv

This generates tab-separated files (ED_pointcloud.tsv, ES_pointcloud.tsv) with columns x, y, z, label, and region for every node of the biventricular template. The labels are 1-4 for the valve rims (MV, AV, TV, PV), 5 LV_ENDO, 6 RV_SEPTUM, 7 RV_FREEWALL, 8 LV_EPI, 9 RV_EPI, and 10-13 for the valve centre nodes (MV_CAP, AV_CAP, TV_CAP, PV_CAP).

The triangulation and region labels come from the biv-me template (Apache-2.0), vendored in src/ukb/data/biv-me.

Usage#

There are three main commands:

surf - Extract surfaces from the atlas and save them in the specified directory as STL files
clip - Clip the surfaces to remove e.g the outflow tracts
mesh - Generate mesh from the surfaces

usage: ukb-atlas [-h] {surf,clip,mesh} ...

UKB-atlas This is a command line interface for extracting surfaces and generating Bi-ventricular meshes from the UK Biobank atlas: https://www.cardiacatlas.org/biventricular-modes/

positional arguments:
  {surf,clip,mesh}
    surf            Extract surfaces from the atlas
    clip            Clip the surfaces
    mesh            Generate mesh from the surfaces

options:
  -h, --help        show this help message and exit

Citing#

If you use this tool to create meshes please cite

@software{Finsberg_fenics-beat_2024,
author = {Henrik Finsberg and Lisa R Pankewitz},
doi = {10.5281/zenodo.13927883},
title = {UK Biobank atlas - mesh generation},
url = {https://github.com/ComputationalPhysiology/ukb-atlas},
version = {0.1.0},
year = {2024}
}

The templates used to generate the meshes are described where developed as part of the following publication (so please cite this paper if you use the templates)

@article{PANKEWITZ2024103091,
title = {A universal biventricular coordinate system incorporating valve annuli: Validation in congenital heart disease},
journal = {Medical Image Analysis},
volume = {93},
pages = {103091},
year = {2024},
issn = {1361-8415},
doi = {https://doi.org/10.1016/j.media.2024.103091},
url = {https://www.sciencedirect.com/science/article/pii/S1361841524000161},
author = {Lisa R Pankewitz and Kristian G Hustad and Sachin Govil and James C Perry and Sanjeet Hegde and Renxiang Tang and Jeffrey H Omens and Alistair A Young and Andrew D McCulloch and Hermenegild J Arevalo},
keywords = {Cardiac geometry, Coordinates, Congenital Heart Disease, Mapping},
}

License#

MIT