ukb-atlas 0.1.0

Generate meshes from UK Biobank data

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

or with pipx

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

Usage

$ ukb-atlas --help
usage: ukb-atlas [-h] [-a] [-m MODE] [-s STD] [--mesh] [--char_length_max CHAR_LENGTH_MAX] [--char_length_min CHAR_LENGTH_MIN] outdir

Generate surfaces and meshes from UK Biobank atlas.

positional arguments:
  outdir                Directory to save the generated surfaces and meshes.

options:
  -h, --help            show this help message and exit
  -a, --all             Download the PCA atlas derived from all 4,329 subjects from the UK Biobank Study.
  -m MODE, --mode MODE  Mode to generate points from. If -1, generate points from the mean shape. If between 0 and the number of modes, generate points from the
                        specified mode. By default -1
  -s STD, --std STD     Standard deviation to scale the mode by, by default 1.5
  --mesh                Create gmsh mesh files from the generated surfaces.
  --char_length_max CHAR_LENGTH_MAX
                        Maximum characteristic length of the mesh elements.
  --char_length_min CHAR_LENGTH_MIN
                        Minimum characteristic length of the mesh elements.

For example, by running the following command

ukb-atlas data --mesh

The tool will generate the following files

data
├── AV_ED.stl
├── AV_ES.stl
├── ED.msh
├── EPI_ED.stl
├── EPI_ES.stl
├── ES.msh
├── LV_ED.stl
├── LV_ES.stl
├── MV_ED.stl
├── MV_ES.stl
├── PV_ED.stl
├── PV_ES.stl
├── RVFW_ED.stl
├── RVFW_ES.stl
├── RV_ED.stl
├── RV_ES.stl
├── TV_ED.stl
├── TV_ES.stl
├── UKBRVLV.h5
└── parameters.json

Which are surfaces for both the end diastolic (ED) and the end systolic (ES) shapes, the PCA atlas (UKBRVLV.h5) and the parameters used to generate the surfaces.

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