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 using mode -1 and std 1.5 INFO:ukb.surface:Saved data/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 INFO:ukb.surface:Saved data/LV_ED.stl INFO:ukb.surface:Saved data/RV_ED.stl INFO:ukb.surface:Saved data/RVFW_ED.stl 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

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_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_ED.stl INFO:ukb.clip:Reading data/RVFW_ED.stl INFO:ukb.clip:Merging RV and RVFW 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/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

Usage

There are three main commands: 1. surf - Extract surfaces from the atlas and save them in the specified directory as STL files 2. clip - Clip the surfaces to remove e.g the outflow tracts 3. 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