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LibHip - A Hip Joint Finite Element Model Repository

teaser

LibHip is an open-access hip joint finite element model repository designed for simulation studies. Our repository consists of clinically verified subject-specific hip joint models along with the algorithms to reproduce them. The main features of the models are listed as below:

  • 11 clinically verified subject-specific bilateral models covering the bones and cartilages in the hip joint area
  • Semi-automated modeling workflow using cutting-edge geometry processing tools
  • A direct geometry processing cartilage reconstruction method using segmented bone models
  • Multi-body volume mesh generation, resulting in high-quality discretization, conforming and congruent shared interfaces, and accurate geometries

Data Structure

The model_repository folder contains all the research data belonging to 11 subjects: the clinical images, the segmentation label maps, the multi-body surface and volume meshes, and the finite element models. Detailed explanation of each research data is provided in the related folder.

Screenshot 2022-07-24 at 22 08 36

Modeling Flowchart and Pipeline

Screenshot 2022-04-28 at 10 50 05

The src, notebooks, and the config folders contain the codes that we used to create these models.

  • The src folder locates the source python functions of our modeling pipeline. These functions are called by the Jupyter notebooks in the notebooks folder.
  • The notebooks folder contains the preprocessing, cartilage generation, the volume mesh generation, and the simulation file generation codes. These notebooks call the source codes from the src folder.
  • The config folder contains the subject-specific configurations you need for each subject. These parameters are called by the files in the notebooks folder during the modeling pipeline.
  • Each time you run the Jupyter notebooks, the output of each step is stored in the model_generation folder.

Installation

First, clone this repository to your local directory and go into that folder. Below, is an example of how to clone this repository using the command line:

git clone https://github.com/diku-dk/libhip.git
cd libhip

Next, create a conda environment named libhip, using the channel conda-forge and the list of packages in the requirements.txt file:

conda create --name libhip -c conda-forge --file requirements.txt

Finally, activate your environment and run the jupyter notebook:

conda activate libhip
jupyter notebook

Further, install fTetWild using CMake and clone RAINBOW on your machine.

Citation

Please cite this work by using this reference:

@article{moshfeghifar226libhip,
  title={LibHip: An open-access hip joint model repository suitable for finite element method simulation},
  author={Moshfeghifar, Faezeh and Gholamalizadeh, Torkan and Ferguson, Zachary and Schneider, Teseo and Nielsen, Michael Bachmann and Panozzo, Daniele and Darkner, Sune and Erleben, Kenny},
  journal={Computer methods and programs in biomedicine},
  volume={226},
  pages={107140}
}

Acknowledgement

🌈 This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 764644. This repository only contains the RAINBOW consortium’s views, and the Research Executive Agency and the Commission are not responsible for any use that may be made of the information it contains.

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🌟 This work was partially supported by the NSF CAREER award under Grant No. 1652515, the NSF grants OAC-1835712, OIA-1937043, CHS-1908767, CHS-1901091, NSERC DGECR-2021-00461, and RGPIN-2021-03707, a Sloan Fellowship, a gift from Adobe Research and a gift from Advanced Micro Devices, Inc.