• Install Dependencies
• Setup HEDI
• How to use HEDI
• Authors
• Citation
• License

Install Dependencies

Install Git

Download and install Git.

Clone the HEDI repository

The repository should be in the directory: %Userprofile%\git. Open the CMD shell and enter:

mkdir git
cd git
git clone https://github.com/biomedisa/hernia-repair.git

Install Anaconda3

Download and install Anaconda3.
Important Note!!!: Anaconda must be installed within the %Userprofile% directory (typically C:\Users\%USERNAME%).

Install Paraview (Version 5.10.1 for Python 3.9)

Install Paraview. If the installation directory differs from C:\Program Files\ParaView 5.10.1-Windows-Python3.9-msvc2017-AMD64 you must create a copy of the hernia-repair\config_base.py file:

copy %Userprofile%\git\hernia-repair\config_base.py %Userprofile%\git\hernia-repair\config.py

and adjust the paraview entry in config.py.

Install NVIDIA Driver

Download and install the correct Nvidia driver NVIDIA.
Choose Windows Driver Type: Standard
Choose Recommended/Beta: Studio Driver

Setup HEDI

Automatic Setup

Within the cloned repository lies the batchfile setup.bat Running this file will automaticly create an enviornment with all dependencies needed to run HEDI. Alternatively, you can run the commands manually as described in the next section.

Manual Setup

Open Anaconda Prompt (e.g. Windows Search Anaconda Prompt) or activate conda within the CMD shell via:

call "%Userprofile%\anaconda3\Scripts\activate.bat"

Create and activate the conda environment:

conda env create -f environment.yml

The .yml file contains all infos about the required packages needed to run HEDI.

You can check if the enviornment was created by:

conda activate biomedisa

Configure the config file

Check all paths in the config_base.py file. If any path in this file needs to be adjusted, you must create a copy of the hernia-repair\config_base.py file:

copy %Userprofile%\git\hernia-repair\config_base.py %Userprofile%\git\hernia-repair\config.py

and adjust the config.py file.

How to use HEDI

HEDI can be started either by running the HEDI.bat batch file or directly from the Anaconda command prompt:

conda activate biomedisa
python "%Userprofile%\git\hernia-repair\HEDI_main.py"

When running the application the user will be asked by a popup window to select the dataset containing the Dicom data of a patient:

The data is then sorted and stored in the directory %Userprofile%\Hernia_Analysis_Results\Patient_Name\Dicom_Data
Next the user will be asked by a popup window to select the directory within the above directory that contains the data at rest in axial direction:

Afterwards the corresponding data during valslva needs to be selected in the same way:

Lastly the user is asked to select a threshold value for the area of instability (default = 15mm):

Depending on your machine the application now runs for 4-20 min. All files are stored in the above mentioned directory %Userprofile%\Hernia_Analysis_Results\Patient_Name. After completion, the final result is presented as an image.

Authors

• Philipp D. Lösel
• Jacob J. Relle

Citation

Please cite the following HEDI preprint: Lösel, P.D. et al. HEDI: First-Time Clinical Application and Results of a Biomechanical Evaluation and Visualisation Tool for Incisional Hernia Repair. Preprint at https://arxiv.org/abs/2307.01502 (2023). https://arxiv.org/abs/2307.01502

License

This project is covered under the EUROPEAN UNION PUBLIC LICENCE v. 1.2 (EUPL).