This repository contains a Docker-based auto-segmentation pipeline example relying on the PyRaDiSe Python package.
Clone the repository by typing the following command in your terminal:
git clone https://github.com/ruefene/SkullStrippingPipeline.git
Navigate to the data/model directory and download the example model file from the PyRaDiSe example data repository:
cd SkullStrippingPipeline/data/model
curl -LJO https://github.com/ruefene/pyradise-example-data/raw/main/model/model.pth
Then, go to the repository folder and build the Docker image by typing the following command:
cd SkullStrippingPipeline
docker build -t ch.unibe.segmentation.skullstripping .
To run the pipeline, type the following command in your terminal:
docker run -p 4000:5000 --name SkullStripper --gpus all ch.unibe.segmentation.skullstripping
After starting the container, you can access the web interface by typing the following URL in your browser:
http://localhost:4000
For running this example without using Docker you need to set several environment variables. The following table shows the required environment variables and their default values:
| Variable | Example value | Description |
|---|---|---|
MODEL_DIR_PATH |
C:\SkullStrippingPipeline\data\model |
The directory where the model is stored. |
INPUT_DATA_DIR |
C:\SkullStrippingPipeline\data\input |
The directory where the input data is uploaded to. |
OUTPUT_DATA_DIR |
C:\SkullStrippingPipeline\data\output |
The directory where the output data will be stored before download. |
SCRATCH_DATA_DIR |
C:\SkullStrippingPipeline\data\scratch |
The directory where the temporary data gets stored. |
This project is licensed under the MIT License - see the LICENSE file for details