CTbet

CTbet is a tool for extracting brain regions from CT images using a Docker container.

Installation

To use CTbet, you need to have Docker installed on your system. See Docker.

Usage

Pull the CTbet Docker image:

docker pull llgneuroresearch/ctbet

Run the CTbet Docker container:

docker run -ti -v /path/to/your/data:/input -v /path/to/your/output:/output -u 0:$(id -g) --gpus all --rm --shm-size 2g avnirlab/ctbet:latest -device cuda

Replace /path/to/your/data with the path to your data directory, and /path/to/your/output with the desired path to your output directory. The –device cuda flag permits to run the inference on GPU. If you want to run the inference on CPU, you can replace cuda by cpu.

Example

Here is an example command to run CTbet:

# Create input and output directories
mkdir output_directory
ls input_data/
    image1.nii.gz  image2.nii.gz

# Run CTbet
docker run -ti -v $(pwd)/input_data:/input -v $(pwd)/output_directory:/output \
-u 0:$(id -g) --gpus all --rm --shm-size 2g avnirlab/ctbet:latest -device cuda

# Check the output
ls output_directory/results
    image1.nii.gz  image2.nii.gz  dataset.json
    plans.json  predict_from_raw_data_args.json