Installation

pip install

With Python 3.9+ (3.10+ for preprocessing), you can install BraTS Orchestrator directly from PyPI:

pip install brats
pip install brats[preprocessing]

Important

BraTS Orchestrator requires Docker or Singularity to run algorithm containers. Most algorithms also need GPU support (NVIDIA Container Toolkit). The algorithm tables indicate which algorithms are CPU compatible.

Docker Setup

• Docker: Installation instructions on the official website
• NVIDIA Container Toolkit: Refer to the NVIDIA install guide and the official GitHub page

Singularity Setup

Singularity provides a container runtime alternative to Docker, commonly used on HPC clusters. Install it following the official guide.

Specify the Singularity backend when running inference:

from brats.constants import Backends

segmenter.infer_single(
    t1c="path/to/t1c.nii.gz",
    output_file="path/to/segmentation.nii.gz",
    backend=Backends.SINGULARITY,
)