brainles-aurora 0.2.6

Segmentation models for cancer metastasis in brain MR.

AURORA

Deep learning models for brain cancer metastasis segmentation based on the manuscripts:

• Identifying core MRI sequences for reliable automatic brain metastasis segmentation
• Development and external validation of an MRI-based neural network for brain metastasis segmentation in the AURORA multicenter study

Installation

With a Python 3.8+ environment, you can install brainles_aurora directly from pypi.org:

pip install brainles-aurora

Recommended Environment

• CUDA 11.4+ (https://developer.nvidia.com/cuda-toolkit)
• Python 3.8+
• GPU with CUDA support and at least 6GB of VRAM

Usage

BrainLes features Jupyter Notebook tutorials with usage instructions.

A minimal example could look like this:

    from brainles_aurora.inferer import AuroraInferer, AuroraInfererConfig

    config = AuroraInfererConfig(
        tta=False, cuda_devices="4"
    )  # disable tta for faster inference in this showcase
    inferer = AuroraInferer(config=config)

    inferer.infer(
        t1="t1.nii.gz",
        t1c="t1c.nii.gz",
        t2="t2.nii.gz",
        fla="fla.nii.gz",
        segmentation_file="segmentation.nii.gz",
        whole_tumor_unbinarized_floats_file="whole_network.nii.gz",
        metastasis_unbinarized_floats_file="metastasis_network.nii.gz",
        log_file="aurora.log",
    )

Citation

Please support our development by citing the following manuscripts:

Identifying core MRI sequences for reliable automatic brain metastasis segmentation

@article{buchner2023identifying,
  title={Identifying core MRI sequences for reliable automatic brain metastasis segmentation},
  author={Buchner, Josef A and Peeken, Jan C and Etzel, Lucas and Ezhov, Ivan and Mayinger, Michael and Christ, Sebastian M and Brunner, Thomas B and Wittig, Andrea and Menze, Bjoern H and Zimmer, Claus and others},
  journal={Radiotherapy and Oncology},
  volume={188},
  pages={109901},
  year={2023},
  publisher={Elsevier}
}

also consider citing the original AURORA manuscript, especially when using the vanilla model (all 4 modalities as input):

Development and external validation of an MRI-based neural network for brain metastasis segmentation in the AURORA multicenter study

@article{buchner2022development,
  title={Development and external validation of an MRI-based neural network for brain metastasis segmentation in the AURORA multicenter study},
  author={Buchner, Josef A and Kofler, Florian and Etzel, Lucas and Mayinger, Michael and Christ, Sebastian M and Brunner, Thomas B and Wittig, Andrea and Menze, Bj{\"o}rn and Zimmer, Claus and Meyer, Bernhard and others},
  journal={Radiotherapy and Oncology},
  year={2022},
  publisher={Elsevier}
}

Contact / Feedback / Questions

If possible please open a GitHub issue here.

For inquiries not suitable for GitHub issues:

Florian Kofler florian.kofler [at] tum.de

Josef Buchner j.buchner [at] tum.de