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
With a Python 3.8+ environment, you can install brainles_aurora directly from pypi.org:
pip install brainles-aurora
- CUDA 11.4+ (https://developer.nvidia.com/cuda-toolkit)
- Python 3.8+
- GPU with CUDA support and at least 6GB of VRAM
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",
)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):
@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}
}
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