AURORA

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

WARNING: This code base is no longer supported. It still works, but we recommended using BrainLes AURORA instead, which offers much more flexibility in a convenient PyPI package.

Installation

1. Clone this repository:

   git clone https://github.com/neuronflow/AURORA
   

2. Go into the repository and install:

   cd AURORA
   pip install -r requirements.txt 
   

Recommended Environment

• CUDA 11.4+
• Python 3.10+
• GPU with at least 8GB of VRAM

further details in requirements.txt

Usuage

run_inference.py: Example script for single inference.

Input: t1_file, t1c_file, t2_file, fla_file

All 4 input files must be nifti (nii.gz) files containing 3D MRIs. Please ensure that all input images are correctly preprocessed (skullstripped, co-registered, registered on SRI-24, you can use BraTS Toolkit for that).

Output: segmentation_file

Add path to your desired output folder.

optional Output: whole_network_outputs_file, enhancing_network_outputs_file

Citation

when using the software please cite https://www.sciencedirect.com/science/article/pii/S0167814022045625

@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}
}

Licensing

This project is licensed under the terms of the GNU Affero General Public License v3.0.

Contact us regarding licensing.

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