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Federated Tumor Segmentation Challenge 2021 (task-2 2nd place solution)

Installation

clone the repository and run the setup.sh file

sh setup.sh

Data Prepration for training only

set the src_path to the nifiti images and dst_path to output dir for .npy data

generate_numpy_data.py --src_path=./data/nifti/train/*/*seg.nii.gz --dst_path=./data/np/train/

Training

cd ./trainingScripts
sh train.sh

Inference

inference.py

Paper:

Pawar, K., Zhong, S., Chen, Z., Egan, G. (2022). Brain Tumor Segmentation Using Two-Stage Convolutional Neural Network for Federated Evaluation. In: Crimi, A., Bakas, S. (eds) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2021. Lecture Notes in Computer Science, vol 12963. Springer, Cham. https://doi.org/10.1007/978-3-031-09002-8_43

https://link.springer.com/chapter/10.1007/978-3-031-09002-8_43