Brats19

This repo contains code for the Brain Tumor Segmentation Challenge 2020, published in Brainlesion 2019:

Pawar K, Chen Z, Shah NJ, Egan GF. An Ensemble of 2D Convolutional Neural Network for 3D Brain Tumor Segmentation. In International MICCAI Brainlesion Workshop 2019 Oct 17 (pp. 359-367). Springer, Cham.

Installation

Clone the repository and run setup.sh as

sh setup.sh

Run

To run prediction, copy all four MRI contrast images ending with names (*.t1.nii.gz, *.t2.nii.gz, *,t1ce.nii.gz, *.flair.nii.gz) into the directory ./data then run the following

cd ./src
python predict_all_no_gt.py

The output will be in ./data/results/

Dependencies

The repository requires dependencies to be installed before runnning the inference. The dependieies are:

nibabel, Keras, Tensoflow

Alternatively, a Docker Container is avalibale here