MSC19950601 / brats2019-1

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Knowledge Distillation for Brain Tumor Segmentation

This code was written for participation in the Brain Tumor Segmentation Challenge (BraTS) 2019. The code is based on the corresponding paper, where we employ knowledge distillation for automatic brain tumor segmentation. First, we annotated unlabeled data with ensemble of different models. Then, we trained simple UNet model with residual blocks. This repository contains the code for inferencing the distilled model.

Network achitecture

drawing

Results

drawing

Data WT ET TC
Cascaded UNet Val 2019 0.9 0.731 0.833
Distilled Val 2019 0.904 0.756 0.842
Distilled Test 2019 0.887 0.794 0.829

Pre-trained model

Download checkpoint with the following link, where the model has the name brain-tumor-segmentation-0002. You can also download onnx version for cpu inference with OpenVino. The onnx model has a few modifications to match ONNX and OpenVino standards:

  • It takes image of size 128x128x128 as an input
  • It uses nearest neighbour upsampling instead of trilinear one
  • It includes group norm operation from OpenVino

How to perform prediction

  1. Download BraTS data
  2. Download pretrained model
  3. Setup directory hierarchy
  4. Run the script

Run the following command. Models root directory is a repository for all models. Change the output directory in the script.

python test.py --name=brain-tumor-segmentation-0002  --models_path=<model's root dir>

Requirements

dicom                  0.9.9.post1
h5py                   2.9.0
jupyter-client         5.2.4      
jupyter-core           4.5.0      
jupyterlab             1.0.1      
jupyterlab-server      1.0.0    
matplotlib             3.1.1  
nibabel                2.4.1
numpy                  1.16.4      
opencv-python-headless 4.1.0.25    
openpyxl               2.6.2
pandas                 0.24.2
pickleshare            0.7.5      
Pillow                 6.1.0
protobuf               3.8.0
pydicom                1.2.2      
Pygments               2.4.2
PyWavelets             1.0.3
scikit-image           0.15.0      
scikit-learn           0.21.2      
scipy                  1.3.0      
seaborn                0.9.0
SimpleITK              1.2.0      
six                    1.12.0      
sklearn                0.0 
tensorboardX           1.8
torch                  1.2.0      
torchvision            0.4.0
tqdm                   4.32.2

Citation

TBD

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License:MIT License


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