D2-Net: Dual Disentanglement Network for Brain Tumor Segmentation with Missing Modalities

This repository is the official PyTorch implementation of D2-Net: Dual Disentanglement Network for Brain Tumor Segmentation with Missing Modalities published on IEEE TMI 2022.

Overview

We propose a Dual Disentanglement Network (D2-Net) for brain tumor segmentation with missing modalities, which consists of a modality disentanglement stage (MD-Stage) and a tumor-region disentanglement stage (TDStage). In the MD-Stage, a spatial-frequency joint modality contrastive learning scheme is designed to directly decouple the modality-specific information from MRI data. To decompose tumor-specific representations and extract discriminative holistic features, we propose an affinity-guided dense tumor-region knowledge distillation mechanism in the TD-Stage through aligning the features of a disentangled binary teacher network with a holistic student network. By explicitly discovering relations among modalities and tumor regions, our model can learn sufficient information for segmentation even if some modalities are missing.

Requirements

All experiments use the PyTorch library. We recommend installing the following package versions:

•    python=3.7

•    pytorch=1.6.0

•    torchvision=0.7.0

Dependency packages can be installed using following command:

pip install -r requirements.txt

Dateset

Download

We use multimodal brain tumor dataset (BraTS 2018) in our experiments. Download the BraTS2018 dataset and change the path:

experiments/PATH.yaml

Data preprocess

Convert the .nii files as .pkl files. Normalization with zero-mean and unit variance .

python preprocess.py

(Optional) Split the training set into k-fold for the cross-validation experiment.

python split.py

Training

D2-Net can be trained by running following command:

sh tool/train.sh

In our experiments, D2-Net is built on the lightweight backbone U2-Net. Training D2-Net requires at least one V100 GPU with 32G memory. The defualt hyperparameters are set in train.py. Running the training code will generate logs files and saved models in a directory name logs and ckpts, respectively.

Inference

D2-Net can be tested with a saved model using following command:

sh tool/inference.sh

The inference code will test all 15 cases with missing modalities together.

Citation

@article{yang2022d2,
  title={D2-Net: Dual Disentanglement Network for Brain Tumor Segmentation with Missing Modalities},
  author={Yang, Qiushi and Guo, Xiaoqing and Chen, Zhen and Woo, Peter YM and Yuan, Yixuan},
  journal={IEEE Transactions on Medical Imaging},
  year={2022},
  publisher={IEEE}
}

Acknowledgement

1. The implementation is based on the repo: DMFNet