lhlm1994/decgan

[MICCAI2019] Chest X-ray decomposition with unpaired CT knowledge

Requirements

pytorch==0.3.1
visdom==0.1.8.5

Introduction

In this study, we propose the decompose X-ray into separate components by taking advantage of the unpaired 3D knowledge from CT in the framework of generative adversarial network (GAN). The main idea of this paper is:

Please refer to the paper for more details.

Results

Out method disentangles different X-ray components in the latent space. It can be applied to modulating different components in X-ray images by changing the corresponding weights of probability maps in the latent space.

For example, it can be applied to bone suppression or lung enhancement by changing alpha_bone or alpha_lung:

Data

Please download the data and put it in ./dataset/. We provide the processed DRR pairs and Chest X-rays (CXRs) from Shenzhen Hospital X-ray Set. Similar experiments can be easily adapated to other datasets such as ChestX-ray14 (by subtituting the CXRs from Shenzhen Hospital X-ray Set). Remember to set less training epoches for ChestX-ray14 because of much more cases (i.e. --niter 5 --niter_decay 5 --lr_decay 3).

Test

Download the pretrained model (Shenzhen or ChestX14), and put it in ./checkpoints/. Run the script, you can modulate your CXR by chaning the alphas! For example, if we want to suppress bone region:

python test_DecGAN.py --dataroot ./dataset/ --name DecGAN_SZ --results_dir ./results --alpha_bone 0 --alpha_lung 1 --alpha_other 1 --gpu_ids 0

Train

• You may want to track the training process by running

python -m visdom.server

1. Train the decomposition network G_Dec using DRR generated from LIDC-IDRI

Because G_Dec is trained with range [-1, 1] but DecGAN IO implies [0, 1], we should modify some preprocessing functions to train G_Dec. (I know it is dummy, it can be done better) I leave some noted in the following files:

• Comments out all the transformless related code (7 lines in total) in ./data/unaligned_dataset.py
• Change the visualization output in ./util/util.py/tensor2im

python train_G_Dec.py --dataroot ./dataset/ --name G_Dec --batchSize 20 --niter 200 --niter_decay 200 --lr_decay_iters 100 --model G_dec --gpu_ids 0

2. Train DecGAN network

• Revert the comments if you train G_Dec like above.
• Put the learned G_Dec in the checkpoints folder. It is not updated in this process. Maybe it can be trained together, but we think it is not necessary and haven't tried.
• The training can be accelerated by increasing batchsize with more gpus.

python train_DecGAN.py --dataroot ./dataset/ --name DecGAN_SZ --batchSize 2 --gpu_ids 0

Acknowledgement

This code borrows heavily from CycleGAN and Unet.

Citation

If you find our work has positively influenced your projects, please kindly consider to cite our work:

@article{li2020high,
  title={High-Resolution Chest X-ray Bone Suppression Using Unpaired CT Structural Priors},
  author={Li, Han and Han, Hu and Li, Zeju and Wang, Lei and Wu, Zhe and Lu, Jingjing and Zhou, S Kevin},
  journal={IEEE Transactions on Medical Imaging},
  year={2020},
  publisher={IEEE}
}

and

@inproceedings{li2019encoding,
  title={Encoding ct anatomy knowledge for unpaired chest X-Ray image decomposition},
  author={Li, Zeju and Li, Han and Han, Hu and Shi, Gonglei and Wang, Jiannan and Zhou, S Kevin},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={275--283},
  year={2019},
  organization={Springer}
}