MedicalNet

This repository contains a Pytorch implementation of Med3D: Transfer Learning for 3D Medical Image Analysis. Many studies have shown that the performance on deep learning is significantly affected by volume of training data. The MedicalNet project aggregated the dataset with diverse modalities, target organs, and pathologies to to build relatively large datasets. Based on this dataset, a series of 3D-ResNet pre-trained models and corresponding transfer-learning training code are provided.

License

MedicalNet is released under the MIT License (refer to the LICENSE file for detailso).

Citing MedicalNet

If you use this code or pre-trained models, please cite the following:

    @article{chen2019med3d,
        title={Med3D: Transfer Learning for 3D Medical Image Analysis},
        author={Chen, Sihong and Ma, Kai and Zheng, Yefeng},
        journal={arXiv preprint arXiv:1904.00625},
        year={2019}
    }

Requirements
Installation
Demo
Experiments
TODO
Acknowledgement

Requirements

Python 3.7.0
PyTorch-0.4.1
CUDA Version 9.0
CUDNN 7.0.5

Installation

Install Python 3.7.0 pip install -r requirements.txt

Demo

Structure of data directories

MedicalNet is used to transfer the pre-trained model to other datasets (here the MRBrainS18 dataset is used as an example).
MedicalNet/
    |--datasets/：Data preprocessing module
    |   |--brains18.py：MRBrainS18 data preprocessing script
	|--models/：Model construction module
    |   |--resnet.py：3D-ResNet network build script
    |--utils/：tools
	|   |--logger.py：Logging script
	|--toy_data/：For CI test
    |--data/：Data storage module
	|   |--MRBrainS18/：MRBrainS18 dataset
	|   |	|.../：A folder named with patient ID
	|   |	|	|reg_T1.nii.gz/：image
	|   |	|	|segm_3label_13_merge.nii.gz/：label
	|   |--train.txt: training data lists
	|   |--val.txt: validation data lists
    |--pretrain/：Pre-trained models storage module
    |--model.py: Network processing script
    |--setting.py: Parameter setting script
    |--train.py: MRBrainS18 training demo script
    |--test.py: MRBrainS18 testing demo script
    |--requirement.txt: Dependent library list
    |--README.md

Network structure parameter settings

Model name   : parameters settings
resnet-10.pth: --model resnet --model_depth 10 --resnet_shortcut B
resnet-18.pth: --model resnet --model_depth 18 --resnet_shortcut A
resnet-34.pth: --model resnet --model_depth 34 --resnet_shortcut A
resnet-50.pth: --model resnet --model_depth 50 --resnet_shortcut B
resnet-101.pth: --model resnet --model_depth 101 --resnet_shortcut B
resnet-152.pth: --model resnet --model_depth 152 --resnet_shortcut B
resnet-200.pth: --model resnet --model_depth 200 --resnet_shortcut B

After successfully completing basic installation, you'll be ready to run the demo.

Clone the MedicalNet repository

git clone https://github.com/cshwhale/MedicalNet

Downloading data & pre-trained models Unzip and move files

mv MedicalNet_pytorch_files.zip MedicalNet/.
cd MedicalNet
unzip MedicalNet_pytorch_files.zip

Running the training code (e.g. 3D-ResNet-50)

python train.py --gpu_id 0 1    # multi-gpu training on gpu 0,1
or
python train.py --gpu_id 0    # single-gpu training on gpu 0

Running the testing code (e.g. 3D-ResNet-50)

python test.py --gpu_id 0 --resume_path trails/models/resnet_50_epoch_200_batch_0.pth --img_list data/val.txt

Experiments

Computational Cost

GPU：NVIDIA Tesla P40

Network	Paramerers (M)	Running time (s)
3D-ResNet10	14.36	0.18
3D-ResNet18	32.99	0.19
3D-ResNet34	63.31	0.22
3D-ResNet50	46.21	0.21
3D-ResNet101	85.31	0.29
3D-ResNet152	117.51	0.34
3D-ResNet200	126.74	0.45

Performance

Visualization of the segmentation results of our approach vs. the comparison ones after the same training epochs. 
It has demonstrated that the efficiency for training convergence and accuracy based on our MedicalNet pre-trained models.

Results of transfer MedicalNet pre-trained models to lung segmentation (LungSeg) and pulmonary nodule classification (NoduleCls) with Dice and accuracy evaluation metrics, respectively.

Network	Pretrain	LungSeg(Dice)	NoduleCls(accuracy)
3D-ResNet10	Train from scratch	71.30%	79.80%
3D-ResNet10	MedicalNet	87.16%	86.87%
3D-ResNet18	Train from scratch	75.22%	80.80%
3D-ResNet18	MedicalNet	87.26%	88.89%
3D-ResNet34	Train from scratch	76.82%	83.84%
3D-ResNet34	MedicalNet	89.31%	89.90%
3D-ResNet50	Train from scratch	71.75%	84.85%
3D-ResNet50	MedicalNet	93.31%	89.90%
3D-ResNet101	Train from scratch	72.10%	81.82%
3D-ResNet101	MedicalNet	92.79%	90.91%
3D-ResNet152	Train from scratch	73.29%	73.74%
3D-ResNet152	MedicalNet	92.33%	90.91%
3D-ResNet200	Train from scratch	71.29%	76.77%
3D-ResNet200	MedicalNet	92.06%	90.91%

Please refer to Med3D: Transfer Learning for 3D Medical Image Analysis for more details：

TODO

3D-ResNet series pre-trained models
Transfer learning training code
Training with multi-gpu
3D efficient pre-trained models（e.g., 3D-MobileNet, 3D-ShuffleNet）
2D medical pre-trained models
Pre-trained MedicalNet models based on more medical dataset

Acknowledgement

We thank 3D-ResNets-PyTorch and MRBrainS18 which we build MedicalNet refer to this releasing code and the dataset.

Contribution

If you want to contribute to MedicalNet, be sure to review the contribution guidelines.

jixing0415/MedicalNet