Winner of MyoPS 2020 Challenge

This repository provides source code for myocardial pathology segmentation (MyoPS) Challenge 2020. The method is detailed in the paper, and it won the 1st place of MyoPS 2020. Our code is based on PyMIC, a pytorch-based toolkit for medical image computing with deep learning, that is lightweight and easy to use, and nnUNet, a self-adaptive segmentation method for medical images.

@inproceedings{zhai2020myocardial,
  title={Myocardial edema and scar segmentation using a coarse-to-fine framework with weighted ensemble},
  author={Zhai, Shuwei and Gu, Ran and Lei, Wenhui and Wang, Guotai},
  booktitle={Myocardial Pathology Segmentation Combining Multi-Sequence CMR Challenge},
  pages={49--59},
  year={2020},
  organization={Springer}
}

Method overview

Our solution is a coarse-to-fine method. PyMIC and nnUNet are used in the coarse and fine stages, respectively.

In the coarse segmentation stage, we use 2D U-Net to segment there foreground classes: complete ring-shaped myocardium, left ventricular (LV) blood pool and rigth ventricular (RV) blood pool. The network is trained with a combination of Dice loss and cross entropy loss.

In the fine stage, we use nnUNet to segment all the five foreground classes: LV blood pool, RV blood pool, LV normal myocardium, LV myocardial edema and LV myocardial scar. The coarse segmentation result will serve as an extra channel for the input of the network, i.e., the first 3 modalities are C0(_0000), DE(_0001) and T2(_0002), respectively. The 4th modality(_0003) is the coarse segmentation result.

Requirements

This code depends on Pytorch, PyMIC, GeodisTK and nnUNet. To install PyMIC and GeodisTK, run:

pip install PYMIC==0.2.4
pip install GeodisTK

To use nnUNet, Download nnUNet, and put them in the ProjectDir such as /mnt/data1/swzhai/projects/MyoPS2020. Other requirements can be found in requirements.txt.

Configure data directories and environmental variables

• Configure data directories in path_confg.py based on your environment. For example, in my case:

path_dict['MyoPS_data_dir'] = "/mnt/data1/swzhai/dataset/MyoPS"
path_dict['nnunet_raw_data_dir'] = "/mnt/data1/swzhai/dataset/MyoPS/nnUNet_raw_data_base/nnUNet_raw_data"

where MyoPS_data_dir is the path of the MyoPS dataset, and nnunet_raw_data_dir is the path of raw data used by nnU-Net in the second stage of our method.

• After installation of nnUNet, set environmental variables as follows.

cd nnUNet
pip install -e .
export nnUNet_raw_data_base="MyoPS_data_dir/nnUNet_raw_data_base"
export nnUNet_preprocessed="MyoPS_data_dir/nnUNet_preprocessed"
export RESULTS_FOLDER="ProjectDir/result/nnunet"

Dataset and Preprocessing

• Download the dataset from MyoPS 2020 and put the dataset in the MyoPS_data_dir, specifically, MyoPS_data_dir/data_raw/imagesTr for training images, MyoPS_data_dir/data_raw/labelsTr for training ground truth and MyoPS_data_dir/data_raw/imagesTs for test images.

• For data preprocessing, Run:

python crop_for_coarse_stage.py

This will crop the images with the maximal bounding box in the training set, and the cropped results are saved in MyoPS_data_dir/data_preprocessed/imagesTr, MyoPS_data_dir/data_preprocessed/labelsTr and MyoPS_data_dir/data_preprocessed/imagesTs respectively. crop_information.json in each folder contains bounding box coordinates that will be used when putting the final segmentation results to the original image space.

Coarse segmentation Model

We use five-fold cross validation for training and validation of the coarse model.

Training and cross validation

• Run the following command to create csv files of training and testing datasets that are required by PyMIC, and split the training data into five folds. The csv files will be saved to config/data.

python write_csv_files.py

• For training and validation of the first fold, run the following command. The segmentation model will be saved in model/unet2d/fold_1, and prediction of the validation data for the first fold will be saved in result/unet2d.

python myops_run.py train config/train_val.cfg 1
python myops_run.py test  config/train_val.cfg 1

• Similarly to the above step, run the code for fold_2-fold_5.
• After training of all the five folds, to see the performance of the five fold cross validation, set ground_truth_folder_root to the correct value in config/evaluation.cfg, and run the following command to see the Dice scores of class 1, 2 and 3.

pymic_evaluate_seg config/evaluation.cfg

• For post processing, run:

python  postprocess.py result/unet2d result/unet2d_post

• The post processed results will be saved in result/unet2d_post. You can set segmentation_folder_root = result/unet2d_post in config/evaluation.cfg and run the evaluation code again. The average dice scores before after post processing on my machine are:

---	class_1	class_2	class_3	average
No postprocess	0.8780	0.9067	0.9180	0.9009
with postprocess	0.8785	0.9095	0.9234	0.9038

Inference for testing data

• We use an ensemble of five models obtained during the five-fold cross validation for inference. Open config/test.cfg and set ckpt_name to the list of the best performing checkpoints of the five folds. The best performing iteration number for fold i can be found in model/unet2d/fold_i/model_best.txt. Run the following command for inference. The results will be saved in result/unet2d_test.

python myops_test.py test config/test.cfg

• Run this command to postprocess the segmentation of the testing images:

python postprocess.py result/unet2d_test result/unet2d_test_post

Fine segmentation

In the fine segmentation stage, we use nnUNet to segment all the classes. This section is highly dependent on nnUNet, so make sure that you have some basic experience of using nnUNet before you do the following operations.

Tips: In order to save unnecessary time, you can change self.max_num_epochs = 1000 to self.max_num_epochs = 300 in nnUNet/nnunet/training/network_training/nnUNetTrainerV2.py.

Data preparation

• Run the following commands to prepare training and testing data for nnUNet. Note that the input of nnUNet has four channels as mentioned above.

python crop_for_fine_stage.py
python create_dataset_json.py

Training

• Dataset conversion and preprocess. Run:

nnUNet_plan_and_preprocess -t 112 --verify_dataset_integrity

• Train 2D UNet. For FOLD in [0, 1, 2, 3, 4], run:

nnUNet_train 2d nnUNetTrainerV2 Task112_MyoPS FOLD --npz

• Train 2.5D(3D) UNet. For FOLD in [0, 1, 2, 3, 4], run:

nnUNet_train 3d_fullres nnUNetTrainerV2 Task112_MyoPS FOLD --npz

Inference

• Here we have 2 fine models, i.e. 2D UNet and 2.5D UNet. To find the best configuration for inference, run:

nnUNet_find_best_configuration -m 2d 3d_fullres -t 112

• The terminal will output some commands for inference with each model and getting their ensemble. In my case, I get the following commands:

nnUNet_predict -i FOLDER_WITH_TEST_CASES -o OUTPUT_FOLDER_MODEL1 -tr nnUNetTrainerV2 -ctr nnUNetTrainerV2CascadeFullRes -m 2d -p nnUNetPlansv2.1 -t Task112_MyoPS

nnUNet_predict -i FOLDER_WITH_TEST_CASES -o OUTPUT_FOLDER_MODEL2 -tr nnUNetTrainerV2 -ctr nnUNetTrainerV2CascadeFullRes -m 3d_fullres -p nnUNetPlansv2.1 -t Task112_MyoPS

nnUNet_ensemble -f OUTPUT_FOLDER_MODEL1 OUTPUT_FOLDER_MODEL2 -o OUTPUT_FOLDER -pp result/nnunet/nnUNet/ensembles/Task112_MyoPS/ensemble_2d__nnUNetTrainerV2__nnUNetPlansv2.1--3d_fullres__nnUNetTrainerV2__nnUNetPlansv2.1/postprocessing.json

• In my case, FOLDER_WITH_TEST_CASES is nnunet_raw_data_dir/Task112_MyoPS/imagesTs. OUTPUT_FOLDER_MODEL1 is result/nnunet/test_2D. OUTPUT_FOLDER_MODEL2 is result/nnunet/test_3D. OUTPUT_FOLDER is result/nnunet/test_ensemble.

• Notice: Add arguments "--save_npz" and "--npz" to save .npz file which are model probability for future ensemble.

• Because we crop the images twice in the whole process for test images, we need to insert the fine segmentation results into the original images space. Run the following command, and the final segmentation results are saved in result/nnunet/test_ensemble_original.

python get_final_test.py result/nnunet/test_ensemble  result/nnunet/test_ensemble_original