MICCAI 2020: Automatic Data Augmentation for 3D Medical Image Segmentation

Requirements

This framework is built based on framework of nnUNet. Being familiar with its pipeline is prerequisite of ASNG.

• python 3
• torch >= 1.0
• Other packages such as tqdm, dicom2nifti, scipy, batchgenerators, numpy, sklearn, SimpleITK etc are listed in ./nnunet.egg-info

Due to version upgrade of nnUNet, it may encounter some troubles such as conflict between batchgenerators and numpy (MIC-DKFZ/nnUNet#145). History version (before Febrary, 2019) of nnUNet is strongly recommended.

The original version nnUNet which ASNG utilized could be downloaded from original_nnUNet.zip with password: ASNG. Comparison between original nnUNet and ASNG may be helpful for debug.

Usage

The same with nnUNet pipeline, dataset must be preprocessed as MSD default format. Other information about MSD can be found from: https://decathlon-10.grand-challenge.org/Home/.

# create environment variables

export nnUNet_base='YOUR_PATH/ASNG/'
export nnUNet_preprocessed='YOUR_PATH/ASNG/nnUNet_preprocessed/'
export RESULTS_FOLDER='YOUR_PATH/ASNG/'

cd YOUR_PATH/ASNG/
rm -r nnUNet_raw_cropped/
rm -r nnUNet_raw_splitted/
cp -r nnUNet_raw/ nnUNet_raw_splitted/

# Task04 Hippocampus is small, very helpful for debug.

cd nnUNet_raw_splitted/Task04_Hippocampus/imagesTr/
for var in *.nii.gz; do mv "$var" "${var%.nii.gz}_0000.nii.gz"; done

cd YOUR_PATH/ASNG/nnunet/
python experiment_planning/plan_and_preprocess_task.py -t Task04_Hippocampus
python run/run_training.py 3d_fullres nnUNetTrainer Task04_Hippocampus 1 --ndet

Notification

• Although ASNG is theoretically much more effectively than other reinforcement learning based algorithms in AutoML, it is still somewhat time-consuming in medical image segmentation tasks.
• Some records such as (1) training logs, (2) nnUNet plans making pickle files and (3) train/valid split infomation are stored at ./TrainingRecord/
• The main difference between ASNG and nnUNet is from: ./nnunet/training/network_training/network_trainer.py where parameters update by Monte Carlo implements.

Acknowledgments

The authors would like to thank Fabian Isensee for his great PyTorch implementation of nnUNet.

Citation

Including the following citation in your work would be highly appreciated:

Ju Xu, Mengzhang Li, and Zhanxing Zhu. "Automatic Data Augmentation for 3D Medical Image Segmentation." International Conference on Medical Image Computing and Computer-Assisted Intervention. Springer, Cham, 2020.