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EfficientSegmentation

Introduction

• EfficientSegmentation is an open source, PyTorch-based segmentation method for 3D medical image.
• For more information about efficientSegmentation, please read the following paper: Efficient Context-Aware Network for Abdominal Multi-organ Segmentation. Please also cite this paper if you are using the method for your research!

Features

• A whole-volume-based coarse-to-fine segmentation framework. The segmentation network is decomposed into different components, including basic encoder, slim decoder and efficient context blocks. Anisotropic convolution block and anisotropic context block are designed for efficient and effective segmentation.
• Pre-process data in multi-process. Distributed and Apex training support. In the inference phase, preprocess and postprocess are computed in GPU.
• This method won the 1st place on the 2021-MICCAI-FLARE challenge. Where participants were required to effectively and efficiently segment multi-organ in abdominal CT.

Benchmark

Installation

Environment

• Ubuntu 16.04.12
• Python 3.6+
• Pytorch 1.5.0+
• CUDA 10.0+

1.Git clone

git clone https://github.com/Shanghai-Aitrox-Technology/EfficientSegmentation.git

2.Install Nvidia Apex

• Perform the following command:

git clone https://github.com/NVIDIA/apex
cd apex
pip install -v --no-cache-dir ./

3.Install dependencies

pip install -r requirements.txt

Get Started

preprocessing

1. Download FLARE21, resulting in 361 training images and masks, 50 validation images.
2. Copy image and mask to 'FlareSeg/dataset/' folder.
3. Edit the 'FlareSeg/data_prepare/config.yaml'. 'DATA_BASE_DIR'(Default: FlareSeg/dataset/) is the base dir of databases. If set the 'IS_SPLIT_5FOLD'(Default: False) to true, 5-fold cross-validation datasets will be generated.
4. Run the data preprocess with the following command:

cd FlareSeg/data_prepare
python run.py

The image data and lmdb file are stored in the following structure:

DATA_BASE_DIR directory structure：
├── train_images
   ├── train_000_0000.nii.gz
   ├── train_001_0000.nii.gz
   ├── train_002_0000.nii.gz
   ├── ...
├── train_mask
   ├── train_000.nii.gz
   ├── train_001.nii.gz
   ├── train_002.nii.gz
   ├── ...
└── val_images
    ├── validation_001_0000.nii.gz
    ├── validation_002_0000.nii.gz
    ├── validation_003_0000.nii.gz
    ├── ...
├── file_list
    ├──'train_series_uids.txt', 
    ├──'val_series_uids.txt',
    ├──'lesion_case.txt',
├── db
    ├──seg_raw_train         # The 361 training data information.
    ├──seg_raw_test          # The 50 validation images information.
    ├──seg_train_database    # The default training database.
    ├──seg_val_database      # The default validation database.
    ├──seg_pre-process_database # Temporary database.
    ├──seg_train_fold_1
    ├──seg_val_fold_1
├── coarse_image
    ├──160_160_160
          ├── train_000.npy
          ├── train_001.npy
          ├── ...
├── coarse_mask
    ├──160_160_160
          ├── train_000.npy
          ├── train_001.npy
          ├── ...
├── fine_image
    ├──192_192_192
          ├── train_000.npy
          ├── train_001.npy
          ├──  ...
├── fine_mask
    ├──192_192_192
          ├── train_000.npy
          ├── train_001.npy
          ├── ...

The data information is stored in the lmdb file with the following format:

{
    series_id = {
        'image_path': data.image_path,
        'mask_path': data.mask_path,
        'smooth_mask_path': data.smooth_mask_path,
        'coarse_image_path': data.coarse_image_path,
        'coarse_mask_path': data.coarse_mask_path,
        'fine_image_path': data.fine_image_path,
        'fine_mask_path': data.fine_mask_path
    }
}

Models

• Models can be downloaded through Baidu Netdisk, password: vjy5
• Put the models in the "FlareSeg/model_weights/" folder.

AbdomenCT-1K models

• We also trained models in AbdomenCT-1K dataset.
• You can download the models through Baidu Netdisk, password:5k77

Training

Remark: Coarse segmentation is trained on Nvidia GeForce 2080Ti(Number:8), while fine segmentation on Nvidia A100(Number:4). If you use different hardware, please set the "ENVIRONMENT.NUM_GPU", "DATA_LOADER.NUM_WORKER" and "DATA_LOADER.BATCH_SIZE" in 'FlareSeg/coarse_base_seg/config.yaml' and 'FlareSeg/fine_efficient_seg/config.yaml' files. You also need to set the 'nproc_per_node' in 'FlareSeg/coarse_base_seg/run.sh' file.

Coarse segmentation:

• Edit the 'FlareSeg/coarse_base_seg/config.yaml' and 'FlareSeg/coarse_base_seg/run.sh'
• Train coarse segmentation with the following command:

cd FlareSeg/coarse_base_seg
sh run.sh

Fine segmentation:

• Put the trained coarse model in the 'FlareSeg/model_weights/base_coarse_model/' folder.
• Edit the 'FlareSeg/fine_efficient_seg/config.yaml'.
• Edit the 'FlareSeg/fine_efficient_seg/run.py', set the 'tune_params' for different experiments.
• Train fine segmentation with the following command:

cd  FlareSeg/fine_efficient_seg
sh run.sh

Inference:

• Put the trained models in the 'FlareSeg/model_weights/' folder.
• Run the inference with the following command:

sh predict.sh

Evaluation:

Refer to FLARE2021 Evaluation.

Contact

This repository is currently maintained by Fan Zhang (zf2016@mail.ustc.edu.cn) and Yu Wang (wangyu@fosun.com)

References

[1] Z. e. a. Zhu, “A 3d coarse-to-fine framework for volumetric medical image segmentation.” 2018 International Conference on 3D Vision (3DV), 2018.

[2] Q. e. a. Hou, “Strip pooling: Rethinking spatial pooling for scene parsing.” 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2020.

Acknowledgement

Thanks for FLARE organizers with the donation of the dataset.