This repository is an unoffical PyTorch implementation of Medical segmentation in 3D and 2D.

Overview

Pytorch Medical Segmentation

Read Chinese Introduction:Here!

Recent Updates

  • 2021.1.8 The train and test codes are released.
  • 2021.2.6 A bug in dice was fixed with the help of Shanshan Li.

Requirements

  • pytorch1.7
  • torchio<=0.18.20
  • python>=3.6

Notice

Prepare Your Dataset

Example1

if your source dataset is :

source_dataset
├── source_1.mhd
├── source_1.zraw
├── source_2.mhd
├── source_2.zraw
├── source_3.mhd
├── source_3.zraw
├── source_4.mhd
├── source_4.zraw
└── ...

and your label dataset is :

label_dataset
├── label_1.mhd
├── label_1.zraw
├── label_2.mhd
├── label_2.zraw
├── label_3.mhd
├── label_3.zraw
├── label_4.mhd
├── label_4.zraw
└── ...

then your should modify fold_arch as *.mhd, source_train_dir as source_dataset and label_train_dir as label_dataset in hparam.py

Example2

if your source dataset is :

source_dataset
├── 1
    ├── source_1.mhd
    ├── source_1.zraw
├── 2
    ├── source_2.mhd
    ├── source_2.zraw
├── 3
    ├── source_3.mhd
    ├── source_3.zraw
├── 4
    ├── source_4.mhd
    ├── source_4.zraw
└── ...

and your label dataset is :

label_dataset
├── 1
    ├── label_1.mhd
    ├── label_1.zraw
├── 2
    ├── label_2.mhd
    ├── label_2.zraw
├── 3
    ├── label_3.mhd
    ├── label_3.zraw
├── 4
    ├── label_4.mhd
    ├── label_4.zraw
└── ...

then your should modify fold_arch as */*.mhd, source_train_dir as source_dataset and label_train_dir as label_dataset in hparam.py

Training

  • without pretrained-model
set hparam.train_or_test to 'train'
python main.py
  • with pretrained-model
set hparam.train_or_test to 'train'
python main.py -k True

Inference

  • testing
set hparam.train_or_test to 'test'
python main.py

Examples

Done

  • 2D
  • 3D

TODO

  • metrics.py to evaluate your results
  • dataset
  • benchmark
  • nnunet

By The Way

This project is not perfect and there are still many problems. If you are using this project and would like to give the author some feedbacks, you can send Kangneng Zhou an email, his wechat number is: ellisgege666

Acknowledgements

This repository is an unoffical PyTorch implementation of Medical segmentation in 3D and 2D and highly based on MedicalZooPytorch and torchio.Thank you for the above repo. Thank you to Cheng Chen, Daiheng Gao, Jie Zhang, Xing Tao, Weili Jiang and Shanshan Li for all the help I received.

Owner
EasyCV-Ellis
公众号【easycv_ellis】博主,欢迎关注! @Easy-Shu 的兄弟公众号!
EasyCV-Ellis
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