hexiaoxiao-cs / recursive-3d-segmentation-of-shoulder-joint-with-coarse-scanned-mr-image

Code for Recursive 3D Segmentation of Shoulder Joint with Coarse-scanned MR Image

This repository contains code for Recursive 3D Segmentation of Shoulder Joint with Coarse-scanned MR Image.

The data for training the network can not be published by the regulation of clinics and Patient Privacy laws.

Please contact:

• * Kang Li [email protected]
• Xiaoxiao He [email protected]
• Chaowei Tan [email protected]
• "*" for the corresponding author

For using this code

We encourage you to use the anaconda for python environment

The following packages are used in the program:

  - SimpleITK
  - keras
  - nibabel
  - pytables
  - nilearn
  - nipype
  - tqdm

Install ANTs N4BiasFieldCorrection and add the location of the ANTs

binaries to the PATH environmental variable.

Add the repository directory to the PYTONPATH system variable:

$ export PYTHONPATH=${PWD}:$PYTHONPATH

Goto Preprocessing folder and run

python preprocessing.py

Goto Training folder and run

python auto-augmentation.py