SpineParseNet: Spine Parsing for Volumetric MR Image by a Two-Stage Segmentation Framework with Semantic Image Representation
This repository is the official implementation of the paper:
Shumao Pang, Chunlan Pang, Lei Zhao, Yangfan Chen, Zhihai Su, Yujia Zhou, Meiyan Huang, Wei Yang, Hai Lu, and Qianjin Feng, "SpineParseNet: Spine Parsing for Volumetric MR Image by a Two-Stage Segmentation Framework with Semantic Image Representation, " IEEE Transactions on Medical Imaging, 2021, doi: 10.1109/TMI.2020.3025087.
Website: https://www.researchgate.net/profile/Shumao_Pang2
Some codes were borrowed from
- Pytorch = 1.5.1
- torchvision
- scipy
- tensorboardX
- numpy
- opencv-python
- matplotlib
- networkx
- The dataset can be downloaded at: https://www.spinesegmentation-challenge.com
- The data structure should look like:
|-- data
|-- coarse
|-- in
|-- h5py
|-- nii
|-- original_mr
|-- Case1.nii.gz
|-- Case2.nii.gz
......
|-- Case215.nii.gz
|-- mask
|-- mask_case1.nii.gz
|-- mask_case2.nii.gz
......
|-- mask_case215.nii.gz
|-- fine
|-- in
|-- h5py
|-- nii
|-- original_mr
|-- Case1.nii.gz
|-- Case2.nii.gz
......
|-- Case215.nii.gz
|-- mask
|-- mask_case1.nii.gz
|-- mask_case2.nii.gz
......
|-- mask_case215.nii.gz
Note that the files in data/coarse/in/nii are the same with those in data/fine/in/nii.
nohup ./main.sh > main.out &
@article{pang2020spineparsenet, title={SpineParseNet: Spine Parsing for Volumetric MR Image by a Two-Stage Segmentation Framework With Semantic Image Representation}, author={Pang, Shumao and Pang, Chunlan and Zhao, Lei and Chen, Yangfan and Su, Zhihai and Zhou, Yujia and Huang, Meiyan and Yang, Wei and Lu, Hai and Feng, Qianjin}, journal={IEEE Transactions on Medical Imaging}, volume={40}, number={1}, pages={262--273}, year={2021}, publisher={IEEE} }