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This repo contains the supported pytorch code and configuration files to reproduce 3D medical image segmentaion results of VT-UNet.
Prepare an environment with python=3.8, and then run the command "pip install -r requirements.txt" for the dependencies.
For experiments we used four datasets:
File structure
BRATS2021
|---Data
| |--- RSNA_ASNR_MICCAI_BraTS2021_TrainingData
| | |--- BraTS2021_00000
| | | |--- BraTS2021_00000_flair...
|
|
|
|
VT-UNet
|---train.py
|---test.py
|---pretrained_ckpt
|---saved_model
...
python train.py --cfg configs/vt_unet_base.yaml --num_classes 3 --epochs 350
python test.py --cfg configs/vt_unet_base.yaml --num_classes 3
This repository makes liberal use of code from open_brats2020, Swin Transformer, Video Swin Transformer and Swin-Unet
@misc{peiris2021volumetric,
title={A Volumetric Transformer for Accurate 3D Tumor Segmentation},
author={Himashi Peiris and Munawar Hayat and Zhaolin Chen and Gary Egan and Mehrtash Harandi},
year={2021},
eprint={2111.13300},
archivePrefix={arXiv},
primaryClass={eess.IV}
}
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