Generative T2-FLAIR mismatch sign in glioma:
Effect of augmenting phenotype for isocitrate dehydrogenase mutation prediction

Dependencies

Install the other packages in requirements.txt, jax, jaxlib, numpy, and opencv-python as following:

pip install -r requirements.txt
pip install jax==0.4.6 jaxlib==0.4.6 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.htm
pip install numpy==1.23.0
pip install opencv-python==4.5.5.64

Prepare your own dataset

For example, you should set dataset path following:

root_path
    ├── train
          ├── <Patient_Folder>
                ├── T1CE
                      ├── 0001.npy
                      ├── 0002.npy
                      └── 0003.npy
                ├── T2
                └── FLAIR
    └── test

Training

python main.py --config='configs/ve/t1t2flair.py' --workdir='result' --mode=train

Model checkpoints and validation samples will be stored in ./result/checkpoints and ./result/samples, respectively.

Sampling

python t1t2flair_sampling.py

Sampling results will be stored in ./result/generated_images as png file.

Acknowledgement

Our main code is heavily based on score_sde_pytorch.