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FDB

Official PyTorch implementation of FDB as described in the paper

Muhammad U. Mirza, Onat Dalmaz, Hasan A. Bedel, Gokberk Elmas, Yilmaz Korkmaz, Alper Gungor, Salman UH Dar, Tolga Çukur, "Learning Fourier-Constrained Diffusion Bridges for MRI Reconstruction", arXiv 2023.

Dependencies

python==3.8.13
blobfile==2.0.2
h5py==3.9.0
imageio==2.22.1
mpi4py==3.1.4
numpy==1.24.4
Pillow==10.0.0
torch==2.0.1

Installation

  • Clone this repo:
git clone https://github.com/icon-lab/FDB
cd FDB

Train


For Single-Coil

python train.py --data_dir /path_to_data/ --log_interval 5000 --save_dir 'model_singlecoil' --save_interval 5000 --image_size 256 --num_channels 128 --num_res_blocks 3 --learn_sigma False --dropout 0.3 --diffusion_steps 1000 --lr 1e-4 --batch_size 1 --lr_anneal_steps 100000 --undersampling_rate 2 --data_type 'singlecoil'

For Multi-Coil

python train.py --data_dir /path_to_data/ --log_interval 5000 --save_dir 'model_multicoil' --save_interval 5000 --image_size 384 --num_channels 128 --num_res_blocks 3 --learn_sigma False --dropout 0.3 --diffusion_steps 1000 --lr 1e-4 --batch_size 1 --lr_anneal_steps 15000 --undersampling_rate 2 --data_type 'multicoil'

Inference


For Single-Coil

python sample.py --model_path model_singlecoil/ema_0.9999_100000.pt --data_path /path_to_data/ --image_size 256 --num_channels 128 --num_res_blocks 3 --learn_sigma False --dropout 0.3 --diffusion_steps 1500 --save_path results_singlecoil --num_samples 1 --batch_size 1 --data_type 'singlecoil' --R 4 --contrast 'T1'

For Multi-Coil

python sample.py --model_path model_multicoil/ema_0.9999_015000.pt --data_path /path_to_data/ --image_size 384 --num_channels 128 --num_res_blocks 3 --learn_sigma False --dropout 0.3 --diffusion_steps 1750 --save_path results_multicoil --num_samples 1 --batch_size 1 --data_type 'multicoil' --R 8 --contrast 'FLAIR'


Citation

You are encouraged to modify/distribute this code. However, please acknowledge this code and cite the paper appropriately.

@misc{mirza2023learning,
      title={Learning Fourier-Constrained Diffusion Bridges for MRI Reconstruction}, 
      author={Muhammad U. Mirza and Onat Dalmaz and Hasan A. Bedel and Gokberk Elmas and Yilmaz Korkmaz and Alper Gungor and Salman UH Dar and Tolga Çukur},
      year={2023},
      eprint={2308.01096},
      archivePrefix={arXiv},
      primaryClass={eess.IV}
}

For any questions, comments and contributions, please contact Usama Mirza (usama.mirza.819[at]gmail.com )

(c) ICON Lab 2023


Acknowledgements

This code uses libraries from DiffuseRecon and Improved DDPM repositories.