povolann / mednerf

MedNeRF: Medical Neural Radiance Fields for Reconstructing 3D-aware CT-Projections from a Single X-ray

Repository copied from: https://github.com/abrilcf/mednerf

Get the Data

You can find all DRR in the following link. Here is a description of the folders:

An instance comprehends 72 DRRs (each at 5 degrees) from a 360 degree rotation of a real CT scan.

chest_xrays all images of the 20 chest instances (.png, res. 128x128).

knee_xrays all images of the 5 knee instances (.png, res. 128x128)

Train a model

Refer to graf-main folder and execute, replacing CONFIG.yaml with knee.yaml or chest.yaml

python train.py configs/CONFIG.yaml

Reconstruction given an X-ray

After training a model, you can test its capacity to reconstruct 3D-aware CT projections given a single X-ray.

Install ray tune for hyperparameter tuning with:

pip install "ray[tune]"

To execute the reconstruction, please refer to graf-main folder and execute:

python finetune_xray.py configs/config-file.yaml --xray_img_path path_to_xray --save_dir path_to_save_dir --model path_to_trained_model configs/knee.yaml

(to use ray for finetuning, please change the runtime environment with your configuration) In my case:

ray.init(runtime_env={"conda": "/home/anya/anaconda3/envs/graf", "py_modules": ["/home/anya/Programs/mednerf/graf-main/submodules", "/home/anya/Programs/mednerf/graf-main/graf", "/home/anya/Programs/mednerf/graf-main/submodules/GAN_stability/", "/home/anya/Programs/mednerf/graf-main/configs"]})

PixelNeRF instructions

To use pixelNeRF model use the following configuration files:

pixel-nerf/conf/exp/ct_single.conf
pixel-nerf/conf/exp/drr.conf

Generate DRR images from CT scans

To generate xrays images (.png) at different angles from CT scans use the script generate_drr.py under the folder data/. To run it you need to install the Plastimatch's build. Version 1.9.3 was used.

An updated version of the script has been added (generate_drr_multiple_dirs.py). Use this script to automatically generate the set of DRRs when you have a global folder with multiple folders containing CT scans. The files do not necessarily need to be in the immediate subfolder. You only need to assign the path location of the global folder and the global folder to save the set of DRRs.

Overview of input arguments

Replace the following variables within the file:

• input_path: path to the .dcm files or .mha file of the CT.
• save_root_path: path where you want the xrays images to be saved.
• plasti_path: path of the build.
• multiple_view_mode <True | False>: generate single xrays from lateral or frontal views or multiple images from a circular rotation around the z axis. If False you need to specify the view with the argument frontal_dir <True | False> (false for lateral view). If True you need to specify num_xrays to generate equally spaced number of views and angles to input the difference between neighboring angles (in degrees).
• preprocessing <True | False>: set this to True if files are .dcm for Hounsfield Units conversion. Set to False if given file is raw (.mha), for which you need to provide its path under the variable raw_input_file.
• detector_size: pair of values in mm
• bg_color: choose either black or white background.
• resolution: size of the output xrays images.

Acknowledgments

This codebase is heavily based on the GRAF code base. We also use the code from pixel-nerf for baseline experiments.

We thank all authors for the wonderful code!

Citation

If you use our model for your research, please cite the following work.

@misc{coronafigueroa2022mednerf,
      title={MedNeRF: Medical Neural Radiance Fields for Reconstructing 3D-aware CT-Projections from a Single X-ray}, 
      author={Abril Corona-Figueroa and Jonathan Frawley and Sam Bond-Taylor and Sarath Bethapudi and Hubert P. H. Shum and Chris G. Willcocks},
      year={2022},
      eprint={2202.01020},
      archivePrefix={arXiv},
      primaryClass={eess.IV}
}