osbm / fastmri_prostate

A large scale dataset and reconstruction script of both raw prostate MRI measurements and images

FastMRI Prostate

[Paper] [Dataset] [Github] [BibTeX]

Updates

02-07-2024: Updated files for slice-, volume-, exam-level labels and their paths for T2 and Diffusion sequences in the fastMRI prostate dataset.

Classification: The classification folder contains code for training deep learning models to detect clinically significant prostate cancer. Reconstruction: The reconstruction folder contains code for training deep learning models for reconstructing diffusion MRI images from undersampled k-space.

Overview

This repository contains code to facilitate the reconstruction of prostate T2 and DWI (Diffusion-Weighted Imaging) images from raw (k-space) data from the fastMRI Prostate dataset. It includes reconstruction methods along with utilities for pre-processing and post-processing the data.

The package is intended to serve as a starting point for those who want to experiment and develop alternate reconstruction techniques.

Installation

The code requires python >= 3.9

Install FastMRI Prostate: clone the repository locally and install with

pip install git+https://github.com/cai2r/fastMRI_prostate.git

Usage

The repository is centered around the fastmri_prostate package. The following breaks down the basic structure:

fastmri_prostate: Contains a number of basic tools for T2 and DWI reconstruction

• fastmri_prostate.data: Provides data utility functions for accessing raw data fields like kspace, calibration, phase correction, and coil sensitivity maps.
• fastmri.reconstruction.t2: Contains functions required for prostate T2 reconstruction
• fastmri.reconstruction.dwi: Contains functions required for prostate DWI reconstruction

fastmri_prostate_recon.py contains code to read files from the dataset and call the T2 and DWI reconstruction functions for a single h5 file.

fastmri_prostate_tutorial.ipynb walks through an example of loading a h5 file from the fastMRI prostate dataset and reconstructing T2/DW images.

To reconstruct T2/DW images from the fastMRI prostate raw data, users can download the dataset and run fastmri_prostate_recon.py with appropriate arguments, specifying the path to the root of the downloaded dataset, output path to store reconstructions, and the sequence (T2, DWI, or both).

python fastmri_prostate_recon.py \  
    --data_path <path to dataset> \  
    --output_path <path to store recons> \  
    --sequence <t2/dwi/both>

Hardware Requirements

The reconstruction algorithms implemented in this package requires the following hardware:

• A computer with at least 32GB of RAM
• A multi-core CPU

Run Time

The run time of a single T2 reconstruction takes ~15 minutes while the Diffusion Weighted reconstructions take ~7 minutes on a multi-core CPU Linux machine with 64GB RAM. A bulk of the time is spent in applying GRAPPA weights to the undersampled raw kspace data.

License

fastMRI_prostate is MIT licensed, as found in LICENSE file

Cite

If you use the fastMRI Prostate data or code in your research, please use the following BibTeX entry.

@misc{tibrewala2023fastmri,
      title={FastMRI Prostate: A Publicly Available, Biparametric MRI Dataset to Advance Machine Learning for Prostate Cancer Imaging}, 
      author={Radhika Tibrewala and Tarun Dutt and Angela Tong and Luke Ginocchio and Mahesh B Keerthivasan and Steven H Baete and Sumit Chopra and Yvonne W Lui and Daniel K Sodickson and Hersh Chandarana and Patricia M Johnson},
      year={2023},
      eprint={2304.09254},
      archivePrefix={arXiv},
      primaryClass={physics.med-ph}
}

Acknowedgements

The code for the GRAPPA technique was based off pygrappa, and ESPIRiT maps provided in the dataset were computed using espirit-python