Pre-CAT

The purpose of this code is to reconstruct and analyze preclinical cardiac CEST data acquired using the method described in the manuscript "Ungated, plug-and-play preclinical cardiac CEST-MRI using radial FLASH with segmented saturation"

Requirements

Dependencies

• Scripts tested on Python 3.9.16

• Dependencies listed in requirements.txt

• A Berkeley Advanced Reconstruction Toolbox (BART) installation is required for reconstruction

  • Install the latest version of BART by following the instructions listed at: https://mrirecon.github.io/bart/installation.html
    • For Mac M1 installation instructions, refer to: mrirecon/bart#326
  • Make sure that BART_TOOLBOX_PATH is set and added to the PATH variable

  Suggested installation routes

  • pip
    • Use pip install -r /path/to/requirements.txt
  • Anaconda
    • Use conda install --file /path/to/requirements.txt

Instructions

Detailed instructions can be found in the instructions folder.

Note: Pixelwise mapping is not included in main script. Refer to /scripts/plot_maps.py for pixelwise mapping.

References

Martin Uecker, Frank Ong, Jonathan I Tamir, Dara Bahri, Patrick Virtue, Joseph Y Cheng, Tao Zhang, and Michael Lustig. Berkeley Advanced Reconstruction Toolbox. Annual Meeting ISMRM, Toronto 2015, In Proc. Intl. Soc. Mag. Reson. Med. 23:2486

This repository is associate with the following paper, please cite this work when using the code published in this repository:

Weigand-Whittier J, Wendland M, Lam B, et al. Ungated, plug-and-play cardiac CEST-MRI using radial FLASH with segmented saturation. Magn Reson Med. 2024. 10.1002/mrm.30382