Rational Approximation of Golden Angles for Simple and Reproducible Radial Sampling

This repository includes the scripts to create the Figures for the publication

Rational Approximation of Golden Angles for Simple and Reproducible Radial Sampling

Scholand, N, Graf, C, Mackner, D, Holme, HCM, Uecker, M.

Submitted to Magnetic Resonance in Medicine

Preprint on ArXiv (DOI: 10.48550/arXiv.2401.02892)

Requirements

This repository has been tested on Debian 11, but is assumed to work on other Linux-based operating systems, too.

Reconstruction

Pre-processing, reconstruction and post-processing is performed with the BART toolbox. The provided scripts are compatible with version 0.9.00 or later. If you experience any compatibility problems with later BART versions please contact us!

For running the reconstructions access to a GPU is recommended. If the CPU should be used, please remove -g flags from all bart pics ..., bart nufft ..., and bart rtnlinv ... calls.

Runtime and Memory Mapping

The time and memory mapping in figure 4 requires the UNIX time tool and Nvidia GPUs with nvidia-smi installed.

Visualizations

The visualizations have been tested with Python (version 3.9.2) and require numpy, copy, matplotlib, mpl_toolkits, sys, os, math, time, pandas, and cv2. Ensure to have set a DISPLAY variable, when the results should be visualized. The figures 3 and 5 require pdflatex and was tested with version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian). Figure 5 requires the command line tool from Inkscape 1.2.2 (b0a8486541, 2022-12-01) and montage included in ImageMagick (tested on version 6.9.11-60 Q16 x86_64 2021-01-25).

Data

The data is hosted on ZENODO and must be downloaded first.

• Manual download: https://doi.org/10.5281/zenodo.10260251
• Download via script: Run the download script in the ./data folder.
  • All files: bash load-all.sh
  • Individual files: bash load.sh 10260251 <FILENAME> .

Note: The data must be stored in the ./data folder!

Folders

Each folder contains a README file explaining how the figure can be reproduced.

Feedback

Please feel free to send us feedback about this scripts! We would be happy to learn how to improve this and future script publications.

License

This work is licensed under a Creative Commons Attribution 4.0 International License. You should have received a copy of the license along with this work. If not, see https://creativecommons.org/licenses/by/4.0/.