This repository includes the scripts to create the Figures for the study
Scholand, N, Wang, X, Roeloffs, V, Rosenzweig, S, Uecker, M. Magn Reson Med. 2023; 1- 19. doi: 10.1002/mrm.29664
This repository has been tested on Debian 11, but is assumed to work on other Linux-based operating systems, too.
Pre-processing, reconstruction and post-processing is performed with the BART toolbox.
The provided scripts are compatible with commit 0c847a2 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 bart moba ..., bart pics ... and bart rtnlinv ... calls.
The visualizations have been tested with Python on version 3.9.2 and require numpy, copy, matplotlib, mpl_toolkits, sys, os, math, time, and scipy. Ensure to have a your DISPLAY variable set, when the results should be visualized.
The data is hosted on ZENODO and must be downloaded first.
- Manual download: https://zenodo.org/record/7654462
- Download via script: Run the download script in the
./datafolder.- All files:
bash load_all.sh - Individual files:
bash load.sh 7654462 <FILENAME> .
- All files:
Note: The data must be stored in the ./data folder!
The folder names represent the corresponding figure numbers in the manuscript.
Folder 00_... only reproduces the gold-standard mapping reference results used in figure 05b.
The reference figures from the manuscript can be found under <folder>/results/.
Each folder contains a README file explaining how the figure can be reproduced.
If you want to reproduce all figures, run
bash reproduce_all.sh
Please feel free to send us feedback about this scripts! We would be happy to learn how to improve this and future script publications.
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/.