This repository includes the scripts to create the Figures and Tables for the publication
N. Scholand, P. Schaten, C. Graf, D. Mackner, H.C.M. Holme, M. Blumenthal, A. Mao, J. Assländer, and M. Uecker
Submitted to Magnetic Resonance in Medicine
it provides basic comments and guidance through the workflows related to this publication. Please find more details in the interactive tutorial about RAGA sampling in BART on Github:mrirecon/raga-tutorial.
This repository has been tested on Debian 12, but is assumed to work on other Linux-based operating systems, too. Virtual environments like a Windows Subsystem for Linux might work, but have not been tested yet.
Preprocessing, reconstruction and postprocessing is performed with the BART toolbox.
The provided scripts are mostly compatible with version 0.9.00, but the GROG calibration and gridding requires at least commit 79fd4a72 or later, which will be included in the next release following version 0.9.00.
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.
The time and memory mapping in figure 4 requires the UNIX time tool and Nvidia GPUs with nvidia-smi installed.
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).
The visualizations require access to the BART toolbox. Therefore, either the environment variable BART_TOOLBOX_PATH or TOOLBOX_PATH needs to be set in the executing shell:
export TOOLBOX_PATH=<Path to BART Toolbox>
or
export BART_TOOLBOX_PATH=<Path to BART Toolbox>
The data is hosted on ZENODO and must be downloaded first.
- Manual download: https://doi.org/10.5281/zenodo.12728657
- Download via script: Run the download script in the
./datafolder.- All files:
bash load-all.sh - Individual files:
bash load.sh 12728657 <FILENAME> .
- All files:
Note: The data must be stored in the ./data folder!
Each folder contains a README file explaining how the figure can be reproduced.
| CPU | GPU | Runtime [min] |
|---|---|---|
| Intel Xeon Gold 6132 | NVIDIA Tesla V100 SXM2 32 GB | ~2 h |
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/.
The authors thank the ISMRM Reproducible Research Study Group for conducting a code review of the code (Version 1: DOI 10.5281/zenodo.11287833) The scope of the code review covered only the code’s ease of download, quality of documentation, and ability to run, but did not consider scientific accuracy or code efficiency.
Please feel free to send us feedback about this scripts! We would be happy to learn how to improve this and future script publications.