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Quantitative Multi-Parameter Mapping in Magnetic Resonance Imaging

This repository includes the scripts to create the Figures for chapter 5 of

Quantitative Multi-Parameter Mapping in Magnetic Resonance Imaging

Scholand, N. Doctoral thesis, 2023. doi: 10.53846/goediss-10028

The scripts for the figures of chapter 4 can be found on Github.

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 commit f1192bc 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.

Visualization

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 set a DISPLAY variable, when the results should be visualized.

Data

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

  • Manual download: https://zenodo.org/record/7837312
  • Download via script: Run the download script in the ./data folder.
    • All files: bash load-all.sh
    • Individual files: bash load.sh 7654462 <FILENAME> . or bash load.sh 6992763 <FILENAME> . for the scripts in the folder init_test

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/.