This repository contains scripts to reproduce the results for the following work

X Wang, H Fan, Z Tan, S Vasylechko, E Yang, R Didier, O Afacan, M Uecker, SK Warfield, A Gholipour

Magnetic Resonance in Medicine (DOI: 10.1002/mrm.30604).

This repository has been tested on Ubuntu 22.04.5 LTS, but is assumed to work on other Linux-based operating systems, too. Image export and display require Python and NumPy.

Pre-processing, reconstruction and post-processing is performed with the BART toolbox. The provided scripts are compatible with commit gefb1de8 or later. 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 moba ... calls.

For the in-vivo example, simply run bash run.sh; For the simulations, navigate to the simulation folder (cd simulation) and run bash run_simu.sh. Alternatively, you can open the Jupyter notebook FetalR2Star.ipynb in Google Colab to reproduce one of the in-vivo results.

If you experience any compatibility problems with later BART versions, or need further help to run the scripts, please let us know! (xiaoqingwang2010@gmail.com or xiaoqing.wang@childrens.harvard.edu)

The expected outputs include water, fat, and quantitative R2* and B0 maps of the simulated phantom and fetal brain, as shown in Figures 1 and 4, respectively.

Quantitative R2* maps (left) and R2*-weighted images (right) at TE = 70 ms for a subject at 27.9 weeks gestational age

Quantitative R2* maps (left) and R2*-weighted images (right) at TE = 70 ms for a subject at 35.6 weeks gestational age