Rapid, High-resolution and Distortion-free R2* Mapping of Fetal Brain using Multi-echo Radial FLASH and Model-based Reconstruction
This repository contains scripts to reproduce the results for the following work
Rapid, High-resolution and Distortion-free R2* Mapping of Fetal Brain using Multi-echo Radial FLASH and Model-based Reconstruction
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