Summary

These scripts reproduce the experiments described in the article:

Free-Breathing Water, Fat, $R_2^*$ and $B_0$ Field Mapping of the Liver Using Multi-Echo Radial FLASH and Regularized Model-based Reconstruction (MERLOT)

The algorithms have been integrated into the Berkeley Advanced Reconstruction Toolbox (BART) [1] (commit a28c18a)

The raw files are hosted on ZENODO

How to download

• Download manually: https://zenodo.org/record/4359744

• Download via bash script:

  • All files: bash load-all.sh
  • Individual file: bash load.sh 4359744 <FILENAME> <dstdir> (please refer to md5sum.txt for FILENAME)

Explanation of directory and raw files

.
├── ### Figure 2 ###
├── simulation_ROIs.[hdr,cfl]                  # 10 regions of interst
├── ### Figure 3 ###
├── phantom_NIST_Cartesian.[hdr,cfl]           # k-space data
├── phantom_NIST_Cartesian_TE.[hdr,cfl]        # TE array
├── phantom_NIST_Radial.[hdr,cfl]              # k-space data
├── phantom_NIST_Radial_TE.[hdr,cfl]           # TE_array
├── phantom_NIST_ROIs.[hdr,cfl]                # 7 ROIs
├── ### Figure 4 ###
├── phantom_WaterFat_Cartesian.[hdr,cfl]       # k-space data
├── phantom_WaterFat_Cartesian_TE.[hdr,cfl]    # TE array
├── phantom_WaterFat_Cartesian_Water.[hdr,cfl] # Water
├── phantom_WaterFat_Cartesian_Fat.[hdr,cfl]   # Fat
├── phantom_WaterFat_Cartesian_FF.[hdr,cfl]    # Fat fraction
├── phantom_WaterFat_Radial.[hdr,cfl]          # k-space data
├── phantom_WaterFat_Radial_TE.[hdr,cfl]       # TE array
├── phantom_WaterFat_ROIs.[hdr,cfl]            # 4 ROIs
├── ### Figures 5, 6 ###
├── liver_2D_s3_scan2.[hdr,cfl]                # k-space data
├── liver_2D_s1_scan1.[hdr,cfl]
├── liver_2D_s2_scan1.[hdr,cfl]
├── liver_2D_s3_scan1.[hdr,cfl]
├── ### Figures 7 ###
├── liver_3D_BH_scan1.[hdr,cfl]
├── liver_3D_BH_scan2.[hdr,cfl]
├── ### Figures 8 ###
├── liver_3D_FB_scan1.[hdr,cfl]
├── liver_3D_FB_scan2.[hdr,cfl]
├── liver_TE.[hdr,cfl]                         # TE array
└── liver_ROIs.[hdr,cfl]                       # 3 ROIs

The bash scritps used for reconstructions and quantitative analysis

After downloading the raw data, you can run the following bash scripts.

Simulation:

bash run_simulation.sh performs:

1. numerical simulation;
2. model-based reconstruction for $R_2^\star$ mapping;
3. comparison of the reconstructed $R_2^\star$ values with the reference values based on the ROI files stored in simulation/simulation_ROIs.[cfl,hdr].

Phantom NIST:

bash run_NIST_Cartesian.sh performs:

1. polarity correction of MGRE Cartesian k-space data;
2. coil combination via ESPIRiT;
3. pixel-wise mobafit.

bash run_NIST_Radial.sh performs:

1. preparation of multi-echo radial FLASH data;
2. calculation of multi-echo radial sampling trajectory;
3. moba reconstruction for quantitative R2* mapping.

Phantom WaterFat:

bash run_WaterFat_Radial.sh performs:

1. preparation of multi-echo radial FLASH data;
2. calculation of multi-echo radial sampling trajectory;
3. moba reconstruction for water/fat separation and R2* mapping.

Liver:

bash run_liver_all.sh runs all liver data (2D and 3D).

bash run_liver_table.sh runs after the reconstruction of all liver data, and computes the mean and standard deviation given the ROIs.

Note:

For the preparation of figures in the article, plots.py is used to export png files from all the above reconstructed files.

If you need further help to run the scripts, we are happy to help you: zhengguo.tan@med.uni-goettingen.de and martin.uecker@med.uni-goettingen.de.

[1]. https://mrirecon.github.io/bart