B0 self-navigation for respiratory motion estimation in liver Look-Locker T1 mapping

Implementation of the Dixon B0 self-navigator to perform respiratory motion estimation in liver Look-Locker T1 mapping using a radial stack-of stars trajectory.

🚀 Setup

Dependencies

• Julia (tested with v1.11)
• Mamba package manager for Python dependencies. Alternatively, conda or virtualenv can be used, but the setup.sh script has to be modified accordingly.
  The latest Miniforge distribution with Mamba can be installed from the terminal using curl or wget (Unix-like platforms):

  curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
  bash Miniforge3-$(uname)-$(uname -m).sh

Install

Clone the repo and run setup script:

git clone https://github.com/BMRRgroup/B0nav-LL.git
cd B0nav-LL
./setup.sh

The setup.sh script creates a new Mamba environment with the Python dependencies and configures the executable Python file from this environment as the Python path for PyCall.jl. An argument can be passed to the setup.sh script to change the name of the Mamba environment (default: B0nav-LL).

Run

Run the Pluto programming environment and open the notebooks (theory_simulation.jl, invivo_example.jl) directly in your browser:

julia -e 'using Pkg; Pkg.activate("."); using Pluto; Pluto.run()'

Data

An example in vivo dataset for running the B0 navigator and motion estimation algorithms are provided in /data.

Expected outputs

theory_simulation.jl: B0 navigator in simplified two-species model

Case 1: $\varrho_1$, $\varrho_2$ water

Estimated $f_{B,nav}$ for the different TIs in Hz: [49.2, 21.7, 69.1, 59.6, 55.9, 53.9, 52.4]

Case 2: $\varrho_1$ water, $\varrho_2$ fat

Estimated $f_{B,nav}$ for the different TIs in Hz (water-fat model): [33.9, 33.2, 70.6, 63.1, 51.4, 44.7, 40.9]

invivo_example.jl: In vivo motion estimation

Median B0 variation amplitude $\gamma$ across slices/coils in Hz: 7.1
Maximum B0 variation amplitude $\gamma$ across slices/coils in Hz: 53.0

License

This project is licensed as given in the LICENSE file. However, used submodules / projects may be licensed differently. Please see the respective licenses.