Simultaneous whole-liver water T1 and T2 mapping

Example source code to perform motion-resolved reconstruction, dual-echo water-fat separation and dictionary matching based on the publication:

Jonathan Stelter, Kilian Weiss, Lisa Steinhelfer, Veronika Spieker, Elizabeth Huaroc Moquillaza, Weitong Zhang, Marcus R. Makowski, Julia A. Schnabel, Bernhard Kainz, Rickmer F. Braren and Dimitrios C. Karampinos; Simultaneous whole‐liver water T1 and T2 mapping with isotropic resolution during free‐breathing, NMR in Biomedicine, DOI: 10.1002/nbm.5216, https://doi.org/10.1002/nbm.5216

🚀 Setup

Requirements

• Julia 1.9 (system-wide installation is recommened)
• Anaconda/mamba environment with Python 3.10

Installing

1. Create a new mamba environment:

   mamba env create --name t1t2mapping --file environment_nocuda.yml
   mamba activate t1t2mapping
   which python

2. Open Julia and instantiate/precompile new Julia environment:

   using Pkg
   Pkg.activate(".")
   Pkg.instantiate()
   ENV["PYTHON"] = "/path/to/envs/t1t2mapping/bin/python"
   Pkg.build("PyCall")

3. Run processing script directly from the shell:

   Replace n_threads with the number of threads you wish to use.

   julia -t n_threads -i scripts/processing_demo.jl

Data

Raw data for the T1 mapping phantom and the dictionary are stored at the Google Drive folder.

Authors and acknowledgment

• Jonathan Stelter - Body Magnetic Resonance Research Group, TUM

Dual-echo water-fat separation: https://github.com/BMRRgroup/2echo-WaterFat-hmrGC

Single-voxel spectroscopy processing: https://github.com/BMRRgroup/alfonso

License

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