Publication	Links to Publications	Corresponding Code
T₁ Variability
T₁ Sensitivity
unpublished edits

T₁ Variability Paper

This code reproduces all results in the paper Magnetization transfer explains most of the T₁ variability in the MRI literature. Please refer to the Documentation for a detailed description of the code.

The code is written in the open-source language Julia and is structured as follows:

• T1_mapping_methods.jl implements the pulse sequence simulations and the mono-exponential fitting routines of each T₁-mapping method.
• Fit_qMT_to_literatureT1.jl is the main script that performs the fit of the qMT models to the variable literature T₁ estimates.
• helper_functions.jl contains implementations of RF pulses, their propagators, and some helper functions, which are less relevant for understanding the simulations.
• Project.toml and Manifest.toml contain information about the packages used by the simulation, facilitating their automated installation.

T₁ Sensitivity Paper

This code also reproduces all results in the paper Sensitivity of literature T₁ mapping methods to the underlying magnetization transfer parameters. Please refer to the Documentation for a detailed description of the code.

In addition to the scripts described above, this analysis uses the following code:

• Derivatives.jl is the main script that calculates the derivatives and performs the mixed effects model fit.
• Derivatives_HelperFunctions.jl contains implementations of the Shapley regression and other helper functions.

Running the code

Julia can be downloaded from https://julialang.org or, on Unix systems, by simply calling

`curl -fsSL https://install.julialang.org | sh`

from the command line.

To run the simulations, place all files in the same folder, cd into this folder, and call

`julia -iq --threads=auto --project=. Fit_qMT_to_literatureT1.jl`

for reproducing the T₁ variability paper and

`julia -iq --threads=auto --project=. Derivaties.jl`

for reproducing the T₁ sensitivity paper.

For a more interactive interface, the code can be called from Visual Studio Code with the Julia extension.