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MRI $RF$ pulse simulation in MALTAB

This repository is a MATLAB application that simulate the response of MRI RadioFrequency (RF) pulses. The app is a GUI, and the code also made to be used purely programmatically.

  1. Open the GUI app
  2. Click on a pulse in the library list.
  3. The selected $RF$ pulse is loaded with default parameters, plotted in the GUI, and it's simulation triggered. The simulation is plotted automatically : magnetization vector across time $M_{xzy}(t)$, slice profile $\Delta Z$, chemical shift profile $\Delta B_0$.

The application is highly object oriented, to take advantage of heritage and composition of several abstract classes.

Also, you can use your own pulses in the app by:

  • A super fast method: fill the $RF$ pulse shape ($B1$ curve $GZ$ curve) in the the USER_DEFINED pulse, then trigger the GUI so simulate the profile.
  • An ergonomic method made for interactivity: add your own $RF$ pulse class in +mri_rf_pulse_sim/+rf_pulse/+local/ so it will appear in the GUI library. This directory is not versioned in this repo

Features

GUI

The GUI have 3 independent panels:

  • Pulse definition: It shows the library of pulses, and the selected pulse, including its shape and the UI parameters. Pulse definition
  • Simulation parameters: You define the range and granularity (number of points) for the slice profile evaluation $\Delta Z$ and the chemical shift $\Delta B_0$ evaluation. Simulation parameters
  • Simulation results: Displays $M_{xzy}(t)$, the slice profile $\Delta Z$, and the chemical shift $\Delta B_0$ profile. Simulation results

Scripting

Here is some examples of non-GUI analysis:

Object oriented programming

All pulses are objects.
Pulses can inherit from others: FOCI is derived from HyperbolicSecant.
Pulses can be composed of several abstract classes. For example, slr_mb_verse is a SLR base waveform, then the MultiBand algorithm is applied to excite several slices, and finally the VERSE algorithm reduces it's duration and $B1_{max}$ using constrains.

Re-usability

One of the objectives here is to centralize the equations/algorithms of $RF$ pulse so they can be almost copy-pasted in other programming environments, like a complete sequence simulator, or a sequence development environment from your manufacturer.
One difficulty when looking in the literature is that different sources can have different vocabulary or different parameters. A typical example is the HyperbolicSecant, which is the extremely well described, but with a large variety of implementation using different input parameters.

Use vendor specific pulses

Bruker

  • Copy your pulses from Bruker into <package_dir>/vendor/bruker/.
  • In the GUI, select "BRUKER", this will fetch all files and display them in a list.
  • Click on a pulse to load it and simulate it.

Examples

HS : Hyperbolic Secant

HS

FOCI : Frequency Offset Corrected Inversion

FOCI

Download and install

  1. Clone the repository with
    • git clone --recurse-submodules https://github.com/benoitberanger/mri_rf_pulse_simulation_matlab.git
  2. In Matlab, cd /path/to/mri_rf_pulse_simulation_matlab
  3. Start the app with mri_rf_pulse_sim.app()

Limitations

  • MATLAB R2023a+ ? maybe few release earlier, but I did not test them.

External dependency

None, except for :

  • For SLR pulses :
    • DSP System Toolbox
    • Signal Processing Toolbox

Tested on

MATLAB R2023a+

Alternatives

In all alternatives that I found, in Python, MATLAB, Julia, all of them have very nice features, but none has the same interactivity and ergonomy.