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Introduction

MCMRSimulator.jl allows simulation of MR signal generation using Monte Carlo simulations. The spin evolution of randomly diffusing particles is tracked under influence of one or more MR sequences. At present, the simulator allows to model

  • Free diffusion and diffusion restricted by Walls, Cylinders, Spheres, and/or a triangular Mesh.
  • R1 and R2 relaxation using global or local R1/R2 parameters.
  • MR sequences consisting of arbitrary RF pulses, gradients, and readouts (built using MRIBuilder or read from pulseq files).
  • Off-resonance magnetic field generation by myelinated cylinders or meshes.
  • Magnetisation transfer between liquid spins and bound spins in membranes.
  • Membrane permeability (i.e., exchange)
  • Surface relaxation
  • Surface tension of membranes causing spins to get temporarily "stuck" when they hit a membrane

Future (potential) features:

  • Macromolecular pool not bound to the membrane
  • Off-resonance field by iron particles
  • Contribution from metabolites (i.e., spectroscopy)

We use the following units throughout (unless otherwise noted):

  • Times are in ms. Equivalently, RF pulse amplitudes and off-resonance magnetic fields are in kHz (i.e., 1/ms).
  • Positions are in um. So, gradients are in kHz/um (not mT/m).
  • Angles are in degrees (not radians). These are used for phases (of spins and RF pulses) as well as RF pulse flip angles.
  • Magnetic susceptibilities are in parts per million (ppm).

How to get started?

  1. If MCMRSimulator is not yet installed, follow the installation instructions.
  2. Look through one of the tutorials. There are two available, depending on which interface you prefer to use:
  3. If you want more information on a specific topic, you can check one of the more dedicated sections:

Contributors

The original simulator was written by Michiel Cottaar.

Other contributors:

  • Zhiyu Zheng

Movie of spins moving through cylinders