Minicourse-19

Light modeling in the brain using Brain2Mesh and MCX/MMC

Qianqian Fang, Northeastern University

Duration: 180 min

Capacity: 40

Level: Introductory, Some coding experience

Monte Carlo Toolbox

Requirements: Laptop; Matlab and toolboxes pre-installed

Synopsis: Accurate three-dimensional (3-D) light transport modeling in the brain is crucial for fNIRS probe design, placement, optimization, quantitative data analysis and comparisons. In this min-course, we will teach participants how to use our open-source Monte Carlo light transport suite – MCX and MMC to model light propagations in complex 3-D brain models. We will cover the preprocessing steps converting segmented MRI images into high-quality multi-layered mesh models using the Brain2Mesh toolbox, creation of 10-20/10-5 positions, probe placement, execution of 3D light transport modeling using GPU-accelerated MCX and MMC (in MATLAB) and visualization of the results.

Learning objectives:

  • How to use our open-source Monte Carlo light transport suite – MCX and MMC to model light propagations in complex 3-D brain models.
  • Brain segmentation and mesh generation using Brain2Mesh
  • MCX basics and designing MCX simulations in MATLAB
  • MMC simulations using Brain mesh models
  • Visualization and post processing

Requirements: You are expected to bring a laptop with Matlab and the toolboxes listed below installed. The laptop shall have a CPU/GPU that is no older than 5 years. The laptop needs to be pre-tested/pre-installed with our software that can be downloaded for free at: