Brain2Mesh

Brain2Mesh generates high-quality, multi-layered 3D brain tetrahedral meshes for anatomically accurate modeling used in functional near-infrared spectroscopy (fNIRS) photon transport simulations.

Key Features:

• MATLAB/Octave implementation: Implemented as a MATLAB/Octave-based 3D mesh generation toolbox.
• Surface-based brain meshing pipeline: Employs a surface-based pipeline to convert segmented volumetric brain scans into detailed multi-layered surfaces and tetrahedral mesh models, typically within a few minutes.
• Tetrahedral mesh output: Produces tetrahedral meshes suitable for numerical simulations of light propagation in brain tissues.
• Simulation compatibility: Generates meshes compatible with Monte Carlo and finite-element-based photon transport simulations.
• Atlas processing: Processes publicly available brain atlases to produce a variety of high-quality mesh models efficiently.
• Comparative anatomical analysis: Enables comparison of voxel-based segmentation, tetrahedral brain mesh, and layered-slab brain models to evaluate discrepancies in brain partial pathlengths.

Scientific Applications:

• fNIRS photon transport simulation: Provide anatomically accurate meshes for simulating photon transport in fNIRS studies to improve quantification of brain activity.
• Numerical modeling of light propagation: Support Monte Carlo and finite-element modeling of light propagation in layered brain tissues.
• Evaluation of anatomical approximations: Assess how anatomical model approximations (voxel-based, tetrahedral, layered-slab) affect partial pathlengths and fNIRS quantification.

Methodology:

Uses a surface-based pipeline that converts segmented volumetric brain scans into multi-layered surfaces and tetrahedral meshes (implemented in MATLAB/Octave) and outputs meshes suitable for Monte Carlo and finite-element photon simulations.