Collins adult brain atlas FEM mesh

Version 1

  • Created by Qianqian Fang <fangq at> =


Please download the latest release (Version 1) at our registration/download page.


Collins adult brain atlas [Collins1998] FEM mesh Version 1 was created on 06/03/2010 by Qianqian Fang with iso2mesh [Fang2009a] version 0.9.8pre.


Please refer to [Fang2010] for details.


The mesh data were saved in matlab/octave .mat format. Please load the .mat file in matlab/octave and export to your FEM simulator.

	node: node coordinates (in mm)
	face: surface triangles, the last column is the surface ID, 
		1-scalp, 2-CSF, 3-gray matter, 4-white matter
	elem: tetrahedral elements, the last column is the region ID, 
		1-scalp and skull layer, 2-CSF, 3-gray matter, 4-white matter

Optical properties

The optical properties of the brain atlas was described in [Fang2010] Table 2 (the same properties were first used in [Fang2009b]). The properties for scalp/skull and cerebro-spinal fluid (CSF) are based on [Custo2006] and those for gray and white matters are based on [Yaroslavsky2002] at 630 nm.

Tissue types μa (mm−1)μs (mm−1) Anisotropy (g)Refract. Index (n)
Scalp & skull 0.019 7.8 0.89 1.37
CSF 0.004 0.009 0.89 1.37
Gray-matter 0.02 9.0 0.89 1.37
White-matter 0.08 40.9 0.84 1.37


If you use this mesh in your publication, please cite the mesh version number to avoid conflict to any further updates of this mesh.


[Collins1998] D. L. Collins, A. P. Zijdenbos, V. Kollokian, J. G. Sled, N. J. Kabani, C. J. Holmes, and A. C. Evans, “Design and construction of a realistic digital brain phantom,” IEEE Trans. Med. Imaging 17(3), 463–468 (1998).

[Fang2010] Q. Fang, "Mesh-based Monte Carlo method using fast ray-tracing in Plucker coordinates," Biomed. Opt. Express 1(1), 165-175 (2010)

[Fang2009a] Q. Fang and D. Boas, “Tetrahedral mesh generation from volumetric binary and gray-scale images,” Proceedings of IEEE International Symposium on Biomedical Imaging 2009, 1142–1145 (2009).

[Fang2009b] Q. Fang and D. A. Boas, “Monte Carlo simulation of photon migration in 3D turbid media accelerated by graphics processing units,” Opt. Express 17(22), 20178–20190 (2009).

[Custo2006] A. Custo, W. M. Wells 3rd, A. H. Barnett, E. M. Hillman, and D. A. Boas, “Effective scattering coefficient of the cerebral spinal fluid in adult head models for diffuse optical imaging,” Appl. Opt. 45(19), 4747–4755 (2006).

[Yaroslavsky2002] A. N. Yaroslavsky, P. C. Schulze, I. V. Yaroslavsky, R. Schober, F. Ulrich, and H.-J. Schwarzmaier, “Optical properties of selected native and coagulated human brain tissues in vitro in the visible and near infrared spectral range,” Phys. Med. Biol. 47(12), 2059–2073 (2002).

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