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Collins adult brain atlas FEM mesh

Collins Atlas Mesh

Version 1

  • Created by Qianqian Fang <fangq at>

1. Download
2. Introduction
3. Format
4. Optical properties
5. Footnote
6. Reference

1. Download

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

2. Introduction

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.

3. Format

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

The mesh contains 69865 nodes, 425224 tetrahedral elements and 120864 triangular surface elements (8108 for scalp surface, 14760 for CSF surface, 15320 for pial surface and 82676 for white-matter surface).

4. 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

5. Footnote

The mesh data is in the public domain.

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

6. Reference

[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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