gdimap (version 0.1-1)

simul.simplefield: Simulation of a Simple Field of Diffusion Profiles for von Mises-Fisher Fibre Orientation Mapping

Description

ODF profiles and fibre directions are estimated using mixtures of von Mises-Fisher (vMF) distributions for directional mapping. The synthesized field of diffusion profiles generated by simul.simplefield are used to reconstruct ODF profiles using GQI or GQI2.

Usage

simul.simplefield(gdi="gqi", ang=60, b=3000, sigma=NULL, threshold=0.5, logplot=TRUE)

Arguments

gdi

method of ODF reconstruction to use c("gqi", "gqi2") (default: "gqi").

ang

angle in degrees of crossing fibres to be used in simulation (default: 60).

b

strength of the magnetic diffusion gradient (default b-value=3000).

sigma

Rician noise level used in simulation; (default NULL).

threshold

thresholding generalized fractional anisotropy (GFA) value at each voxel (default: 0.5).

logplot

logical variable for selecting log-scale (default TRUE).

Value

• simul.simplefield plots the reconstructed field of ODF profiles together with the vMF-estimated fiber directions.

concept

• Simulation
• ODF visualization
• Glyph field mapping

Details

The number of fibres is automatically estimated from the diffusion profile. Noisy profiles may be simulated by adding Rician noise to the simulated diffusion profile, with a user defined standard deviation level specified as $\sigma$ (SNR=1/$\sigma$).

References

Ferreira da Silva, A. R. Facing the Challenge of Estimating Human Brain White Matter Pathways. In Proc. of the 4th International Joint Conference on Computational Intelligence (Oct. 2012), K. Madani, J. Kacprzyk, and J. Filipe, Eds., SciTePress, pp. 709-714.

Hornik, K., and Gruen, B. movMF: Mixtures of von Mises-Fisher Distributions, 2012. R package version 0.1-0.

Adler, D., and Murdoch, D. rgl: 3D visualization device system (OpenGL), 2012. R package version 0.92.880.

Barber, C. B., Habel, K., Grasman, R., Gramacy, R. B., Stahel, A., and Sterratt, D. C. geometry: Mesh generation and surface tessellation, 2012. R package version 0.3-2.

See Also

simulglyph.vmf, simul.fandtasia, synthfiberss2z, plotglyph, gqi.odfvmflines, rgbvolmap, gqi.odfpeaks, gqi.odfpeaklines, gqi.odfvxgrid

Examples

simul.simplefield(ang=60, b=3000, sigma=NULL)
  simul.simplefield(gdi="gqi2", ang=60, b=3000, sigma=NULL)
  ##
  simul.simplefield(ang=60, b=3000, sigma=NULL, logplot=FALSE)
  simul.simplefield(gdi="gqi2", ang=60, b=3000, sigma=NULL, logplot=FALSE)
  ##
  simul.simplefield(ang=60, b=3000, sigma=0.033, logplot=FALSE)
  simul.simplefield(gdi="gqi2", ang=60, b=3000, sigma=0.033, logplot=FALSE)