simul.simplefield: Simulation of a Simple Field of Diffusion Profiles for von...
In gdimap: Generalized Diffusion Magnetic Resonance Imaging

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

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simul.simplefield(gdi="gqi", b=3000, sigma=NULL,
 clusterthr=0.6, logplot=TRUE, savedir=tempdir(),
 fmask="m1", ang=NULL, ...)

`gdi`	method of ODF reconstruction to use `c("gqi", "gqi2")` (default: `"gqi"`).
`b`	strength of the magnetic diffusion gradient (default b-value=3000).
`sigma`	Rician noise level used in simulation; (default `NULL`).
`clusterthr`	thresholding orientations based on ODF values at each voxel for directional clustering (default: 0.6).
`logplot`	logical variable for selecting log-scale (default `TRUE`).
`savedir`	directory for saving processed results (default: `tempdir()`.
`fmask`	choice of field mask among a table of pre-defined mask models for simple field simulations. Models are built by indexing array masks. Models `c( "m1","m2","m3")` simulate single fiber fields. Models `c("mx1","mx2", "mx3"` simulates crossing-fiber fields.
`ang`	angle in degrees to be cutomize `fmask` models (default: `NULL` - pre-defined angles are used).
`...`	optional specification of non-default control parameters as detailed in `movMF`.

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 σ (SNR=1/σ).

simul.simplefield plots the reconstructed field of ODF profiles together with the vMF-estimated fiber directions. It outputs three data files in NIfTI format named
‘data_V1_gqi.nii.gz’, ‘data_V2_gqi.nii.gz’, and ‘data_gfa_gqi.nii.gz’. The first and second main fibre directions per voxel are contained in ‘data_V1_gqi.nii.gz’, ‘data_V2_gqi.nii.gz’, respectively. The file ‘data_gfa_gqi.nii.gz’ contains the GFA metric per voxel.

Adelino Ferreira da Silva, Universidade Nova de Lisboa, Faculdade de Ciencias e Tecnologia, Portugal, afs at fct.unl.pt

Ferreira da Silva, A. R. Computational Representation of White Matter Fiber Orientations, International Journal of Biomedical Imaging, Vol. 2013, Article ID 232143, Hindawi Publishing Corporation http://dx.doi.org/10.1155/2013/232143.

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.

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

## Not run: 
  simul.simplefield(fmask="m1")
  simul.simplefield(gdi="gqi2", fmask="m1")
  ##
  simul.simplefield(logplot=FALSE, fmask="m3")
  simul.simplefield(gdi="gqi2", logplot=FALSE, fmask="m3")
  ##
  simul.simplefield(sigma=0.033, logplot=FALSE, fmask="mx1")
  simul.simplefield(gdi="gqi2", sigma=0.033, logplot=FALSE, fmask="mx1")

## End(Not run)