simul.simplefield: Simulation of a Simple Field of Diffusion Profiles for von...

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

View source: R/simul.simplefield.R

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

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

Arguments

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.

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 σ (SNR=1/σ).

Value

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.

Author(s)

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

References

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.

See Also

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

Examples

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## 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)

gdimap documentation built on May 29, 2017, 11:03 p.m.