gdimap (version 0.1-3)

sph.odfpeaklines: Fibre Orientation Mapping Based on Local Peak Detection with QBI Reconstruction

Description

sph.odfpeaklines produces line-maps of ODF profiles for diffusion data slices using a regularized spheric harmonics method for ODF reconstruction.

Usage

sph.odfpeaklines(run=TRUE, fbase=NULL, roi=NULL, rg=c(1,1), btoption=1,
 swap=FALSE, threshold=0.4, kdir=2,  zfactor=5, showglyph=FALSE,
 snapshot=FALSE, showimage="linesgfa", bview="coronal", savedir=tempdir(),
 pngfig="odfpeak", bg="white", order=4, texture=NULL, ...)

Arguments

run

logical variable enabling loading previously processed data (default: TRUE).

fbase

Directory where the required input data files are located.

roi

Region of Interest (ROI) to use as mask; default mask (roi=NULL) uses an all brain mask for the supplied data set.

rg

range of slices to process (default option rg=c(1,1)); rg=NULL processes all slices.

btoption

b-table selection using the included data file btable.txt (btoption=1) or user defined files. With btoption=2, diffusion data files data.bvec and data.bval are selected for input, as used

swap

toggle radiological/neurological orientation (default: FALSE).

threshold

thresholding generalized fractional anisotropy (GFA) value at each voxel (default: 0.4).

kdir

maximum number of fibre directions to map (default: 2).

zfactor

parameter controlling z-value in relief overlay maps (default: 5).

showglyph

logical variable controlling visualization of voxel glyphs (default: FALSE).

snapshot

logical variable controlling line-map snapshots (default: FALSE).

showimage

object controlling visualization of line-maps (default: "linesgfa"). Alternative options are: c("none", "gfa", "lines", "linesgfa", "linesrgbmap", "linesdata") (see Details).

bview

MRI slice view selection in {axial, coronal, sagittal} (default: "coronal").

savedir

directory for saving/loading processed results (default: tempdir()).

pngfig

base-name of the PNG file when snapshot is TRUE (default "odfpeak").

bg

map background colour (default "white")

order

parameter associated with the order of the spherical harmonics approximation (default: 4).

texture

name of the PNG file to be used as RGB map overlay in some 'showimage' options (default NULL - no texture).

...

additional material properties for geometry appearance as specified in rgl.material.

Value

• sph.odfpeaklines produces line-maps of ODF profiles for diffusion data slices. The line-maps may be overlayed with generalized fractional anisotropy (GFA) relief maps, diffusion data maps or ROI maps. The file V1list.RData containing the first main orientation directions for all processed voxels is output for further posterior orientation processing.

concept

• QBI Reconstruction
• ODF Line-maps
• Peak Detection

Details

The identification of fibre directions is performed by extracting the local maxima of the reconstructed ODF, where this function surpasses a certain threshold. The Q-ball reconstruction method with Aganj regularization as implemented in dti (Tabelow and Polzehl) is used for orientation distribution function (ODF) reconstruction. sph.odfpeaklines implements the standard method of fibre orientation detection. Local maxima of the reconstructed ODF are located simply by selecting a large number of sampled points on the sphere and searching within a fixed radius neighbourhood. For a single main fibre orientation the method performs well. However, for crossing fibres and other complex fibre configurations the peaks of the ODF profiles identified by the methods do not necessarily match the orientations of the distinct fibre populations. A more robust method is implemented in sph.odfvmflines.

Starting with the raw high angular resolution diffusion signal acquired on a S2-shell of q-space, the ODF profile is reconstructed at each voxel, considering a sampling density of unit vectors on a unit S2 shell. Q-ball imaging (QBI) is used for orientation distribution function (ODF) reconstruction. For comparison with GQI, the b-table btable.txt has been used in the examples. This b-table has 203 points distributed on a S2-shell.

Slice map display and overlay selection is controlled by specifying one the arguments c("none", "gfa", "lines", "linesgfa", "linesrgbmap", "linesdata") for showimages. Meanings are as follows: "none" - no visualization; "gfa" - GFA map only; "lines" - line map only; "linesgfa" - GFA overlayed on line map; "linesrgbmap" - lines overlayed on RGB map (if available); "linesdata" - data_brain.nii.gz is overlayed on line map.

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.

Tuch D. S., Q-Ball Imaging, Magnetic Resonance in Medicine 52 (2004), 1358-1372.

Tabelow K., Polzehl J.: dti: DTI/DWI Analysis, 2012. R package version 1.1-0.

See Also

sph.odfpeaks, sph.odfvmf, sph.odfvmflines, gqi.odfvxgrid, s2tessel.zorder, plotglyph, rgbvolmap, simulglyph.vmf, simul.fandtasia, simul.simplefield, data, data.bval, data.bvec, btable

Examples

##-------------
  ## Line map using ODF peak detection 
  sph.odfpeaklines(run=TRUE, showimage="lines")
  ## display line-map overlayed on GFA map 
  sph.odfpeaklines(run=FALSE, showimage="linesgfa")
  ##-------------
  ## Show examples of reconstructed glyphs in ODF processing 
  sph.odfpeaklines(showimage="lines", showglyph=TRUE)
  ##------------
  ## using a ROI overlay
  sph.odfpeaklines(roi="slfcst", showimage="linesgfa")
  ## using data overlay
  sph.odfpeaklines(showimage="linesdata")