gdimap (version 0.0-3)

gqi.odfvxgrid: Glyph Maps

Description

gqi.odfvxgrid produces glyph-map fields of reconstructed ODF profiles for voxels in slices.

Usage

gqi.odfvxgrid(fbase=NULL, rg=c(1,1), swap=FALSE, mddratio=1.24,
 depth=3, btoption=2, threshold=0.4, kdir=4, zfactor=5,
 snapshot=FALSE, showimage="glyphgfa", bview="coronal",
 savedir=tempdir(), pngfig="odfglyphs", bg="white", texturefile=NA)

Arguments

fbase

Directory where the required input data files are located.

rg

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

swap

toggle radiological/neurological orientation (default: FALSE).

mddratio

GQI parameter (default: 1.24).

depth

sampling density on the hemisphere used in simulation (default N=321; depth=3).

btoption

b-table selection between dsi203_bmax4000.txt (btoption=1), and the 3D-DSI grid b-table extracted from the diffusion data set (data.bvec and data.bval). By default, the 3D-DSI grid b-table is used (

threshold

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

kdir

maximum number of fibre directions to map (default: 4).

zfactor

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

snapshot

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

showimage

object controlling visualization of line-maps (default: "glyphgfa"). Alternative options are: c("none", "gfa", "glyph", "glyphgfa", "glyphrgbmap", "glyphdata") (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 "odfglyphs").

bg

map background colour (default "white")

texturefile

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

concept

• GQI Volume Processing
• Glyph maps

Details

Generalized q-Sampling Imaging (GQI) is used for orientation distribution function (ODF) reconstruction. Slice glyph map display and overlay selection is controlled by specifying one the arguments c("none", "gfa", "glyph", "glyphgfa", "glyphrgbmap", "glyphdata") for showimages. Meanings are as follows: "none" - no overlay; "gfa" - GFA map only; "glyph" - glyph map only; "glyphgfa" - GFA overlayed on glyph map; "glyphrgbmap" - glyphs overlayed on RGB map (if available); "glyphdata" - data_brain.nii.gz is overlayed on line map.

References

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

Auguie, B. gridExtra: functions in Grid graphics, 2012. R package version 0.9.1.

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

Zeileis, A., Hornik, K., and Murrell, P. Escaping RGBland: Selecting colors for statistical graphics. Computational Statistics & Data Analysis 53 (2009), 3259-3270.

See Also

gqi.odfpeaks, gqi.odfvmf, gqi.odfvmflines, s2tessel.zorder, plotglyph, rgbvolmap, simulglyph.vmf, simul.fandtasia, simul.simplefield

Examples

## show glyph-map for selected slice
  gqi.odfvxgrid(threshold=0.5, depth=2, showimage="glyphgfa")
  ##----
  ## generate slice RGB map as texture
  rgbvolmap(texture=TRUE, transp=TRUE)
  ## coronal glyphs + RGBmap
  gqi.odfvxgrid(threshold=0.5, depth=2, showimage="glyphrgbmap",
    texturefile=paste(tempdir(),"/rgbmap.png", sep=""))