gqi.odfvxgrid: Glyph Maps

Description

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

Usage

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

Arguments

gdi

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

fbase

Directory where the required input data files are located.

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

swap

toggle radiological/neurological orientation (default: FALSE).

lambda

diffusion sampling length in gdi="gqi" and gdi="gqi2". By default the following default values are used when lambda=NULL is specified: 1.24 in "gqi", 3 in "gqi2".

depth

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

btoption

b-table selection between btable.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 (btoption

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").

map background colour (default "white")

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.

concept

GQI Volume Processing
Glyph maps

Details

GQI (Yeh et.al. 2010) or GQI2 (Garyfallidis 2012) may be used for 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.

Examples

Run this code

## show glyph-map for selected slice
  gqi.odfvxgrid(threshold=0.5, depth=2, showimage="glyphgfa")
  gqi.odfvxgrid(gdi="gqi", threshold=0.5, depth=2, showimage="glyphgfa")
  ##----
  ## generate slice RGB map as texture
  texturefname <- file.path(tempdir(),"rgbmap.png")
  rgbvolmap(texture=texturefname, bg="transparent")
  ## coronal glyphs + RGBmap
  gqi.odfvxgrid(threshold=0.5, depth=2, showimage="glyphrgbmap",
    texture=texturefname)

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