gdimap (version 0.1-9)

sph.odfvxgrid: Glyph Maps

Description

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

Usage

sph.odfvxgrid(fbase=NULL, rg=c(1,1), swap=FALSE, btoption=2, threshold=0.4, kdir=4, zfactor=5, showimage="glyphgfa", bview="coronal", savedir=tempdir(), bg="white", order=4, texture=NULL, ...)

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).

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=2).

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).

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().

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.

Details

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.

Q-ball imaging (QBI) is used for orientation distribution function (ODF) reconstruction. One QBI-compatible b-table defining the acquisition setup on a S2-shell is included in the package. The b-table ‘btable.txt’ has 203 points distributed on a S2-shell.

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, s2tessel.zorder, plotglyph, rgbvolmap, simulglyph.vmf, simul.fandtasia, simul.simplefield

Examples

## Not run: 
#   ## show glyph-map for selected slice
#   sph.odfvxgrid(threshold=0.5, showimage="glyphgfa")
#   ##----
#   ## generate slice RGB map as texture
#   rgbvolmap(texture=TRUE, transp=TRUE)
#   ## coronal glyphs + RGBmap
#   sph.odfvxgrid(threshold=0.5, showimage="glyphrgbmap",
#     texture=file.path(tempdir(),"rgbmap.png"))
# ## End(Not run)