gqi.odfpeaklines: Fibre Orientation Mapping Based on Local Peak Detection

Description

gqi.odfpeaklines produces line-maps of ODF profiles for diffusion data slices.

Usage

gqi.odfpeaklines(gdi="gqi", run=TRUE, fbase=NULL, roi=NULL, rg=c(1,1),
 swap=FALSE, lambda=NULL, depth=3, btoption=2, threshold=0.4, kdir=2,
 zfactor=5, showglyph=FALSE, snapshot=FALSE, showimage="linesgfa",
 bview="coronal", savedir=tempdir(), pngfig="odfpeak", bg="white",
 texture=NULL, ...)

Arguments

gdi

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

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.

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 (btopti

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").

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.

Value

gqi.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

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

Starting with the raw high angular resolution diffusion signal acquired on a grid of q-space, the ODF profile is reconstructed at each voxel, considering a sampling density of unit vectors on a unit S2 grid. Generalized q-Sampling Imaging (GQI) is used for orientation distribution function (ODF) reconstruction. Two b-tables defining the acquisition setup are specified. One is a b-table for a S2-like grid denoted by btable.txt. The other is the b-table for the 3D-DSI sampling scheme used in the DICOM data acquisition. This b-table has 203 points uniformly distributed on a 3D grid limited to the volume of the unit sphere. In both tables, the b-values range from 0 to 4000.

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.

Yeh, F.-C., Wedeen, V. J., and Tseng, W.-Y. I. Generalized q-Sampling Imaging. IEEE Transactions on Medical Imaging 29, 9 (2010), 1626-1635.

Garyfallidis E., Towards an Accurate Brain Tractography, 2012, PhD Thesis, University of Cambridge.

Examples

Run this code

##-------------
  ## Line map using ODF peak detection 
  gqi.odfpeaklines(run=TRUE, showimage="lines")
  ## idem with "gqi2"
  gqi.odfpeaklines(gdi="gqi2", run=TRUE, showimage="lines")
  ## display line-map overlayed on GFA map 
  gqi.odfpeaklines(run=FALSE, showimage="linesgfa")
  ##-------------
  ## generate slice texture first from default data file
  texturefname <- file.path(tempdir(),"rgbmap.png")
  rgbvolmap(texture=texturefname, bg="transparent")
  ## Line map with RGB map overlay
  gqi.odfpeaklines(run=TRUE, showimage="linesrgbmap",
    texture=texturefname)
  ##-------------
  ## Show examples of reconstructed glyphs in ODF processing 
  gqi.odfpeaklines(showimage="lines", showglyph=TRUE)
  ##------------
  ## using a ROI overlay
  gqi.odfpeaklines(roi="slfcst", showimage="linesgfa")
  ## using data overlay
  gqi.odfpeaklines(showimage="linesdata")

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