gdimap (version 0.1-9)

sph.odfpeaks: Main Fibre Orientation Determination via Peak Detection with Q-ball Reconstruction

Description

The Q-ball reconstruction method with Aganj regularization as implemented in dti (Tabelow and Polzehl) is used for orientation distribution function (ODF) reconstruction. For identifying voxel fibre directions, the local maxima of the reconstructed ODF are identified, where this function surpasses a certain threshold.

Usage

sph.odfpeaks(fbase=NULL, rg=NULL, swap=FALSE, btoption=2,
 threshold=0.4, showglyph=FALSE, bview="coronal", savedir=tempdir(), order=4)

Arguments

fbase

Directory where the required input data files are located.

rg

range of slices to process; default option rg=NULL processes all slices.

swap

toggle radiological/neurological orientation (default: FALSE).

btoption

b-table selection between btable.txt (btoption=1), and 3D-DSI grid b-table supplied with the diffusion data set (default btoption=2).

threshold

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

showglyph

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

bview

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

savedir

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

order

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

Value

• sph.odfpeaks outputs two data files in NIfTI format named data_V1_sph.nii.gz and data_gfa_sph.nii.gz. The first main fibre directions per voxel are contained in data_V1_sph.nii.gz. The file data_gfa_sph.nii.gz contains the GFA values per voxel.

concept

• Diffusion Magnetic Resonance
• GQI Reconstruction
• Orientation Distribution Function
• RGB maps

Details

The most commonly used approach for identifying fibre directions is to extract the local maxima of the reconstructed ODF, where this function surpasses a certain threshold. The application of the approach is based on the assumption that the principal directions extracted from the ODF can be interpreted as principal directions of the underlying fibre architecture. Thresholding avoids selecting smaller ODF peaks that may appear due to noise. 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.

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.

The output files data_V1_sph.nii.gz and data_gfa_sph.nii.gz are used to visualize RGB maps through rgbvolmap() or via the "FSL/fslview" tool. These files may also be used to perform white matter fibre tractography.

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.

Jenkinson, M., Beckmann, C. F., Behrens, T. E., Woolrich, M. W., and Smith, S. M. FSL. NeuroImage 62, 2 (2012), 782-790.

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

Examples

##-------------
    ## Generate ODF volumes (GQI volume processing) for
    ## range of slices using deterministic find peaks algorithm
    sph.odfpeaks(rg=c(1,1), bview="coronal", showglyph=FALSE)
    ## Show RGB maps for range of slices processed by sph.odfpeaks()
    rgbvolmap(fbase=tempdir())
    ##-------------
    ## Process whole volume: generate NIfTI files
    ##   data_gfa_sph.nii.gz and data_V1_sph.nii.gz
    sph.odfpeaks(rg=NULL)
    rgbvolmap(fbase=tempdir(), rg=NULL, bview="coronal")
    ##-------------
    ## Show reconstructed glyphs in ODF processing 
    ## for principal direction determination
    sph.odfpeaks(rg=c(1,1), bview="coronal", showglyph=TRUE)