gdimap (version 0.1-9)

sph.odfvmf: Fibre Orientation Estimation Based on von Mises Distributions with Q-ball Reconstruction

Description

Fibre orientations in multiple fibre voxels are estimated using a mixture of von Mises-Fisher (vMF) distributions. This statistical estimation procedure is used to resolve crossing fibre mappings.

Usage

sph.odfvmf(run=TRUE, fbase=NULL, savedir=tempdir(), rg=NULL, swap=FALSE,
 btoption=2, threshold=0.4, showglyph=FALSE, bview="coronal", order=4,
 clusterthr=0.6, aniso=NULL, ...)

Arguments

run

logical variable enabling loading previously processed data (default: TRUE).

fbase

Directory where the required input data files are located.

savedir

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

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 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).

bview

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

showglyph

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

order

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

clusterthr

thresholding orientations based on ODF values at each voxel for directional clustering (default: 0.6).

aniso

anisotropic parameter in the range "[0,1)" or NULL to use in ODF pos-processing default: NULL.

...

optional specification of non-default control parameters as detailed in movMF.

Value

• sph.odfvmf outputs three data files in NIfTI format named data_V1_sph.nii.gz, data_V2_sph.nii.gz, and data_gfa_sph.nii.gz. The first and second main fibre directions per voxel are contained in data_V1_sph.nii.gz, data_V2_sph.nii.gz, respectively. The file data_gfa_sph.nii.gz contains the GFA metric per voxel.

concept

• Diffusion Magnetic Resonance
• QBI Reconstruction
• von Mises distributions
• Orientation Distribution Function
• RGB maps

Details

For directional clustering estimation sph.odfvmf uses a mixture of 2 and 4 von Mises-Fisher (vMF) distributions that serves as a model for directional ODF profile data, corresponding to multiple fibre orientations. Statistical orientation estimation in sph.odfvmf is based on von Mises clustering procedures provided by the R-package movMF, by Kurt Hornik and Bettina Gruen.

Starting with the raw diffusion signal acquired on a grid of q-space, the ODF profile is estimated at each voxel, considering a sampling density of unit vectors on a unit S2 grid. When a threshold is applied to the estimated ODF at each voxel, the non-thresholded unit vectors provide directional statistics information about the estimated ODF profile. The main ODF orientations at each voxel relevant for fibre tracking may be estimated by clustering the non-thresholded unit vectors. The Q-ball reconstruction method with Aganj regularization as implemented in dti (Tabelow and Polzehl) is used for orientation distribution function (ODF) reconstruction.

The main diffusion data set used in the examples is a DICOM data set provided by the "Advanced Biomedical MRI Lab, National Taiwan University Hospital", which is included in the "DSI Studio" package, publicly available from the NITRC repository (http://www.nitrc.org). One QBI-compatible b-table defining the acquisition setup on a S2-shell is included in the package. The b-table for the shell acquisition used in 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, data_V2_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 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.

Hornik, K., and Gruen, B. movMF: Mixtures of von Mises-Fisher Distributions, 2012. R package version 0.1-0.

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

Examples

## Generate ODF volumes (QBI volume processing)
    ## for a range of slices using von Mises-Fisher clustering
    sph.odfvmf(showglyph=FALSE, threshold=0.5, savedir=tempdir())
    ## RGB maps for range of slices processed by sph.odfvmf()
    rgbvolmap(fbase=tempdir(), rg=c(1,4), bview="coronal")
    ##-------------
    ## Show reconstructed glyphs in ODF processing 
    ## for first and second main fibre direction determination
    sph.odfvmf(rg=c(1,1), bview="coronal", showglyph=TRUE, threshold=0.5)