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, ...)
TRUE
).tempdir()
.rg=NULL
processes all slices.FALSE
).btoption=1
), and the 3D-DSI grid b-table extracted from the diffusion data set (btoption
axial, coronal, sagittal
} (default: "coronal"
).FALSE
).NULL
to use in ODF pos-processing default: NULL
.movMF
.sph.odfvmf
outputs three data files in NIfTI format named
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 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
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 (
The output files rgbvolmap()
or via the "FSL/fslview" tool.
These files may be used to perform white matter fibre tractography.
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.
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.:
sph.odfvmflines
,
sph.odfpeaklines
,
gqi.odfvxgrid
,
rgbvolmap
,
sph.odfpeaks
,
s2tessel.zorder
,
plotglyph
,
simulglyph.vmf
,
simul.fandtasia
,
simul.simplefield
,
data
,
data.bval
,
data.bvec
,
btable
## 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)
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