Description Usage Arguments Details Value Author(s) References See Also Examples
Generalized q-Sampling Imaging (GQI) 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.
1 2 3 |
gdi |
method of ODF reconstruction to use |
fbase |
Directory where the required input data files are located. |
rg |
range of slices to process; default option |
swap |
toggle radiological/neurological orientation (default: |
lambda |
diffusion sampling length in |
depth |
sampling density on the hemisphere used in simulation (default N=321; depth=3). |
btoption |
b-table selection between ‘btable.txt’ ( |
threshold |
thresholding generalized fractional anisotropy (GFA) value at each voxel (default: 0.4). |
showglyph |
logical variable controlling visualization of voxel glyphs (default: |
bview |
MRI slice view selection in { |
savedir |
directory for saving/loading processed results (default: |
aniso |
anisotropic parameter in the range "[0,1)" or |
GQI specifies an operational sampling scheme in q-space from which the ODF can be estimated. 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. GQI (Yeh et.al. 2010) or GQI2 (Garyfallidis 2012) may be used for ODF reconstruction.
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.
The output files ‘data_V1_gqi.nii.gz’ and ‘data_gfa_gqi.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.
gqi.odfpeaks
outputs two data files in NIfTI format named
‘data_V1_gqi.nii.gz’ and ‘data_gfa_gqi.nii.gz’.
The first main fibre directions per voxel are contained in ‘data_V1_gqi.nii.gz’.
The file ‘data_gfa_gqi.nii.gz’ contains the GFA values per voxel.
Adelino Ferreira da Silva, Universidade Nova de Lisboa, Faculdade de Ciencias e Tecnologia, Portugal, afs at fct.unl.pt
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.
gqi.odfpeaklines
,
plotglyph
,
gqi.odfvmf
,
gqi.odfvmflines
,
gqi.odfvxgrid
,
s2tessel.zorder
,
rgbvolmap
,
simulglyph.vmf
,
simul.fandtasia
,
simul.simplefield
,
data
,
data.bval
,
data.bvec
,
btable
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## Not run:
##-------------
## Generate ODF volumes (GQI volume processing) for
## range of slices using deterministic find peaks algorithm
gqi.odfpeaks(rg=c(1,1), bview="coronal", showglyph=FALSE)
## Show RGB maps for range of slices processed by gqi.odfpeaks()
rgbvolmap(fbase=tempdir())
##-------------
## Process whole volume: generate NIfTI files
## data_gfa_gqi.nii.gz and data_V1_gqi.nii.gz
gqi.odfpeaks(rg=NULL)
rgbvolmap(fbase=tempdir(), rg=NULL, bview="coronal")
##-------------
## Visualization of RBG maps based on processed volumes
## "data_gfa_gqi.nii.gz and "data_V1_gqi.nii.gz"
## (visualization compatible with the FSL/fslview tool)
rgbvolmap(rg=NULL, bview="coronal")
##-------------
## Show reconstructed glyphs in ODF processing
## for principal direction determination
gqi.odfpeaks(rg=c(1,1), bview="coronal", showglyph=TRUE, depth=3)
## End(Not run)
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