gdimap: Generalized Diffusion Magnetic Resonance Imaging

Diffusion anisotropy has been used to characterize white matter neuronal pathways in the human brain, and infer global connectivity in the central nervous system. The package implements algorithms to estimate and visualize the orientation of neuronal pathways in model-free methods (q-space imaging methods). For estimating fibre orientations two methods have been implemented. One method implements fibre orientation detection through local maxima extraction. A second more robust method is based on directional statistical clustering of ODF voxel data. 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 configurations. Reconstruction of orientation distribution function (ODF) profiles may be performed using the standard generalized q-sampling imaging (GQI) approach, Garyfallidis' GQI (GQI2) approach, or Aganj's variant of the Q-ball imaging (CSA-QBI) approach. Procedures for the visualization of RGB-maps, line-maps and glyph-maps of real diffusion magnetic resonance imaging (dMRI) data-sets are included in the package.

Author
Adelino Ferreira da Silva <afs@fct.unl.pt>
Date of publication
2015-01-07 17:51:06
Maintainer
Adelino Ferreira da Silva <afs@fct.unl.pt>
License
GPL (>= 2)
Version
0.1-9
URLs

View on CRAN

Man pages

btable
b-Table File for Shell Data
data
A Real Dataset for Diffusion MRI Analysis
data_brain_mask
Example of Mask File Used in Diffusion MRI Processing
data.bval
b-Table File
data.bvec
3D b-table Vectors for Data Acquisition
data_gfa
Generalized Fractional Anisotropy (GFA) File
data_V1
ODF First Principal Directions File
data_V2
ODF Second Principal Directions File
dec
Directionally-Encoded Color (DEC) Representation
gdimap-package
Generalized Diffusion Magnetic Resonance Imaging
gqi.odfpeaklines
Fibre Orientation Mapping Based on Local Peak Detection
gqi.odfpeaks
Main Fibre Orientation Determination via Peak Detection with...
gqi.odfvmf
Fibre Orientation Estimation Based on von Mises Distributions...
gqi.odfvmflines
Fibre Orientation Mapping Based on von Mises-Fisher...
gqi.odfvxgrid
Glyph Maps
niinorm
Normalization of Principal Diffusion Directions
plotglyph
3D Glyph Visualization
rgbvolmap
Generalized Fractional Anisotropy (GFA) Maps (RGB Maps)
s2tessel.zorder
3D Shell Grid Tessellation
simul.fandtasia
Simulation of Curved Fibre Bundles for von Mises-Fisher Fibre...
simul.fandtasiaSignal
Simulation of Crossing-Fibre Diffusion Profiles
simulglyph.vmf
Voxel Diffusion Profile Simulation and von Mises-Fisher Fibre...
simul.simplefield
Simulation of a Simple Field of Diffusion Profiles for von...
slfcst
A Region-of-Interest (ROI) File for Diffusion MRI Analysis
sph.odfpeaklines
Fibre Orientation Mapping Based on Local Peak Detection with...
sph.odfpeaks
Main Fibre Orientation Determination via Peak Detection with...
sph.odfvmf
Fibre Orientation Estimation Based on von Mises Distributions...
sph.odfvmflines
Fibre Orientation Mapping Based on von Mises-Fisher...
sph.odfvxgrid
Glyph Maps
synthfiberss2z
Voxel Diffusion Profiles for Multiple Fibre Simulation

Files in this package

gdimap
gdimap/inst
gdimap/inst/extdata
gdimap/inst/extdata/data_V1.nii.gz
gdimap/inst/extdata/data.bvec
gdimap/inst/extdata/slfcst.nii.gz
gdimap/inst/extdata/data.bval
gdimap/inst/extdata/data.nii.gz
gdimap/inst/extdata/data_brain_mask.nii.gz
gdimap/inst/extdata/data_gfa.nii.gz
gdimap/inst/extdata/btable.txt
gdimap/inst/extdata/data_V2.nii.gz
gdimap/NAMESPACE
gdimap/NEWS
gdimap/R
gdimap/R/sph.odfvxgrid.R
gdimap/R/simul.fandtasiaSignal.R
gdimap/R/gqi.odfpeaklines.R
gdimap/R/sph.odfpeaklines.R
gdimap/R/niinorm.R
gdimap/R/sph.odfpeaks.R
gdimap/R/rgbvolmap.R
gdimap/R/plotglyph.R
gdimap/R/sphutils.R
gdimap/R/dec.R
gdimap/R/sph.odfvmf.R
gdimap/R/readutils.R
gdimap/R/gqi.odfpeaks.R
gdimap/R/simul.simplefield.R
gdimap/R/gqi.odfvxgrid.R
gdimap/R/s2tessel.zorder.R
gdimap/R/synthfiberss2z.R
gdimap/R/gdiutils.R
gdimap/R/simul.fandtasia.R
gdimap/R/sph.odfvmflines.R
gdimap/R/gqi.odfvmf.R
gdimap/R/simulglyph.vmf.R
gdimap/R/gqi.odfvmflines.R
gdimap/MD5
gdimap/DESCRIPTION
gdimap/man
gdimap/man/simul.fandtasia.Rd
gdimap/man/gdimap-package.Rd
gdimap/man/sph.odfpeaklines.Rd
gdimap/man/sph.odfvmflines.Rd
gdimap/man/sph.odfvmf.Rd
gdimap/man/dec.Rd
gdimap/man/data_brain_mask.Rd
gdimap/man/niinorm.Rd
gdimap/man/slfcst.Rd
gdimap/man/gqi.odfpeaklines.Rd
gdimap/man/plotglyph.Rd
gdimap/man/gqi.odfvxgrid.Rd
gdimap/man/synthfiberss2z.Rd
gdimap/man/rgbvolmap.Rd
gdimap/man/data_V2.Rd
gdimap/man/s2tessel.zorder.Rd
gdimap/man/simul.simplefield.Rd
gdimap/man/sph.odfpeaks.Rd
gdimap/man/gqi.odfvmf.Rd
gdimap/man/data.Rd
gdimap/man/data.bval.Rd
gdimap/man/data_V1.Rd
gdimap/man/simulglyph.vmf.Rd
gdimap/man/btable.Rd
gdimap/man/data.bvec.Rd
gdimap/man/simul.fandtasiaSignal.Rd
gdimap/man/gqi.odfvmflines.Rd
gdimap/man/gqi.odfpeaks.Rd
gdimap/man/sph.odfvxgrid.Rd
gdimap/man/data_gfa.Rd