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.

Install the latest version of this package by entering the following in R:
AuthorAdelino Ferreira da Silva <>
Date of publication2015-01-07 17:51:06
MaintainerAdelino Ferreira da Silva <>
LicenseGPL (>= 2)

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


btable Man page
data Man page
data_brain_mask Man page
data.bval Man page
data.bvec Man page
data_gfa Man page
data_V1 Man page
data_V2 Man page
dec Man page
gdimap-package Man page
gqi.odfpeaklines Man page
gqi.odfpeaks Man page
gqi.odfvmf Man page
gqi.odfvmflines Man page
gqi.odfvxgrid Man page
niinorm Man page
plotglyph Man page
rgbvolmap Man page
s2tessel.zorder Man page
simul.fandtasia Man page
simul.fandtasiaSignal Man page
simulglyph.vmf Man page
simul.simplefield Man page
slfcst Man page
sph.odfpeaklines Man page
sph.odfpeaks Man page
sph.odfvmf Man page
sph.odfvmflines Man page
sph.odfvxgrid Man page
synthfiberss2z Man page

Questions? Problems? Suggestions? or email at

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.