gdimap: Generalized Diffusion Magnetic Resonance Imaging
Version 0.1-9

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.

Browse man pages Browse package API and functions Browse package files

AuthorAdelino Ferreira da Silva <afs@fct.unl.pt>
Date of publication2015-01-07 17:51:06
MaintainerAdelino Ferreira da Silva <afs@fct.unl.pt>
LicenseGPL (>= 2)
Version0.1-9
URL http://www.r-project.org
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("gdimap")

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

Functions

SimulateDWMRI Source code
anglev Source code
anisofn Source code
basisN Source code
btable Man page
cflush Source code
data Man page
data.bval Man page
data.bvec Man page
data_V1 Man page
data_V2 Man page
data_brain_mask Man page
data_gfa Man page
datatrans Source code
dec Man page Source code
design.spheven Source code
estimate.vmf.lines Source code
field.gqi Source code
fieldtestodf.gqi Source code
findpeak Source code
fnorm Source code
gdi.vmf Source code
gdimap-package Man page
genfa Source code
getsphericalharmonicsall Source code
getsphericalharmonicseven Source code
gfasurf3d Source code
gqi.odfpeaklines Man page Source code
gqi.odfpeaks Man page Source code
gqi.odfvmf Man page Source code
gqi.odfvmflines Man page Source code
gqi.odfvxgrid Man page Source code
gqifn Source code
gqifn2 Source code
m1 Source code
m2 Source code
m3 Source code
maxone Source code
mx1 Source code
mx2 Source code
mx3 Source code
myglyph.synthsimul Source code
niinorm Man page Source code
norm01 Source code
plotglyph Man page Source code
plotodfvmf Source code
plotodfvxgrid Source code
plzero Source code
premask Source code
read.slice Source code
readniidata Source code
readtable Source code
repmat Source code
rgbvolmap Man page Source code
rglinit Source code
rglstart Source code
s2tessel.zorder Man page Source code
scantable Source code
simul.fandtasia Man page Source code
simul.fandtasiaSignal Man page Source code
simul.simplefield Man page Source code
simulglyph.vmf Man page Source code
slfcst Man page
sph.odfpeaklines Man page Source code
sph.odfpeaks Man page Source code
sph.odfvmf Man page Source code
sph.odfvmflines Man page Source code
sph.odfvxgrid Man page Source code
sphcoord Source code
sphodf Source code
surf.tri Source code
synthfiberss2z Man page Source code
testfilexist Source code

Files

inst
inst/extdata
inst/extdata/data_V1.nii.gz
inst/extdata/data.bvec
inst/extdata/slfcst.nii.gz
inst/extdata/data.bval
inst/extdata/data.nii.gz
inst/extdata/data_brain_mask.nii.gz
inst/extdata/data_gfa.nii.gz
inst/extdata/btable.txt
inst/extdata/data_V2.nii.gz
NAMESPACE
NEWS
R
R/sph.odfvxgrid.R
R/simul.fandtasiaSignal.R
R/gqi.odfpeaklines.R
R/sph.odfpeaklines.R
R/niinorm.R
R/sph.odfpeaks.R
R/rgbvolmap.R
R/plotglyph.R
R/sphutils.R
R/dec.R
R/sph.odfvmf.R
R/readutils.R
R/gqi.odfpeaks.R
R/simul.simplefield.R
R/gqi.odfvxgrid.R
R/s2tessel.zorder.R
R/synthfiberss2z.R
R/gdiutils.R
R/simul.fandtasia.R
R/sph.odfvmflines.R
R/gqi.odfvmf.R
R/simulglyph.vmf.R
R/gqi.odfvmflines.R
MD5
DESCRIPTION
man
man/simul.fandtasia.Rd
man/gdimap-package.Rd
man/sph.odfpeaklines.Rd
man/sph.odfvmflines.Rd
man/sph.odfvmf.Rd
man/dec.Rd
man/data_brain_mask.Rd
man/niinorm.Rd
man/slfcst.Rd
man/gqi.odfpeaklines.Rd
man/plotglyph.Rd
man/gqi.odfvxgrid.Rd
man/synthfiberss2z.Rd
man/rgbvolmap.Rd
man/data_V2.Rd
man/s2tessel.zorder.Rd
man/simul.simplefield.Rd
man/sph.odfpeaks.Rd
man/gqi.odfvmf.Rd
man/data.Rd
man/data.bval.Rd
man/data_V1.Rd
man/simulglyph.vmf.Rd
man/btable.Rd
man/data.bvec.Rd
man/simul.fandtasiaSignal.Rd
man/gqi.odfvmflines.Rd
man/gqi.odfpeaks.Rd
man/sph.odfvxgrid.Rd
man/data_gfa.Rd
gdimap documentation built on May 29, 2017, 11:03 p.m.