dti: Analysis of Diffusion Weighted Imaging (DWI) Data
Version 1.2-6.1

Diffusion Weighted Imaging (DWI) is a Magnetic Resonance Imaging modality, that measures diffusion of water in tissues like the human brain. The package contains R-functions to process diffusion-weighted data. The functionality includes diffusion tensor imaging (DTI), diffusion kurtosis imaging (DKI), modeling for high angular resolution diffusion weighted imaging (HARDI) using Q-ball-reconstruction and tensor mixture models, several methods for structural adaptive smoothing including POAS and msPOAS, and a streamline fiber tracking for tensor and tensor mixture models. The package provides functionality to manipulate and visualize results in 2D and 3D.

AuthorKarsten Tabelow [aut, cre], Joerg Polzehl [aut], Felix Anker [ctb]
Date of publication2016-10-10 13:51:51
MaintainerKarsten Tabelow <karsten.tabelow@wias-berlin.de>
LicenseGPL (>= 2)
Version1.2-6.1
URL http://www.wias-berlin.de/research/ats/imaging/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("dti")

Getting started

Package overview

Popular man pages

dtiIndices-methods: Methods for Function 'dtiIndices' in Package 'dti'
dti.smooth-methods: Methods for Function 'dti.smooth' in Package 'dti'
dwiSqrtODF-methods: Methods for positive definite EAP and ODF estimation in...
extract-methods: Methods for Function 'extract' and '[' in Package 'dti'
getsdofsb-methods: Estimate the noise standard deviation
medinria: Read/Write Diffusion Tensor Data from/to NIFTI File
optgrad: Optimal gradient directions
See all...

All man pages Function index File listing

Man pages

awssigmc: Estimate noise variance for multicoil MR systems
colqFA: FA map color scheme
combineDWIdata: Combine two objects of class "dtiData")
dkiTensor-methods: Diffusion Kurtosis Imaging (DKI)
dti-class: Class "dwi"
dtiIndices-methods: Methods for Function 'dtiIndices' in Package 'dti'
dti-package: Analysis of diffusion weighted imaging (DWI) data
dti.smooth-methods: Methods for Function 'dti.smooth' in Package 'dti'
dtiTensor-methods: Methods for Function 'dtiTensor' in Package 'dti'
dwiMD-methods: Methods for Function 'dwiMD' in Package 'dti'
dwiMixtensor-methods: Methods for Function 'dwiMixtensor' in Package 'dti'
dwiQball-methods: Methods for Function 'dwiQball' in Package 'dti'
dwiRiceBias-methods: Correction for Rician Bias
dwi.smooth-methods: Smooth DWI data
dwiSqrtODF-methods: Methods for positive definite EAP and ODF estimation in...
extract-methods: Methods for Function 'extract' and '[' in Package 'dti'
getmask-methods: Methods for Function 'getmask' in Package 'dti'
getsdofsb-methods: Estimate the noise standard deviation
medinria: Read/Write Diffusion Tensor Data from/to NIFTI File
optgrad: Optimal gradient directions
optgradients: Optimal gradient directions for number of gradients between 6...
plot-methods: Methods for Function 'plot' in Package 'dti'
pmatrix: Parallelize columnwise computations on a matrix using forking...
polyeder: Polyeders derived from the Icosahedron (icosa0) by sequential...
print-methods: Methods for Function 'print' in Package 'dti'
readDWIdata: Read Diffusion Weighted Data
sdpar-methods: Methods for Function 'sdpar' in Package 'dti'
show3d-methods: Methods for Function 'show3d' in Package 'dti'
showFAColorScale: Writes an image with the colqFA colorscale to disk.
show-methods: Methods for Function 'show' in Package 'dti'
subsetg: Create an objects of class "dtiData" containing only a subset...
summary-methods: Methods for Function 'summary' in Package 'dti'
tracking-methods: Methods for Function 'tracking' in Package 'dti'

Functions

D2Rall Source code
IQRdiff Source code
MedINRIA Man page
R2Dall Source code
Spatialvar.gauss Source code
Varcor.gauss Source code
[,ANY-method Man page
[,dkiIndices-method Man page
[,dkiTensor-method Man page
[,dtiData-method Man page
[,dtiIndices-method Man page
[,dtiTensor-method Man page
[,dwiMixtensor-method Man page
[,dwiQball-method Man page
[-methods Man page
aflsigmc Man page Source code
afsigmc Man page Source code
andir.image Source code
andir2.image Source code
awsgfamily Source code
awsgsigma2 Source code
awslinsd Source code
awslsigmc Man page Source code
awssigmc Man page Source code
betagamma Source code
colqFA Man page
combineDWIdata Man page Source code
combineFibers Man page Source code
combineFibers,dwiFiber,dwiFiber-method Man page
combineFibers-methods Man page
compactFibers Source code
connect.mask Source code
corrrisk Source code
create.designmatrix.dti Source code
defineKurtosisTensor Source code
design.spheven Source code
dkiDesign Source code
dkiIndices Man page Source code
dkiIndices,ANY-method Man page
dkiIndices,dkiTensor-method Man page
dkiIndices-class Man page
dkiIndices-methods Man page
dkiTensor Man page Source code
dkiTensor,ANY-method Man page
dkiTensor,dtiData-method Man page
dkiTensor-class Man page
dkiTensor-methods Man page
drskmb2 Source code
dti Man page
dti-package Man page
dti.smooth Man page Source code
dti.smooth,ANY-method Man page
dti.smooth,dtiData-method Man page
dti.smooth,dtiTensor-method Man page
dti.smooth-methods Man page
dti3Dall Source code
dti3Dand Source code
dti3Dev Source code
dti3Dreg Source code
dtiData Man page Source code
dtiData-class Man page
dtiIndices Man page Source code
dtiIndices,ANY-method Man page
dtiIndices,dtiTensor-method Man page
dtiIndices-class Man page
dtiIndices-methods Man page
dtiTensJKN Source code
dtiTensor Man page Source code
dtiTensor,ANY-method Man page
dtiTensor,dtiData-method Man page
dtiTensor-class Man page
dtiTensor-methods Man page
dtieigen Source code
dtiind3D Source code
dtilin.smooth Source code
dtireg.smooth Source code
dwi Source code
dwi-class Man page
dwi.smooth Man page Source code
dwi.smooth,ANY-method Man page
dwi.smooth,dtiData-method Man page
dwi.smooth-methods Man page
dwi.smooth.ms Man page Source code
dwi.smooth.ms,ANY-method Man page
dwi.smooth.ms,dtiData-method Man page
dwi.smooth.ms.wghts Source code
dwi.smooth.testprop Source code
dwiFiber-class Man page
dwiMD Man page Source code
dwiMD,ANY-method Man page
dwiMD,dtiData-method Man page
dwiMD,dtiTensor-method Man page
dwiMD-methods Man page
dwiMixtensor Man page Source code
dwiMixtensor,ANY-method Man page
dwiMixtensor,dtiData-method Man page
dwiMixtensor-class Man page
dwiMixtensor-methods Man page
dwiMtCombine Man page Source code
dwiMtCombine,ANY-method Man page
dwiMtCombine,dwiMixtensor,dwiMixtensor-method Man page
dwiMtCombine-methods Man page
dwiQball Man page Source code
dwiQball,ANY-method Man page
dwiQball,dtiData-method Man page
dwiQball-class Man page
dwiQball-methods Man page
dwiRiceBias Man page Source code
dwiRiceBias,ANY-method Man page
dwiRiceBias,dtiData-method Man page
dwiRiceBias-methods Man page
dwiSqrtODF Man page
dwiSqrtODF,ANY-method Man page
dwiSqrtODF,dtiData-method Man page
dwiSqrtODF-methods Man page
expandFibers Source code
extract Man page
extract,ANY-method Man page
extract,dtiData-method Man page
extract,dtiIndices-method Man page
extract,dtiTensor-method Man page
extract,dwiMixtensor-method Man page
extract,dwiQball-method Man page
extract-methods Man page
fmixureb Source code
fncchir Source code
fncchis Source code
fncchiv Source code
fwhm2bw Source code
gethani Source code
gethseqfullse3 Source code
gethseqfullse3msh Source code
getkappas Source code
getkappas3 Source code
getkappasmsh Source code
getkappasmsh3 Source code
getmask Man page Source code
getmask,ANY-method Man page
getmask,array-method Man page
getmask,dtiData-method Man page
getmask-methods Man page
getnext3g Source code
getsdofsb Man page Source code
getsdofsb,ANY-method Man page
getsdofsb,dtiData-method Man page
getsdofsb-methods Man page
getsiind2 Source code
getsiind3 Source code
getsiindbv Source code
getsphericalharmonicseven Source code
getsphwghts Source code
getvofh Source code
hg1f1 Source code
icosa0 Man page
icosa1 Man page
icosa2 Man page
icosa3 Man page
icosa4 Man page
ident.fibers Source code
identifyFA Source code
imtfb0 Source code
imtfb1 Source code
imtfbv Source code
imtgrb0 Source code
imtgrb1 Source code
imtgrbv Source code
interpolatesphere Source code
interpolatesphere0 Source code
interpolatesphere1 Source code
kldist Source code
kurtosisFunctionF1 Source code
kurtosisFunctionF2 Source code
likesigmaf Source code
lkfulls0 Source code
lkfullse3 Source code
lkfullse3msh Source code
matrm Source code
mcorr Source code
median1 Source code
mediansm3d Source code
medinria Man page
medinria2tensor Man page Source code
mlikesigmaf Source code
mtfb0 Source code
mtfb1 Source code
mtfbv Source code
mtgrb0 Source code
mtgrb1 Source code
mtgrbv Source code
mthomogen Source code
optgrad Man page
optgradients Man page
pdkiQP Source code
pgetsii30 Source code
pgetsii31 Source code
pgetsiind2 Source code
pgetsiindbv Source code
plmatrix Man page Source code
plot,ANY-method Man page
plot,dkiIndices-method Man page
plot,dtiData-method Man page
plot,dtiIndices-method Man page
plot,dtiTensor-method Man page
plot,dwi-method Man page
plot,dwiFiber-method Man page
plot,dwiMixtensor-method Man page
plot-methods Man page
plotse3wghts Source code
plzero Source code
plzeroaganji Source code
pmatrix Man page Source code
pmixtens Source code
pmixtn0b Source code
pmixtn1b Source code
pmixtn2b Source code
pmixtns0 Source code
pmixtns1 Source code
pmixtns2 Source code
pnlrdtirg Source code
polyeder Man page
print,ANY-method Man page
print,dkiIndices-method Man page
print,dkiTensor-method Man page
print,dtiData-method Man page
print,dtiIndices-method Man page
print,dtiTensor-method Man page
print,dwi-method Man page
print,dwiFiber-method Man page
print,dwiMixtensor-method Man page
print,dwiQball-method Man page
print-methods Man page
pseudoinverseSVD Source code
ptenschi Source code
ptensnl Source code
readDWIdata Man page Source code
reduceFibers Man page Source code
reduceFibers,dwiFiber-method Man page
reduceMixtens Source code
reduceparam Source code
replind Source code
ricebiascorr Source code
rotateKurtosis Source code
rskmixb2 Source code
sdpar Man page Source code
sdpar,ANY-method Man page
sdpar,dtiData-method Man page
sdpar-methods Man page
selectCube Source code
selectFibers Man page Source code
selectFibers,dwiFiber-method Man page
selectFibers-methods Man page
selisample Source code
setawsdefaults Source code
show,ANY-method Man page
show,dkiIndices-method Man page
show,dkiTensor-method Man page
show,dti-method Man page
show,dtiData-method Man page
show,dtiIndices-method Man page
show,dtiTensor-method Man page
show,dwiFiber-method Man page
show,dwiMixtensor-method Man page
show-methods Man page
show3d Man page Source code
show3d,ANY-method Man page
show3d,dkiTensor-method Man page
show3d,dtiData-method Man page
show3d,dtiIndices-method Man page
show3d,dtiTensor-method Man page
show3d,dwiFiber-method Man page
show3d,dwiMixtensor-method Man page
show3d,dwiQball-method Man page
show3d-methods Man page
show3dCdata Source code
show3dData Source code
show3dODF Source code
show3dTens Source code
showFAColorScale Man page Source code
showse3wghts Source code
sioutlier Source code
sioutlier1 Source code
sofmchi Source code
sortFibers Source code
sphcoord Source code
sphtrarea1 Source code
subsetg Man page Source code
suggestkappa Source code
summary,ANY-method Man page
summary,dkiIndices-method Man page
summary,dkiTensor-method Man page
summary,dtiData-method Man page
summary,dtiIndices-method Man page
summary,dtiTensor-method Man page
summary,dwi-method Man page
summary,dwiFiber-method Man page
summary,dwiMixtensor-method Man page
summary,dwiQball-method Man page
summary-methods Man page
tchi Source code
tensor2medinria Man page Source code
thcorr3D Source code
touchingFibers Man page Source code
touchingFibers,dwiFiber,dwiFiber-method Man page
touchingFibers-methods Man page
tracking Man page Source code
tracking,ANY-method Man page
tracking,dtiIndices-method Man page
tracking,dtiTensor-method Man page
tracking,dwiMixtensor-method Man page
tracking-methods Man page
unifybvals Source code
vcrossp Source code
vredsphere Source code

Files

inst
inst/rcode
inst/rcode/generatedata2.r
inst/rcode/generatedata3.r
inst/rcode/mousecallbacks.r
inst/rcode/smse3_tests.r
inst/rcode/createpolyeders.r
inst/rcode/generatedata.r
inst/rcode/gen_mixtens.r
inst/rcode/create_data_from_mtobj.r
inst/CITATION
inst/dat
inst/dat/S0ofFA.txt
inst/dat/b-directions.txt
inst/dat/hardi-grad.txt
src
src/esiglike.f
src/Fiber.cpp
src/Voxel.h
src/bmixtensorpl.c
src/Makevars
src/Fibertracking.cpp
src/nlrdtirg.f
src/tensor.f
src/bessel.c
src/mixtensorpl.c
src/mixtensl.f
src/aniso.f
src/smse3w.f
src/Fibertracking.h
src/Converter.cpp
src/sqrtODF.f
src/Converter.h
src/fibers.f
src/awsvar.f
src/VectorList.cpp
src/Voxel.cpp
src/VectorList.h
src/design.f
src/Fiber.h
src/mixtenbv.f
src/mixtens.f
src/Vector.cpp
src/TrackingInterface.cpp
src/varest.f
src/lmixtensorpl.c
src/tensorc.c
src/show3d.f
src/misc.f
src/init.c
src/dtinraw2.f
src/smse3.f
src/LawsonHansonnnls.f
src/rice.f
src/Vector.h
src/miscmt.f
src/dtifull.f
NAMESPACE
demo
demo/dti_art.r
demo/00Index
demo/mixtens_art.r
data
data/polyeders.rda
data/colqFA.rda
data/optgradients.rda
R
R/smse3misc.r
R/varest.r
R/mixtensnew.r
R/MD.r
R/aws.r
R/plot.r
R/fibers.r
R/misc.r
R/show3d.r
R/Classes.r
R/ricebias.r
R/awsse3ms.r
R/dtijkn.r
R/spherharm.r
R/utilities.r
R/awsse3mswghts.r
R/dtineu.r
R/multishell.r
R/awsse3.r
R/tracking.r
R/improve.r
R/dkimisc.r
R/parallel.r
R/mixtensorpl.r
R/dki.r
R/hardi.r
R/awsse3mstestprop.r
R/aws2.r
R/paramse3.r
R/io.r
MD5
DESCRIPTION
ChangeLog
man
man/summary-methods.Rd
man/colqFA.Rd
man/subsetg.Rd
man/showFAColorScale.Rd
man/dkiTensor-methods.Rd
man/combineDWIdata.Rd
man/sdpar-methods.Rd
man/plot-methods.Rd
man/getmask-methods.Rd
man/dwiSqrtODF-methods.Rd
man/polyeder.Rd
man/dwiMD-methods.Rd
man/show3d-methods.Rd
man/dtiTensor-methods.Rd
man/dwiMixtensor-methods.Rd
man/optgrad.Rd
man/dwi.smooth-methods.Rd
man/dtiIndices-methods.Rd
man/extract-methods.Rd
man/dwiRiceBias-methods.Rd
man/dti.smooth-methods.Rd
man/pmatrix.Rd
man/dti-class.Rd
man/print-methods.Rd
man/optgradients.Rd
man/getsdofsb-methods.Rd
man/readDWIdata.Rd
man/dti-package.Rd
man/dwiQball-methods.Rd
man/tracking-methods.Rd
man/awssigmc.Rd
man/medinria.Rd
man/show-methods.Rd
dti documentation built on May 19, 2017, 1:39 p.m.

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