dti: Analysis of Diffusion Weighted Imaging (DWI) Data

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.

Install the latest version of this package by entering the following in R:
install.packages("dti")
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
http://www.wias-berlin.de/research/ats/imaging/

View on CRAN

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

aflsigmc Man page
afsigmc Man page
[,ANY-method Man page
awslsigmc Man page
awssigmc Man page
colqFA Man page
combineDWIdata Man page
combineFibers Man page
combineFibers,dwiFiber,dwiFiber-method Man page
combineFibers-methods Man page
dkiIndices Man page
dkiIndices,ANY-method Man page
dkiIndices-class Man page
dkiIndices,dkiTensor-method Man page
[,dkiIndices-method Man page
dkiIndices-methods Man page
dkiTensor Man page
dkiTensor,ANY-method Man page
dkiTensor-class Man page
dkiTensor,dtiData-method Man page
[,dkiTensor-method Man page
dkiTensor-methods Man page
dti Man page
dtiData Man page
dtiData-class Man page
[,dtiData-method Man page
dtiIndices Man page
dtiIndices,ANY-method Man page
dtiIndices-class Man page
dtiIndices,dtiTensor-method Man page
[,dtiIndices-method Man page
dtiIndices-methods Man page
dti-package Man page
dti.smooth Man page
dti.smooth,ANY-method Man page
dti.smooth,dtiData-method Man page
dti.smooth,dtiTensor-method Man page
dti.smooth-methods Man page
dtiTensor Man page
dtiTensor,ANY-method Man page
dtiTensor-class Man page
dtiTensor,dtiData-method Man page
[,dtiTensor-method Man page
dtiTensor-methods Man page
dwi-class Man page
dwiFiber-class Man page
dwiMD Man page
dwiMD,ANY-method Man page
dwiMD,dtiData-method Man page
dwiMD,dtiTensor-method Man page
dwiMD-methods Man page
dwiMixtensor Man page
dwiMixtensor,ANY-method Man page
dwiMixtensor-class Man page
dwiMixtensor,dtiData-method Man page
[,dwiMixtensor-method Man page
dwiMixtensor-methods Man page
dwiMtCombine Man page
dwiMtCombine,ANY-method Man page
dwiMtCombine,dwiMixtensor,dwiMixtensor-method Man page
dwiMtCombine-methods Man page
dwiQball Man page
dwiQball,ANY-method Man page
dwiQball-class Man page
dwiQball,dtiData-method Man page
[,dwiQball-method Man page
dwiQball-methods Man page
dwiRiceBias Man page
dwiRiceBias,ANY-method Man page
dwiRiceBias,dtiData-method Man page
dwiRiceBias-methods Man page
dwi.smooth Man page
dwi.smooth,ANY-method Man page
dwi.smooth,dtiData-method Man page
dwi.smooth-methods Man page
dwi.smooth.ms Man page
dwi.smooth.ms,ANY-method Man page
dwi.smooth.ms,dtiData-method Man page
dwiSqrtODF Man page
dwiSqrtODF,ANY-method Man page
dwiSqrtODF,dtiData-method Man page
dwiSqrtODF-methods Man page
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
getmask Man page
getmask,ANY-method Man page
getmask,array-method Man page
getmask,dtiData-method Man page
getmask-methods Man page
getsdofsb Man page
getsdofsb,ANY-method Man page
getsdofsb,dtiData-method Man page
getsdofsb-methods Man page
icosa0 Man page
icosa1 Man page
icosa2 Man page
icosa3 Man page
icosa4 Man page
medinria Man page
MedINRIA Man page
medinria2tensor Man page
[-methods Man page
optgrad Man page
optgradients Man page
plmatrix Man page
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,dwiFiber-method Man page
plot,dwi-method Man page
plot,dwiMixtensor-method Man page
plot-methods Man page
pmatrix Man page
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,dwiFiber-method Man page
print,dwi-method Man page
print,dwiMixtensor-method Man page
print,dwiQball-method Man page
print-methods Man page
readDWIdata Man page
reduceFibers Man page
reduceFibers,dwiFiber-method Man page
sdpar Man page
sdpar,ANY-method Man page
sdpar,dtiData-method Man page
sdpar-methods Man page
selectFibers Man page
selectFibers,dwiFiber-method Man page
selectFibers-methods Man page
show3d Man page
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
show,ANY-method Man page
show,dkiIndices-method Man page
show,dkiTensor-method Man page
show,dtiData-method Man page
show,dtiIndices-method Man page
show,dti-method Man page
show,dtiTensor-method Man page
show,dwiFiber-method Man page
show,dwiMixtensor-method Man page
showFAColorScale Man page
show-methods Man page
subsetg Man page
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,dwiFiber-method Man page
summary,dwi-method Man page
summary,dwiMixtensor-method Man page
summary,dwiQball-method Man page
summary-methods Man page
tensor2medinria Man page
touchingFibers Man page
touchingFibers,dwiFiber,dwiFiber-method Man page
touchingFibers-methods Man page
tracking Man page
tracking,ANY-method Man page
tracking,dtiIndices-method Man page
tracking,dtiTensor-method Man page
tracking,dwiMixtensor-method Man page
tracking-methods Man page

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

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