# Analysis of Diffusion Weighted Imaging (DWI) Data

## Documentation for package ‘dti’ version 1.5.4.3

- DESCRIPTION file.
- Code demos. Use demo() to run them.

## Help Pages

A C D E G I M O P R S T misc

dti-package | Analysis of Diffusion Weighted Imaging (DWI) Data

## -- A --

AdjacencyMatrix | Create an adjacency matrix from fiber tracking results
aflsigmc | Estimate noise variance for multicoil MR systems
afsigmc | Estimate noise variance for multicoil MR systems
awslsigmc | Estimate noise variance for multicoil MR systems
awssigmc | Estimate noise variance for multicoil MR systems

## -- C --

colqFA | FA map color scheme
combineDWIdata | Combine two objects of class "dtiData")
combineFibers | Methods for Function 'tracking' in Package 'dti'
combineFibers-method | Methods for Function 'tracking' in Package 'dti'
combineFibers-methods | Methods for Function 'tracking' in Package 'dti'

## -- D --

dkiIndices | Diffusion Kurtosis Imaging (DKI)
dkiIndices-class | Class "dwi"
dkiIndices-method | Diffusion Kurtosis Imaging (DKI)
dkiIndices-methods | Diffusion Kurtosis Imaging (DKI)
dkiTensor | Diffusion Kurtosis Imaging (DKI)
dkiTensor-class | Class "dwi"
dkiTensor-method | Diffusion Kurtosis Imaging (DKI)
dkiTensor-methods | Diffusion Kurtosis Imaging (DKI)
dti | Analysis of Diffusion Weighted Imaging (DWI) Data
dti.options | Set and manipulate image orientations for plots.
dti.smooth | Methods for Function 'dti.smooth' in Package 'dti'
dti.smooth-method | Methods for Function 'dti.smooth' in Package 'dti'
dti.smooth-methods | Methods for Function 'dti.smooth' in Package 'dti'
dtiData | Read Diffusion Weighted Data
dtiData-class | Class "dwi"
dtiIndices | Methods for Function 'dtiIndices' in Package 'dti'
dtiIndices-class | Class "dwi"
dtiIndices-method | Methods for Function 'dtiIndices' in Package 'dti'
dtiIndices-methods | Methods for Function 'dtiIndices' in Package 'dti'
dtiTensor | Methods for Function 'dtiTensor' in Package 'dti'
dtiTensor-class | Class "dwi"
dtiTensor-method | Methods for Function 'dtiTensor' in Package 'dti'
dtiTensor-methods | Methods for Function 'dtiTensor' in Package 'dti'
dwi-class | Class "dwi"
dwi.smooth | Smooth DWI data
dwi.smooth-method | Smooth DWI data
dwi.smooth-methods | Smooth DWI data
dwi.smooth.ms | Smooth DWI data
dwi.smooth.ms-method | Smooth DWI data
dwiFiber-class | Class "dwi"
dwiMD | Methods for Mean Diffusivity in Package 'dti'
dwiMD-method | Methods for Mean Diffusivity in Package 'dti'
dwiMixtensor | Methods for Function 'dwiMixtensor' in Package 'dti'
dwiMixtensor-class | Class "dwi"
dwiMixtensor-method | Methods for Function 'dwiMixtensor' in Package 'dti'
dwiMixtensor-methods | Methods for Function 'dwiMixtensor' in Package 'dti'
dwiMtCombine | Methods for Function 'dwiMixtensor' in Package 'dti'
dwiMtCombine-method | Methods for Function 'dwiMixtensor' in Package 'dti'
dwiMtCombine-methods | Methods for Function 'dwiMixtensor' in Package 'dti'
dwiQball | Methods for Function 'dwiQball' in Package 'dti'
dwiQball-class | Class "dwi"
dwiQball-method | Methods for Function 'dwiQball' in Package 'dti'
dwiQball-methods | Methods for Function 'dwiQball' in Package 'dti'
dwiRiceBias | Correction for Rician Bias
dwiRiceBias-method | Correction for Rician Bias
dwiRiceBias-methods | Correction for Rician Bias
dwiSqrtODF | Methods for positive definite EAP and ODF estimation in Package 'dti'
dwiSqrtODF-method | Methods for positive definite EAP and ODF estimation in Package 'dti'
dwiSqrtODF-methods | Methods for positive definite EAP and ODF estimation in Package 'dti'

## -- E --

extract | Methods for Function 'extract' and '[' in Package 'dti'
extract-method | Methods for Function 'extract' and '[' in Package 'dti'
extract-methods | Methods for Function 'extract' and '[' in Package 'dti'

## -- G --

getmask | Methods for Function 'getmask' in Package 'dti'
getmask-method | Methods for Function 'getmask' in Package 'dti'
getmask-methods | Methods for Function 'getmask' in Package 'dti'
getsdofsb | Estimate the noise standard deviation
getsdofsb-method | Estimate the noise standard deviation
getsdofsb-methods | Estimate the noise standard deviation

## -- I --

icosa0 | Polyeders derived from the Icosahedron (icosa0) by sequential triangulation of surface triangles
icosa1 | Polyeders derived from the Icosahedron (icosa0) by sequential triangulation of surface triangles
icosa2 | Polyeders derived from the Icosahedron (icosa0) by sequential triangulation of surface triangles
icosa3 | Polyeders derived from the Icosahedron (icosa0) by sequential triangulation of surface triangles
icosa4 | Polyeders derived from the Icosahedron (icosa0) by sequential triangulation of surface triangles

## -- M --

MedINRIA | Read/Write Diffusion Tensor Data from/to NIFTI File
medinria | Read/Write Diffusion Tensor Data from/to NIFTI File
medinria2tensor | Read/Write Diffusion Tensor Data from/to NIFTI File

## -- O --

optgrad | Optimal gradient directions
optgradients | Optimal gradient directions for number of gradients between 6 and 162

## -- P --

plot-method | Methods for Function 'plot' in Package 'dti'
plot-methods | Methods for Function 'plot' in Package 'dti'
polyeder | Polyeders derived from the Icosahedron (icosa0) by sequential triangulation of surface triangles
print-method | Methods for Function 'print' in Package 'dti'
print-methods | Methods for Function 'print' in Package 'dti'

## -- R --

readDWIdata | Read Diffusion Weighted Data
reduceFibers | Methods for Function 'tracking' in Package 'dti'
reduceFibers-method | Methods for Function 'tracking' in Package 'dti'

## -- S --

sdpar | Methods for Function 'sdpar' in Package 'dti'
sdpar-method | Methods for Function 'sdpar' in Package 'dti'
sdpar-methods | Methods for Function 'sdpar' in Package 'dti'
selectFibers | Methods for Function 'tracking' in Package 'dti'
selectFibers-method | Methods for Function 'tracking' in Package 'dti'
selectFibers-methods | Methods for Function 'tracking' in Package 'dti'
setmask | Methods for Function 'setmask' in Package 'dti'
setmask-method | Methods for Function 'setmask' in Package 'dti'
setmask-methods | Methods for Function 'setmask' in Package 'dti'
show-method | Methods for Function 'show' in Package 'dti'
show-methods | Methods for Function 'show' in Package 'dti'
show3d | Methods for Function 'show3d' in Package 'dti'
show3d-method | Methods for Function 'show3d' in Package 'dti'
show3d-methods | Methods for Function 'show3d' in Package 'dti'
showFAColorScale | Writes an image with the colqFA colorscale to disk.
subsetg | Create an objects of class "dtiData" containing only a subset of gradient directions.
summary-method | Methods for Function 'summary' in Package 'dti'
summary-methods | Methods for Function 'summary' in Package 'dti'

## -- T --

tensor2medinria | Read/Write Diffusion Tensor Data from/to NIFTI File
touchingFibers | Methods for Function 'tracking' in Package 'dti'
touchingFibers-method | Methods for Function 'tracking' in Package 'dti'
touchingFibers-methods | Methods for Function 'tracking' in Package 'dti'
tracking | Methods for Function 'tracking' in Package 'dti'
tracking-method | Methods for Function 'tracking' in Package 'dti'
tracking-methods | Methods for Function 'tracking' in Package 'dti'

## -- misc --

[-method | Methods for Function 'extract' and '[' in Package 'dti'
[-methods | Methods for Function 'extract' and '[' in Package 'dti'