Package: dti 1.5.4.3

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.

Authors:Karsten Tabelow [aut, cre], Joerg Polzehl [aut], Felix Anker [ctb]

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dti.pdf |dti.html
dti/json (API)

# Install 'dti' in R:
install.packages('dti', repos = c('https://ktabelow.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • colqFA - FA map color scheme
  • 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
  • optgrad - Optimal gradient directions

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.20 score 16 scripts 863 downloads 2 mentions 40 exports 40 dependencies

Last updated 2 months agofrom:6461869b28. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-win-x86_64OKOct 27 2024
R-4.5-linux-x86_64OKOct 27 2024
R-4.4-win-x86_64OKOct 27 2024
R-4.4-mac-x86_64OKOct 27 2024
R-4.4-mac-aarch64OKOct 27 2024
R-4.3-win-x86_64OKOct 27 2024
R-4.3-mac-x86_64OKOct 27 2024
R-4.3-mac-aarch64OKOct 27 2024

Exports:AdjacencyMatrixaflsigmcafsigmcawslsigmcawssigmccombineDWIdatacombineFibersdkiIndicesdkiTensordti.optionsdti.smoothdtiDatadtiIndicesdtiTensordwi.smoothdwi.smooth.msdwiMDdwiMixtensordwiMtCombinedwiQballdwiRiceBiasextractgetmaskgetsdofsbmedinria2tensorplotprintreadDWIdatareduceFiberssdparselectFiberssetmaskshowshow3dshowFAColorScalesubsetgsummarytensor2medinriatouchingFiberstracking

Dependencies:abindadimproawsawsMethodsbase64encbitopsbslibcachemclidigestevaluatefastmapfontawesomefsgluegslhighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimeoro.dicomoro.niftiquadprogR6rappdirsRcpprglrlangrmarkdownRNiftisasstinytexxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Analysis of Diffusion Weighted Imaging (DWI) Datadti-package dti
Create an adjacency matrix from fiber tracking resultsAdjacencyMatrix
Estimate noise variance for multicoil MR systemsaflsigmc afsigmc awslsigmc awssigmc
FA map color schemecolqFA
Combine two objects of class "dtiData")combineDWIdata
Diffusion Kurtosis Imaging (DKI)dkiIndices dkiIndices,ANY-method dkiIndices,dkiTensor-method dkiIndices-methods dkiTensor dkiTensor,ANY-method dkiTensor,dtiData-method dkiTensor-methods
Set and manipulate image orientations for plots.dti.options
Methods for Function `dti.smooth' in Package `dti'dti.smooth dti.smooth,ANY-method dti.smooth,dtiData-method dti.smooth,dtiTensor-method dti.smooth-methods
Methods for Function `dtiIndices' in Package `dti'dtiIndices dtiIndices,ANY-method dtiIndices,dtiTensor-method dtiIndices-methods
Methods for Function `dtiTensor' in Package `dti'dtiTensor dtiTensor,ANY-method dtiTensor,dtiData-method dtiTensor-methods
Class "dwi"dkiIndices-class dkiTensor-class dtiData-class dtiIndices-class dtiTensor-class dwi-class dwiFiber-class dwiMixtensor-class dwiQball-class
Smooth DWI datadwi.smooth dwi.smooth,ANY-method dwi.smooth,dtiData-method dwi.smooth-methods dwi.smooth.ms dwi.smooth.ms,ANY-method dwi.smooth.ms,dtiData-method
Methods for Mean Diffusivity in Package `dti'dwiMD dwiMD,ANY-method dwiMD,dtiData-method dwiMD,dtiTensor-method
Methods for Function `dwiMixtensor' in Package `dti'dwiMixtensor dwiMixtensor,ANY-method dwiMixtensor,dtiData-method dwiMixtensor-methods dwiMtCombine dwiMtCombine,ANY-method dwiMtCombine,dwiMixtensor,dwiMixtensor-method dwiMtCombine-methods
Methods for Function `dwiQball' in Package `dti'dwiQball dwiQball,ANY-method dwiQball,dtiData-method dwiQball-methods
Correction for Rician BiasdwiRiceBias dwiRiceBias,ANY-method dwiRiceBias,dtiData-method dwiRiceBias-methods
Methods for positive definite EAP and ODF estimation in Package 'dti'dwiSqrtODF dwiSqrtODF,ANY-method dwiSqrtODF,dtiData-method dwiSqrtODF-methods
Methods for Function `extract' and `[' in Package `dti'extract extract,ANY-method extract,dtiData-method extract,dtiIndices-method extract,dtiTensor-method extract,dwiMixtensor-method extract,dwiQball-method extract-methods [,ANY-method [,dkiIndices-method [,dkiTensor-method [,dtiData-method [,dtiIndices-method [,dtiTensor-method [,dwiMixtensor-method [,dwiQball-method [-methods
Methods for Function `getmask' in Package `dti'getmask getmask,ANY-method getmask,array-method getmask,dtiData-method getmask-methods
Estimate the noise standard deviationgetsdofsb getsdofsb,ANY-method getsdofsb,dtiData-method getsdofsb-methods
Read/Write Diffusion Tensor Data from/to NIFTI FileMedINRIA medinria medinria2tensor tensor2medinria
Optimal gradient directionsoptgrad
Optimal gradient directions for number of gradients between 6 and 162optgradients
Methods for Function `plot' in Package `dti'plot,ANY-method plot,dkiIndices-method plot,dtiData-method plot,dtiIndices-method plot,dtiTensor-method plot,dwi-method plot,dwiFiber-method plot,dwiMixtensor-method plot-methods
Polyeders derived from the Icosahedron (icosa0) by sequential triangulation of surface trianglesicosa0 icosa1 icosa2 icosa3 icosa4 polyeder
Methods for Function `print' in Package `dti'print,ANY-method print,dkiIndices-method print,dkiTensor-method print,dtiData-method print,dtiIndices-method print,dtiTensor-method print,dwi-method print,dwiFiber-method print,dwiMixtensor-method print,dwiQball-method print-methods
Read Diffusion Weighted DatadtiData readDWIdata
Methods for Function `sdpar' in Package `dti'sdpar sdpar,ANY-method sdpar,dtiData-method sdpar-methods
Methods for Function `setmask' in Package `dti'setmask setmask,ANY-method setmask,dtiData-method setmask-methods
Methods for Function `show' in Package `dti'show,ANY-method show,dkiIndices-method show,dkiTensor-method show,dti-method show,dtiData-method show,dtiIndices-method show,dtiTensor-method show,dwiFiber-method show,dwiMixtensor-method show-methods
Methods for Function `show3d' in Package `dti'show3d show3d,ANY-method show3d,dkiTensor-method show3d,dtiData-method show3d,dtiIndices-method show3d,dtiTensor-method show3d,dwiFiber-method show3d,dwiMixtensor-method show3d,dwiQball-method show3d-methods
Writes an image with the colqFA colorscale to disk.showFAColorScale
Create an objects of class "dtiData" containing only a subset of gradient directions.subsetg
Methods for Function `summary' in Package `dti'summary,ANY-method summary,dkiIndices-method summary,dkiTensor-method summary,dtiData-method summary,dtiIndices-method summary,dtiTensor-method summary,dwi-method summary,dwiFiber-method summary,dwiMixtensor-method summary,dwiQball-method summary-methods
Methods for Function `tracking' in Package `dti'combineFibers combineFibers,dwiFiber,dwiFiber-method combineFibers-methods reduceFibers reduceFibers,dwiFiber-method selectFibers selectFibers,dwiFiber-method selectFibers-methods touchingFibers touchingFibers,dwiFiber,dwiFiber-method touchingFibers-methods tracking tracking,ANY-method tracking,dtiIndices-method tracking,dtiTensor-method tracking,dwiMixtensor-method tracking-methods