Package: dti 1.5.4.3
Karsten Tabelow
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:
dti_1.5.4.3.tar.gz
dti_1.5.4.3.tar.gz(r-4.5-noble)dti_1.5.4.3.tar.gz(r-4.4-noble)
dti_1.5.4.3.tgz(r-4.4-emscripten)dti_1.5.4.3.tgz(r-4.3-emscripten)
dti.pdf |dti.html✨
dti/json (API)
| # Install 'dti' in R: |
| install.packages('dti', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- 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
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 30 days agofrom:6461869b28. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 27 2024 |
| R-4.5-linux-x86_64 | OK | Sep 27 2024 |
Exports:AdjacencyMatrixaflsigmcafsigmcawslsigmcawssigmccombineDWIdatacombineFibersdkiIndicesdkiTensordti.optionsdti.smoothdtiDatadtiIndicesdtiTensordwi.smoothdwi.smooth.msdwiMDdwiMixtensordwiMtCombinedwiQballdwiRiceBiasextractgetmaskgetsdofsbmedinria2tensorplotprintreadDWIdatareduceFiberssdparselectFiberssetmaskshowshow3dshowFAColorScalesubsetgsummarytensor2medinriatouchingFiberstracking
Dependencies:abindadimproawsawsMethodsbase64encbitopsbslibcachemclidigestevaluatefastmapfontawesomefsgluegslhighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimeoro.dicomoro.niftiquadprogR6rappdirsRcpprglrlangrmarkdownRNiftisasstinytexxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Analysis of Diffusion Weighted Imaging (DWI) Data | dti-package dti |
| Create an adjacency matrix from fiber tracking results | AdjacencyMatrix |
| Estimate noise variance for multicoil MR systems | aflsigmc afsigmc awslsigmc awssigmc |
| FA map color scheme | colqFA |
| 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 data | dwi.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 Bias | dwiRiceBias 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 deviation | getsdofsb getsdofsb,ANY-method getsdofsb,dtiData-method getsdofsb-methods |
| Read/Write Diffusion Tensor Data from/to NIFTI File | MedINRIA medinria medinria2tensor tensor2medinria |
| Optimal gradient directions | optgrad |
| Optimal gradient directions for number of gradients between 6 and 162 | optgradients |
| 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 triangles | icosa0 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 Data | dtiData 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 |
