ANTsR

ANTs in R: Quantification Tools for Biomedical Images

ANTsR interfaces state of the art image processing with R statistical methods. The project grew out of the need, at University of Pennsylvania, to develop large-scale analytics pipelines that track provenance from scanner to scientific study. ANTsR wraps an ANTs and ITK C++ core via Rcpp to access these frameworks from within R and support reproducible analyses. Specialized functionality in ANTsR includes image segmentation and registration along imaging specific variations of principal component and canonical correlation analysis.

Author: Brian B. Avants

Maintainer: Brian B. Avants < stnava at gmail.com >

Citation (from within R, entercitation("ANTsR")):

To cite package 'ANTsR' in publications use:

Brian B. Avants, Benjamin M. Kandel, Jeff T. Duda, Philip A. Cook,
Nicholas J. Tustison and Shrinidhi KL (2016). ANTsR: ANTs in R:
quantification tools for biomedical images. R package version 0.3.3.

A BibTeX entry for LaTeX users is

@Manual{,
title = {ANTsR: ANTs in R: quantification tools for biomedical images},
author = {Brian B. Avants and Benjamin M. Kandel and Jeff T. Duda and Philip A. Cook and Nicholas J. Tustison and Shrinidhi KL},
year = {2016},
note = {R package version 0.3.3},
}

Issues

If you have any problems with this package you can open a new issue or check the already existing ones here.

Package Versions

Stable

VersionUNIX CI testsOSX CI testsWindows CI testsCoverageLogs
0.6.1view

Current

VersionUNIX CI testsOSX CI testsWindows CI testsCoverageLogs
0.6.1view

All Versions

VersionStableCurrentCoverageLogs
Unix CI testsOSX CI testsWindows CI testsUnix CI testsOSX CI testsWindows CI tests
0.6.1view

Installation

To install this package, start R and enter:

source("https://neuroconductor.org/neurocLite.R")
neuroc_install("ANTsR")


More detailed installation instructions can be found here.

Details

Initally submitted on 2017-10-05 09:58:02
Package type standard
Source GitHub URLhttps://github.com/stnava/ANTsR
Neuroconductor GitHub URLhttps://github.com/neuroconductor/ANTsR
System requirementscmake, git, clang
Dependsmethods, ANTsRCore (0.2)
Importsgraphics, grDevices, magic, magrittr, psych, rsvd, stats, utils
LinkingToRcpp, ITKR, ANTsRCore
Suggestsabind, BGLR, caret, cluster, corpcor, DMwR, dplyr, e1071, extremevalues, fastICA, fpc, ggplot2, glasso, glmnet, grid, h5, igraph, irlba, knitr, MASS, Matrix, mFilter, misc3d, moments, nabor, networkD3, pixmap, png, pracma, randomForest, RANN, Rcpp, RcppEigen, rflann, rgl, rmarkdown, robust, robustbase, signal, sna, testthat, tools, viridis, visreg, wmtsa, xgboost
Reverse importsextrantsr (0.6)

Documentation

LinkFile nameTitle
HTMLANTsRTransformations and statistical representations for images in R
HTMLMultiChannelMultichannel image proccessing
HTMLRestingBOLDResting BOLD (basic analyses using ANTsR)
HTMLantsrTransformUsing the antsrTransform class
HTMLdeformationSimulationSimulate a deformation field with ANTsR
HTMLiMathiMath (mathematical operations inside ANTsR)
HTMLmultivarTemplateCoordinatesmultivariate template coordinates example for eigenanatomy
HTMLrfLesionSegMulti-resolution voxel-wise neighborhood random forest (MRV-NRF) lesion segmentation

Search Neuroconductor for ANTsR