Brief Introduction to using ANTs in R¶

There is a general tutorial here ANTsR-Tutorial .

Once installation is successful, the ANTsR package can be used in R as follows:

Load the package

> library( ANTsR )

List the available functions in the namespace ANTsR

> ANTsR::<double-tab>

Use any function in the core ANTS namespace by providing arguments almost exactly as in the command-line version.

For example, call the antsImageRead routine and some standard ANTs functions.

tfn <- getANTsRData("r16")  # download example data
antsimage <- antsImageRead(tfn, 2)
imgn3 <- antsImageClone(antsimage)
N3BiasFieldCorrection(list(antsimage@dimension, antsimage, imgn3, "4"))

Installation Method: OSX and LINUX variants¶

We created an install script ( ANTsR-Install-Script ) that uses Homebrew or apt-get (on LINUX)

to install CMake, git, R, wget ( on osx ) and ANTsR package dependencies.

NOTE: If you see errors like “Undefined symbols for architecture x86_64” , edit the script to use

$ R –arch=x86_64 CMD INSTALL ANTsR