README.md

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The neuroim2 package is currently in development. The goal of the project is to to provide basic functionality for working with neuroimaging data in R. neuroim2 It is an effort to modify and upgrade the neuroim package (https://github.com/bbuchsbaum/neuroim).

Installation

You can install the development version of neuroim2 (v. 0.1.0) from Github with:

# install.packages("devtools")
devtools::install_github("bbuchsbaum/neuroim2")

Usage

To read in a volumetric NIFTI formatted image, use the read_vol function:

library(neuroim2)
## Loading required package: Matrix
fname <- system.file("extdata", "global_mask.nii", package="neuroim2")
vol <- read_vol(fname)

Now, vol can be treated as a three-dimensional array:

v1 <- vol[1,1,1]
vol2 <- vol + vol
vol3 <- vol2 - vol
all(vol == vol3)
## [1] TRUE

We can create a 4D image, by concatenating several 3D volumes:

vec <- concat(vol, vol, vol2)
series1 <- vec[1,1,1,]
length(series1)
## [1] 3

Vignettes

See examples of use of neuroim2 in the vignettes.



bbuchsbaum/neuroim2 documentation built on Oct. 26, 2019, 12:18 p.m.