Data structures and I/O for volumetric brain imaging with a focus on
fMRI. This is the successor to
neuroim with improved S4
classes, sparse/dense 3D–4D representations, and fast
resampling/filtering.
Website: https://bbuchsbaum.github.io/neuroim2/
CRAN: https://cran.r-project.org/package=neuroim2
Cheatsheet: neuroim2_cheatsheet.md
install.packages("neuroim2")install.packages("neuroim2",
repos = c("https://bbuchsbaum.r-universe.dev", "https://cloud.r-project.org"))# install.packages("remotes")
remotes::install_github("bbuchsbaum/neuroim2")Read a NIFTI image and perform simple operations:
library(neuroim2)## Loading required package: Matrix
##
## Attaching package: 'neuroim2'
## The following object is masked from 'package:base':
##
## scale
fname <- system.file("extdata", "global_mask_v4.nii", package="neuroim2")
vol <- read_vol(fname)
v1 <- vol[1,1,1]
vol2 <- vol + vol
all(vol == (vol2 - vol))## [1] TRUE
Create a 4D image from volumes:
vec <- vec_from_vols(list(vol, vol, vol2))
series1 <- vec[1,1,1,]
length(series1)## [1] 3
See examples of use of neuroim2 in the
vignettes.
This package uses the albersdown theme. Vignettes are styled with vignettes/albers.css and a local vignettes/albers.js; the palette family is provided via params$family (default 'red'). The pkgdown site uses template: { package: albersdown }.