https://github.com/bbuchsbaum/neuroim2

R data structures and function for fMRI-focused neuroimaging analysis
https://github.com/bbuchsbaum/neuroim2

fmri neuroimaging r

Last synced: about 2 months ago
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R data structures and function for fMRI-focused neuroimaging analysis

• Host: GitHub
• URL: https://github.com/bbuchsbaum/neuroim2
• Owner: bbuchsbaum
• License: other
• Created: 2017-11-01T01:02:03.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2026-02-08T19:12:17.000Z (about 2 months ago)
• Last Synced: 2026-02-11T21:44:31.894Z (about 2 months ago)
• Topics: fmri, neuroimaging, r
• Language: R
• Homepage: https://bbuchsbaum.github.io/neuroim2/
• Size: 18.8 MB
• Stars: 3
• Watchers: 1
• Forks: 0
• Open Issues: 8
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • License: LICENSE

Awesome Lists containing this project

README

          
---

title: "neuroim2"

output:

  md_document:

    variant: markdown_github

---

```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = TRUE)

```

# neuroim2 

[![CRAN status](https://www.r-pkg.org/badges/version/neuroim2)](https://cran.r-project.org/package=neuroim2)

[![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/neuroim2)](https://cran.r-project.org/package=neuroim2)

[![R-CMD-check](https://github.com/bbuchsbaum/neuroim2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bbuchsbaum/neuroim2/actions/workflows/R-CMD-check.yaml)

[![pkgdown](https://github.com/bbuchsbaum/neuroim2/actions/workflows/pkgdown.yaml/badge.svg)](https://bbuchsbaum.github.io/neuroim2/)

[![codecov](https://codecov.io/gh/bbuchsbaum/neuroim2/branch/master/graph/badge.svg)](https://app.codecov.io/gh/bbuchsbaum/neuroim2)

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE.md)

Data structures and I/O for volumetric brain imaging with a focus on fMRI. This is the successor to [`neuroim`](https://github.com/bbuchsbaum/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](neuroim2_cheatsheet.md)

## Installation

### CRAN

```r

install.packages("neuroim2")

```

### R-universe (daily builds)

```r

install.packages("neuroim2",

  repos = c("https://bbuchsbaum.r-universe.dev", "https://cloud.r-project.org"))

```

### Development version (GitHub)

```r

# install.packages("remotes")

remotes::install_github("bbuchsbaum/neuroim2")

```

## Usage

Read a NIFTI image and perform simple operations:

```{r}

library(neuroim2)

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))

```

Create a 4D image from volumes:

```{r}

vec <- vec_from_vols(list(vol, vol, vol2))

series1 <- vec[1,1,1,]

length(series1)

```

## Vignettes

See examples of use of `neuroim2` in the [vignettes](https://bbuchsbaum.github.io/neuroim2/articles/index.html).

### Visualization

- Slice visualization vignette: https://bbuchsbaum.github.io/neuroim2/articles/slice-visualization.html

Quick montage example (robust scaling and shared colorbar):

```r

# Not run in README

# library(neuroim2)

# vol <- read_vol(system.file("extdata","global_mask_v4.nii", package="neuroim2"))

# z <- unique(round(seq(round(dim(vol)[3]*.25), round(dim(vol)[3]*.85), length.out = 12)))

# plot_montage(vol, zlevels = z, along = 3, cmap = "grays", range = "robust", ncol = 6)

```