neuroim2

R data structures and function for fMRI-focused neuroimaging analysis

https://github.com/bbuchsbaum/neuroim2

Science Score: 26.0%

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Scientific vocabulary similarity
Low similarity (15.0%) to scientific vocabulary

Keywords

fmri neuroimaging r

Last synced: 10 months ago · JSON representation

Repository

R data structures and function for fMRI-focused neuroimaging analysis

Basic Info

Host: GitHub
Owner: bbuchsbaum
License: other
Language: R
Default Branch: master
Homepage: https://bbuchsbaum.github.io/neuroim2/
Size: 15 MB

Statistics

Stars: 3
Watchers: 1
Forks: 0
Open Issues: 7
Releases: 0

Topics

fmri neuroimaging r

Created over 8 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog License

README.Rmd

---
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

- Elegant slice visualization vignette: https://bbuchsbaum.github.io/neuroim2/articles/elegant-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)
```

Owner

Login: bbuchsbaum
Kind: user

Repositories: 56
Profile: https://github.com/bbuchsbaum

GitHub Events

Total

Issues event: 1
Watch event: 1
Push event: 57
Pull request event: 4
Create event: 5

Last Year

Issues event: 1
Watch event: 1
Push event: 57
Pull request event: 4
Create event: 5

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 7
Total pull requests: 10
Average time to close issues: almost 3 years
Average time to close pull requests: less than a minute
Total issue authors: 3
Total pull request authors: 1
Average comments per issue: 0.57
Average comments per pull request: 0.0
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 10
Average time to close issues: N/A
Average time to close pull requests: less than a minute
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

bbuchsbaum (5)
dipterix (1)
seantma (1)

Pull Request Authors

bbuchsbaum (10)

Top Labels

Issue Labels

Pull Request Labels

codex (10)

Packages

Total packages: 1
Total downloads:
- cran 210 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 1
Total maintainers: 1

cran.r-project.org: neuroim2

Data Structures for Brain Imaging Data

Homepage: https://github.com/bbuchsbaum/neuroim2
Documentation: http://cran.r-project.org/web/packages/neuroim2/neuroim2.pdf
License: MIT + file LICENSE
Latest release: 0.8.1
published about 1 year ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 210 Last month

Rankings

Dependent packages count: 26.8%

Dependent repos count: 33.0%

Average: 48.8%

Downloads: 86.7%

Maintainers (1)

brad.buchsbaum@gmail.com