{"id":28423940,"url":"https://github.com/bbuchsbaum/neuroim2","last_synced_at":"2026-02-20T03:04:04.793Z","repository":{"id":66678539,"uuid":"109069233","full_name":"bbuchsbaum/neuroim2","owner":"bbuchsbaum","description":"R data structures and function for fMRI-focused neuroimaging analysis","archived":false,"fork":false,"pushed_at":"2026-02-08T19:12:17.000Z","size":19765,"stargazers_count":3,"open_issues_count":8,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-02-11T21:44:31.894Z","etag":null,"topics":["fmri","neuroimaging","r"],"latest_commit_sha":null,"homepage":"https://bbuchsbaum.github.io/neuroim2/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bbuchsbaum.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2017-11-01T01:02:03.000Z","updated_at":"2026-02-08T19:12:20.000Z","dependencies_parsed_at":"2024-03-27T14:45:30.693Z","dependency_job_id":"eca9e6f9-a4d2-4d4b-99f4-6676ecd9cb51","html_url":"https://github.com/bbuchsbaum/neuroim2","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bbuchsbaum/neuroim2","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbuchsbaum%2Fneuroim2","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbuchsbaum%2Fneuroim2/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbuchsbaum%2Fneuroim2/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbuchsbaum%2Fneuroim2/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bbuchsbaum","download_url":"https://codeload.github.com/bbuchsbaum/neuroim2/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bbuchsbaum%2Fneuroim2/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29639809,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-19T22:32:43.237Z","status":"online","status_checked_at":"2026-02-20T02:00:07.535Z","response_time":59,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["fmri","neuroimaging","r"],"created_at":"2025-06-05T09:09:47.367Z","updated_at":"2026-02-20T03:04:04.788Z","avatar_url":"https://github.com/bbuchsbaum.png","language":"R","readme":"---\ntitle: \"neuroim2\"\noutput:\n  md_document:\n    variant: markdown_github\n---\n\n```{r setup, include=FALSE}\nknitr::opts_chunk$set(echo = TRUE)\n```\n\n# neuroim2 \u003cimg src=\"https://raw.githubusercontent.com/bbuchsbaum/neuroim2/master/docs/hex-neuroim2.png\" align=\"right\" width=\"120\" /\u003e\n\u003c!-- badges: start --\u003e\n[![CRAN status](https://www.r-pkg.org/badges/version/neuroim2)](https://cran.r-project.org/package=neuroim2)\n[![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/neuroim2)](https://cran.r-project.org/package=neuroim2)\n[![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)\n[![pkgdown](https://github.com/bbuchsbaum/neuroim2/actions/workflows/pkgdown.yaml/badge.svg)](https://bbuchsbaum.github.io/neuroim2/)\n[![codecov](https://codecov.io/gh/bbuchsbaum/neuroim2/branch/master/graph/badge.svg)](https://app.codecov.io/gh/bbuchsbaum/neuroim2)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE.md)\n\u003c!-- badges: end --\u003e\n\nData 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.  \n\n**Website:** https://bbuchsbaum.github.io/neuroim2/  \n**CRAN:** https://cran.r-project.org/package=neuroim2  \n**Cheatsheet:** [neuroim2_cheatsheet.md](neuroim2_cheatsheet.md)\n\n\n## Installation\n\n### CRAN\n\n```r\ninstall.packages(\"neuroim2\")\n```\n\n### R-universe (daily builds)\n\n```r\ninstall.packages(\"neuroim2\",\n  repos = c(\"https://bbuchsbaum.r-universe.dev\", \"https://cloud.r-project.org\"))\n```\n\n### Development version (GitHub)\n\n```r\n# install.packages(\"remotes\")\nremotes::install_github(\"bbuchsbaum/neuroim2\")\n```\n\n## Usage\n\nRead a NIFTI image and perform simple operations:\n\n```{r}\nlibrary(neuroim2)\nfname \u003c- system.file(\"extdata\", \"global_mask_v4.nii\", package=\"neuroim2\")\nvol \u003c- read_vol(fname)\n\nv1 \u003c- vol[1,1,1]\nvol2 \u003c- vol + vol\nall(vol == (vol2 - vol))\n```\n\nCreate a 4D image from volumes:\n\n```{r}\nvec \u003c- vec_from_vols(list(vol, vol, vol2))\nseries1 \u003c- vec[1,1,1,]\nlength(series1)\n```\n\n## Vignettes\n\nSee examples of use of `neuroim2` in the [vignettes](https://bbuchsbaum.github.io/neuroim2/articles/index.html).\n\n### Visualization\n\n- Slice visualization vignette: https://bbuchsbaum.github.io/neuroim2/articles/slice-visualization.html\n\nQuick montage example (robust scaling and shared colorbar):\n\n```r\n# Not run in README\n# library(neuroim2)\n# vol \u003c- read_vol(system.file(\"extdata\",\"global_mask_v4.nii\", package=\"neuroim2\"))\n# z \u003c- unique(round(seq(round(dim(vol)[3]*.25), round(dim(vol)[3]*.85), length.out = 12)))\n# plot_montage(vol, zlevels = z, along = 3, cmap = \"grays\", range = \"robust\", ncol = 6)\n```\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbbuchsbaum%2Fneuroim2","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbbuchsbaum%2Fneuroim2","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbbuchsbaum%2Fneuroim2/lists"}