freesurferformats

1.0.1

Read and Write 'FreeSurfer' Neuroimaging File Formats

8packages depend

22.4Kdownloads / year

85.4%test coverage

12/13checks pass

Overview

About

Maintained by Tim SchäferFirst published 2019-09-0421 releasesCRAN page ↗GitHub ↗

Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' http://freesurfer.net/ formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("freesurferformats", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("dfsp-spirit/freesurferformats")

Development version from dfsp-spirit/freesurferformats. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-freesurferformats

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-freesurferformats

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-freesurferformats

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 4.8 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.31

85.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 51%
Documented parameters: 96%
Return-value docs: 88%
References docs: 7%

Downloads

22.4K

CRAN downloads in the past year

Rank #2,822 · ~61/day · ~1.9K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

5.6K90 days

22.4K1 year

Compare downloads with other packages →

Also on230 r2u3 autocran1.1K conda_forge45 c2d4u

Repository

GitHub ↗ dfsp-spirit/freesurferformats

23Stars

5Forks

0Open issues

0Open PRs

22Releases

881Commits

4Contributors

freesurferrfileformatsneuroimagingbrainmrisurfacemesh

881 commits · Last activity 2026-07-30

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/dfsp-spirit/freesurferformats on 2026-07-31.

Continuous integration (2)

GitHub ActionsAppVeyor

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Lint, format, editor (1)

RStudio project

Show all practices

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

utilspkgfilecache xml2

LinkingTo (0)

none

Suggests (7)

knitr rmarkdown curl testthat oro.nifti (>= 0.9)gifti cifti

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

8direct

1indirect

VertexWiseR fsbrain ieegio threeBrain wal ggseg.meshes neuromapr ravetools

Code & Tests

People & History

People (1)

Maintainer (1)

Tim Schäfer

Author, Maintainer

Authors (1)

Tim Schäfer

Author, Maintainer

Package Timeline

21 releases. Pick two to compare their code metrics. R releases are shown for context.

1.0.1Latest
2026-07-08 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.0
2025-09-08 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.18
2024-02-02 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.17
2022-02-11 · diff ↗
0.1.16
2021-11-07 · diff ↗
0.1.15
2021-05-25 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.14
2021-01-17 · diff ↗
0.1.13
2020-09-21 · diff ↗
0.1.12
2020-08-26 · diff ↗
0.1.11
2020-06-17 · diff ↗

Show 13 earlier events

0.1.10
2020-05-13 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.9
2020-04-14 · diff ↗
0.1.8
2020-02-17 · diff ↗
0.1.7
2020-01-07 · diff ↗
0.1.6
2019-11-27 · diff ↗
0.1.5
2019-11-12 · diff ↗
0.1.4
2019-11-06 · diff ↗
0.1.3
2019-10-15 · diff ↗
0.1.2
2019-10-02 · diff ↗
0.1.1
2019-09-13 · diff ↗
0.1.0
2019-09-04
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-09-04
Total releases: 21 / 7 yrs
License: MIT + file LICENSE OSI
Download size: 3.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Medical Image Analysis

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