R Observatory: Metrics for ciftiTools version 0.21.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ciftiTools

0.21.1Package record

Tools for Reading, Writing, Viewing and Manipulating CIFTI Files

3packages dependsuggested by 5

8.5Kdownloads / year

0.4%test coverage

9/13flavors OK

Overview

About

Maintained by Amanda MejiaCRAN page ↗GitHub ↗Issues ↗

CIFTI files contain brain imaging data in "grayordinates," which represent the gray matter as cortical surface vertices (left and right) and subcortical voxels (cerebellum, basal ganglia, and other deep gray matter). 'ciftiTools' provides a unified environment for reading, writing, visualizing and manipulating CIFTI-format data. It supports the "dscalar," "dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti" object, which is structured for convenient access to the data and metadata, and includes support for surface geometry files to enable spatially-dependent functionality such as static or interactive visualizations and smoothing.

Install

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

install.packages("ciftiTools", 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("mandymejia/ciftiTools")

Development version from mandymejia/ciftiTools. 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-ciftitools

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-ciftiTools

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-ciftiTools

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

4ERROR9OK

Check messages

ERRORre-building of vignette outputsr-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-release-macos-arm64, r-release-macos-x86_64

r-oldrel-macos-arm64

Error(s) in re-building vignettes:
--- re-building ‘ciftiTools_vignette_mini.Rmd’ using rmarkdown
2026-10-18 16:44:54.979 R[38810:364865] XType: Using static font registry.

Quitting from ciftiTools_vignette_mini.Rmd:85-92 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `knitr::include_graphics()`:
! Cannot find the file(s): "../../../../../../../../../Temp/tmp/RtmpidncMr/file979afe50f74.png"
---
Backtrace:
    ▆
 1. └─knitr::include_graphics(xii_plt, dpi = 200)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ciftiTools_vignette_mini.Rmd' failed with diagnostics:
Cannot find the file(s): "../../../../../../../../../Temp/tmp/RtmpidncMr/file979afe50f74.png"
--- failed re-building ‘ciftiTools_vignette_mini.Rmd’

SUMMARY: processing the following file failed:
  ‘ciftiTools_vignette_mini.Rmd’

Error: Vignette re-building failed.
Execution halted

r-oldrel-macos-x86_64

Error(s) in re-building vignettes:
--- re-building ‘ciftiTools_vignette_mini.Rmd’ using rmarkdown

Quitting from ciftiTools_vignette_mini.Rmd:85-92 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `knitr::include_graphics()`:
! Cannot find the file(s): "../../../../../../../../../Temp/tmp/Rtmp2xSJXq/fileb712147a63c3.png"
---
Backtrace:
    ▆
 1. └─knitr::include_graphics(xii_plt, dpi = 200)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ciftiTools_vignette_mini.Rmd' failed with diagnostics:
Cannot find the file(s): "../../../../../../../../../Temp/tmp/Rtmp2xSJXq/fileb712147a63c3.png"
--- failed re-building ‘ciftiTools_vignette_mini.Rmd’

SUMMARY: processing the following file failed:
  ‘ciftiTools_vignette_mini.Rmd’

Error: Vignette re-building failed.
Execution halted

r-release-macos-arm64

Error(s) in re-building vignettes:
--- re-building ‘ciftiTools_vignette_mini.Rmd’ using rmarkdown

Quitting from ciftiTools_vignette_mini.Rmd:85-92 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `knitr::include_graphics()`:
! Cannot find the file(s): "../../../../../../../../../Temp/tmp/RtmpsMf1Lo/file34621c91b7c9.png"
---
Backtrace:
    ▆
 1. └─knitr::include_graphics(xii_plt, dpi = 200)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ciftiTools_vignette_mini.Rmd' failed with diagnostics:
Cannot find the file(s): "../../../../../../../../../Temp/tmp/RtmpsMf1Lo/file34621c91b7c9.png"
--- failed re-building ‘ciftiTools_vignette_mini.Rmd’

SUMMARY: processing the following file failed:
  ‘ciftiTools_vignette_mini.Rmd’

Error: Vignette re-building failed.
Execution halted

r-release-macos-x86_64

Error(s) in re-building vignettes:
--- re-building ‘ciftiTools_vignette_mini.Rmd’ using rmarkdown

Quitting from ciftiTools_vignette_mini.Rmd:85-92 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `knitr::include_graphics()`:
! Cannot find the file(s): "../../../../../../../../../Temp/tmp/RtmpK5sQwX/file52833a8c58d.png"
---
Backtrace:
    ▆
 1. └─knitr::include_graphics(xii_plt, dpi = 200)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ciftiTools_vignette_mini.Rmd' failed with diagnostics:
Cannot find the file(s): "../../../../../../../../../Temp/tmp/RtmpK5sQwX/file52833a8c58d.png"
--- failed re-building ‘ciftiTools_vignette_mini.Rmd’

SUMMARY: processing the following file failed:
  ‘ciftiTools_vignette_mini.Rmd’

Error: Vignette re-building failed.
Execution halted

CRAN check page ↗

Slowest check: 5.5 min · r-release-macos-x86_64

Status changes

ERROR9 OK, 4 ERRORNow
ERROR8 OK, 2 NOTE, 3 ERROR2026-09-10
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.21.1

READMEYes · 1,263 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · does not mention 0.21.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 193 (113 internal)includes a package overview page
Examples that run: 0%1 never run
Exported functions with examples: 1%
Documented parameters: 81%
Return-value docs: 97%
Help pages citing references: 0%

Vignettes (1)

`ciftiTools` Mini Demo

How these are measured

Downloads

8.5K

CRAN downloads in the past year

Rank #3,840 · ~23/day · ~708/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

2.4K90 days

8.5K1 year

Compare downloads with other packages →

Also on286 r2u6 autocran934 conda_forge

How downloads are counted

Repository

mandymejia/ciftitools ↗Account: mandymejia

60Stars

10Forks

2Open issues

1Open PRs

17Releases

1,003Commits

18Commit identities

License file reads as GPL-3.0 · 1,003 commits · Last activity 2026-09-09 · +1.7% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 93%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-08 · 512026-10-16 · 60

How these are measured

PracticesBeta

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

Checks run against github.com/mandymejia/ciftitools on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (1)

README.Rmd

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing ciftiTools adds 44 packages (24 with compiled code, 42 MB of source tarballs). Heaviest: bslib 5.6 MB, oro.nifti 5.0 MB, rgl 4.0 MB.

Depends (1)

R >= 3.5.0

Imports (10)

fields giftigrDeviceshtmltools oro.nifti RNifti RColorBrewer rgl viridisLite xml2

LinkingTo (0)

none

Suggests (14)

chromote covr ggplot2 ggpubrgridgridExtra htmlwidgets manipulateWidgetMatrixwebshot2 knitr rmarkdown png testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

Imports 3

Suggested by 5

Depends, Imports or LinkingTo, most downloaded first

BayesfMRI hrf SparseICA

Suggests, most downloaded first

fMRItools fMRIscrub templateICAr BayesBrainMap neuromapr

How these are counted

Code & Tests

Datasets

People & History

People (3)

Amanda Mejia

Author, Maintainer since 0.1.6.0 (2020)

Damon Pham

Author

John Muschelli

Contributor · added in 0.4.3

Releases (19)

Pick two releases to compare their code metrics.

0.21.1Latest
record
2026-09-09 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.19.0
record
2026-03-19 · diff ↗
0.18.0
record
2025-12-20 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.17.4
record
2025-01-23 · diff ↗ ·
added 1 export
impute_xifti
0.16.1
record
2024-09-20 · diff ↗ ·
added 2 exports
move_from_submask, move_to_submask
0.15.1
record
2024-06-25 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.14.0
record
2024-02-24 · diff ↗
0.13.4
record
2024-01-21 · diff ↗ ·
added 11 exports
convert_to_dlabel, convert_to_dscalar, convert_to_dtseries, parc_add_subcortex, parc_vals_to_xifti, remapCIfTI, remap_cifti, remap_gifti, remap_xifti, remapcii, surf_area
0.12.2
record
2023-08-15 · diff ↗ ·
added 3 exports
apply_parc, even_vert_samp, set_names_xifti
R
R 4.3.0 released · 2023-04-21
0.11.0
record
2023-01-23 · diff ↗ ·
removed 1 export
unmask_cortex

added 5 exports
boundary_mask_surf, dilate_mask_surf, edit_mask_surf, erode_mask_surf, mask_surf
0.10.2
record
2022-07-01 · diff ↗
0.9.0
record
2022-05-16 · diff ↗

Show 10 earlier eventsHide 10 earlier events

R
R 4.2.0 released · 2022-04-22
0.8.0
record
2022-01-31 · diff ↗ ·
added 2 exports
infer_resolution, scale_xifti
0.7.0
record
2021-11-17 · diff ↗ ·
added 2 exports
view_comp, write_xifti2
0.6.1
record
2021-09-16 · diff ↗
0.4.3
record
2021-08-19 · diff ↗ ·
removed 2 exports
demo_files, unmask_vol

added 9 exports
apply_xifti, ciftiTools.files, fix_xifti, load_parc, load_surf, move_from_mwall, move_to_mwall, unmask_subcortex, write_surf
0.3.1
record
2021-06-17 · diff ↗ ·
removed 4 exports
concat_xifti, convert_to_dlabel, convert_to_dscalar, gifti_to_surf

added 8 exports
combine_xifti, convert_xifti, merge_xifti, read_surf, read_xifti2, smoothGIfTI, smooth_gifti, smoothgii
R
R 4.1.0 released · 2021-05-18
0.2.2
record
2021-03-16 · diff ↗ ·
added 10 exports
concat_xifti, convert_to_dlabel, convert_to_dscalar, newdata_xifti, remove_xifti, rotate_surf, run_wb_cmd, select_xifti, smooth_xifti, transform_xifti
0.1.6.0
record
2020-11-20
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-20
Total releases: 19 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 5.2 MB

Appears in task views

Medical Image Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ciftiTools")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for ciftiTools version 0.21.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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