Package: ciftiTools 0.19.0

ciftiTools: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files

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.

Authors:Amanda Mejia [aut, cre], Damon Pham [aut], John Muschelli [ctb]

ciftiTools_0.19.0.tar.gz
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ciftiTools_0.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ciftiTools/json (API)

# Install 'ciftiTools' in R:

install.packages('ciftiTools', repos = c('https://mandymejia.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mandymejia/ciftitools/issues

On CRAN:

8.60 score 58 stars 3 packages 252 scripts 825 downloads 115 exports 44 dependencies

Last updated from:1dc7110788. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	225
source / vignettes	OK	319
linux-release-x86_64	OK	221
macos-release-arm64	OK	167
macos-oldrel-arm64	OK	146
windows-devel	OK	134
windows-release	OK	125
windows-oldrel	OK	126
wasm-release	OK	183

Exports:add_surf apply_parc apply_xifti as_cifti as_xifti as.cifti as.xifti boundary_mask_surf ciftiTools.files ciftiTools.getOption ciftiTools.listOptions ciftiTools.setOption combine_xifti convert_to_dlabel convert_to_dscalar convert_to_dtseries convert_xifti dilate_mask_surf edit_mask_surf erode_mask_surf even_vert_samp expand_color_pal fix_xifti get_wb_cmd_path impute_xifti infer_resolution info_cifti infoCIfTI infocii is_cifti is_xifti is.cifti is.surf is.xifti isCIfTI load_parc load_surf make_color_pal make_surf mask_surf merge_xifti move_from_mwall move_from_submask move_to_mwall move_to_submask newdata_xifti parc_add_subcortex parc_borders parc_vals_to_xifti read_cifti read_surf read_xifti read_xifti2 readCIfTI readcii remap_cifti remap_gifti remap_xifti remapCIfTI remapcii remove_xifti resample_cifti resample_cifti_from_template resample_gifti resample_surf resample_xifti resampleCIfTI resamplecii resampleGIfTI resamplegii rotate_surf ROY_BIG_BL run_wb_cmd scale_xifti select_xifti separate_cifti separateCIfTI separatecii set_names_xifti smooth_cifti smooth_gifti smooth_xifti smoothCIfTI smoothcii smoothGIfTI smoothgii substructure_table supported_intents surf_area transform_xifti unmask_subcortex use_color_pal view_cifti view_cifti_surface view_cifti_volume view_comp view_surf view_xifti view_xifti_surface view_xifti_volume viewCIfTI viewCIfTI_surface viewCIfTI_volume viewcii viewcii_surface viewcii_volume write_cifti write_metric_gifti write_subcort_nifti write_surf write_surf_gifti write_xifti write_xifti2 writeCIfTI writecii

Dependencies:abind base64enc bitops bslib cachem cli digest dotCall64 evaluate fastmap fields fontawesome fs gifti highr htmltools htmlwidgets jquerylib jsonlite knitr lifecycle magrittr maps memoise mime oro.nifti R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp rgl rlang rmarkdown RNifti sass spam tinytex viridisLite xfun xml2 yaml

ciftiTools Mini Demo

Visualization | Manipulation | Citing ciftiTools

Rendered fromciftiTools_vignette_mini.Rmdusingknitr::rmarkdown

Last update: 2025-01-23
Started: 2025-01-18

Help page	Topics
Add HCP surface(s) to a '"xifti"'	add_surf
Apply function over locations in each parcel	apply_parc
Apply a function along the rows or columns of a '"xifti"'	apply_xifti
Convert a '"xifti"' to a matrix	as.matrix.xifti
Assemble a '"xifti"' from data	as.cifti as.xifti as_cifti as_xifti
Boundary region of a mask	boundary_mask_surf
ciftiTools: Tools for Reading and Visualizing CIFTI Brain Files	ciftiTools-package ciftiTools
'ciftiTools' files	ciftiTools.files
Get a 'ciftiTools' option	ciftiTools.getOption
List 'ciftiTools' options	ciftiTools.listOptions
Set a 'ciftiTools' option	ciftiTools.setOption
Combine '"xifti"'s with non-overlapping brain structures	combine_xifti
Convert '"xifti"'	convert_to_dlabel convert_to_dscalar convert_to_dtseries convert_xifti
Dimensions of a '"xifti"'	dim.xifti
Edit mask on surface	dilate_mask_surf edit_mask_surf erode_mask_surf
Evenly sample vertices of mesh	even_vert_samp
Interpolates between entries in the input palette to make a larger palette with COLOR_RES entries.	expand_color_pal
faces	faces_Param
Fix a '"xifti"'	fix_xifti
Get the Connectome Workbench command path	get_wb_cmd_path
Impute '"xifti"' data	impute_xifti
Infer resolution from '"xifti"' and surfaces	infer_resolution
Get CIFTI metadata	infoCIfTI infocii info_cifti
Validate a '"xifti"' object	is.cifti isCIfTI is_cifti
Validate a '"surf"' object (vertices + faces)	is.surf
Validate a '"xifti"' object.	is.xifti is_xifti
Load a parcellation included in 'ciftiTools'	load_parc
Load a '"surf"' included in 'ciftiTools'	load_surf
Make a color palette.	make_color_pal
mask: vertices	mask_Param_vertices
Mask surface	mask_surf
Concatenate '"xifti"'s	merge_xifti
Move data locations from medial wall	move_from_mwall
Move data locations from subcortex mask	move_from_submask
Move data locations to the medial wall	move_to_mwall
Move data locations to the subcortex mask	move_to_submask
Replace the data in a '"xifti"'	newdata_xifti
Add subcortex to cortical parcellation	parc_add_subcortex
Parcellation borders	parc_borders
Convert parcellation values to '"xifti"'	parc_vals_to_xifti
S3 method: plot surface	plot.surf
S3 method: use 'view_xifti' to plot a '"xifti"' object	plot.xifti
Read a CIFTI file	readCIfTI readcii read_cifti read_xifti
Get a '"surf"' object	make_surf read_surf
Read in GIFTI files as a '"xifti"' object	read_xifti2
Remap CIFTI data	remapCIfTI remapcii remap_cifti remap_xifti
Remap GIFTI metric or label data	remap_gifti
Remove a component from a '"xifti"'	remove_xifti
Resample CIFTI data	resampleCIfTI resamplecii resample_cifti resample_xifti
Resample a CIFTI from a template	resample_cifti_from_template
Resample a GIFTI file (with its ROI)	resampleGIfTI resamplegii resample_gifti
Resample a '"surf"' object	resample_surf
Rotate a '"surf"' object	rotate_surf
"ROY_BIG_BL" color palette	ROY_BIG_BL
Wrapper for Connectome Workbench Commands	run_wb_cmd
'"xifti"' S3 Math methods	Math.xifti S3_Math
'"xifti"' S3 Ops methods	Ops.xifti S3_Ops
'"xifti"' S3 Summary methods	S3_Summary Summary.xifti
Scale CIFTI	scale_xifti
Select columns of a '"xifti"'	select_xifti
Separate a CIFTI file	separateCIfTI separatecii separate_cifti
Set '"xifti"' column names	set_names_xifti
Smooth CIFTI data	smoothCIfTI smoothcii smooth_cifti smooth_xifti
Smooth a metric GIFTI file	smoothGIfTI smoothgii smooth_gifti
Substructure table	substructure_table
Summarize a '"surf"' object	print.summary.surf print.surf summary.surf
Summarize a '"xifti"' object	print.summary.xifti print.xifti summary.xifti
The NIFTI intents supported by 'ciftiTools'	supported_intents
Surface area calculation	surf_area
Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.	transform_xifti
Undo the volumetric mask to the subcortex	unmask_subcortex
Use a color palette	use_color_pal
vertices	vertices_Param
View composite of images	view_comp
View '"surf"' object(s)	view_surf
View a '"xifti"' object	viewCIfTI viewcii view_cifti view_xifti
View cortical surface data in a '"xifti"'	viewCIfTI_surface viewcii_surface view_cifti_surface view_xifti_surface
View subcortical data in a '"xifti"'	viewCIfTI_volume viewcii_volume view_cifti_volume view_xifti_volume
Write a CIFTI file from a '"xifti"' object	writeCIfTI writecii write_cifti write_xifti
Write a data matrix to a GIFTI metric file	write_metric_gifti
Write subcortical data to NIFTI files	write_subcort_nifti
Write a '"surf"' to a GIFTI surface file	write_surf write_surf_gifti
Write a '"xifti"' object to GIFTI and NIFTI files	write_xifti2

Package: ciftiTools 0.19.0

ciftiTools: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files

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