Package: ciftiTools 0.17.4

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]

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ciftiTools.pdf |ciftiTools.html✨
ciftiTools/json (API)
NEWS

# 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:

9.04 score 47 stars 4 packages 176 scripts 553 downloads 115 exports 45 dependencies

Last updated 19 days agofrom:e5659c1c3e. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 30 2025
R-4.5-winOKJan 30 2025
R-4.5-macOKJan 30 2025
R-4.5-linuxOKJan 30 2025
R-4.4-winOKJan 30 2025
R-4.4-macOKJan 30 2025
R-4.3-winOKJan 30 2025
R-4.3-macOKJan 30 2025

Exports:add_surfapply_parcapply_xiftias_ciftias_xiftias.ciftias.xiftiboundary_mask_surfciftiTools.filesciftiTools.getOptionciftiTools.listOptionsciftiTools.setOptioncombine_xifticonvert_to_dlabelconvert_to_dscalarconvert_to_dtseriesconvert_xiftidilate_mask_surfedit_mask_surferode_mask_surfeven_vert_sampexpand_color_palfix_xiftiget_wb_cmd_pathimpute_xiftiinfer_resolutioninfo_ciftiinfoCIfTIinfociiis_ciftiis_xiftiis.ciftiis.surfis.xiftiisCIfTIload_parcload_surfmake_color_palmake_surfmask_surfmerge_xiftimove_from_mwallmove_from_submaskmove_to_mwallmove_to_submasknewdata_xiftiparc_add_subcortexparc_bordersparc_vals_to_xiftiread_ciftiread_surfread_xiftiread_xifti2readCIfTIreadciiremap_ciftiremap_giftiremap_xiftiremapCIfTIremapciiremove_xiftiresample_ciftiresample_cifti_from_templateresample_giftiresample_surfresample_xiftiresampleCIfTIresampleciiresampleGIfTIresamplegiirotate_surfROY_BIG_BLrun_wb_cmdscale_xiftiselect_xiftiseparate_ciftiseparateCIfTIseparateciiset_names_xiftismooth_ciftismooth_giftismooth_xiftismoothCIfTIsmoothciismoothGIfTIsmoothgiisubstructure_tablesupported_intentssurf_areatransform_xiftiunmask_subcortexuse_color_palview_ciftiview_cifti_surfaceview_cifti_volumeview_compview_surfview_xiftiview_xifti_surfaceview_xifti_volumeviewCIfTIviewCIfTI_surfaceviewCIfTI_volumeviewciiviewcii_surfaceviewcii_volumewrite_ciftiwrite_metric_giftiwrite_subcort_niftiwrite_surfwrite_surf_giftiwrite_xiftiwrite_xifti2writeCIfTIwritecii

Dependencies:abindbase64encbitopsbslibcachemclidigestdotCall64evaluatefastmapfieldsfontawesomefsgiftigluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmapsmemoisemimeoro.niftiR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcpprglrlangrmarkdownRNiftisassspamtinytexviridisLitexfunxml2yaml

ciftiTools Mini Demo

Damon Pham & Amanda Mejia

Rendered fromciftiTools_vignette_mini.Rmdusingknitr::rmarkdownon Jan 30 2025.

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

Readme and manuals

Help Manual

Help pageTopics
Add HCP surface(s) to a '"xifti"'add_surf
Apply function over locations in each parcelapply_parc
Apply a function along the rows or columns of a '"xifti"'apply_xifti
Convert a '"xifti"' to a matrixas.matrix.xifti
Assemble a '"xifti"' from dataas.cifti as.xifti as_cifti as_xifti
Boundary region of a maskboundary_mask_surf
ciftiTools: Tools for Reading and Visualizing CIFTI Brain FilesciftiTools-package ciftiTools
'ciftiTools' filesciftiTools.files
Get a 'ciftiTools' optionciftiTools.getOption
List 'ciftiTools' optionsciftiTools.listOptions
Set a 'ciftiTools' optionciftiTools.setOption
Combine '"xifti"'s with non-overlapping brain structurescombine_xifti
Convert '"xifti"'convert_to_dlabel convert_to_dscalar convert_to_dtseries convert_xifti
Dimensions of a '"xifti"'dim.xifti
Edit mask on surfacedilate_mask_surf edit_mask_surf erode_mask_surf
Evenly sample vertices of mesheven_vert_samp
Interpolates between entries in the input palette to make a larger palette with COLOR_RES entries.expand_color_pal
facesfaces_Param
Fix a '"xifti"'fix_xifti
Get the Connectome Workbench command pathget_wb_cmd_path
Impute '"xifti"' dataimpute_xifti
Infer resolution from '"xifti"' and surfacesinfer_resolution
Get CIFTI metadatainfoCIfTI infocii info_cifti
Validate a '"xifti"' objectis.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: verticesmask_Param_vertices
Mask surfacemask_surf
Concatenate '"xifti"'smerge_xifti
Move data locations from medial wallmove_from_mwall
Move data locations from subcortex maskmove_from_submask
Move data locations to the medial wallmove_to_mwall
Move data locations to the subcortex maskmove_to_submask
Replace the data in a '"xifti"'newdata_xifti
Add subcortex to cortical parcellationparc_add_subcortex
Parcellation bordersparc_borders
Convert parcellation values to '"xifti"'parc_vals_to_xifti
S3 method: plot surfaceplot.surf
S3 method: use 'view_xifti' to plot a '"xifti"' objectplot.xifti
Read a CIFTI filereadCIfTI readcii read_cifti read_xifti
Get a '"surf"' objectmake_surf read_surf
Read in GIFTI files as a '"xifti"' objectread_xifti2
Remap CIFTI dataremapCIfTI remapcii remap_cifti remap_xifti
Remap GIFTI metric or label dataremap_gifti
Remove a component from a '"xifti"'remove_xifti
Resample CIFTI dataresampleCIfTI resamplecii resample_cifti resample_xifti
Resample a CIFTI from a templateresample_cifti_from_template
Resample a GIFTI file (with its ROI)resampleGIfTI resamplegii resample_gifti
Resample a '"surf"' objectresample_surf
Rotate a '"surf"' objectrotate_surf
"ROY_BIG_BL" color paletteROY_BIG_BL
Wrapper for Connectome Workbench Commandsrun_wb_cmd
'"xifti"' S3 Math methodsMath.xifti S3_Math
'"xifti"' S3 Ops methodsOps.xifti S3_Ops
'"xifti"' S3 Summary methodsS3_Summary Summary.xifti
Scale CIFTIscale_xifti
Select columns of a '"xifti"'select_xifti
Separate a CIFTI fileseparateCIfTI separatecii separate_cifti
Set '"xifti"' column namesset_names_xifti
Smooth CIFTI datasmoothCIfTI smoothcii smooth_cifti smooth_xifti
Smooth a metric GIFTI filesmoothGIfTI smoothgii smooth_gifti
Substructure tablesubstructure_table
Summarize a '"surf"' objectprint.summary.surf print.surf summary.surf
Summarize a '"xifti"' objectprint.summary.xifti print.xifti summary.xifti
The NIFTI intents supported by 'ciftiTools'supported_intents
Surface area calculationsurf_area
Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.transform_xifti
Undo the volumetric mask to the subcortexunmask_subcortex
Use a color paletteuse_color_pal
verticesvertices_Param
View composite of imagesview_comp
View '"surf"' object(s)view_surf
View a '"xifti"' objectviewCIfTI 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"' objectwriteCIfTI writecii write_cifti write_xifti
Write a data matrix to a GIFTI metric filewrite_metric_gifti
Write subcortical data to NIFTI fileswrite_subcort_nifti
Write a '"surf"' to a GIFTI surface filewrite_surf write_surf_gifti
Write a '"xifti"' object to GIFTI and NIFTI fileswrite_xifti2