Tools for Reading, Writing, Viewing and Manipulating CIFTI Files

Documentation for package ‘ciftiTools’ version 0.15.1

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ciftiTools: Tools for Reading and Visualizing CIFTI Brain Files

-- A --

add_surf	Add surface(s) to a '"xifti"'
apply_parc	Apply function over locations in each parcel
apply_xifti	Apply a function along the rows or columns of a '"xifti"'
as.cifti	Assemble a '"xifti"' from data
as.matrix.xifti	Convert a '"xifti"' to a matrix
as.xifti	Assemble a '"xifti"' from data
as_cifti	Assemble a '"xifti"' from data
as_xifti	Assemble a '"xifti"' from data

-- B --

Boundary region of a mask

-- C --

ciftiTools	ciftiTools: Tools for Reading and Visualizing CIFTI Brain Files
ciftiTools.files	'ciftiTools' files
ciftiTools.getOption	Get a 'ciftiTools' option
ciftiTools.listOptions	List 'ciftiTools' options
ciftiTools.setOption	Set a 'ciftiTools' option
combine_xifti	Combine '"xifti"'s with non-overlapping brain structures
convert_to_dlabel	Convert the intent of a CIFTI file or '"xifti"' object
convert_to_dscalar	Convert the intent of a CIFTI file or '"xifti"' object
convert_to_dtseries	Convert the intent of a CIFTI file or '"xifti"' object
convert_xifti	Convert the intent of a CIFTI file or '"xifti"' object

-- D --

dilate_mask_surf	Edit mask on surface
dim.xifti	Dimensions of a '"xifti"'

-- E --

edit_mask_surf	Edit mask on surface
erode_mask_surf	Edit mask on surface
even_vert_samp	Evenly sample vertices of mesh
expand_color_pal	Interpolates between entries in the input palette to make a larger palette with COLOR_RES entries.

-- F --

faces_Param	faces
fix_xifti	Fix a '"xifti"'

-- G --

Get the Connectome Workbench command path

-- I --

infer_resolution	Infer resolution from '"xifti"' and surfaces
infoCIfTI	Get CIFTI metadata
infocii	Get CIFTI metadata
info_cifti	Get CIFTI metadata
is.cifti	Validate a '"xifti"' object
is.surf	Validate a '"surf"' object (vertices + faces)
is.xifti	Validate a '"xifti"' object.
isCIfTI	Validate a '"xifti"' object
is_cifti	Validate a '"xifti"' object
is_xifti	Validate a '"xifti"' object.

-- L --

load_parc	Load a parcellation included in 'ciftiTools'
load_surf	Load a '"surf"' included in 'ciftiTools'

-- M --

make_color_pal	Make a color palette.
make_surf	Get a '"surf"' object
mask_Param_vertices	mask: vertices
mask_surf	Mask surface
Math.xifti	'"xifti"' S3 Math methods
merge_xifti	Concatenate '"xifti"'s
move_from_mwall	Move data locations from medial wall
move_to_mwall	Move data locations to the medial wall

-- N --

Replace the data in a '"xifti"'

-- O --

'"xifti"' S3 Ops methods

-- P --

parc_add_subcortex	Add subcortex to cortical parcellation
parc_borders	Parcellation borders
parc_vals_to_xifti	Convert parcellation values to '"xifti"'
plot.surf	S3 method: plot surface
plot.xifti	S3 method: use 'view_xifti' to plot a '"xifti"' object
print.summary.surf	Summarize a '"surf"' object
print.summary.xifti	Summarize a '"xifti"' object
print.surf	Summarize a '"surf"' object
print.xifti	Summarize a '"xifti"' object

-- R --

readCIfTI	Read a CIFTI file
readcii	Read a CIFTI file
read_cifti	Read a CIFTI file
read_surf	Get a '"surf"' object
read_xifti	Read a CIFTI file
read_xifti2	Read in GIFTI files as a '"xifti"' object
remapCIfTI	Remap CIFTI data
remapcii	Remap CIFTI data
remap_cifti	Remap CIFTI data
remap_gifti	Remap GIFTI metric or label data
remap_xifti	Remap CIFTI data
remove_xifti	Remove a component from a '"xifti"'
resampleCIfTI	Resample CIFTI data
resamplecii	Resample CIFTI data
resampleGIfTI	Resample a GIFTI file (with its ROI)
resamplegii	Resample a GIFTI file (with its ROI)
resample_cifti	Resample CIFTI data
resample_cifti_from_template	Resample a CIFTI from a template
resample_gifti	Resample a GIFTI file (with its ROI)
resample_surf	Resample a '"surf"' object
resample_xifti	Resample CIFTI data
rotate_surf	Rotate a '"surf"' object
ROY_BIG_BL	"ROY_BIG_BL" color palette
run_wb_cmd	Wrapper for Connectome Workbench Commands

-- S --

S3_Math	'"xifti"' S3 Math methods
S3_Ops	'"xifti"' S3 Ops methods
S3_Summary	'"xifti"' S3 Summary methods
scale_xifti	Scale CIFTI
select_xifti	Select columns of a '"xifti"'
separateCIfTI	Separate a CIFTI file
separatecii	Separate a CIFTI file
separate_cifti	Separate a CIFTI file
set_names_xifti	Set '"xifti"' column names
smoothCIfTI	Smooth CIFTI data
smoothcii	Smooth CIFTI data
smoothGIfTI	Smooth a metric GIFTI file
smoothgii	Smooth a metric GIFTI file
smooth_cifti	Smooth CIFTI data
smooth_gifti	Smooth a metric GIFTI file
smooth_xifti	Smooth CIFTI data
substructure_table	Substructure table
summary.surf	Summarize a '"surf"' object
Summary.xifti	'"xifti"' S3 Summary methods
summary.xifti	Summarize a '"xifti"' object
supported_intents	The NIFTI intents supported by 'ciftiTools'
surf_area	Surface area calculation

-- T --

Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.

-- U --

unmask_subcortex	Undo the volumetric mask to the subcortex
use_color_pal	Use a color palette

-- V --

vertices_Param	vertices
viewCIfTI	View a '"xifti"' object
viewCIfTI_surface	View cortical surface data in a '"xifti"'
viewCIfTI_volume	View subcortical data in a '"xifti"'
viewcii	View a '"xifti"' object
viewcii_surface	View cortical surface data in a '"xifti"'
viewcii_volume	View subcortical data in a '"xifti"'
view_cifti	View a '"xifti"' object
view_cifti_surface	View cortical surface data in a '"xifti"'
view_cifti_volume	View subcortical data in a '"xifti"'
view_comp	View composite of images
view_surf	View '"surf"' object(s)
view_xifti	View a '"xifti"' object
view_xifti_surface	View cortical surface data in a '"xifti"'
view_xifti_volume	View subcortical data in a '"xifti"'

-- W --

writeCIfTI	Write a CIFTI file from a '"xifti"' object
writecii	Write a CIFTI file from a '"xifti"' object
write_cifti	Write a CIFTI file from a '"xifti"' object
write_metric_gifti	Write a data matrix to a GIFTI metric file
write_subcort_nifti	Write subcortical data to NIFTI files
write_surf	Write a '"surf"' to a GIFTI surface file
write_surf_gifti	Write a '"surf"' to a GIFTI surface file
write_xifti	Write a CIFTI file from a '"xifti"' object
write_xifti2	Write a '"xifti"' object to GIFTI and NIFTI files