Tools for Reading, Writing, Viewing and Manipulating CIFTI Files

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Documentation for package ‘ciftiTools’ version 0.8.0

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A C D E F G I L M N P R S T U V W misc

-- A --

abs.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
add_surf Add surface(s) to a '"xifti"'
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

-- C --

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

-- D --

dim.xifti Dimensions of a '"xifti"'

-- E --

exp.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
expand_color_pal Interpolates between entries in the input palette to make a larger palette with COLOR_RES entries.

-- F --

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

-- G --

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

-- M --

make_color_pal Make a color palette.
make_surf Get a '"surf"' object
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 --

newdata_xifti Replace the data in a '"xifti"'

-- P --

parc_borders Parcellation borders
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
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
round.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
ROY_BIG_BL "ROY_BIG_BL" color palette
run_wb_cmd Wrapper for Connectome Workbench Commands

-- S --

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
sign.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
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
sqrt.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
substructure_table Substructure table
summary.surf Summarize a '"surf"' object
summary.xifti Summarize a '"xifti"' object
supported_intents The NIFTI intents supported by 'ciftiTools'

-- T --

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

-- U --

unmask_cortex Unmask cortex
unmask_subcortex Undo a volumetric mask
use_color_pal Use a color palette

-- V --

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

-- misc --

!=.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
%%.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
%/%.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
*.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
+.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
-.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
/.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
<.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
<=.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
==.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
>.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
>=.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.
^.xifti Apply a univariate transformation to a '"xifti"' or pair of '"xifti"'s.