# Tools for Reading, Writing, Viewing and Manipulating CIFTI Files

## Documentation for package ‘ciftiTools’ version 0.19.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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

ciftiTools-package | ciftiTools: Tools for Reading and Visualizing CIFTI Brain Files

## -- A --

add_surf | Add HCP 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_mask_surf | 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 '"xifti"'
convert_to_dscalar | Convert '"xifti"'
convert_to_dtseries | Convert '"xifti"'
convert_xifti | Convert '"xifti"'

## -- 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_wb_cmd_path | Get the Connectome Workbench command path

## -- I --

impute_xifti | Impute '"xifti"' data
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_from_submask | Move data locations from subcortex mask
move_to_mwall | Move data locations to the medial wall
move_to_submask | Move data locations to the subcortex mask

## -- N --

newdata_xifti | Replace the data in a '"xifti"'

## -- O --

Ops.xifti | '"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 --

transform_xifti | 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