Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
Add HCP surface(s) to a "xifti"
All integers?
Apply function over locations in each parcel
Apply a function along the rows or columns of a "xifti"
area_original_Param
area_target_Param
Convert a "xifti" to a matrix
Format metric data as a "gifti"
Format surface data as a "gifti"
Assemble a "xifti" from data
Assure this is a parcellation
Boundary region of a mask
brainstructures
Check CIFTI type
Get CIFTI component suffix default
cifti_fname
Print suppressible message
Print suppressible warning
Validate a ciftiTools option and value
ciftiTools files
Get a ciftiTools option
List ciftiTools options
ciftiTools: Tools for Reading and Visualizing CIFTI Brain Files
Set a ciftiTools option
Combine "xifti"s with non-overlapping brain structures
Confirm the Connectome Workbench command path
Convert "xifti"
Convert coordinate list to volume
Crop image
Crop a 3D array
Dimensions of a "xifti"
Distance from mask on surface
Message on attach
Edit mask on surface
Evenly sample vertices of mesh
Interpolates between entries in the input palette to make a larger pal...
Expect these "xifti"s to match
faces
Fix GIFTI medial wall
Fix a "xifti"
Flatten a "xifti"
Format a path
Get CIFTI file extension
Extract data-related metadata from CIFTI
Extract intent-specific metadata from CIFTI
Get kwargs
Extract misc metadata from CIFTI
Get the Connectome Workbench command path
Get NIFTI header (of a CIFTI)
idx
Impute "xifti" data
Infer resolution from "xifti" and surfaces
Get CIFTI metadata
Validate a 3d binary mask
Validate a "xifti" object
Is this an existing file path?
Validate a numeric matrix
Validate a factor vector of subcortical labels
Validate a "surf" object (vertices + faces)
Validate the "data" component of a "xifti" object
Validate the "meta" component of a "xifti" object
Validate a "xifti" object.
labels
Load a parcellation included in ciftiTools
Load subcortical parcellation
Load a "surf" included in ciftiTools
Make a color palette.
Make the cortical components of a "xifti"
Make the subcortical components of a "xifti"
Make the subcortical transformation matrix
Assemble a "xifti" object
mask: vertices
Mask surface
Apply Mask With Boundary To Mesh
Do these character vectors match exactly?
Match user inputs to expected values
Merges two kwargs
Concatenate "xifti"s
Move data locations from medial wall
Move data locations from subcortex mask
Move data locations to the medial wall
Move data locations to the subcortex mask
Counts the number of columns in a "xifti".
Replace the data in a "xifti"
Counts the number of rows (vertices + voxels) in a "xifti".
original_fnames: for remapping
original_fnames: for resampling
Pad a 3D Array
Add subcortex to cortical parcellation
Parcellation borders
Make parcellation mean matrix
Convert parcellation values to "xifti"
S3 method: plot surface
S3 method: use view_xifti to plot a "xifti" object
Order Vertices on Circular Manifold
Read a CIFTI file quickly
Read only the data matrix in a CIFTI file
Read a CIFTI file with optional resampling
Read a CIFTI file
read_dir: separated files
Get a "surf" object
Read in GIFTI files as a "xifti" object
remap_cifti wrapper
Remap CIFTI data
Remap GIFTI metric or label data
Remove a component from a "xifti"
resamp_method
resamp_res: optional
resamp_res: required
Resample a series of GIFTIs related to a CIFTI file
Get resampled file name default
Resample a CIFTI from a template
resample_cifti wrapper
Resample CIFTI data
Resample a GIFTI file (with its ROI)
Resample a "surf" object
Navigating and Embedding the Interactive Plots
Embedding the Static Plots
ROI_brainstructures
Rotate a "surf" object
"ROY_BIG_BL" color palette
Wrapper for Connectome Workbench Commands
"xifti" S3 Math methods
"xifti" S3 Ops methods
"xifti" S3 Summary methods
Scale CIFTI
Select columns of a "xifti"
Separate CIFTI: file names
separate_cifti wrapper
Separate a CIFTI file
Set "xifti" column names
Smooth CIFTI data
Smooth a metric GIFTI file
Substructure table
Summarize a "surf" object
Summarize a "xifti" object
The NIFTI intents supported by ciftiTools
Surface area calculation
Surface plot
surfL_fname
surfL_original_fname
surfL
surfL_target_fname
surfR_fname
surfR_original_fname
surfR
surfR_target_fname
Format a path for system
Make a template "xifti" object
Apply a univariate transformation to a "xifti" or pair of "xifti"s...
Unmask cortex
Undo the volumetric mask to the subcortex
Convert vectorized data back to volume
Use a color palette
verbose: FALSE
verbose: TRUE
Vertex Adjacency Matrix
vertices
View composite of images
View "surf" object(s)
Get the palettes and data color mapping for view_xifti_surface
Draw brain hemisphere mesh in RGL
Draw title in RGL
Get the mesh(es) and data values for view_xifti_surface
View cortical surface data in a "xifti"
Sort out surface & hemisphere args for view_xifti_surface
View subcortical data in a "xifti"
Make the colorbar for view_xifti_surface
Draw color legend for qualitative mode
View a "xifti" object
Get title for view_xifti_surface or view_xifti_volume
Get spatial locations of each voxel
Request "wb_path"
Welcome message
Write a CIFTI file from NIFTI and GIFTI files
Write a CIFTI file from a "xifti" object
write_dir: generic
Write label table to text file
Write a data matrix to a GIFTI metric file
Generate GIFTI sphere surface files
Write subcortical data to NIFTI files
Write a "surf" to a GIFTI surface file
Write a "xifti" object to GIFTI and NIFTI files
x: xifti
xifti
Get XML of a CIFTI
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.
Useful links