ciftiTools v0.1.6.0

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Tools for Reading and Visualizing CIFTI Brain Files

CIFTI files contain brain imaging data in "gray-ordinates", which represent the gray matter as cortical surface vertices (left and right) and subcortical voxels (cerebellum, basal ganglia, and other deep gray matter). 'ciftiTools' uses the Connectome Workbench to read CIFTI files into R and apply common pre-processing steps (e.g. smoothing, resampling). It also provides tools for visualizing the cortical surface with GIFTI files, and for visualizing the subcortical volume.

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ciftiTools

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Tools for reading and visualizing CIFTI brain imaging files.

CIFTI files contain brain imaging data in “gray-ordinates”, which represent the gray matter as cortical surface vertices (left and right) and subcortical voxels (cerebellum, basal ganglia, and other deep gray matter).ciftiTools uses the Connectome Workbench to read CIFTI files into R and apply common pre-processing steps (e.g. smoothing, resampling). It also provides tools for visualizing the cortical surface with GIFTI files, and for visualizing the subcortical volume.

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("mandymejia/ciftiTools")

Vignette

See this link to view the tutorial: https://htmlpreview.github.io/?https://github.com/mandymejia/ciftiTools/blob/master/vignettes/ciftiTools_vignette.html

Functions in ciftiTools

Name Description
Connectome_Workbench_Description Connectome_Workbench
add_surf Add surface(s) to a "xifti" object
as.surf_gifti Format surface data as a "gifti" object
ROY_BIG_BL "ROY_BIG_BL" color palette
brainstructures_Param_LR brainstructures
ROI_brainstructures_Param_LR ROI_brainstructures
all_integers All Integers?
cifti_fname_Param cifti_fname
check_cifti_type Check CIFTI type
as.metric_gifti Format metric data as a "gifti" object
coordlist_to_vol Convert coordinate list to volume.
as.xifti Assemble a "xifti" object from data
brainstructures_Param_all brainstructures
ciftiTools.getOption Get ciftiTools option
ciftiTools_warn Print Suppressable Warning
ciftiTools.setOption Set ciftiTools option
is.xifti Validate a "xifti" object.
ciftiTools_msg Print Suppressable Message
ciftiTools.listOptions List ciftiTools options
get_cifti_extn Get CIFTI file extension
cifti_component_suffix Get CIFTI component suffix default
merge_kwargs Merges two kwargs
is.xifti_data Validate the "data" component of a "xifti" object
original_fnames_Param_resampled original_fnames: for resampling
run_wb_cmd Wrapper for Connectome Workbench Commands
rgl_static_plots_Description Embedding the Static Plots
expand_color_pal Interpolates between entries in the input palette to make a larger palette with at least MIN_COLOR_RES entries.
.onAttach Message on attach
expect_equal_xifti Expect these CIFTIs to match
crop_vol Crop a 3D array
get_data_meta_from_cifti_xml Extract data-related metadata from CIFTI
is.surf Validate a surface (vertices + faces)
info_cifti Get CIFTI metadata
summary.surf Summarise cifti objects
demo_files Get example files
get_kwargs Get kwargs
get_intn_meta_from_cifti_xml Extract intent-specific metadata from CIFTI
is.subcort_labs Validate a factor vector of subcortical labels
header_cifti Get NIFTI header (of a CIFTI)
is.3D_mask Validate a 3d binary mask
is.cifti Validate a "xifti" object
ciftiTools.checkOption Validate a ciftiTools option and value
make_color_pal Make a color palette.
is.fname File name check
labels_Description labels
plot.surf S3 method: plot surface
plot.xifti S3 method: use view_xifti to plot a "xifti" object
is.nummat Validate a numeric matrix
fix_gifti_mwall Fix GIFTI medial wall
flatten_xifti Flatten a "xifti" object
is.xifti_meta Validate the "meta" component of a "xifti" object
read_cifti_flat Read only the data matrix in a CIFTI file
pad_vol Pad a 3D Array
resamp_fnames_Param resamp_fnames
format_path Format a path
surfR_original_fname_Param surfR_original_fname
surfR_fname_Param surfR_fname
summary.xifti Summarise cifti objects
use_color_pal Use a color palette
separate_cifti Separate a CIFTI file
parc_borders Parcellation borders
read_cifti_separate Read a CIFTI file with optional resampling
make_cortex Make "xifti" cortical components
verbose_Param_FALSE verbose: FALSE
match_exactly Do these character vectors match exactly?
view_xifti_volume View subcortex
view_xifti_surface.surf_hemi Sort out surface & hemispehre args for view_xifti_surface
template_xifti Make a template "xifti" object
separate_cifti_wrapper separate_cifti wrapper
sys_path Format a path for system.
read_cifti Read a CIFTI file
resamp_keep_Param resamp_keep
match_input Match user inputs to expected values
read_cifti_convert Read a CIFTI file quickly
resample_cifti_default_fname Get resampled file name default
view_xifti View a "xifti" object
view_xifti_surface View cortical surface
write_cifti Write a CIFTI file from a "xifti" object.
remove_xifti Remove "xifti" component
resample_surf Resample a "surf" object
read_dir_Param_separated read_dir: separated files
write_cifti_components Write CIFTI component files from a "xifti" object.
get_misc_meta_from_cifti_xml Extract misc metadata from CIFTI
get_wb_cmd_path Get the Connectome Workbench command path
make_surf Convert input to a "surf" object
xifti_Param xifti
write_spheres Generate GIFTI sphere surface files
make_subcort Make "xifti" subcortical components
make_trans_mat Make the subcortical transformation matrix
resamp_res_Param_optional resamp_res: optional
make_xifti Assemble a "xifti" object
write_subcort_nifti Write subcortical data to NIFTI files
resample_cifti_from_template Resample a CIFTI from a template
resamp_res_Param_required resamp_res: required
xml_cifti Get XML of a CIFTI
write_dir_Param_intermediate write_dir: intermediate separated/resampled files
surfL_target_fname_Param surfL_target_fname
surfR_Param_optional surfR
rgl_interactive_plots_Description Navigating and Embedding the Interactive Plots
write_metric_gifti Write CIFTI cortex data to GIFTI
resample_gifti Resample a GIFTI file (with its ROI)
resample_cifti_wrapper resample_cifti wrapper
sep_fnames_Param sep_fnames
sep_keep_Param sep_keep
surfR_target_fname_Param surfR_target_fname
resample_cifti_components Resample a series of GIFTIs related to a CIFTI file
resample_cifti Resample CIFTI Data
surface_plot_Params surface plot
unmask_vol Undo a volumetric mask
unmask_cortex Unmask cortex
view_xifti_surface.mesh_val Get the mesh(es) and data values for view_xifti_surface
smooth_cifti Smooth a CIFTI
substructure_table Substructure table
write_dir_Param_generic write_dir: generic
view_xifti_surface.draw_title Draw title in RGL
write_cifti_from_separate Make CIFTI file
supported_intents The NIFTI intents supported by ciftiTools
surfL_Param_optional surfL
surfL_fname_Param surfL_fname
view_xifti_surface.cbar Make the colorbar for view_xifti_surface
surfL_original_fname_Param surfL_original_fname
wb_path_Param wb_path
view_xifti_surface.cleg Draw color legend for qualitative mode
wb_path_request Request "wb_path"
verbose_Param_TRUE verbose: TRUE
view_xifti_surface.draw_mesh Draw brain hemisphere mesh in RGL
view_surf View "surf" object(s)
view_xifti_surface.color Get the palettes and data color mapping for view_xifti_surface
x_Param_xifti x: xifti
write_surf_gifti Write CIFTI surface data to GIFTI
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Details

Type Package
License GPL-3
Encoding UTF-8
LazyData true
RoxygenNote 7.1.1
URL https://github.com/mandymejia/ciftiTools
BugReports https://github.com/mandymejia/ciftiTools/issues
NeedsCompilation no
Packaged 2020-11-19 02:52:18 UTC; damon
Repository CRAN
Date/Publication 2020-11-20 10:20:05 UTC

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