ciftiTools v0.1.6.0
0
Monthly downloads
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.
Readme
ciftiTools
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 | |
| No Results! | ||
Last month downloads
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 |
| suggests | covr , fields , ggplot2 , ggpubr , knitr , papayar , rgl , rmarkdown , testthat (>= 2.1.0) |
| imports | gifti (> 0.7.5) , grDevices , oro.nifti , RColorBrewer , RNifti , xml2 |
| depends | R (>= 3.5.0) |
| Contributors | Damon Pham |
Include our badge in your README
[](http://www.rdocumentation.org/packages/ciftiTools)