Man pages for mandymejia/ciftiTools
Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
| add_surf | Add HCP surface(s) to a '"xifti"' |
| all_integers | All integers? |
| apply_parc | Apply function over locations in each parcel |
| apply_xifti | Apply a function along the rows or columns of a '"xifti"' |
| area_original_Param | area_original_Param |
| area_target_Param | area_target_Param |
| as.matrix.xifti | Convert a '"xifti"' to a matrix |
| as.metric_gifti | Format metric data as a '"gifti"' |
| assure_parc | Assure this is a parcellation |
| as.surf_gifti | Format surface data as a '"gifti"' |
| as.xifti | Assemble a '"xifti"' from data |
| boundary_mask_surf | Boundary region of a mask |
| brainstructures_Param_existing | brainstructures |
| check_cifti_type | Check CIFTI type |
| cifti_component_suffix | Get CIFTI component suffix default |
| cifti_fname_Param | cifti_fname |
| ciftiTools | ciftiTools: Tools for Reading and Visualizing CIFTI Brain... |
| ciftiTools.checkOption | Validate a 'ciftiTools' option and value |
| ciftiTools.files | 'ciftiTools' files |
| ciftiTools.getOption | Get a 'ciftiTools' option |
| ciftiTools.listOptions | List 'ciftiTools' options |
| ciftiTools_msg | Print suppressible message |
| ciftiTools.setOption | Set a 'ciftiTools' option |
| ciftiTools_warn | Print suppressible warning |
| combine_xifti | Combine '"xifti"'s with non-overlapping brain structures |
| confirm_wb_cmd_path | Confirm the Connectome Workbench command path |
| convert_xifti | Convert '"xifti"' |
| coordlist_to_vol | Convert coordinate list to volume |
| crop_image | Crop image |
| crop_vol | Crop a 3D array |
| dim.xifti | Dimensions of a '"xifti"' |
| dist_from_mask_surf | Distance from mask on surface |
| dot-onAttach | Message on attach |
| edit_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... |
| expect_equal_xifti | Expect these '"xifti"'s to match |
| faces_Param | faces |
| fix_gifti_mwall | Fix GIFTI medial wall |
| fix_xifti | Fix a '"xifti"' |
| flatten_xifti | Flatten a '"xifti"' |
| format_path | Format a path |
| get_cifti_extn | Get CIFTI file extension |
| get_data_meta_from_cifti_xml | Extract data-related metadata from CIFTI |
| get_intn_meta_from_cifti_xml | Extract intent-specific metadata from CIFTI |
| get_kwargs | Get kwargs |
| get_misc_meta_from_cifti_xml | Extract misc metadata from CIFTI |
| get_wb_cmd_path | Get the Connectome Workbench command path |
| header_cifti | Get NIFTI header (of a CIFTI) |
| idx_Param | idx |
| impute_xifti | Impute '"xifti"' data |
| infer_resolution | Infer resolution from '"xifti"' and surfaces |
| info_cifti | Get CIFTI metadata |
| is.3D_mask | Validate a 3d binary mask |
| is.cifti | Validate a '"xifti"' object |
| is.fname | Is this an existing file path? |
| is.nummat | Validate a numeric matrix |
| is.subcort_labs | Validate a factor vector of subcortical labels |
| is.surf | Validate a '"surf"' object (vertices + faces) |
| is.xifti | Validate a '"xifti"' object. |
| is.xifti_data | Validate the "data" component of a '"xifti"' object |
| is.xifti_meta | Validate the '"meta"' component of a '"xifti"' object |
| labels_Description | labels |
| load_parc | Load a parcellation included in 'ciftiTools' |
| load_sub_parc | Load subcortical parcellation |
| load_surf | Load a '"surf"' included in 'ciftiTools' |
| make_color_pal | Make a color palette. |
| make_cortex | Make the cortical components of a '"xifti"' |
| make_subcort | Make the subcortical components of a '"xifti"' |
| make_trans_mat | Make the subcortical transformation matrix |
| make_xifti | Assemble a '"xifti"' object |
| mask_Param_vertices | mask: vertices |
| mask_surf | Mask surface |
| mask_with_boundary_surf | Apply Mask With Boundary To Mesh |
| match_exactly | Do these character vectors match exactly? |
| match_input | Match user inputs to expected values |
| merge_kwargs | Merges two kwargs |
| 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 |
| ncol_xifti | Counts the number of columns in a '"xifti"'. |
| newdata_xifti | Replace the data in a '"xifti"' |
| nrow_xifti | Counts the number of rows (vertices + voxels) in a '"xifti"'. |
| original_fnames_Param_remapped | original_fnames: for remapping |
| original_fnames_Param_resampled | original_fnames: for resampling |
| pad_vol | Pad a 3D Array |
| parc_add_subcortex | Add subcortex to cortical parcellation |
| parc_borders | Parcellation borders |
| parc_mean_mat | Make parcellation mean matrix |
| 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 |
| radial_order_surf | Order Vertices on Circular Manifold |
| read_cifti | Read a CIFTI file |
| read_cifti_convert | Read a CIFTI file quickly |
| read_cifti_flat | Read only the data matrix in a CIFTI file |
| read_cifti_separate | Read a CIFTI file with optional resampling |
| read_dir_Param_separated | read_dir: separated files |
| read_surf | Get a '"surf"' object |
| read_xifti2 | Read in GIFTI files as a '"xifti"' object |
| remap_cifti | Remap CIFTI data |
| remap_cifti_wrapper | 'remap_cifti' wrapper |
| remap_gifti | Remap GIFTI metric or label data |
| remove_xifti | Remove a component from a '"xifti"' |
| resample_cifti | Resample CIFTI data |
| resample_cifti_components | Resample a series of GIFTIs related to a CIFTI file |
| resample_cifti_default_fname | Get resampled file name default |
| resample_cifti_from_template | Resample a CIFTI from a template |
| resample_cifti_wrapper | 'resample_cifti' wrapper |
| resample_gifti | Resample a GIFTI file (with its ROI) |
| resample_surf | Resample a '"surf"' object |
| resamp_method_Param | resamp_method |
| resamp_res_Param_optional | resamp_res: optional |
| resamp_res_Param_required | resamp_res: required |
| rgl_interactive_plots_Description | Navigating and Embedding the Interactive Plots |
| rgl_static_plots_Description | Embedding the Static Plots |
| ROI_brainstructures_Param_all | ROI_brainstructures |
| rotate_surf | Rotate a '"surf"' object |
| ROY_BIG_BL | "ROY_BIG_BL" color palette |
| run_wb_cmd | Wrapper for Connectome Workbench Commands |
| 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"' |
| separate_cifti | Separate a CIFTI file |
| separate_cifti_files | Separate CIFTI: file names |
| separate_cifti_wrapper | 'separate_cifti' wrapper |
| set_names_xifti | Set '"xifti"' column names |
| smooth_cifti | Smooth CIFTI data |
| smooth_gifti | Smooth a metric GIFTI file |
| substructure_table | Substructure table |
| summary.surf | Summarize a '"surf"' object |
| summary.xifti | Summarize a '"xifti"' object |
| supported_intents | The NIFTI intents supported by 'ciftiTools' |
| surface_plot_Params | Surface plot |
| surf_area | Surface area calculation |
| surfL_fname_Param | surfL_fname |
| surfL_original_fname_Param | surfL_original_fname |
| surfL_Param_optional | surfL |
| surfL_target_fname_Param | surfL_target_fname |
| surfR_fname_Param | surfR_fname |
| surfR_original_fname_Param | surfR_original_fname |
| surfR_Param_optional | surfR |
| surfR_target_fname_Param | surfR_target_fname |
| sys_path | Format a path for 'system' |
| template_xifti | Make a template '"xifti"' object |
| transform_xifti | Apply a univariate transformation to a '"xifti"' or pair of... |
| unmask_cortex | Unmask cortex |
| unmask_subcortex | Undo the volumetric mask to the subcortex |
| unvec_vol | Convert vectorized data back to volume |
| use_color_pal | Use a color palette |
| verbose_Param_FALSE | verbose: FALSE |
| verbose_Param_TRUE | verbose: TRUE |
| vert_adjacency | Vertex Adjacency Matrix |
| vertices_Param | vertices |
| view_comp | View composite of images |
| view_surf | View '"surf"' object(s) |
| view_xifti | View a '"xifti"' object |
| view_xifti.cbar | Make the colorbar for 'view_xifti_surface' |
| view_xifti.cleg | Draw color legend for qualitative mode |
| view_xifti_surface | View cortical surface data in a '"xifti"' |
| view_xifti_surface.color | Get the palettes and data color mapping for... |
| view_xifti_surface.draw_mesh | Draw brain hemisphere mesh in RGL |
| view_xifti_surface.draw_title | Draw title in RGL |
| view_xifti_surface.mesh_val | Get the mesh(es) and data values for 'view_xifti_surface' |
| view_xifti_surface.surf_hemi | Sort out surface & hemisphere args for 'view_xifti_surface' |
| view_xifti.title | Get title for 'view_xifti_surface' or 'view_xifti_volume' |
| view_xifti_volume | View subcortical data in a '"xifti"' |
| vox_locations | Get spatial locations of each voxel |
| wb_path_request | Request '"wb_path"' |
| welcome_msg | Welcome message |
| write_cifti | Write a CIFTI file from a '"xifti"' object |
| write_cifti_from_separate | Write a CIFTI file from NIFTI and GIFTI files |
| write_dir_Param_generic | write_dir: generic |
| write_label_table | Write label table to text file |
| write_metric_gifti | Write a data matrix to a GIFTI metric file |
| write_spheres | Generate GIFTI sphere surface files |
| write_subcort_nifti | Write subcortical data to NIFTI files |
| write_surf_gifti | Write a '"surf"' to a GIFTI surface file |
| write_xifti2 | Write a '"xifti"' object to GIFTI and NIFTI files |
| xifti_Param | xifti |
| xml_cifti | Get XML of a CIFTI |
| x_Param_xifti | x: xifti |
