Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
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Documentation for package ‘ravetools’ version 0.3.0
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A B C D E F G H I L M N P R S V W
-- A --
| apply_transform3d | Apply a linear RAS transform to resample a 3D volume |
| as_matrix4 | Create a 'Matrix4' instance for "Affine" transform |
| as_quaternion | Create a 'Quaternion' instance to store '3D' rotation |
| as_vector3 | Create a 'Vector3' instance to store '3D' points |
-- B --
| band_pass | Band-pass signals |
| band_pass1 | Band-pass signals |
| band_pass2 | Band-pass signals |
| baseline_array | Calculate Contrasts of Arrays in Different Methods |
| baseline_array.array | Calculate Contrasts of Arrays in Different Methods |
| blackman | Filter window functions |
| blackmanharris | Filter window functions |
| blackmannuttall | Filter window functions |
| bohmanwin | Filter window functions |
| bpc | Basis Profile Curve (BPC) identification |
| butter_max_order | 'Butterworth' filter with maximum order |
-- C --
| carla | Common Average Re-referencing by Least Anti-Correlation (CARLA) |
| catmull_rom_3d | Catmull-Rom 3D Spline Curve |
| check_filter | Check 'Arma' filter |
| collapse | Collapse array |
| collapse.array | Collapse array |
| color_ramp_continuous | Map continuous values to colors |
| convolve | Convolution of '1D', '2D', '3D' data via 'FFT' |
| convolve_image | Convolution of '1D', '2D', '3D' data via 'FFT' |
| convolve_signal | Convolution of '1D', '2D', '3D' data via 'FFT' |
| convolve_volume | Convolution of '1D', '2D', '3D' data via 'FFT' |
| crp | Canonical Response Parameterization (CRP) |
| crp_cluster | Cluster electrodes by their canonical CRP response shape |
-- D --
| decimate | Decimate with 'FIR' or 'IIR' filter |
| design_filter | Design a digital filter |
| design_filter_fir | Design "FIR" filter using 'firls' |
| design_filter_iir | Design an 'IIR' filter |
| detect_threads | Set or get thread options |
| detrend | Remove the trend for one or more signals |
| diagnose_channel | Show channel signals with diagnostic plots |
| diagnose_filter | Diagnose digital filter |
| dijkstras-path | Calculate distances along a surface |
| dijkstras_surface_distance | Calculate distances along a surface |
-- E --
| ensure_mesh3d | Coerce a surface object to a "mesh3d" mesh |
-- F --
| fast_cov | Calculate massive covariance matrix in parallel |
| fast_median | Compute quantiles |
| fast_mvmedian | Compute quantiles |
| fast_mvquantile | Compute quantiles |
| fast_quantile | Compute quantiles |
| fftw-internal | Low-level 'FFTW3' wrappers |
| fftw_c2c | Low-level 'FFTW3' wrappers |
| fftw_c2c_2d | Low-level 'FFTW3' wrappers |
| fftw_c2c_3d | Low-level 'FFTW3' wrappers |
| fftw_c2r | Low-level 'FFTW3' wrappers |
| fftw_r2c | Low-level 'FFTW3' wrappers |
| fftw_r2c_2d | Low-level 'FFTW3' wrappers |
| fftw_r2c_3d | Low-level 'FFTW3' wrappers |
| fill_surface | Fill a volume cube based on water-tight surface |
| filter-window | Filter window functions |
| filter_signal | Filter one-dimensional signal |
| filtfilt | Forward and reverse filter a one-dimensional signal |
| find_peaks | Find peaks of a signal |
| fir1 | Window-based 'FIR' filter design |
| firls | Least-squares linear-phase 'FIR' filter design |
| flattopwin | Filter window functions |
| freqz2 | Frequency response of digital filter |
-- G --
| gammatone_fast | Apply gamma-tone filters to obtain auditory envelopes |
| grow_volume | Grow volume mask |
-- H --
| hamming | Filter window functions |
| hanning | Filter window functions |
-- I --
| internal_rave_function | Get external function from 'RAVE' |
-- L --
| left_hippocampus_mask | Left 'Hippocampus' of 'N27-Collin' brain |
| load_registration | Save or load a registration result in 'ANTs'-compatible files |
-- M --
| matlab_palette | 'Matlab' heat-map plot palette |
| mesh_from_volume | Generate 3D mesh surface from volume data |
| morlet_wavelet | 'Morlet' wavelet transform (Discrete) |
| mris_curvature | Estimate per-node curvature of a surface mesh |
| mris_inflate | Inflate a cortical surface mesh |
| mris_make_surfaces | Localize white-matter and pial surfaces from an intensity volume |
| mris_remesh | Isotropic re-triangulation of a surface mesh |
| mris_smooth | Smooth a surface mesh |
| mris_sphere | Project a surface onto a sphere and relax metric distortion |
| multitaper | Compute 'multitaper' spectral densities of time-series data |
| multitaper_config | Compute 'multitaper' spectral densities of time-series data |
| mvfftw_c2c | Low-level 'FFTW3' wrappers |
| mvfftw_c2r | Low-level 'FFTW3' wrappers |
| mvfftw_r2c | Low-level 'FFTW3' wrappers |
| mv_pwelch | Calculate 'Welch Periodogram' |
-- N --
| naive_nmf | A naive implementation of non-negative matrix factorization |
| new_matrix4 | Create a 'Matrix4' instance for "Affine" transform |
| new_quaternion | Create a 'Quaternion' instance to store '3D' rotation |
| new_vector3 | Create a 'Vector3' instance to store '3D' points |
| notch_filter | Apply 'Notch' filter |
-- P --
| parallel-options | Set or get thread options |
| plane_geometry | Create a two-dimensional plane in three dimensional space |
| plot.ravetools-pwelch | Calculate 'Welch Periodogram' |
| plot.ravetools_bpc | Plot Basis Profile Curve results |
| plot.ravetools_crp | Plot CRP results |
| plot.ravetools_crp_cluster | Plot electrode clustering results |
| plot.ravetools_curve | Plot method for 'ravetools_curve' |
| plot_mesh_dotcloud | Render one or more meshes as an orthographic dot cloud in base R |
| plot_mesh_polygon | Render one or more meshes as flat-shaded triangles in base R |
| plot_signals | Plot one or more signal traces in the same figure |
| print.ravetools-pwelch | Calculate 'Welch Periodogram' |
| print.ravetools_curve | Print method for 'ravetools_curve' |
| project_plane | Project plane to a surface |
| pwelch | Calculate 'Welch Periodogram' |
-- R --
| ravetools_threads | Set or get thread options |
| raw-to-sexp | Convert raw vectors to R vectors |
| raw_to_float | Convert raw vectors to R vectors |
| raw_to_int16 | Convert raw vectors to R vectors |
| raw_to_int32 | Convert raw vectors to R vectors |
| raw_to_int64 | Convert raw vectors to R vectors |
| raw_to_int8 | Convert raw vectors to R vectors |
| raw_to_string | Convert raw vectors to R vectors |
| raw_to_uint16 | Convert raw vectors to R vectors |
| raw_to_uint32 | Convert raw vectors to R vectors |
| raw_to_uint8 | Convert raw vectors to R vectors |
| rcond_filter_ar | Computer reciprocal condition number of an 'Arma' filter |
| read_ants_transform | Read and write an 'ITK'/'ANTs' affine transform |
| read_ants_warp | Read and write an 'ANTs' deformation (warp) field |
| register_volume | Imaging registration using "NiftyReg" |
| register_volume3d | Native 3D volume registration ("rigid", "affine", or "SyN") |
| resample_3d_volume | Sample '3D' volume in the world (anatomical "RAS") space |
| rgl-call | Safe ways to call package "rgl" without requiring "x11" |
| rgl_call | Safe ways to call package "rgl" without requiring "x11" |
| rgl_plot_normals | Safe ways to call package "rgl" without requiring "x11" |
| rgl_view | Safe ways to call package "rgl" without requiring "x11" |
-- S --
| save_registration | Save or load a registration result in 'ANTs'-compatible files |
| save_registration.default | Save or load a registration result in 'ANTs'-compatible files |
| save_registration.ravetools_register_volume3d | Save or load a registration result in 'ANTs'-compatible files |
| shift_array | Shift array by index |
| stimpulse_align | Find and interpolate stimulation pulses |
| stimpulse_extract | Find and interpolate stimulation pulses |
| stimpulse_find | Find and interpolate stimulation pulses |
| stimpulse_interpolate | Find and interpolate stimulation pulses |
| stimulation_signal | Sample stimulation recording |
| surface_path | Calculate distances along a surface |
-- V --
| vcg_average_edge_length | Compute the average edge length of a triangular mesh |
| vcg_count_edge_defects | Count boundary and non-manifold edges of a triangular mesh |
| vcg_detect_collision | Detect collisions between two geometries |
| vcg_fix_defects | Detect and repair defects in a triangular surface mesh |
| vcg_isosurface | Create surface mesh from 3D-array |
| vcg_kdtree_nearest | Find nearest 'k' points |
| vcg_max_edge_length | Maximum edge length of a triangular mesh |
| vcg_mesh_patch | Split a mesh into two patches along a geodesic boundary |
| vcg_mesh_volume | Compute volume for manifold meshes |
| vcg_raycaster | Cast rays to intersect with mesh |
| vcg_smooth | Implicitly smooth a triangular mesh |
| vcg_smooth_explicit | Implicitly smooth a triangular mesh |
| vcg_smooth_implicit | Implicitly smooth a triangular mesh |
| vcg_sphere | Simple 3-dimensional sphere mesh |
| vcg_subdivide_max_edge_length | Selectively subdivide mesh edges that exceed a length threshold |
| vcg_subdivision | Sub-divide (up-sample) a triangular mesh |
| vcg_subset_vertex | Subset mesh by vertex |
| vcg_uniform_remesh | Sample a surface mesh uniformly |
| vcg_update_normals | Update vertex normal |
-- W --
| wavelet | 'Morlet' wavelet transform (Discrete) |
| wavelet_cycles_suggest | 'Morlet' wavelet transform (Discrete) |
| wavelet_kernels | 'Morlet' wavelet transform (Discrete) |
| write_ants_transform | Read and write an 'ITK'/'ANTs' affine transform |
| write_ants_warp | Read and write an 'ANTs' deformation (warp) field |