# Signal and Image Processing Toolbox for Analyzing Intracranial Electroencephalography Data

## Documentation for package ‘ravetools’ version 0.3.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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