Package: ravetools 0.4.0

ravetools: Signal and Image Processing Toolbox for Analyzing Intracranial Electroencephalography Data

Implemented fast and memory-efficient Notch-filter, Welch-periodogram, discrete wavelet spectrogram for minutes of high-resolution signals, fast 3D convolution, image registration, 3D mesh manipulation; providing fundamental toolbox for intracranial Electroencephalography (iEEG) pipelines. Documentation and examples about 'RAVE' project are provided at <https://rave.wiki>, and the paper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp (2020) <doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for details.

Authors:Zhengjia Wang [aut, cre], John Magnotti [aut], Michael Beauchamp [aut], Trustees of the University of Pennsylvania [cph], Karim Rahim [cph, ctb], Thomas Possidente [cph, ctb], Michael Prerau [cph, ctb], Marcus Geelnard [ctb, cph], Stefan Schlager [ctb, cph], Visual Computing Lab, ISTI [ctb, cph]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ravetools/json (API)

# Install 'ravetools' in R:

install.packages('ravetools', repos = c('https://dipterix.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dipterix/ravetools/issues

Pkgdown/docs site:https://dipterix.org

Uses libs:

fftw3– Library for computing Fast Fourier Transforms
c++– GNU Standard C++ Library v3

Datasets:

left_hippocampus_mask - Left 'Hippocampus' of 'N27-Collin' brain
stimulation_signal - Sample stimulation recording

On CRAN:

fftw3 cpp

6.66 score 3 stars 2 packages 30 scripts 486 downloads 153 exports 14 dependencies

Last updated from:24d8b1428f. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	323
linux-devel-x86_64	OK	367
source / vignettes	OK	489
linux-release-arm64	OK	346
linux-release-x86_64	OK	372
macos-release-arm64	OK	257
macos-release-x86_64	OK	593
macos-oldrel-arm64	OK	241
macos-oldrel-x86_64	OK	721
windows-devel-arm64	OK	638
windows-devel-x86_64	OK	1010
windows-release-arm64	OK	491
windows-release-x86_64	OK	464
windows-oldrel-x86_64	OK	447
wasm-release	OK	537

Exports:apply_transform3d apply_transform3d_points apply_transform3d_volume as_matrix4 as_quaternion as_vector3 band_pass1 band_pass2 baseline_array bias_correction_n4 blackman blackmanharris blackmannuttall bohmanwin bpc buttap butter butter_max_order buttord carla catmull_rom_3d cheb1ap cheb1ord cheb2ap cheb2ord cheby1 cheby2 check_filter collapse color_ramp_continuous convolve_image convolve_signal convolve_volume crp crp_cluster decimate design_filter design_filter_fir design_filter_iir detect_threads detrend diagnose_channel diagnose_filter dijkstras_surface_distance ellip ellipap ellipord ensure_mesh3d fast_cov fast_median fast_mvmedian fast_mvquantile fast_quantile fftw_c2c fftw_c2c_2d fftw_c2c_3d fftw_c2r fftw_r2c fftw_r2c_2d fftw_r2c_3d fill_surface filter_signal filtfilt find_peaks fir1 firls flattopwin freqz2 gammatone_fast grow_volume hamming hanning hilbert internal_rave_function is_not_cran load_registration matlab_palette mesh_from_volume morlet_wavelet mris_curvature mris_inflate mris_make_surfaces mris_remesh mris_smooth mris_sphere multitaper multitaper_config mv_pwelch mvfftw_c2c mvfftw_c2r mvfftw_r2c naive_nmf new_matrix4 new_quaternion new_vector3 notch_filter plane_geometry plot_mesh_dotcloud plot_mesh_polygon plot_signals project_plane pwelch ravetools_threads raw_to_float raw_to_int16 raw_to_int32 raw_to_int64 raw_to_int8 raw_to_string raw_to_uint16 raw_to_uint32 raw_to_uint8 rcond_filter_ar read_ants_transform read_ants_warp register_volume register_volume3d resample resample_3d_volume rgl_call rgl_plot_normals rgl_view save_registration segment_volume_tissue_gmm shift_array stimpulse_align stimpulse_extract stimpulse_find stimpulse_interpolate surface_path vcg_average_edge_length vcg_count_edge_defects vcg_decimate vcg_detect_collision vcg_fix_defects vcg_isosurface vcg_kdtree_nearest vcg_max_edge_length vcg_mesh_patch vcg_mesh_volume vcg_raycaster vcg_smooth_explicit vcg_smooth_implicit vcg_sphere vcg_subdivide_max_edge_length vcg_subdivision vcg_subset_vertex vcg_uniform_remesh vcg_update_normals wavelet_cycles_suggest wavelet_kernels write_ants_transform write_ants_warp

Dependencies:BH digest fastmap filearray gsignal multitaper pracma R6 Rcpp RcppEigen RNifti RNiftyReg uuid waveslim

Mesh geometry

Rendered frommesh-geometry.Rmdusingknitr::rmarkdown

Last update: 2026-08-29
Started: 2026-08-29

Help page	Topics
Apply a linear RAS transform to resample a 3D volume	apply_transform3d
Apply a registration (linear and/or deformable) to a volume or to points	apply_transform3d_points apply_transform3d_volume
Band-pass signals	band_pass band_pass1 band_pass2
Calculate Contrasts of Arrays in Different Methods	baseline_array baseline_array.array
Correct the intensity non-uniformity (bias field) of a 3D volume with the 'N4' algorithm	bias_correction_n4
Basis Profile Curve (BPC) identification	bpc
'Butterworth' filter with maximum order	butter_max_order
Common Average Re-referencing by Least Anti-Correlation (CARLA)	carla
Catmull-Rom 3D Spline Curve	catmull_rom_3d
Check 'Arma' filter	check_filter
Collapse array	collapse collapse.array
Map continuous values to colors	color_ramp_continuous
Convolution of '1D', '2D', '3D' data via 'FFT'	convolve convolve_image convolve_signal convolve_volume
Canonical Response Parameterization (CRP)	crp
Cluster electrodes by their canonical CRP response shape	crp_cluster
Decimate with 'FIR' or 'IIR' filter	decimate
Design a digital filter	design_filter
Design ''FIR'' filter using 'firls'	design_filter_fir
Design an 'IIR' filter	design_filter_iir
Remove the trend for one or more signals	detrend
Show channel signals with diagnostic plots	diagnose_channel
Diagnose digital filter	diagnose_filter
Calculate distances along a surface	dijkstras-path dijkstras_surface_distance surface_path
Coerce a surface object to a ''mesh3d'' mesh	ensure_mesh3d
Calculate massive covariance matrix in parallel	fast_cov
Compute quantiles	fast_median fast_mvmedian fast_mvquantile fast_quantile
Low-level 'FFTW3' wrappers	fftw-internal fftw_c2c fftw_c2c_2d fftw_c2c_3d fftw_c2r fftw_r2c fftw_r2c_2d fftw_r2c_3d mvfftw_c2c mvfftw_c2r mvfftw_r2c
Fill a volume cube based on water-tight surface	fill_surface
Filter one-dimensional signal	filter_signal
Filter window functions	blackman blackmanharris blackmannuttall bohmanwin filter-window flattopwin hamming hanning
Forward and reverse filter a one-dimensional signal	filtfilt
Find peaks of a signal	find_peaks
Window-based 'FIR' filter design	fir1
Least-squares linear-phase 'FIR' filter design	firls
Frequency response of digital filter	freqz2
Apply gamma-tone filters to obtain auditory envelopes	gammatone_fast
Grow volume mask	grow_volume
Get external function from 'RAVE'	internal_rave_function
Left 'Hippocampus' of 'N27-Collin' brain	left_hippocampus_mask
'Matlab' heat-map plot palette	matlab_palette
Generate 3D mesh surface from volume data	mesh_from_volume
Estimate per-node curvature of a surface mesh	mris_curvature
Inflate a cortical surface mesh	mris_inflate
Localize white-matter and pial surfaces from an intensity volume	mris_make_surfaces
Isotropic re-triangulation of a surface mesh	mris_remesh
Smooth a surface mesh	mris_smooth
Project a surface onto a sphere and relax metric distortion	mris_sphere
Compute 'multitaper' spectral densities of time-series data	multitaper multitaper_config
A naive implementation of non-negative matrix factorization	naive_nmf
Create a 'Matrix4' instance for ''Affine'' transform	as_matrix4 new_matrix4
Create a 'Quaternion' instance to store '3D' rotation	as_quaternion new_quaternion
Create a 'Vector3' instance to store '3D' points	as_vector3 new_vector3
Apply 'Notch' filter	notch_filter
Set or get thread options	detect_threads parallel-options ravetools_threads
Create a two-dimensional plane in three dimensional space	plane_geometry
Render one or more meshes as an orthographic dot cloud in base R	plot_mesh_dotcloud
Render one or more meshes as flat-shaded triangles in base R	plot_mesh_polygon
Plot one or more signal traces in the same figure	plot_signals
Plot Basis Profile Curve results	plot.ravetools_bpc
Plot CRP results	plot.ravetools_crp
Plot electrode clustering results	plot.ravetools_crp_cluster
Plot method for 'ravetools_curve'	plot.ravetools_curve
Print method for 'ravetools_curve'	print.ravetools_curve
Project plane to a surface	project_plane
Calculate 'Welch Periodogram'	mv_pwelch plot.ravetools-pwelch print.ravetools-pwelch pwelch
Convert raw vectors to R vectors	raw-to-sexp raw_to_float raw_to_int16 raw_to_int32 raw_to_int64 raw_to_int8 raw_to_string raw_to_uint16 raw_to_uint32 raw_to_uint8
Computer reciprocal condition number of an 'Arma' filter	rcond_filter_ar
Imaging registration using ''NiftyReg''	register_volume
Native 3D volume registration (''rigid'', ''affine'', or ''SyN'')	register_volume3d
Sample '3D' volume in the world (anatomical ''RAS'') space	resample_3d_volume
Safe ways to call package ''rgl'' without requiring ''x11''	rgl-call rgl_call rgl_plot_normals rgl_view
Save or load a registration result in 'ANTs'-compatible files	load_registration save_registration save_registration.default save_registration.ravetools_register_volume3d
Prior-guided tissue segmentation with a Gaussian mixture and an MRF	segment_volume_tissue_gmm
Shift array by index	shift_array
Find and interpolate stimulation pulses	stimpulse_align stimpulse_extract stimpulse_find stimpulse_interpolate
Sample stimulation recording	stimulation_signal
Compute the average edge length of a triangular mesh	vcg_average_edge_length
Count boundary and non-manifold edges of a triangular mesh	vcg_count_edge_defects
Simplify a triangular mesh by quadric edge collapse	vcg_decimate
Detect collisions between two geometries	vcg_detect_collision
Detect and repair defects in a triangular surface mesh	vcg_fix_defects
Create surface mesh from 3D-array	vcg_isosurface
Find nearest 'k' points	vcg_kdtree_nearest
Maximum edge length of a triangular mesh	vcg_max_edge_length
Split a mesh into two patches along a geodesic boundary	vcg_mesh_patch
Compute volume for manifold meshes	vcg_mesh_volume
Cast rays to intersect with mesh	vcg_raycaster
Implicitly smooth a triangular mesh	vcg_smooth vcg_smooth_explicit vcg_smooth_implicit
Simple 3-dimensional sphere mesh	vcg_sphere
Selectively subdivide mesh edges that exceed a length threshold	vcg_subdivide_max_edge_length
Sub-divide (up-sample) a triangular mesh	vcg_subdivision
Subset mesh by vertex	vcg_subset_vertex
Sample a surface mesh uniformly	vcg_uniform_remesh
Update vertex normal	vcg_update_normals
'Morlet' wavelet transform (Discrete)	morlet_wavelet wavelet wavelet_cycles_suggest wavelet_kernels
Read and write an 'ITK'/'ANTs' affine transform	read_ants_transform write_ants_transform
Read and write an 'ANTs' deformation (warp) field	read_ants_warp write_ants_warp

Package: ravetools 0.4.0

ravetools: Signal and Image Processing Toolbox for Analyzing Intracranial Electroencephalography Data

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