Core File Structures and Workflows for 'RAVE'

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Documentation for package ‘ravecore’ version 0.1.0

• DESCRIPTION file.
• Package NEWS.

Help Pages

A B C E G H I L M N P R S T V Y

-- A --

ants_coreg	Register a computerized tomography (CT) image to MRI via 'ANTs'
archive_subject	Archive and share a subject
as_rave_project	Convert character to 'RAVEProject' instance
as_rave_project.character	Convert character to 'RAVEProject' instance
as_rave_subject	Get 'RAVESubject' instance from character
as_yael_process	Create a 'YAEL' imaging processing instance
Auxiliary_electrode	Class definition for auxiliary channels

-- B --

backup_file

Back up and rename the file or directory

-- C --

cache_path	Manipulate cached data on the file systems
cache_root	Manipulate cached data on the file systems
clear_cached_files	Manipulate cached data on the file systems
cmd-external	External shell commands for 'RAVE'
cmd_afni_home	Find external command-line tools
cmd_dcm2niix	Find external command-line tools
cmd_dry_run	Find external command-line tools
cmd_execute	External shell commands for 'RAVE'
cmd_freesurfer_home	Find external command-line tools
cmd_fsl_home	Find external command-line tools
cmd_homebrew	Find external command-line tools
cmd_run_3dAllineate	Align images using 'AFNI'
cmd_run_ants_coreg	Register a computerized tomography (CT) image to MRI via 'ANTs'
cmd_run_dcm2niix	Convert DICOM to NIfTI via "dcm2niix"
cmd_run_freesurfer_recon_all	Workflow: 'FreeSurfer' surface reconstruction
cmd_run_freesurfer_recon_all_clinical	Workflow: 'FreeSurfer' surface reconstruction
cmd_run_fsl_flirt	Run 'FSL' linear registration
cmd_run_niftyreg_coreg	Register a computerized tomography (CT) image to MRI via "NiftyReg"
cmd_run_nipy_coreg	Register a computerized tomography (CT) image to MRI via "nipy"
cmd_run_r	External shell commands for 'RAVE'
cmd_run_yael_preprocess	Run a built-in 'YAEL' imaging processing workflow
collapse2	Collapse high-dimensional tensor array
collapse2.array	Collapse high-dimensional tensor array
collapse2.FileArray	Collapse high-dimensional tensor array
collapse2.RAVEFileArray	Collapse high-dimensional tensor array
collapse2.Tensor	Collapse high-dimensional tensor array
collapse_power	Collapse power array with given analysis cubes
collapse_power.array	Collapse power array with given analysis cubes
collapse_power.FileArray	Collapse power array with given analysis cubes
compose_channel	Compose a phantom channel from existing electrodes
convert_electrode_table_to_bids	Convert electrode table

-- E --

export_table

Export data frame to different common formats

-- G --

generate_reference	Generate common average reference signal for 'RAVE' subjects
get_projects	Get all possible projects in 'RAVE' default directory
glimpse-repository	Visualizes repositories with interactive plots
glimpse_voltage_filearray	Visualizes repositories with interactive plots
glimpse_voltage_repository_with_blocks	Visualizes repositories with interactive plots

-- H --

has_rave_subject

Get 'RAVESubject' instance from character

-- I --

import-signals	Import signal data into 'RAVE'
IMPORT_FORMATS	'RAVE' constants
import_from_brainvis	Import signal data into 'RAVE'
import_from_edf	Import signal data into 'RAVE'
import_from_h5_mat_per_block	Import signal data into 'RAVE'
import_from_h5_mat_per_channel	Import signal data into 'RAVE'
import_from_nevnsx	Import signal data into 'RAVE'
import_table	Export data frame to different common formats
install_openneuro	Install data-sets from OpenNeuro
install_subject	Install a subject from the internet, a zip file or a directory

-- L --

LFP_electrode	Definitions of electrode with local field potential signal type
LFP_reference	Definitions of reference with local field potential signal type
load_meta2	Load or save meta data to 'RAVE' subject
LOCATION_TYPES	'RAVE' constants

-- M --

meta-data	Load or save meta data to 'RAVE' subject
MNI305_to_MNI152	'RAVE' constants

-- N --

new_electrode	Create new electrode channel instance or a reference signal instance
new_rave_subject	Get 'RAVESubject' instance from character
new_reference	Create new electrode channel instance or a reference signal instance
niftyreg_coreg	Register a computerized tomography (CT) image to MRI via "NiftyReg"
normalize_commandline_path	Find external command-line tools

-- P --

plot_volume_slices	Plot volume slices into scalable vector graphics SVG images
power_baseline	Calculate power baseline
power_baseline.array	Calculate power baseline
power_baseline.FileArray	Calculate power baseline
power_baseline.rave_prepare_power	Calculate power baseline
prepare_subject_bare	'RAVE' repository: basic
prepare_subject_bare0	'RAVE' repository: basic
prepare_subject_phase_with_blocks	'RAVE' repository: with entire recording blocks
prepare_subject_phase_with_epochs	'RAVE' repository: with epochs
prepare_subject_power	'RAVE' repository: with epochs
prepare_subject_power_with_blocks	'RAVE' repository: with entire recording blocks
prepare_subject_power_with_epochs	'RAVE' repository: with epochs
prepare_subject_raw_voltage_with_blocks	'RAVE' repository: with entire recording blocks
prepare_subject_raw_voltage_with_epochs	'RAVE' repository: with epochs
prepare_subject_time_frequency_coefficients_with_blocks	'RAVE' repository: with entire recording blocks
prepare_subject_time_frequency_coefficients_with_epochs	'RAVE' repository: with epochs
prepare_subject_voltage_with_blocks	'RAVE' repository: with entire recording blocks
prepare_subject_voltage_with_epochs	'RAVE' repository: with epochs
prepare_subject_with_blocks	'RAVE' repository: with entire recording blocks
prepare_subject_with_epochs	'RAVE' repository: with epochs
py_nipy_coreg	Register a computerized tomography (CT) image to MRI via "nipy"

-- R --

RAVEAbstarctElectrode	Abstract definition of electrode class in 'RAVE'
ravecore-constants	'RAVE' constants
RAVEEpoch	Definition for epoch class
RAVEPreprocessSettings	Defines preprocess configurations
RAVEProject	Definition for 'RAVE' project class
RAVESubject	Defines 'RAVE' subject class
RAVESubjectBaseRepository	'RAVE' class for base repository
RAVESubjectEpochPhaseRepository	'RAVE' class for epoch repository - time-frequency phase
RAVESubjectEpochPowerRepository	'RAVE' class for epoch repository - time-frequency power
RAVESubjectEpochRawVoltageRepository	'RAVE' class for epoch repository - raw voltage
RAVESubjectEpochRepository	'RAVE' class for epoch repository
RAVESubjectEpochTimeFreqBaseRepository	'RAVE' class for epoch repository - time-frequency (internal)
RAVESubjectEpochTimeFreqCoefRepository	'RAVE' class for epoch repository - time-frequency
RAVESubjectEpochVoltageRepository	'RAVE' class for epoch repository - voltage
RAVESubjectRecordingBlockPhaseRepository	'RAVE' class for loading time-frequency phase components
RAVESubjectRecordingBlockPowerRepository	'RAVE' class for loading time-frequency power components
RAVESubjectRecordingBlockRawVoltageRepository	'RAVE' class for blocks of voltage repository
RAVESubjectRecordingBlockRepository	'RAVE' class for loading entire recording block repository
RAVESubjectRecordingBlockTimeFreqBaseRepository	'RAVE' class for loading entire block of time-frequency coefficients
RAVESubjectRecordingBlockTimeFreqCoefRepository	'RAVE' class for loading time-frequency coefficients
RAVESubjectRecordingBlockVoltageRepository	'RAVE' class for blocks of voltage repository
rave_brain	Load 'FreeSurfer' brain from 'RAVE'
rave_cmd_tools	Find external command-line tools
rave_legacy_subject_format_conversion	Legacy support for 'RAVE' 1.0 format
rave_path	Find file paths based on storage
rscript_path	Find external command-line tools
run_wavelet	Apply Morlet-Wavelet to subject

-- S --

save_meta2	Load or save meta data to 'RAVE' subject
SIGNAL_TYPES	'RAVE' constants
Spike_electrode	Class definition for micro-wire spike channels

-- T --

transform_point_to_template	Calculate template 'MNI' coordinates for points on native brain
transform_thinfilm_to_mni152	Calculate template 'MNI' coordinates for points on native brain

-- V --

validate_subject	Validate subject data integrity
validate_time_window	Validate time windows to be used

-- Y --

YAELProcess	Class definition of 'YAEL' image pipeline
YAEL_IMAGE_TYPES	'RAVE' constants
yael_preprocess	Run a built-in 'YAEL' imaging processing workflow