# Core File Structures and Workflows for 'RAVE'

## Documentation for package ‘ravecore’ version 0.1.1

- DESCRIPTION file
- Package NEWS
- Package README

## 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_atlases_from_template | Create brain atlases from template
generate_reference | Generate common average reference signal for 'RAVE' subjects
get_available_morph_to_template | Get names of available non-linear transforms to the templates
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
snapshot_project | Create overview report for given project or subject
snapshot_subject | Create overview report for given project or subject
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