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All functions

BlackrockFile
Class definition to load data from 'BlackRock' 'Micro-systems' files
ECoGTensor
'iEEG/ECoG' Tensor class inherit from Tensor
LFP_electrode
Definitions of electrode with 'LFP' signal type
LFP_reference
Definitions of reference with 'LFP' signal type
LazyFST
R6 Class to Load 'fst' Files
LazyH5
Lazy 'HDF5' file loader
PipelineCollections
Connect and schedule pipelines
PipelineResult
Pipeline result object
PipelineTools
Class definition for pipeline tools
RAVEAbstarctElectrode
Abstract definition of electrode class in RAVE
RAVEEpoch
Definition for epoch class
RAVEMetaSubject
Defines 'RAVE' subject class for meta analyses
RAVEPreprocessSettings
Defines preprocess configurations
RAVEProject
Definition for 'RAVE' project class
RAVESubject
Defines 'RAVE' subject class
Tensor
R6 Class for large Tensor (Array) in Hybrid Mode
ants_coreg() cmd_run_ants_coreg() ants_mri_to_template() cmd_run_ants_mri_to_template() ants_morph_electrode()
Register 'CT' or 'MR' images via 'ANTs'
ants_preprocessing()
Process 'T1' weighted 'MRI' using ANTs
archive_subject()
Archive and share a subject
as_rave_project()
Convert character to RAVEProject instance
as_rave_subject()
Get RAVESubject instance from character
as_rave_unit()
Convert numeric number into print-friendly format
auto_process_blackrock()
Monitors 'BlackRock' output folder and automatically import data into 'RAVE'
backup_file()
Back up and rename the file or directory
cache_root() clear_cached_files()
Manipulate cached data on the file systems
cache_to_filearray()
Generate and automatically cache a file array
catgl()
Print colored messages
cmd_run_3dAllineate() cmd_execute() cmd_run_r() cmd_run_dcm2niix() cmd_run_flirt() cmd_run_recon_all() cmd_run_yael_preprocess_t1() cmd_run_recon_all_clinical()
External shell commands for 'RAVE'
collapse2()
Collapse high-dimensional tensor array
collapse_power()
Collapse power array with given analysis cubes
compose_channel()
Compose a "phantom" channel from existing electrodes
convert_fst_to_hdf5() convert_fst_to_csv()
Convert 'fst' files to other formats
convert_blackrock()
Convert 'BlackRock' 'NEV/NSx' files
convert_electrode_table_to_bids()
Convert electrode table
dir_create2()
Force creating directory with checks
export_table() import_table()
Export data frame to different common formats
find_path()
Try to find path along the root directory
generate_reference()
Generate common average reference signal for 'RAVE' subjects
get_projects()
Get all possible projects in 'RAVE' directory
get_val2()
Get value or return default if invalid
global_preferences() use_global_preferences()
Global preferences for pipelines and modules
h5_names()
Returns all names contained in 'HDF5' file
h5_valid()
Check whether a 'HDF5' file can be opened for read/write
import_electrode_table()
Import electrode table into subject meta folder
install_modules()
Install 'RAVE' modules
install_subject()
Install a subject from the internet, a zip file or a directory
is.blank()
Check If Input Has Blank String
is.zerolenth()
Check If Input Has Zero Length
is_on_cran()
Check if current session is on 'CRAN'
is_valid_ish()
Check if data is close to ``valid"
join_tensors()
Join Multiple Tensors into One Tensor
lapply_async()
Run lapply in parallel
load_bids_ieeg_header()
Read in description files from 'BIDS-iEEG' format
load_fst_or_h5()
Function try to load 'fst' arrays, if not found, read 'HDF5' arrays
load_h5()
Lazy Load 'HDF5' File via hdf5r-package
load_meta2()
Load 'RAVE' subject meta data
load_yaml()
A port to read_yaml
mgh_to_nii()
Convert 'FreeSurfer' 'mgh' to 'Nifti'
module_add()
Add new 'RAVE' (2.0) module to current project
module_registry() module_registry2() get_modules_registries() get_module_description() add_module_registry()
'RAVE' module registry
new_electrode() new_reference()
Create new electrode channel instance or a reference signal instance
niftyreg_coreg() cmd_run_niftyreg_coreg()
Register 'CT' to 'MR' images via 'NiftyReg'
configure_knitr() pipeline_setup_rmd()
Configure 'rmarkdown' files to build 'RAVE' pipelines
pipeline() pipeline_from_path()
Creates 'RAVE' pipeline instance
pipeline_collection()
Combine and execute pipelines
pipeline_install_local() pipeline_install_github()
Install 'RAVE' pipelines
pipeline_settings_set() pipeline_settings_get()
Get or change pipeline input parameter settings
power_baseline()
Calculate power baseline
progress_with_logger()
Enhanced progress with logger message
py_nipy_coreg() cmd_run_nipy_coreg()
Register 'CT' to 'MR' images via 'nipy' script
pipeline_root() pipeline_list() pipeline_find() pipeline_attach() pipeline_run() pipeline_clean() pipeline_run_bare() load_targets() pipeline_target_names() pipeline_debug() pipeline_eval() pipeline_visualize() pipeline_progress() pipeline_fork() pipeline_build() pipeline_read() pipeline_vartable() pipeline_hasname() pipeline_watch() pipeline_create_template() pipeline_create_subject_pipeline() pipeline_description() pipeline_load_extdata() pipeline_save_extdata() pipeline_shared()
'RAVE' pipeline functions
prepare_subject_bare0() prepare_subject_bare() prepare_subject_with_epoch() prepare_subject_with_blocks() prepare_subject_phase() prepare_subject_power() prepare_subject_wavelet() prepare_subject_raw_voltage_with_epoch() prepare_subject_voltage_with_epoch()
Prepare 'RAVE' single-subject data
validate_raw_file() IMPORT_FORMATS
Validate raw files in 'rave' directory
rave_server_install() rave_server_configure()
Install and configure 'RAVE' server as background service using shiny-server
update_local_snippet() load_snippet()
'RAVE' code snippets
rave_brain()
Load 'FreeSurfer' or 'AFNI/SUMA' brain from 'RAVE'
normalize_commandline_path() cmd_dcm2niix() cmd_freesurfer_home() cmd_fsl_home() cmd_afni_home() cmd_homebrew() is_dry_run()
Find and execute external command-line tools
rave_directories()
Returns a list of 'RAVE' directories
rave_export()
Export 'RAVE' data
rave_import()
Import data into 'rave' projects
rave_subject_format_conversion()
Compatibility support for 'RAVE' 1.0 format
SIGNAL_TYPES LOCATION_TYPES MNI305_to_MNI152 PIPELINE_FORK_PATTERN
The constant variables
raveio_setopt() raveio_resetopt() raveio_getopt() raveio_confpath()
Set/Get 'raveio' option
read_eeg_header() read_eeg_marker() read_eeg_data()
Load from 'BrainVision' file
save_fst() load_fst()
Read a 'fst' file
read_csv_ieeg()
Read comma separated value file and ignore headers
read_edf_header()
Read 'EDF(+)' or 'BDF(+)' file headers
read_edf_signal()
Read 'EDF(+)' or 'BDF(+)' file signals
read_mat() read_mat2()
Read 'Matlab' files
read_nsx_nev()
Read 'BlackRock' event and signal files
safe_read_csv()
Read comma separated value files with given column classes
safe_write_csv()
Save data to comma separated value files with backups
save_h5()
Save objects to 'HDF5' file without trivial checks
save_json() load_json()
Save or load R object in 'JSON' format
save_meta2()
Function to save meta data to 'RAVE' subject
save_yaml()
Write named list to file
test_hdspeed()
Simple hard disk speed test
time_diff2()
Calculate time difference in seconds
url_neurosynth()
Get 'Neurosynth' website address using 'MNI152' coordinates
validate_subject
Validate subject data integrity
validate_time_window()
Validate time windows to be used
voltage_baseline()
Calculate voltage baseline
with_future_parallel()
Enable parallel computing provided by 'future' package within the context
yael_preprocess_t1() yael_coregistration() yael_preprocess() yael_postprocess()
'YAEL' imaging processing