Package index • raveio

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

RAVEVariable: Class definition of 'RAVE' constrained variable

RAVEVariableCollection: Class definition of 'RAVE' constrained variable collection

RAVEVariableConstraints: Class definition for 'RAVE' variable constraints

Tensor: R6 Class for large Tensor (Array) in Hybrid Mode

YAELProcess: Class definition of 'YAEL' image pipeline

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

as_yael_process(): Create a 'YAEL' imaging processing instance

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_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

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_constraints() new_constrained_variable() new_constrained_binding(): Create 'RAVE' constrained variables

new_electrode() new_reference(): Create new electrode channel instance or a reference signal instance

new_variable_collection(): Create a collection of constraint variables

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_dep_targets() 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() pipeline_set_preferences() pipeline_get_preferences() pipeline_has_preferences(): '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 YAEL_IMAGE_TYPES 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

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

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

cmd_run_yael_preprocess() yael_preprocess(): Process brain images for 'YAEL'