rave_import: Import data into 'rave' projects

In raveio: File-System Toolbox for RAVE Project

Import data into 'rave' projects

Description

Import files with predefined structures. Supported file formats include 'Matlab', 'HDF5', 'EDF(+)', 'BrainVision' ('.eeg/.dat/.vhdr'). Supported file structures include 'rave' native structure and 'BIDS' (very limited) format. Please see https://openwetware.org/wiki/RAVE:ravepreprocess for tutorials.

Usage

rave_import(
  project_name,
  subject_code,
  blocks,
  electrodes,
  format,
  sample_rate,
  conversion = NA,
  data_type = "LFP",
  task_runs = NULL,
  add = FALSE,
  ...
)

Arguments

project_name	project name, for 'rave' native structure, this can be any character; for 'BIDS' format, this must be consistent with 'BIDS' project name. For subjects with multiple tasks, see Section "'RAVE' Project"
subject_code	subject code in character. For 'rave' native structure, this is a folder name under raw directory. For 'BIDS', this is subject label without "sub-" prefix
blocks	characters, for 'rave' native format, this is the folder names subject directory; for 'BIDS', this is session name with "ses-". Section "Block vs. Session" for different meaning of "blocks" in 'rave' and 'BIDS'
electrodes	integers electrode numbers
format	integer from 1 to 6, or character. For characters, you can get options by running names(IMPORT_FORMATS)
sample_rate	sample frequency, must be positive
conversion	physical unit conversion, choices are NA, V, mV, uV
data_type	electrode signal type; see SIGNAL_TYPES
task_runs	for 'BIDS' formats only, see Section "Block vs. Session"
add	whether to add electrodes. If set to true, then only new electrodes are allowed to be imported, blocks will be ignored and trying to import electrodes that have been imported will still result in error.
...	other parameters

Value

None

'RAVE' Project

A 'rave' project can be very flexible. A project can refer to a task, a research objective, or "arbitrarily" as long as you find common research interests among subjects. One subject can appear in multiple projects with different blocks, hence project_name should be objective-based. There is no concept of "project" in 'rave' raw directory. When importing data, you choose subset of blocks from subjects forming a project.

When importing 'BIDS' data into 'rave', project_name must be consistent with 'BIDS' project name as a compromise. Once imported, you may change the project folder name in imported rave data directory to other names. Because once raw traces are imported, 'rave' data will become self-contained and 'BIDS' data are no longer required for analysis. This naming inconsistency will also be ignored.

Block vs. Session

'rave' and 'BIDS' have different definitions for a "chunk" of signals. In 'rave', we use "block". it means combination of session (days), task, and run, i.e. a block of continuous signals captured. Raw data files are supposed to be stored in file hierarchy of <raw-root>/<subject_code>/<block>/<datafiles>. In 'BIDS', sessions, tasks, and runs are separated, and only session names are indicated under subject folder. Because some previous compatibility issues, argument 'block' refers to direct folder names under subject directories. This means when importing data from 'BIDS' format, block argument needs to be session names to comply with 'subject/block' structure, and there is an additional mandatory argument task_runs especially designed for 'BIDS' format.

For 'rave' native raw data format, block will be as-is once imported.
For 'BIDS' format, task_runs will be treated as blocks once imported.

File Formats

Following file structure. Here use project "demo" and subject "YAB" and block "008"), electrode 14 as an example.

format=1, or ".mat/.h5 file per electrode per block"

folder <raw>/YAB/008 contains 'Matlab' or 'HDF5' files per electrode. Data file name should look like "xxx_14.mat"

format=2, or "Single .mat/.h5 file per block"

<raw>/YAB/008 contains only one 'Matlab' or 'HDF5' file. Data within the file should be a 2-dimensional matrix, where the column 14 is signal recorded from electrode 14

format=3, or "Single EDF(+) file per block"

<raw>/YAB/008 contains only one 'edf' file

format=4, or "Single BrainVision file (.vhdr+.eeg, .vhdr+.dat) per block"

<raw>/YAB/008 contains only one 'vhdr' file, and the data file must be inferred from the header file

format=5, or "BIDS & EDF(+)"

<bids>/demo/sub-YAB/ses-008/ must contains *_electrodes.tsv, each run must have channel file. The channel files and electrode file must be consistent in names.
Argument task_runs is mandatory, characters, combination of session, task name, and run number. For example, a task header file in BIDS with name 'sub-YAB_ses-008_task-visual_run-01_ieeg.edf' has task_runs name as '008-visual-01', where the first '008' refers to session, 'visual' is task name, and the second '01' is run number.

format=6, or "BIDS & BrainVision (.vhdr+.eeg, .vhdr+.dat)"

Same as previous format "BIDS & EDF(+)", but data files have 'BrainVision' formats.

raveio documentation built on July 26, 2023, 5:29 p.m.