Import signal data into 'RAVE'

Import signal data from different file formats; supports 'EDF', 'BrainVision', 'BlackRock', 'HDF5', and 'Matlab' formats under either native or 'BIDS' standard. It is recommended to use 'RAVE' user interfaces to import data.

Usage

import_from_brainvis(
  subject,
  blocks,
  electrodes,
  sample_rate,
  add = FALSE,
  data_type = "LFP",
  ...
)

import_from_edf(
  subject,
  blocks,
  electrodes,
  sample_rate,
  add = FALSE,
  data_type = "LFP",
  skip_validation = FALSE,
  ...
)

import_from_h5_mat_per_block(
  subject,
  blocks,
  electrodes,
  sample_rate,
  add = FALSE,
  data_type = "LFP",
  skip_validation = FALSE,
  ...
)

import_from_h5_mat_per_channel(
  subject,
  blocks,
  electrodes,
  sample_rate,
  add = FALSE,
  data_type = "LFP",
  skip_validation = FALSE,
  ...
)

import_from_nevnsx(
  subject,
  blocks,
  electrodes,
  sample_rate,
  add = FALSE,
  data_type = "LFP",
  skip_validation = FALSE,
  ...
)

Arguments

subject

a 'RAVE' subject or subject ID, consists of a project name, a forward slash, followed by a subject code; for example, 'demo/DemoSubject' refers to a 'RAVE' native subject 'DemoSubject' under the project 'demo'; while 'demo@bids:ds001/01' refers to subject 'sub-01' from the 'BIDS' data set 'ds001', under its 'RAVE' project 'demo' under the derivative folder.

blocks

recording block; see Section 'Recording Blocks' for details

electrodes

electrode (channels) to import, must be a vector of integers (channel numbers) or a character that can be interpreted as integers; for example, integer vector 1:10 stands for the first 10 channels, while '1,3-10,15' refers to channels 1, 3 to 10, then 15. Notice some formats might not have definition of the channel numbers, see Section 'Channel Numbers' for details

sample_rate

sampling frequency of the channel, must be positive. 'RAVE' only accepts unified consistent sample rate across all channels with the same type. For example, if one 'LFP' channel is 2000 Hz, then all 'LFP' channels must be 2000 Hz. Channels with different sample rates will be either decimate (if possible, with a 'FIR' filter) or resample (fractional ratio) during import. Different channel types (such as 'Spike', 'Auxiliary', ...) can have different sample rates

add

whether the operation is to add new channels; default is false to protect data integrity

data_type

channel signal data type, can be 'LFP', 'Spike', or 'Auxiliary'

...

passed to or reserved for other methods

skip_validation

whether to skip data validation, default is false (recommended)

Recording Blocks

The term "recording block" is defined as a continuous block of signals recorded during the experiment, typically during one run of the experiment, depending on the setups and format standards:

In the context of native standard, the raw 'RAVE' data is typically stored in the '~/rave_data/raw_dir' directory ('~' stands for your home directory, or documents directory under Windows). Each subject is stored under a folder named after the subject code. For example, subject 'DemoSubject' has a raw folder path '~/rave_data/raw_dir/DemoSubject'. The block folders are stored under this subject folder (such as '008', '010', ...). Each block folder contains a 5-min recording from an experiment.

In the context of 'BIDS' standard, there is no official definition of a 'block', instead, 'BIDS' has an explicit definition of sessions, tasks, and runs. We typically consider that a combination of a session, a task, and a run consists of a recording block. For example, 'ses-01_task-01_run-01' or 'ses-01_run-01', depending on the existence of the 'BIDS' entities.

Channel Numbers

(Electrode) channel numbers refer to vectors of integers, or characters that can be interpreted as integers. For integers, this is straightforward: c(1:10, 21:30) refers to channel 1 to 20, then 21 to 30. For characters, this is converted to integer internally via an unexported function ravecore:::parse_svec.

The channel numbers must be an integer. In some data formats (such as 'EDF') or some standards ('BIDS'), the channel number is not officially explicitly defined: they use the channel labels as the identifiers. To deal with this situation, 'RAVE' treats the channel order as their numbers. In some cases, this is less ideal because the channel labels might implicitly encode the channel numbers. 'RAVE' will ignore such information for consistent behavior.