Pipeline inputs

Input file paths

Argument	Description	Example
vhdr_files (required)	List of raw EEG file paths	c("raw/Vp01.vhdr", "raw/Vp02.vhdr", ...)
	Nested list if (some) participants have multiple EEG files or	list(c("raw/Vp01_a.vhdr", "raw/Vp01_b.vhdr"), "raw/Vp02.vhdr", ...)
	Directory path with raw EEG files	"raw"
log_files (required)	List of behavioral log file paths	c("log/Vp01.txt", "log/Vp02.txt", ...)
	Directory of raw EEG files	"log"

Output file paths

Argument	Description	Example
output_dir (required)	Output directory	"data/output"
clean_dir (default: NULL)	Cleaned (continuous) data output directory	"data/clean"
epochs_dir (default: NULL)	Epoched data output directory	"data/clean"
report_dir (default: NULL)	HTML quality control report output directory	"data/reports"
to_df (default: TRUE)	Save outputs as data frames with comma-separated values or	TRUE
	Save outputs as MNE-Python (.fif) files or	FALSE
	Save outputs as data frames and MNE-Python files	"both"

Preprocessing options

Argument	Description	Example
downsample_sfreq (default: NULL)	Downsample to lower sampling rate or	250.0
	Do not downsample	NULL
veog_channels (default: "auto")	Construct bipolar VEOG from two EEG or EOG channels or	c("Fp1", "IO1")
	Construct VEOG from default channels or	"auto"
	Do not construct a new VEOG channel	NULL
heog_channels (default: "auto")	Construct bipolar HEOG from two EEG or EOG channels or	c("F9", "F10")
	Construct HEOG from default channels or	"auto"
	Do not construct a new HEOG channel	NULL
montage (default: "easycap-M1")	Standard EEG montage name or	"easycap-M1"
	Custom EEG montage file path	"data/chanlocs.elc"
ref_channels (default: "average")	List of channels to re-reference EEG channels to or	c("M1", "M2")
	Re-reference EEG channels to an average reference or	"average"
	Use the Reference Electrode Standardization Technique (REST)	"REST"
bad_channels (default: NULL)	Lists of bad channels for each participant or	list(c("P7", "Oz"), c("Fp2"), ...)
	Dict with participant labels and their list of bad channels or	list("Vp05" = list("PO8", "O2"), ...)
	Auto-detect bad channels based on standard error across epochs or	"auto"
	Don’t interpolate any bad channels	NULL
besa_files (default: NULL)	Directory of BESA/MSEC correction matrix files or	"data/cali"
	List of BESA/MSEC correction matrix file paths or	c("data/cali/Vp01.matrix", "data/cali/Vp02.matrix", ...)
	Don’t use BESA/MSEC ocular correction	NULL
ica_method (default: NULL)	ICA method or	"fastica" or "infomax" or "picard"
	Don’t apply ICA	NULL
ica_n_components (default: NULL)	Number of ICA components to use or	15
	Proportion of variance explained by ICA components or	0.99
	Use (almost) all possible ICA components	NULL
highpass_freq (default: 0.1)	High-pass filter cutoff frequency or	0.1
	Do not apply high-pass filter	NULL
lowpass_freq (default: 40.0)	Low-pass filter cutoff frequency or	40.0
	Do not apply low-pass filter	NULL

Epoching options

Argument	Description	Example
triggers (recommended, default: NULL)	Numerical EEG triggers for events of interest	c(201, 202)
triggers_column (default: NULL)	Name of log file column with EEG triggers for automatic matching	"trigger"
epochs_tmin (default: -0.5)	Start of epochs relative to event onset (in s)	-0.5
epochs_tmax (default: 1.5)	End of epochs relative to event onset (in s)	1.5
baseline (default: c(-0.2, 0.0))	Time window for baseline correction (in s) or	c(-0.2, 0.0)
	Use entire prestimulus interval or	c(NULL, 0.0)
	Do not perform baseline correction	NULL
reject_peak_to_peak (default: 200.0)	Peak-to-peak threshold for rejecting epochs (in µV) or	200.0
	Do not reject epochs based on peak-to-peak amplitude	NULL
components (recommended, default: NULL)	Definition of single trial ERP components of interest	list("name" = list("P1", "N170"), "tmin" = list(0.08, 0.15), "tmax" = list(0.13, 0.2), "roi" = list(c("PO3", ...), c("P7", ...)))

Averaging options

Argument	Description	Example
average_by (recommended, default: NULL)	Selection of (combinations of) conditions to create by-participant averages for (keys = custom condition labels, values = Pandas query)	list("neg_unrel" = "context == 'negative' & semantics == 'unrelated' & rt < 3000", ...)

Time-frequency analsis options

Argument	Description	Example
perform_tfr (default: FALSE)	Enable time-frequency analysis or	TRUE or FALSE
tfr_subtract_evoked (default: FALSE)	Subtract evoked activity from epochs before time-frequency analysis or	TRUE or FALSE
tfr_freqs (default: seq(4.0, 40.0, length.out = 37))	Frequencies for the family of Morlet wavelets	seq(6.0, 41.0, by = 2.0)
tfr_cycles (default: seq(2.0, 20.0, length.out = 37))	Numbers of cycles for the family of Morlet wavelets	seq(2.0, 21.0, by = 1.0)
tfr_mode (default: "percent")	Method for divisive baseline correction of event-related power using the full epoch interval (Delorme & Grandchamp, 2012)	"percent" or "ratio" or "logratio" or "zscore" or "zlogratio" or NULL
tfr_baseline (default: c(-0.45, -0.05))	Time window for subtractive baseline correction of event-related power	c(-0.45, -0.05)
tfr_components (default: NULL)	Similar to components, the definition of single trial event-related power bands of interest	list("name" = list("alpha"), "tmin" = list(0.05), "tmax" = list(0.25), "fmin" = list(8.0), "fmax" = list(13.0), "roi" = list(c("PO9", ...)))

Permutation test options

Argument	Description	Example
perm_contrasts (default: NULL)	Contrast(s) between condition labels (see average_by) to compute cluster-based permutation tests for	list(c("related", "unrelated"))
perm_tmin (default: 0.0)	Start of time window (in s relative to stimulus onset) for restricting the permutation test	0.0 or NULL (i.e., use entire epoch)
perm_tmax (default: 1.0)	End of time window (in s relative to stimulus onset) for restricting the permutation test	1.0 or NULL (i.e., use entire epoch)
perm_channels (default: NULL)	Selection of channels for restricting the permutation test	c("C1", "Cz", "C2", ...) or NULL (i.e., use all channels)
perm_fmin (default: NULL)	Lowest frequency (in Hz) for restricting the permutation test (event-related power only)	8.0 or NULL (i.e., use all frequencies)
perm_fmax (default: NULL)	Highest frequency (in Hz) for restricting the permutation test (event-related power only)	30.0 or NULL (i.e., use all frequencies)

Performance options

Argument	Description	Example
n_jobs (default: 1)	Number of jobs (i.e., participants) to be processed in parallel	4 or -1 (i.e., use all CPUs)