CTAP configuration

CTAP configuration struct "Cfg" - Required fields and structure

The tables below list fields that might exist in the Cfg struct. Fields marked in italics must always be set by the user. Some fields are directly defined by the user (generated by: user) or automatically generated using information provided by the user (generated by: CTAP/user).

Descriptions of table columns

Fieldname: name of the struct field

generated by: how the field gets populated

type: data type of the field

allowed / default values: allowed values of default values for the field if applicable

description: description of the field

Cfg.env

What: analysis environment setup

Created by: CTAP based on user provided configuration

Fieldname	generated by	type	allowed / default values	description
Cfg.env.paths				Important directories used by CTAP.
.ctapRoot	user	string	NA	The root directory of all pipes (non-branched or branched). This directory usually contains the .analysisRoot directory for non-branched pipes and the starting pipe directory for branched pipes.
.analysisRoot	user/CTAP	string	NA	The root directory of all result files of the current pipe. Use cfg_create_paths() to create this in branched settings.
.branchSource	CTAP	string	NA	EEG source directory for current pipe, if not raw EEG from MC.measurement. Use cfg_create_paths() to create. Used only in branched settings.
.featuresRoot	CTAP	string	NA	Root directory for extracted features
.exportRoot	CTAP	string	NA	Root directory for exported features (csv or SQL), or extracted non- EEG signals (e.g. EDA)
.qualityControlRoot	CTAP	string	NA	Root directory for quality control material
.logRoot	CTAP	string	NA	Root directory for logging
Cfg.env
.measurementInfo	user	string	NA	Full filename of the measurement configuration (MC) file
.logFile	CTAP	string	NA	Full filename for storing log text

Cfg.eeg

What: EEG related config

Created by: CTAP based on user provided configuration

Fieldname	generated by	type	allowed / default values	description
.reference	user	cell of strings	list of channel names, "average"	Desired channel reference
.veogChannelNames	user	cell of strings	NA	Channel names of VEOG channels
.heogChannelNames	user	cell of strings	NA	Channels names of HEOG channels
Cfg.eeg.chanlocs				Channel locations specification needed to load channel locations
.file	user	string	NA	Full filename of the channel locations file
.filetype	optional	string	NA	For EEGLAB readlocs(), see 'help readlocs'
.format	optional	cell array	NA	For EEGLAB readlocs(), see 'help readlocs'
.skiplines	optional	integer	NA	For EEGLAB readlocs(), see 'help readlocs'

Cfg.MC

What: measurement configuration data

Created by: CTAP or user

Fieldname	generated by	type	allowed / default values	description
.< fields >	NA	NA	NA	Data is loaded from an external file that is either autogenerated or manually crafted. See specifications below and in TODO.

Cfg.pipe

What: analysis steps, generated based on the analysis pipe definition that the user provides.

Created by: CTAP

Fieldname	generated by	type	allowed / default values	description
runMeasurements	CTAP	cell of strings	NA	"Casenames" of the set of measurements to run. Casenames are unique IDs used in MC.
stepSets	CTAP	struct	NA	List of all available step sets.
runSets	CTAP	cell of strings	NA	ID strings of step sets to run.

Cfg.ctap

What: Analysis step related configurations: each field corresponds to a function CTAP_< fieldname >.m. Each function has its own set of defaults that can be overridden using Cfg.ctap.. Some of the frequently used functions are listed below. Full list of functions can be found in TODO. All arguments are defined as keyword-value pairs, here stored as structs with keywords as struct fields.

Created by: CTAP based on user definitions in configuration

Fieldname	generated by	type	allowed / default values	description
detect_bad_channels	optional	struct	keyword-value pairs as structs	Bad channel detection
detect_bad_comps	optional	struct	keyword-value pairs as structs	Bad ICA component detection
detect_bad_epochs	optional	struct	keyword-value pairs as structs	Bad epoch detection
epoch_data	optional	struct	keyword-value pairs as structs	Epoching of dataset
export	optional	struct	keyword-value pairs as structs	Exporting features
extract_peripherals	optional	struct	keyword-value pairs as structs	Removal of unwanted channels
filter_data	optional	struct	keyword-value pairs as structs	Filtering of data
interp_chan	optional	struct	keyword-value pairs as structs	Interpolation of channels
load_chanlocs	optional	struct	keyword-value pairs as structs	Loading channel locations
load_data	optional	struct	keyword-value pairs as structs	Loading data
load_events	optional	struct	keyword-value pairs as structs	Loading events
reject_data	optional	struct	keyword-value pairs as structs	Rejecting detected bad channels/components/events/etc.
reref_data	optional	struct	keyword-value pairs as structs	Re-referencing data
run_ica	optional	struct	keyword-value pairs as structs	Running ICA
select_data	optional	struct	keyword-value pairs as structs	Selecting data
tidy_chanloc	optional	struct	keyword-value pairs as structs	Allows channel type naming, deletion of type-less channels

Cfg.event

What: event naming etc.

Created by: CTAP based on user definitions in configuration

Fieldname	generated by	type	allowed / default values	description
badSegement	CTAP	string	"badSegment"	EEG.event.type string for events representing bad segments
blink	CTAP	string	"blink"	EEG.event.type string for events representing blinks
csegEvent	CTAP or user	string	NA	Event type of the events that define calculation segments. Either some existing user defined event or generated using CTAP_generate_cseg.m.

Cfg.grfx

What: graphical settings

Created by: CTAP based on user definitions in configuration

Fieldname	generated by	type	allowed / default values	description
on	optional	boolean	true/false	Global flag controls whether functions create quality assurance plots. Functions that plot can accept their own flags which override this.

Cfg.export

What: feature export related stuff

Created by: CTAP based on user definitions in configuration

Fieldname	generated by	type	allowed / default values	description
csegMetaVariableNames	optional	cell of strings	all available	Names of variables to include in calculation segment metadata.