To run an analysis, you must define a few required parameters, including time windows of interest (timeRange) and the baseline period (baselineTime). Additional optional settings can be customized through the cfg struct to control how the analyses are run and plotted.

Example: Defining Required Fields

% Required analysis definitions
baselineTime = [-250 -50];

timeRange = struct();
timeRange.time1 = [0 500];
timeRange.time2 = [500 1000];
timeRange.time3 = [1000 1500];

Example: Optional Config Definition

cfg = struct();
cfg.vars2plot    = {'NeuralVarName'};
cfg.freq2plot    = {'theta','alpha','beta'};
cfg.times2plot   = {'time1'};
cfg.combinations = [1 2];
cfg.groups2plot  = [1 2];
cfg.chans2plot   = 'all';         % or e.g., {'Cz', 'Pz'}
cfg.errorType    = 'none';
cfg.FDRflag      = 1;
cfg.toPlot       = 1;
cfg.isnormal     = 'auto';

Required Parameters

Field	Description
baselineTime	A 1×2 vector specifying the baseline correction window (in ms), aligned to project.info.timeAxis. If you do not want baseline correction, this can be left as an empty vector []. Example: [-250, -50]
timeRange	A structure defining labeled time windows of interest, where each field is a 1×2 vector of [start, end] times (in ms). These labels are used later in cfg.times2plot. Example: timeRange.time1 = [0, 500]; timeRange.time2 = [500, 1000];

⏱️ Note: These time windows must match the scale of project.info.timeAxis.

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Configuring Analysis (cfg Struct)

The cfg struct allows you to customize analysis options. This is not required for data formatting, but is passed when running main analysis functions like analyzeScalp() or analyzeSource().

Default values are assigned automatically if not provided by the user.

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cfg Field Reference

Field	Description
vars2plot	Cell array of variable names to analyze. Must be a subset of project.info.variables. Default: all variables
freq2plot	Cell array of frequency bands to include. Must match project.info.freq_list. Default: all frequencies
times2plot	Cell array of time window labels defined in project.info.timeRange. Default: all available time ranges
combinations	Nx2 matrix of group index pairs to compare. Default: all 2-group combinations
groups2plot	Vector of group indices to include (e.g., [1 2]). Default: all groups
chans2plot	'all' (all significant) or a cell array of specific channels (e.g., {'Pz', 'Cz'}). Default: 'all'
rois2plot	Numeric vector of ROIs to include (source analysis). _Default: all rois 1:length(project.info.roi)
errorType	Type of error bars for ERP plot: 'none', 'sem', or '95CI'. Default: 'none'
FDRflag	Boolean flag (1/0) to perform FDR correction. Default: 1
toPlot	Boolean flag to enable initial topographic/brain ROI plotting. Default: 1
isnormal	Specifies assumption about data normality: 'auto' (determine automatically with adtest()), 1 (normal), or 0 (non-normal). Default: 'auto'
color_list	Cell array of color codes (e.g., {'r','b','g'}) to use for plotting. Default: MATLAB color set
hmFile	Path to head model file for plotting (if needed). Default: Uses default headmodel from dsi ''
netConMethod	Method used in network connectivity: 'net' or 'roi'(if applicable). Default: 'net'

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