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function [stat] = ft_freqstatistics(cfg, varargin)
% FT_FREQSTATISTICS computes significance probabilities and/or critical
% values of a parametric statistical test or a non-parametric permutation
% test.
% Use as
% [stat] = ft_freqstatistics(cfg, freq1, freq2, ...)
% where the input data is the result from FT_FREQANALYSIS, FT_FREQDESCRIPTIVES
% The configuration can contain the following options for data selection
% = Nx1 cell-array with selection of channels (default = 'all'),
% see FT_CHANNELSELECTION for details
% cfg.latency = [begin end] in seconds or 'all' (default = 'all')
% cfg.frequency = [begin end], can be 'all' (default = 'all')
% cfg.avgoverchan = 'yes' or 'no' (default = 'no')
% cfg.avgovertime = 'yes' or 'no' (default = 'no')
% cfg.avgoverfreq = 'yes' or 'no' (default = 'no')
% cfg.parameter = string (default = 'powspctrm')
% If you specify cfg.correctm='cluster', then the following is required
% cfg.neighbours = neighbourhood structure, see FT_PREPARE_NEIGHBOURS
% Furthermore, the configuration should contain
% cfg.method = different methods for calculating the significance probability and/or critical value
% 'montecarlo' get Monte-Carlo estimates of the significance probabilities and/or critical values from the permutation distribution,
% 'analytic' get significance probabilities and/or critical values from the analytic reference distribution (typically, the sampling distribution under the null hypothesis),
% 'stats' use a parametric test from the MATLAB statistics toolbox,
% 'crossvalidate' use crossvalidation to compute predictive performance
% = Nxnumobservations: design matrix (for examples/advice, please see the Fieldtrip wiki,
% especially cluster-permutation tutorial and the 'walkthrough' design-matrix section)
% The other cfg options depend on the method that you select. You
% should read the help of the respective subfunction FT_STATISTICS_XXX
% for the corresponding configuration options and for a detailed
% explanation of each method.
% To facilitate data-handling and distributed computing you can use
% cfg.inputfile = ...
% cfg.outputfile = ...
% If you specify one of these (or both) the input data will be read from a *.mat
% file on disk and/or the output data will be written to a *.mat file. These mat
% files should contain only a single variable, corresponding with the
% input/output structure.
% Copyright (C) 2005-2014, Robert Oostenveld & Jan-Mathijs Schoffelen
% This file is part of FieldTrip, see
% for the documentation and details.
% FieldTrip is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
% FieldTrip is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% GNU General Public License for more details.
% You should have received a copy of the GNU General Public License
% along with FieldTrip. If not, see <>.
% $Id$
% these are used by the ft_preamble/ft_postamble function and scripts
ft_revision = '$Id$';
ft_nargin = nargin;
ft_nargout = nargout;
% do the general setup of the function
ft_preamble init
ft_preamble debug
ft_preamble loadvar varargin
ft_preamble provenance varargin
ft_preamble randomseed
% the ft_abort variable is set to true or false in ft_preamble_init
if ft_abort
% check if the input data is valid for this function
for i=1:length(varargin)
varargin{i} = ft_checkdata(varargin{i}, 'datatype', 'freq', 'feedback', 'no');
% check if the input cfg is valid for this function
cfg = ft_checkconfig(cfg, 'forbidden', {'channels'}); % prevent accidental typos, see issue 1729
cfg = ft_checkconfig(cfg, 'required', {'method', 'design'});
cfg = ft_checkconfig(cfg, 'renamed', {'approach', 'method'});
cfg = ft_checkconfig(cfg, 'forbidden', {'transform'});
cfg = ft_checkconfig(cfg, 'forbidden', {'trials'}); % this used to be present until 24 Dec 2014, but was deemed too confusing by Robert
% set the defaults
cfg.parameter = ft_getopt(cfg, 'parameter'); % default is set below
cfg.correctm = ft_getopt(cfg, 'correctm'); = ft_getopt(cfg, 'channel', 'all');
cfg.latency = ft_getopt(cfg, 'latency', 'all');
cfg.frequency = ft_getopt(cfg, 'frequency', 'all');
cfg.avgoverchan = ft_getopt(cfg, 'avgoverchan', 'no');
cfg.avgovertime = ft_getopt(cfg, 'avgovertime', 'no');
cfg.avgoverfreq = ft_getopt(cfg, 'avgoverfreq', 'no');
if isempty(cfg.parameter)
if isfield(varargin{1}, 'powspctrm')
cfg.parameter = 'powspctrm';
% ensure that the data in all inputs has the same channels, time-axis, etc.
tmpcfg = keepfields(cfg, {'frequency', 'avgoverfreq', 'latency', 'avgovertime', 'channel', 'avgoverchan', 'parameter', 'select', 'nanmean', 'showcallinfo', 'trackcallinfo', 'trackusage', 'trackdatainfo', 'trackmeminfo', 'tracktimeinfo'});
[varargin{:}] = ft_selectdata(tmpcfg, varargin{:});
% restore the provenance information
[cfg, varargin{:}] = rollback_provenance(cfg, varargin{:});
% neighbours are required for clustering with multiple channels
if strcmp(cfg.correctm, 'cluster') && length(varargin{1}.label)>1
% this is limited to reading neighbours from disk and/or selecting channels
% the user should call FT_PREPARE_NEIGHBOURS directly for the actual construction
tmpcfg = keepfields(cfg, {'neighbours', 'channel', 'showcallinfo', 'trackcallinfo', 'trackusage', 'trackdatainfo', 'trackmeminfo', 'tracktimeinfo'});
cfg.neighbours = ft_prepare_neighbours(tmpcfg);
dimord = getdimord(varargin{1}, cfg.parameter);
dimtok = tokenize(dimord, '_');
dimsiz = getdimsiz(varargin{1}, cfg.parameter, numel(dimtok));
rptdim = find( strcmp(dimtok, 'subj') | strcmp(dimtok, 'rpt') | strcmp(dimtok, 'rpttap'));
datdim = find(~strcmp(dimtok, 'subj') & ~strcmp(dimtok, 'rpt') & ~strcmp(dimtok, 'rpttap'));
datsiz = dimsiz(datdim);
% pass these fields to the low-level functions, they should be removed further down
cfg.dimord = sprintf('%s_', dimtok{datdim});
cfg.dimord = cfg.dimord(1:end-1); % remove trailing _
cfg.dim = dimsiz(datdim);
if isempty(rptdim)
% repetitions are across multiple inputs
dat = nan(prod(dimsiz), length(varargin));
for i=1:length(varargin)
tmp = varargin{i}.(cfg.parameter);
dat(:,i) = tmp(:);
% repetitions are within inputs
dat = cell(size(varargin));
for i=1:length(varargin)
tmp = varargin{i}.(cfg.parameter);
if rptdim~=1
% move the repetitions to the first dimension
tmp = permute(tmp, [rptdim datdim]);
dat{i} = reshape(tmp, size(tmp,1), []);
dat = cat(1, dat{:}); % repetitions along 1st dimension
dat = dat'; % repetitions along 2nd dimension
if size(,2)~=size(dat,2) = transpose(;
design =;
% fetch function handle to the intermediate-level statistics function
statmethod = ft_getuserfun(cfg.method, 'statistics');
if isempty(statmethod)
ft_error('could not find the corresponding function for cfg.method="%s"\n', cfg.method);
ft_info('using "%s" for the statistical testing\n', func2str(statmethod));
% check that the design completely describes the data
if size(dat,2) ~= size(,2)
ft_error('the length of the design matrix (%d) does not match the number of observations in the data (%d)', size(,2), size(dat,2));
% determine the number of output arguments
% the nargout function in MATLAB 6.5 and older does not work on function handles
num = nargout(statmethod);
num = 1;
% perform the statistical test
if num>1
[stat, cfg] = statmethod(cfg, dat, design);
cfg = rollback_provenance(cfg); % ensure that changes to the cfg are passed back to the right level
[stat] = statmethod(cfg, dat, design);
if ~isstruct(stat)
% only the probability was returned as a single matrix, reformat into a structure
stat = struct('prob', stat);
% the statistical output contains multiple elements, e.g. F-value, beta-weights and probability
fn = fieldnames(stat);
for i=1:length(fn)
if numel(stat.(fn{i}))==prod(datsiz)
% reformat into the same dimensions as the input data
stat.(fn{i}) = reshape(stat.(fn{i}), [datsiz 1]);
% describe the dimensions of the output data
stat.dimord = cfg.dimord;
% copy the descripive fields into the output
stat = copyfields(varargin{1}, stat, {'freq', 'time', 'label', 'elec', 'grad', 'opto'});
% these were only present to inform the low-level functions
cfg = removefields(cfg, {'dim', 'dimord'});
% do the general cleanup and bookkeeping at the end of the function
ft_postamble debug
ft_postamble randomseed
ft_postamble previous varargin
ft_postamble provenance stat
ft_postamble history stat
ft_postamble savevar stat