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ft_baddata.m
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function [data] = ft_baddata(cfg, data)
% FT_BADDATA identifies bad data in a MEG or EEG dataset by looping over all trials
% and all channels. Each channel in each trial is considered separately, in the
% remainder of the help we will refer to this as "traces". Different methods are
% implemented, these are largely shared with those implemented in FT_REJECTVISUAL
% with the "summary" method. The methods are shortly described in detail below. Bad
% traces are replaced in the output data with nan.
%
% VAR, STD, MIN, MAX, MAXABS, RANGE, KURTOSIS, ZVALUE - compute the specified metric
% for each channel in each trial and check whether it exceeds the threshold.
%
% NEIGHBEXPVAR - identifies channels that cannot be explained very well by a linear
% combination of their neighbours. A general linear model is used to compute the
% explained variance. A value close to 1 means that a channel is similar to its
% neighbours, a value close to 0 indicates a "bad" channel.
%
% Use as
% [data_clean] = ft_baddata(cfg, data)
% where the input data corresponds to the output from FT_PREPROCESSING.
%
% The configuration should contain
% cfg.metric = string, describes the metric that should be computed in summary mode for each channel in each trial, can be
% 'var' variance within each channel (default)
% 'std' standard deviation within each channel
% 'db' decibel value within each channel
% 'mad' median absolute deviation within each channel
% '1/var' inverse variance within each channel
% 'min' minimum value in each channel
% 'max' maximum value in each channel
% 'maxabs' maximum absolute value in each channel
% 'range' range from min to max in each channel
% 'kurtosis' kurtosis, i.e. measure of peakedness of the amplitude distribution in trace
% 'zvalue' mean and std computed over all time and trials, per channel
% 'neighbexpvar' relative variance explained by neighboring channels in each trial
% cfg.threshold = scalar, the appropriate value depends on the data characteristics and the metric
% cfg.feedback = 'yes' or 'no', whether to show an image of the neighbour values (default = 'no')
%
% The following options allow you to make a pre-selection
% cfg.channel = Nx1 cell-array with selection of channels (default = 'all'), see FT_CHANNELSELECTION for details
% cfg.trials = 'all' or a selection given as a 1xN vector (default = 'all')
%
% See also FT_BADCHANNEL, FT_BADSEGMENT, FT_REJECTVISUAL, FT_CHANNELREPAIR
% Undocumented options
% cfg.thresholdside = above or below
% Copyright (C) 2024, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% 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
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% 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 <http://www.gnu.org/licenses/>.
%
% $Id$
% 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_defaults
ft_preamble init
ft_preamble debug
ft_preamble loadvar data
ft_preamble provenance
% the ft_abort variable is set to true or false in ft_preamble_init
if ft_abort
return
end
% check if the input data is valid for this function
data = ft_checkdata(data, 'datatype', 'raw', 'feedback', 'yes');
% check if the input cfg is valid for this function
cfg = ft_checkconfig(cfg, 'forbidden', {'channels', 'trial'}); % prevent accidental typos, see issue 1729
cfg = ft_checkconfig(cfg, 'required', 'metric');
% ensure that the preproc specific options are located in the cfg.preproc substructure
cfg = ft_checkconfig(cfg, 'createsubcfg', {'preproc'});
% set the defaults
cfg.channel = ft_getopt(cfg, 'channel', 'all');
cfg.trials = ft_getopt(cfg, 'trials', 'all', true);
cfg.neighbours = ft_getopt(cfg, 'neighbours');
cfg.nbdetect = ft_getopt(cfg, 'nbdetect', 'median');
cfg.feedback = ft_getopt(cfg, 'feedback', 'no');
cfg.thresholdside = ft_getopt(cfg, 'thresholdside', []); % the default depends on cfg.metric, see below
if isempty(cfg.thresholdside)
if ismember(cfg.metric, {'var', 'std', 'db', 'mad', '1/var', 'max', 'maxabs', 'range', 'kurtosis', 'zvalue', 'maxzvalue', 'neighbstdratio'})
% large positive values indicate an artifact, so check for values ABOVE the threshold
cfg.thresholdside = 'above';
elseif ismember(cfg.metric, {'min', 'neighbexpvar', 'neighbcorr'})
% very negative values or small positive values indicate an artifact, so check for values BELOW the threshold
cfg.thresholdside = 'below';
else
% there are also a few where one could look at either side, these require the user to make a choice
ft_error('you must specify cfg.thresholdside');
end
end
% select trials and channels of interest
tmpcfg = keepfields(cfg, {'trials', 'channel', 'tolerance', 'latency', 'showcallinfo', 'trackcallinfo', 'trackusage', 'trackdatainfo', 'trackmeminfo', 'tracktimeinfo', 'checksize'});
data = ft_selectdata(tmpcfg, data);
% restore the provenance information
[cfg, data] = rollback_provenance(cfg, data);
ntrl = length(data.trial);
nchan = length(data.label);
if contains(cfg.metric, 'zvalue')
% cellmean and cellstd (see FT_DENOISE_PCA) would work instead of for-loops, but they are too memory-intensive
runsum = zeros(nchan, 1);
runss = zeros(nchan, 1);
runnum = 0;
for trl=1:ntrl
dat = preproc(data.trial{trl}, data.label, data.time{trl}, cfg.preproc);
runsum = runsum + nansum(dat, 2);
runss = runss + nansum(dat.^2, 2);
runnum = runnum + sum(isfinite(dat), 2);
end
mval = runsum./runnum;
sd = sqrt(runss./runnum - (runsum./runnum).^2);
else
mval = [];
sd = [];
end
if contains(cfg.metric, 'neighb')
cfg = ft_checkconfig(cfg, 'required', 'neighbours');
% creates a NxN Boolean matrix that describes whether channels are connected as neighbours
connectivity = channelconnectivity(cfg, data);
else
connectivity = [];
end
% compute the artifact value for each trial and each channel
level = nan(nchan, ntrl);
for trl=1:ntrl
dat = preproc(data.trial{trl}, data.label, data.time{trl}, cfg.preproc);
level(:,trl) = artifact_level(dat, cfg.metric, mval, sd, connectivity);
end
% find channels and trials with a value that exceeds the threshold
switch cfg.thresholdside
case 'below'
bad = level<cfg.threshold;
case 'above'
bad = level>cfg.threshold;
end
ft_info('identified %d out of %d traces as bad (%.0f %%)\n', sum(bad(:)), length(bad(:)), 100*mean(bad(:)));
for trl=1:ntrl
for chan=1:nchan
if bad(chan,trl)
data.trial{trl}(chan,:) = nan;
end
end
end
% do the general cleanup and bookkeeping at the end of the function
ft_postamble debug
ft_postamble previous data
ft_postamble provenance data
ft_postamble history data
ft_postamble savevar data