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function [timelock] = ft_timelockbaseline(cfg, timelock)
% FT_TIMELOCKBASELINE performs baseline correction for ERF and ERP data. To apply
% baseline correction to data that is not timelocked, use ft_preprocessing instead.
%
% Use as
% [timelock] = ft_timelockbaseline(cfg, timelock)
% where the timelock data is the output from FT_TIMELOCKANALYSIS, and the
% configuration should contain
% cfg.baseline = [begin end] (default = 'no')
% cfg.channel = cell-array, see FT_CHANNELSELECTION
% cfg.parameter = field for which to apply baseline normalization, or
% cell-array of strings to specify multiple fields to normalize
% (default = 'avg')
% 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.
%
% See also FT_TIMELOCKANALYSIS, FT_FREQBASELINE, FT_TIMELOCKGRANDAVERAGE, FT_DATATYPE_TIMELOCK
% Undocumented local options:
% cfg.baselinewindow
% cfg.previous
% cfg.version
% Copyright (C) 2022, 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 timelock
ft_preamble provenance timelock
% 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
israw = ft_datatype(timelock, 'raw');
iscomp = ft_datatype(timelock, 'comp');
if israw || iscomp
% the type 'raw' also captures component data
ft_warning('The input data is expected to be of datatype ''timelock''. Consider using ft_preprocessing instead, to avoid unexpected sideeffects. The datatype will be temporarily converted.');
end
timelock = ft_checkdata(timelock, 'datatype', {'timelock+comp', 'timelock'}, 'feedback', 'yes');
% 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, 'renamed', {'blc', 'demean'});
cfg = ft_checkconfig(cfg, 'renamed', {'blcwindow', 'baselinewindow'});
cfg = ft_checkconfig(cfg, 'forbidden', 'baselinetype');
% set the defaults
cfg.baseline = ft_getopt(cfg, 'baseline', 'no');
cfg.channel = ft_getopt(cfg, 'channel', 'all');
cfg.parameter = ft_getopt(cfg, 'parameter', '');
if isempty(cfg.parameter)
if isfield(timelock, 'avg')
cfg.parameter = 'avg';
elseif strcmp(timelock.dimord, 'rpt_chan_time')
cfg.parameter = 'trial';
elseif strcmp(timelock.dimord, 'subj_chan_time')
cfg.parameter = 'individual';
end
end
% make sure cfg.parameter is a cell-array of strings
if (~isa(cfg.parameter, 'cell'))
cfg.parameter = {cfg.parameter};
end
% the cfg.blc/blcwindow options are used in preprocessing and in
% ft_timelockanalysis (i.e. in private/preproc), hence make sure that
% they can also be used here for consistency
if isfield(cfg, 'baseline') && (isfield(cfg, 'demean') || isfield(cfg, 'baselinewindow'))
ft_error('conflicting configuration options, you should use cfg.baseline');
elseif isfield(cfg, 'demean') && strcmp(cfg.demean, 'no')
cfg.baseline = 'no';
cfg = rmfield(cfg, 'demean');
cfg = rmfield(cfg, 'baselinewindow');
elseif isfield(cfg, 'demean') && strcmp(cfg.demean, 'yes')
cfg.baseline = cfg.baselinewindow;
cfg = rmfield(cfg, 'demean');
cfg = rmfield(cfg, 'baselinewindow');
end
if ischar(cfg.baseline)
if strcmp(cfg.baseline, 'yes')
% do correction on the whole time interval
cfg.baseline = [-inf inf];
elseif strcmp(cfg.baseline, 'all')
% do correction on the whole time interval
cfg.baseline = [-inf inf];
% is input consistent?
elseif strcmp(cfg.baseline, 'no')
ft_warning('no baseline correction done');
end
end
cfg.channel = ft_channelselection(cfg.channel, timelock.label);
chansel = match_str(timelock.label, cfg.channel);
if ~(ischar(cfg.baseline) && strcmp(cfg.baseline, 'no'))
% determine the time interval on which to apply baseline correction
tbeg = nearest(timelock.time, cfg.baseline(1));
tend = nearest(timelock.time, cfg.baseline(2));
% update the configuration
cfg.baseline(1) = timelock.time(tbeg);
cfg.baseline(2) = timelock.time(tend);
for k = 1:numel(cfg.parameter)
par = cfg.parameter{k};
% this if-statement is just there to give more specific text output
if isequal(par, 'trial')
fprintf('applying baseline correction on each individual trial\n');
ntrial = size(timelock.(par),1);
for i=1:ntrial
timelock.(par)(i,chansel,:) = ft_preproc_baselinecorrect(shiftdim(timelock.(par)(i,chansel,:),1), tbeg, tend);
end
elseif isequal(par, 'individual')
fprintf('applying baseline correction on each individual subject\n');
nsubj = size(timelock.(par),1);
for i=1:nsubj
timelock.(par)(i,chansel,:) = ft_preproc_baselinecorrect(shiftdim(timelock.(par)(i,chansel,:),1), tbeg, tend);
end
else
fprintf('applying baseline correction on %s\n', par);
d = ndims(timelock.(par));
if d == 3
for i=1:size(timelock.(par),1)
timelock.(par)(i,chansel,:) = ft_preproc_baselinecorrect(shiftdim(timelock.(par)(i,chansel,:),1), tbeg, tend);
end
elseif d == 2
timelock.(par)(chansel,:) = ft_preproc_baselinecorrect(timelock.(par)(chansel,:), tbeg, tend);
else
ft_warning('Not doing anything - matrices up to only three dimensions are supported');
end
end
if isfield(timelock, 'var')
fprintf('baseline correction invalidates previous variance estimate, removing var\n');
timelock = rmfield(timelock, 'var');
end
if isfield(timelock, 'cov')
fprintf('baseline correction invalidates previous covariance estimate, removing cov\n');
timelock = rmfield(timelock, 'cov');
end
end
end % ~strcmp(cfg.baseline, 'no')
if iscomp
timelock = ft_checkdata(timelock, 'datatype', 'raw+comp');
elseif israw
% convert the timelock structure back into a raw structure
timelock = ft_checkdata(timelock, 'datatype', 'raw');
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Output scaffolding
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if numel(cfg.parameter)==1
% convert from cell-array to string
cfg.parameter = cfg.parameter{1};
end
% do the general cleanup and bookkeeping at the end of the function
ft_postamble debug
ft_postamble previous timelock
ft_postamble provenance timelock
ft_postamble history timelock
ft_postamble savevar timelock