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ft_dipolesimulation.m
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ft_dipolesimulation.m
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function [data] = ft_dipolesimulation(cfg)
% FT_DIPOLESIMULATION simulates channel-level time-series data that consists of the
% the spatial distribution of the the field or potential of one or multiple dipoles.
%
% Use as
% data = ft_dipolesimulation(cfg)
% which will return a raw data structure that resembles the output of
% FT_PREPROCESSING.
%
% The dipoles position and orientation have to be specified with
% cfg.sourcemodel.pos = [Rx Ry Rz] (size Nx3)
% cfg.sourcemodel.mom = [Qx Qy Qz] (size 3xN)
% cfg.sourcemodel.unit = string, can be 'mm', 'cm', 'm' (default is automatic)
%
% The timecourse of the dipole activity is given as a cell-array with one
% dipole signal per trial
% cfg.sourcemodel.signal = cell-array with one dipole signal per trial
% or by specifying the parameters of a sine-wave signal
% cfg.sourcemodel.frequency = in Hz
% cfg.sourcemodel.phase = in radians
% cfg.sourcemodel.amplitude = per dipole
%
% The number of trials and the time axes of the trials can be specified by
% cfg.fsample = simulated sample frequency (default = 1000)
% cfg.trllen = length of simulated trials in seconds (default = 1)
% cfg.numtrl = number of simulated trials (default = 10)
% cfg.baseline = number (default = 0.3)
% or by
% cfg.time = cell-array with one time axis per trial, for example obtained from an existing dataset
%
% Random white noise can be added to the data in each trial, either by
% specifying an absolute or a relative noise level
% cfg.relnoise = add noise with level relative to data signal
% cfg.absnoise = add noise with absolute level
% cfg.randomseed = 'yes' or a number or vector with the seed value (default = 'yes')
%
% Optional input arguments are
% cfg.channel = Nx1 cell-array with selection of channels (default = 'all'),
% see FT_CHANNELSELECTION for details
% cfg.dipoleunit = units for dipole amplitude (default nA*m)
% cfg.chanunit = Nx1 cell-array with units for the channel data
%
% Optionally, you can modify the leadfields by reducing the rank, i.e. remove the weakest orientation
% cfg.reducerank = 'no', or number (default = 3 for EEG, 2 for MEG)
% cfg.backproject = 'yes' or 'no', determines when reducerank is applied whether the
% lower rank leadfield is projected back onto the original linear
% subspace, or not (default = 'yes')
%
% The volume conduction model of the head should be specified as
% cfg.headmodel = structure with volume conduction model, see FT_PREPARE_HEADMODEL
%
% The EEG or MEG sensor positions should be specified as
% cfg.elec = structure with electrode positions or filename, see FT_READ_SENS
% cfg.grad = structure with gradiometer definition or filename, see FT_READ_SENS
%
% See also FT_SOURCEANALYSIS, FT_DIPOLEFITTING, FT_TIMELOCKSIMULATION,
% FT_FREQSIMULATION, FT_CONNECTIVITYSIMULATION
% Undocumented local options
% cfg.feedback
% cfg.previous
% cfg.version
% Copyright (C) 2004, Robert Oostenveld
%
% This file is part of FieldTrip, see http:https://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:https://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 provenance
ft_preamble randomseed
% the ft_abort variable is set to true or false in ft_preamble_init
if ft_abort
return
end
% 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', {'elecfile', 'elec'});
cfg = ft_checkconfig(cfg, 'renamed', {'gradfile', 'grad'});
cfg = ft_checkconfig(cfg, 'renamed', {'optofile', 'opto'});
cfg = ft_checkconfig(cfg, 'renamed', {'hdmfile', 'headmodel'});
cfg = ft_checkconfig(cfg, 'renamed', {'vol', 'headmodel'});
cfg = ft_checkconfig(cfg, 'renamed', {'dip', 'sourcemodel'});
% for consistency with FT_TIMELOCKSIMULUATION and FT_FREQSIMULATION
cfg = ft_checkconfig(cfg, 'createsubcfg', 'sourcemodel');
cfg = ft_checkconfig(cfg, 'renamed', {'ntrials', 'numtrl'});
cfg = ft_checkconfig(cfg, 'renamed', {'triallength', 'trllen'});
% set the defaults
cfg.sourcemodel = ft_getopt(cfg, 'sourcemodel', []);
cfg.sourcemodel.pos = ft_getopt(cfg.sourcemodel, 'pos', [-5 0 15]);
cfg.sourcemodel.mom = ft_getopt(cfg.sourcemodel, 'mom', [1 0 0]');
cfg.sourcemodel.time = ft_getopt(cfg.sourcemodel, 'time', {});
cfg.sourcemodel.signal = ft_getopt(cfg.sourcemodel, 'signal', {});
cfg.fsample = ft_getopt(cfg, 'fsample', 250);
cfg.relnoise = ft_getopt(cfg, 'relnoise', 0);
cfg.absnoise = ft_getopt(cfg, 'absnoise', 0);
cfg.feedback = ft_getopt(cfg, 'feedback', 'text');
cfg.channel = ft_getopt(cfg, 'channel', 'all');
cfg.dipoleunit = ft_getopt(cfg, 'dipoleunit', 'nA*m');
cfg.chanunit = ft_getopt(cfg, 'chanunit', {});
% collect and preprocess the electrodes/gradiometer and head model
% this will also update cfg.channel to match the electrodes/gradiometers
[headmodel, sens, cfg] = prepare_headmodel(cfg, []);
% construct the low-level options for the leadfield computation as key-value pairs, these are passed to FT_COMPUTE_LEADFIELD
leadfieldopt = {};
leadfieldopt = ft_setopt(leadfieldopt, 'reducerank', ft_getopt(cfg, 'reducerank'));
leadfieldopt = ft_setopt(leadfieldopt, 'backproject', ft_getopt(cfg, 'backproject'));
leadfieldopt = ft_setopt(leadfieldopt, 'normalize', ft_getopt(cfg, 'normalize'));
leadfieldopt = ft_setopt(leadfieldopt, 'normalizeparam', ft_getopt(cfg, 'normalizeparam'));
leadfieldopt = ft_setopt(leadfieldopt, 'weight', ft_getopt(cfg, 'weight'));
cfg.sourcemodel = fixdipole(cfg.sourcemodel);
Ndipoles = size(cfg.sourcemodel.pos,1);
% in case no time or signal was given, set some additional defaults
if ~isempty(cfg.sourcemodel.time) && ~isempty(cfg.sourcemodel.signal)
assert(length(cfg.sourcemodel.signal)==length(cfg.sourcemodel.time)); % these must match
cfg.numtrl = length(cfg.sourcemodel.time);
cfg.fsample = 1/mean(diff(cfg.sourcemodel.time{1})); % determine from time-axis
cfg.trllen = length(cfg.sourcemodel.time{1})/cfg.fsample;
cfg.baseline = -cfg.sourcemodel.time{1}(1);
elseif ~isempty(cfg.sourcemodel.time)
cfg.numtrl = length(cfg.sourcemodel.time);
cfg.fsample = 1/mean(diff(cfg.sourcemodel.time{1})); % determine from time-axis
cfg.trllen = length(cfg.sourcemodel.time{1})/cfg.fsample;
cfg.baseline = -cfg.sourcemodel.time{1}(1);
elseif ~isempty(cfg.sourcemodel.signal)
cfg.numtrl = length(cfg.sourcemodel.signal);
cfg.fsample = ft_getopt(cfg, 'fsample', 1000);
cfg.trllen = length(cfg.sourcemodel.signal{1})/cfg.fsample;
cfg.baseline = ft_getopt(cfg, 'baseline', 0);
else
cfg.numtrl = ft_getopt(cfg, 'numtrl', 10);
cfg.fsample = ft_getopt(cfg, 'fsample', 1000);
cfg.trllen = ft_getopt(cfg, 'trllen', 1);
cfg.baseline = ft_getopt(cfg, 'baseline', 0);
end
% no signal was given, set some additional defaults
if isempty(cfg.sourcemodel.signal)
cfg.sourcemodel.frequency = ft_getopt(cfg, 'frequency', ones(Ndipoles,1)*10);
cfg.sourcemodel.phase = ft_getopt(cfg, 'phase', zeros(Ndipoles,1));
cfg.sourcemodel.amplitude = ft_getopt(cfg, 'amplitude', ones(Ndipoles,1));
end
if isfield(cfg.sourcemodel, 'frequency')
% this should be a column vector
cfg.sourcemodel.frequency = cfg.sourcemodel.frequency(:);
end
if isfield(cfg.sourcemodel, 'phase')
% this should be a column vector
cfg.sourcemodel.phase = cfg.sourcemodel.phase(:);
end
if ~isempty(cfg.sourcemodel.time)
% use the user-supplied time vectors
diptime = cfg.sourcemodel.time;
else
% construct a time axis for every trial
nsample = round(cfg.trllen*cfg.fsample);
diptime = cell(1, cfg.numtrl);
for iTr = 1:cfg.numtrl
diptime{iTr} = (((1:nsample)-1)/cfg.fsample) - cfg.baseline;
end
end
if ~isempty(cfg.sourcemodel.signal)
% use the user-supplied signal for the dipoles
dipsignal = cfg.sourcemodel.signal;
else
dipsignal = cell(1, cfg.numtrl);
for iTr = 1:cfg.numtrl
% compute a cosine signal with the desired frequency, phase and amplitude for each dipole
for i=1:Ndipoles
dipsignal{iTr}(i,:) = cos(cfg.sourcemodel.frequency(i)*diptime{iTr}*2*pi + cfg.sourcemodel.phase(i)) * cfg.sourcemodel.amplitude(i);
end
end
end
dippos = cfg.sourcemodel.pos;
dipmom = cfg.sourcemodel.mom;
if ~iscell(dipmom)
dipmom = {dipmom};
end
if ~iscell(dippos)
dippos = {dippos};
end
if length(dippos)==1
dippos = repmat(dippos, 1, cfg.numtrl);
elseif length(dippos)~=cfg.numtrl
ft_error('incorrect number of trials specified in the dipole position');
end
if length(dipmom)==1
dipmom = repmat(dipmom, 1, cfg.numtrl);
elseif length(dipmom)~=cfg.numtrl
ft_error('incorrect number of trials specified in the dipole moment');
end
data.time = diptime;
data.trial = {};
ft_progress('init', cfg.feedback, 'computing data data');
for trial=1:cfg.numtrl
ft_progress(trial/cfg.numtrl, 'computing data data for trial %d\n', trial);
if numel(cfg.chanunit) == numel(cfg.channel)
lf = ft_compute_leadfield(dippos{trial}, sens, headmodel, 'dipoleunit', cfg.dipoleunit, 'chanunit', cfg.chanunit, leadfieldopt{:});
else
lf = ft_compute_leadfield(dippos{trial}, sens, headmodel, leadfieldopt{:});
end
nsamples = size(dipsignal{trial},2);
nchannels = size(lf,1);
data.trial{trial} = zeros(nchannels,nsamples);
for i = 1:3
data.trial{trial} = data.trial{trial} + ...
lf(:,i:3:end) * (repmat(dipmom{trial}(i:3:end),1,nsamples) .* dipsignal{trial});
end
end
ft_progress('close');
if ft_senstype(sens, 'meg')
data.grad = sens;
elseif ft_senstype(sens, 'eeg')
data.elec = sens;
end
% determine RMS value of data data
ss = 0;
sc = 0;
for trial=1:cfg.numtrl
ss = ss + sum(data.trial{trial}(:).^2);
sc = sc + length(data.trial{trial}(:));
end
rms = sqrt(ss/sc);
ft_info('RMS value of data data is %g\n', rms);
% add noise to the data data
for trial=1:cfg.numtrl
relnoise = randn(size(data.trial{trial})) * cfg.relnoise * rms;
absnoise = randn(size(data.trial{trial})) * cfg.absnoise;
data.trial{trial} = data.trial{trial} + relnoise + absnoise;
end
data.fsample = cfg.fsample;
data.label = sens.label;
% do the general cleanup and bookkeeping at the end of the function
ft_postamble debug
ft_postamble randomseed
ft_postamble provenance data
ft_postamble history data
ft_postamble savevar data