function DEM_demo_induced_fMRI
% Demonstration of DCM for CSD (fMRI) with simulated responses
%__________________________________________________________________________
% This demonstration compares generalised filtering and deterministic DCM 
% (generating complex cross spectra) in the context of a nonlinear 
% convolution (fMRI) model using simulated data. Here, the dynamic
% convolution model for fMRI responses is converted into a static
% non-linear model by generating not the timeseries per se but their
% second-order statistics – in the form of cross spectra and covariance
% functions. This enables model parameters to the estimated using the
% second order data features through minimisation of variational free
% energy. For comparison, the same data are inverted (in timeseries form)
% using generalised filtering. This example uses a particularly difficult
% problem – with limited data - to emphasise the differences.
%
% NB - the generalised filtering trakes much longer than the deterministic
% scheme
%__________________________________________________________________________
% Copyright (C) 2010 Wellcome Trust Centre for Neuroimaging
 
% Karl Friston
% $Id: DEM_demo_induced_fMRI.m 6759 2016-03-27 19:45:17Z karl $
 
% Simulate timeseries
%==========================================================================
rng('default')
 
% DEM Structure: create random inputs
% -------------------------------------------------------------------------
T  = 512;                             % number of observations (scans)
TR = 2;                               % repetition time or timing
t  = (1:T)*TR;                        % observation times
n  = 3;                               % number of regions or nodes
u  = spm_rand_mar(T,n,1/2)/4;         % endogenous fluctuations
 
% experimental inputs (Cu = 0 to suppress)
% -------------------------------------------------------------------------
Cu  = [1; 0; 0] * 0;
E   = cos(2*pi*TR*(1:T)/24) * 0;

% priors
% -------------------------------------------------------------------------
options.nonlinear  = 0;
options.two_state  = 0;
options.stochastic = 1;
options.centre     = 1;
options.induced    = 1;
options.maxit      = 8;
 
A   = ones(n,n);
B   = zeros(n,n,0);
C   = zeros(n,n);
D   = zeros(n,n,0);
pP  = spm_dcm_fmri_priors(A,B,C,D,options);
 
 
% true parameters (reciprocal connectivity)
% -------------------------------------------------------------------------
pP.A = [  0  -.2    0;
        -.3    0   .3
          0   .2    0];
pP.C = eye(n,n);
pP.transit = randn(n,1)/16;
 
% simulate response to endogenous fluctuations
%==========================================================================
 
% integrate states
% -------------------------------------------------------------------------
M.f  = 'spm_fx_fmri';
M.x  = sparse(n,5);
U.u  = u + (Cu*E)';
U.dt = TR;
x    = spm_int_J(pP,M,U);
 
% haemodynamic observer
% -------------------------------------------------------------------------
for i = 1:T
    y(i,:) = spm_gx_fmri(spm_unvec(x(i,:),M.x),[],pP)';
end
 
% observation noise process
% -------------------------------------------------------------------------
e    = spm_rand_mar(T,n,1/2)/8;
 
% show simulated response
%--------------------------------------------------------------------------
i = 1:128;
spm_figure('Getwin','Figure 1'); clf
subplot(2,2,1)
plot(t(i),u(i,:))
title('Endogenous fluctuations','FontSize',16)
xlabel('Time (seconds)')
ylabel('Amplitude')
axis square
 
subplot(2,2,2), hold off
plot(t(i),x(i,n + 1:end),'c'), hold on
plot(t(i),x(i,1:n)), hold off
title('Hidden states','FontSize',16)
xlabel('Time (seconds)')
ylabel('Amplitude')
axis square
 
subplot(2,2,3)
plot(t(i),y(i,:),t(i),e(i,:),':')
title('Hemodynamic response and noise','FontSize',16)
xlabel('Time (seconds)')
ylabel('Amplitude')
axis square
 
 
% nonlinear system identification (DCM for CSD)
%==========================================================================
DCM.options = options;
 
DCM.a    = logical(pP.A);
DCM.b    = zeros(n,n,0);
DCM.c    = logical(Cu);
DCM.d    = zeros(n,n,0);
 
% response
% -------------------------------------------------------------------------
DCM.Y.y  = y + e;
DCM.Y.dt = TR;
DCM.U.u  = E';
DCM.U.dt = TR;

 
% nonlinear system identification (Variational Laplace) - deterministic DCM
% =========================================================================
CSD = spm_dcm_fmri_csd(DCM);
 
% summary
% -------------------------------------------------------------------------
spm_figure('Getwin','Figure 2'); clf
 
subplot(2,1,1); hold off
spm_plot_ci(CSD.Ep.A(:),CSD.Cp(1:n*n,1:n*n)), hold on
bar(pP.A(:),1/4), hold off
title('True and MAP connections (Deterministic)','FontSize',16)
axis square


% Bayesian deconvolution (Generalised filtering) - stochastic DCM
% =========================================================================

% initialise parameters using deterministic estimates
% -------------------------------------------------------------------------
DCM.options.P = rmfield(CSD.Ep,{'a','b','c'});

% invert
% -------------------------------------------------------------------------
LAP = spm_dcm_estimate(DCM);
 
% summary
% -------------------------------------------------------------------------
spm_figure('Getwin','Figure 2');
 
subplot(2,1,2); hold off
spm_plot_ci(LAP.Ep.A(:),LAP.Cp(1:n*n,1:n*n)), hold on
bar(pP.A(:),1/4), hold off
title('True and MAP connections (Stochastic)','FontSize',16)
axis square
 

