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Slepi/Code/Utilities/spm12/spm_dcm_specify_ui.m
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spm_dcm_specify_ui.m
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function DCM = spm_dcm_specify_ui(SPM,xY)
% Interface for stepping the user through creating a DCM
% FORMAT DCM = spm_dcm_specify_ui(SPM,xY)
%
% SPM - SPM structure from SPM.mat
% xY - (optional) VOI structures to be inserted into the DCM
%
% DCM - DCM structure (see spm_dcm_ui)
%__________________________________________________________________________
% Copyright (C) 2002-2015 Wellcome Trust Centre for Neuroimaging
% Karl Friston
% $Id: spm_dcm_specify_ui.m 6399 2015-04-07 16:05:10Z guillaume $
%-Interactive window
%--------------------------------------------------------------------------
Finter = spm_figure('GetWin','Interactive');
bcolor = get(Finter,'Color');
WS = spm('WinScale');
dx = 20;
spm_input('Specify DCM:... ',1,'d');
%==========================================================================
% Outputs
%==========================================================================
%-Get cell array of region structures
%--------------------------------------------------------------------------
if nargin < 2 || isempty(xY)
swd = SPM.swd;
[P, sts] = spm_select([1 8],'^VOI.*\.mat$',{'select VOIs'},'',swd);
if ~sts, DCM = []; return; end
P = cellstr(P);
m = numel(P);
xY = [];
for i = 1:m
p = load(P{i},'xY');
xY = spm_cat_struct(xY,p.xY);
end
else
m = numel(xY);
end
%==========================================================================
% Inputs
%==========================================================================
%-Get (nc) 'causes' or inputs U
%--------------------------------------------------------------------------
spm_input('Input specification:... ',1,'d');
Sess = SPM.Sess(xY(1).Sess);
if isempty(Sess.U)
% spontaneous activity, i.e. no stimuli
nc = 0;
U = [];
else
% with stimuli
U.dt = Sess.U(1).dt;
u = length(Sess.U);
U.name = {};
U.u = [];
for i = 1:u
for j = 1:length(Sess.U(i).name)
str = ['include ' Sess.U(i).name{j} '?'];
if spm_input(str,'+1','y/n',[1 0],1)
U.u = [U.u Sess.U(i).u(33:end,j)];
U.name{end + 1} = Sess.U(i).name{j};
end
end
end
nc = size(U.u,2);
end
%==========================================================================
% Timings
%==========================================================================
spm_input('Timing information:... ',-1,'d');
%-VOI timings
%--------------------------------------------------------------------------
RT = SPM.xY.RT;
t0 = spm_get_defaults('stats.fmri.t0');
t = spm_get_defaults('stats.fmri.t');
T0 = RT * t0 / t;
delays = spm_input('VOI timings [s]','+1','r', repmat(T0,1,m),m,[0 RT]);
%-Echo time (TE) of data acquisition
%--------------------------------------------------------------------------
TE = 0.04;
TE_ok = 0;
while ~TE_ok
TE = spm_input('Echo time, TE [s]', '+1', 'r', TE);
if ~TE || (TE < 0) || (TE > 0.1)
str = { 'Extreme value for TE or TE undefined.',...
'Please re-enter TE (in seconds!)'};
spm_input(str,'+1','bd','OK',[1],1);
else
TE_ok = 1;
end
end
%==========================================================================
% Model options
%==========================================================================
if nc % there are inputs
spm_input('Model options:... ',-1,'d');
options.nonlinear = spm_input('modulatory effects','+1','b',{'bilinear','nonlinear'},[0 1],1);
options.two_state = spm_input('states per region', '+1','b',{'one','two'},[0 1],1);
options.stochastic = spm_input('stochastic effects','+1','b',{'no','yes'},[0 1],1);
options.centre = spm_input('centre input', '+1','b',{'no','yes'},[0 1],1);
else
options.nonlinear = 0;
options.two_state = 0;
options.stochastic = 1;
options.centre = 1;
end
%==========================================================================
% Graph connections
%==========================================================================
a = zeros(m,m);
b = zeros(m,m,nc);
c = zeros(m,nc);
d = zeros(m,m,0);
%-Endogenous connections (A matrix)
%==========================================================================
%-Buttons and labels
%--------------------------------------------------------------------------
spm_input('Specify endogenous (fixed) connections from',1,'d')
spm_input('to',3,'d')
for i = 1:m
str = sprintf('%s %i',xY(i).name,i);
h1(i) = uicontrol(Finter,'String',str,...
'Style','text',...
'FontSize',10,...
'BackgroundColor',bcolor,...
'HorizontalAlignment','right',...
'Position',[080 350-dx*i 080 020].*WS);
h2(i) = uicontrol(Finter,'String',sprintf('%i',i),...
'Style','text',...
'FontSize',10,...
'BackgroundColor',bcolor,...
'Position',[180+dx*i 350 010 020].*WS);
end
for i = 1:m
for j = 1:m
h3(i,j) = uicontrol(Finter,...
'Position',[180+dx*j 350-dx*i 020 020].*WS,...
'BackgroundColor',bcolor,...
'Style','radiobutton');
if i == j
set(h3(i,j),'Value',1,...
'enable','off');
else
set(h3(i,j),'enable','on','TooltipString', ...
sprintf('from %s to %s',xY(j).name,xY(i).name));
end
if nc && i~=j
set(h3(i,j),'Value',0);
else
set(h3(i,j),'Value',1);
end
end
end
uicontrol(Finter,'String','done','Position', [300 100 060 020].*WS,...
'Callback', 'uiresume(gcbf)');
uiwait(Finter);
%-Get a
%--------------------------------------------------------------------------
for i = 1:m
for j = 1:m
a(i,j) = get(h3(i,j),'Value');
end
end
delete(findobj(get(Finter,'Children'),'flat'));
%-Effects of causes (B and C matrices)
%==========================================================================
uicontrol(Finter,'String','done','Position', [300 100 060 020].*WS,...
'Callback', 'uiresume(gcbf)');
for k = 1:nc
%-Buttons and labels
%----------------------------------------------------------------------
str = sprintf(...
'Effects of %-12s on regions... and connections',...
U.name{k});
spm_input(str,1,'d');
for i = 1:m
h1(i) = uicontrol(Finter,'String',xY(i).name,...
'Style','text',...
'BackgroundColor',bcolor,...
'FontSize',10,...
'Position',[080 350-dx*i 080 020].*WS);
h2(i) = uicontrol(Finter,...
'Position',[160 360-dx*i 020 020].*WS,...
'BackgroundColor',bcolor,...
'Style','radiobutton');
end
for i = 1:m
for j = 1:m
if a(i,j) == 1
% Allow modulation of endogenous connections
%----------------------------------------------------------
h3(i,j) = uicontrol(Finter,...
'Position',[220+dx*j 360-dx*i 020 020].*WS,...
'BackgroundColor',bcolor,...
'Style','radiobutton');
set(h3(i,j),'TooltipString', ...
sprintf('from %s to %s',xY(j).name,xY(i).name));
end
end
end
uiwait(Finter);
%-Get c
%----------------------------------------------------------------------
for i = 1:m
c(i,k) = get(h2(i),'Value');
end
%-Get b allowing any 2nd order effects
%----------------------------------------------------------------------
for i = 1:m
for j = 1:m
if a(i,j)==1
b(i,j,k) = get(h3(i,j),'Value');
end
end
end
delete([h1(:); h2(:); h3(a==1)])
end
delete(findobj(get(Finter,'Children'),'flat'));
%-Effects of nonlinear modulations (D matrices)
%==========================================================================
if options.nonlinear
uicontrol(Finter,'String','done','Position', [300 100 060 020].*WS,...
'Callback', 'uiresume(gcbf)');
for k = 1:m
%-Buttons and labels
%------------------------------------------------------------------
str = sprintf('Effects of %-12s activity on connections',xY(k).name);
spm_input(str,1,'d');
for i = 1:m
for j = 1:m
if a(i,j)==1
% Allow modulation of endogenous connections
%------------------------------------------------------
h4(i,j) = uicontrol(Finter,...
'Position',[220+dx*j 360-dx*i 020 020].*WS,...
'BackgroundColor',bcolor,...
'Style','radiobutton');
end
end
end
uiwait(Finter);
%-Get d allowing any 2nd order effects
%------------------------------------------------------------------
for i = 1:m
for j = 1:m
if a(i,j)==1
d(i,j,k) = get(h4(i,j),'Value');
end
end
end
delete(h4(a==1))
end
end
delete(findobj(get(Finter,'Children'),'flat'));
spm_input('Thank you',1,'d')
%==========================================================================
% Response
%==========================================================================
%-Response variables & confounds (NB: the data have been whitened)
%--------------------------------------------------------------------------
n = length(xY); % number of regions
v = length(xY(1).u); % number of time points
Y.dt = SPM.xY.RT;
Y.X0 = xY(1).X0;
for i = 1:n
Y.y(:,i) = xY(i).u;
Y.name{i} = xY(i).name;
end
%-Error precision components (one for each region) - i.i.d. (because of W)
%--------------------------------------------------------------------------
Y.Q = spm_Ce(ones(1,n)*v);
%==========================================================================
% DCM structure
%==========================================================================
% Endogenous input specification
if isempty(U)
U.u = zeros(v,1);
U.name = {'null'};
end
%-Store all variables in DCM structure
%--------------------------------------------------------------------------
DCM.a = a;
DCM.b = b;
DCM.c = c;
DCM.d = d;
DCM.U = U;
DCM.Y = Y;
DCM.xY = xY;
DCM.v = v;
DCM.n = n;
DCM.TE = TE;
DCM.delays = delays;
DCM.options = options;
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