Revert "fixed conflict"

This reverts commit e6250c8.

VBA_bDCM_lesion.m

@@ -1,4 +1,4 @@
-function results=VBA_bDCM_lesion(posterior,out)
+function results=VBA_lesionAnalysis(posterior,out)
 
 %% Get normal profile
 
@@ -22,9 +22,7 @@
         posterior.muTheta,...
         posterior.muPhi,...
         out.u,...
-        Inf, ...
-        inf(size(posterior.a_sigma)), ...
-        out.options,...
+        Inf,Inf,out.options,...
         posterior.muX0);
 
         rnormal.y=yp-er;
@@ -43,9 +41,7 @@
         posterior_l.muTheta,...
         posterior.muPhi,...
         out.u,...
-        Inf, ...
-        inf(size(posterior.a_sigma)), ...
-        out.options,...
+        Inf,Inf,out.options,...
         posterior.muX0);
 
         rlesion(iRegion).y=yp-er;

subfunctions/prepare_fullDCM.m

@@ -0,0 +1,149 @@
+function [options] = prepare_fullDCM(A,B,C,D,TR,microDT,homogeneous,hA,hB,hC,hD,sources)
+% precalculates intermediary variables for the VB inversion of DCM for fMRI
+% function [options] = prepare_fullDCM(A,B,C,D,TR,microDT,homogeneous)
+% IN:
+%   - A: binary matrix indicating where the connections are
+%   - B: cell-array of binary matrices of modulatory effects
+%   - C: binary matrix of input-state coupling
+%   - D: cell-array of binay matrices for gating effects
+%   - TR: fMRI reptition time (data sampling period)
+%   - microDT: micro-time resolution for ODE integration
+%   - homogeneous: flag for indicating whether the observation parameters
+%   of the Ballon model are identical across ROIs
+% OUT:
+%   - options: incomplete optinal structure for VB inversion of the
+%   specified model (this does not include priors)...
+
+if nargin < 7
+    homogeneous = 0;
+else
+    homogeneous = ~~homogeneous;
+end
+
+if ~exist('sources','var')
+    sources(1).out=size(A,1);
+    if exist('hA','var')
+        sources(2).out=size(hA,1);
+    end
+end
+extended = numel(sources)>1;
+
+%- prepare neural evolution function parameters indices and matrices
+[inF] = prepare_dcm(A,B,C,D);
+
+dim.n = size(A,1);
+dim.n_u = size(B,2);
+
+
+%- prepare decoding function parameters indices and matrices
+if extended
+    [inF,nresp] = extend_dcm(inF,hA,hB,hC,hD,dim,sources);  
+else
+    nresp = 0;
+end
+
+%- define hemodynamic parameters indices
+nreg=dim.n;
+if extended
+    offset = inF.indhself(end);
+else
+    offset = inF.indself;
+end
+inF.ind1 = [1:5:5*nreg] + offset;
+inF.ind2 = [2:5:5*nreg] + offset;
+inF.ind3 = [3:5:5*nreg] + offset;
+inF.ind4 = [4:5:5*nreg] + offset;
+inF.ind5 = [5:5:5*nreg] + offset;
+
+
+%- define hidden states indices
+inF.n1 = 1:5:5*nreg;
+inF.n2 = 2:5:5*nreg;
+inF.n3 = 3:5:5*nreg;
+inF.n4 = 4:5:5*nreg;
+inF.n5 = 5:5:5*nreg;
+
+if extended
+    try
+        offset = inF.n5(end);
+    catch
+        offset=0;
+    end
+    inF.r =  (1:nresp) + offset;
+end
+inG.n1 = inF.n1;
+inG.n2 = inF.n2;
+inG.n3 = inF.n3;
+inG.n4 = inF.n4;
+inG.n5 = inF.n5;
+
+if extended
+    inG.r = offset+(1:nresp);        
+    for i=2:numel(sources)
+        sourceRespIdx{i-1} = sources(i).out - sources(1).out(end);
+    end
+    inG.sourceRespIdx = sourceRespIdx;
+end
+
+
+%- prepare observation function parameters indices and matrices
+if ~homogeneous
+    inG.ind1 = 1:2:2*nreg;
+    inG.ind2 = 2:2:2*nreg;
+else
+    inG.ind1 = 1;
+    inG.ind2 = 2;
+end
+%- define decoding parameters indices
+if extended
+    inG.indr = [];
+    for i=2:length(sources)
+        inG.indr = [inG.indr,sources(i).out];
+    end
+%     inG.indr = inG.ind2(end) + (1:sum([sources.type]~=0));
+end
+
+% dimensions 
+dim.n_theta = inF.ind5(end);
+if extended
+    dim.n_phi = inG.indr(end);
+else
+    dim.n_phi = inG.ind2(end);
+end
+dim.p = nreg + nresp ;
+dim.n = 5*nreg+nresp;
+
+%- finalize options structure
+options.decim = max([1,ceil(TR./microDT)]);
+inF.deltat = TR./options.decim;
+inF = orderfields(inF);
+inF.confounds.indu = 1:size(C,2);
+inF.confounds.indp = [];
+inF.fullDCM = 1;
+inF.linearized = 0;
+inF.xshift = 0;
+inF.logx2 = 1;
+inG.fullDCM = 1;
+inG.homogeneous = homogeneous;
+inG.TE = 0.04;
+inG.confounds.indu = 1:size(C,2);
+inG.confounds.indt = [];
+inG.confounds.X0 = [];
+inG.confounds.indp = [];
+
+inF.extended=extended;
+inG.extended=extended;
+options.extended=extended;
+
+
+if extended
+    options.sources=sources;
+end
+
+options.inF = inF;
+options.inG = inG;
+
+options.dim = dim;
+
+
+