Update coupling2.m

coupling2.m

@@ -1,12 +1,12 @@
 
 
 
-function mtd = coupling2(data,window,direction,trim)
-%COUPLING2       Time-resolved connectivity
+function mtd = coupling(data,window,direction,trim)
+%COUPLING        Time-resolved connectivity
 %
-%   MTD = coupling2(data,window);
-%   MTD = coupling2(data,window,direction);
-%   MTD = coupling2(data,window,direction,trim);
+%   MTD = coupling(data,window);
+%   MTD = coupling(data,window,direction);
+%   MTD = coupling(data,window,direction,trim);
 %
 %	Creates a functional coupling metric from an input matrix 'data'
 %	data: should be organized in 'time x nodes' matrix
@@ -28,90 +28,67 @@
 %   Outputs:
 %       MTD,
 %           time-varying connectivity matrix
-%
-%
-%
-%
-%
-
 
 
-    if isempty(direction)
+    % check inputs and define variables
+
+    if nargin==2
+        direction=0; trim=0;
+    elseif nargin==2
         trim=0;
     end
 
-    if isempty(trim)
-        trim=0;
-    end
-
-    %define variables
     [ts,nodes] = size(data);
 
     %calculate temporal derivative
     td = diff(data);
 
-
     %standardize data
     data_std = std(td);
 
-
     for i = 1:nodes
-
-        td(:,i) = td(:,i) / data_std(1,i);
-
+         td(:,i) = td(:,i) / data_std(1,i);
     end
 
 
     % [...] = zscore(X,FLAG,DIM) standardizes X by working along the dimension
-    %    DIM of X. Pass in FLAG==0 to use the default normalization by N-1, or 1
-    %    to use N.
+    %    DIM of X. Pass in FLAG==0 to use the default normalization by N-1, or 1 to use N.
 
 
     %functional coupling score
-
     fc = bsxfun(@times,permute(td,[1,3,2]),permute(td,[1,2,3]));
 
 
 
     %temporal smoothing (credit: T. C. O'Haver, 2008.)
-
     mtd_temp = zeros(nodes,nodes,ts-1);
-
-
+
     for j = 1:nodes
         for k = 1:nodes
             mtd_temp(j,k,:) = smooth(squeeze(fc(:,j,k)),window);
         end
     end
 
 
-    %window type
+    %window type (0 = middle; 1 = forward facing)
 
     mtd = zeros(nodes,nodes,ts);
 
     if direction == 1
-
         mtd(:,:,1:ts-round(window/2+1)) = mtd_temp(:,:,round(window/2+1):end);
-
     elseif direction == 0
-
         mtd(:,:,1:ts-1) = mtd_temp;
-
     end
 
 
 
-    %trim ends?
+    %trim ends (0 = no; 1 = yes)?
 
     if trim == 1 && direction == 0
-
         mtd(:,:,ts-round(window/2):end) = [];
         mtd(:,:,1:round(window/2)) = [];
-
     elseif trim == 1 && direction == 1
-
         mtd(:,:,(ts-window):end) = [];
-
     end
 
 end