Current Version Jan 15

fslcc.cc

-//     fslcc.cc cross-correlate two time series
+//     fslcc.cc cross-correlate two time series timepoint by timepoint
 //     Steve Smith and Matthew Webster, FMRIB Image Analysis Group
-//     Copyright (C) 2001-2010 University of Oxford  
+//     Copyright (C) 2001-2015 University of Oxford  
 //     CCOPYRIGHT  
 
 #include "newimage/newimageall.h"
@@ -36,43 +36,43 @@ int fmrib_main(int argc, char *argv[])
   read_volume4D(input_volume1,input_name1);
   read_volume4D(input_volume2,input_name2);
 
-  if (input_volume1.maxx() != input_volume2.maxx() ||  input_volume1.maxy() != input_volume2.maxy()  ||  input_volume1.maxz() != input_volume2.maxz())
+  if (!samesize(input_volume1,input_volume2,3))
   {
     cerr << "Error: Mismatch in image dimensions" << endl; 
     return 1;
   }
 
-  if ( !nodemean.value() ) {
-    input_volume1-=input_volume1.mean();
-    input_volume2-=input_volume2.mean();
-   }
-
+  volume<T> mask;
+  if(fnmask.value().length()>0){
+	read_volume(mask,fnmask.value());
+	if(!samesize(input_volume1,mask,3)){  	
+	  cerr << "Error: Mismatch in mask dimensions" << endl; 
+	  return 1;
+	}
+  } else {
+    mask=input_volume1[0];
+    mask=1;
+  }
 
-  volume<T> theMask;
-  if( fnmask.value().length() > 0 ) {
-    read_volume(theMask,fnmask.value());
-    if(!samesize(input_volume1[0],theMask)){        
-      cerr << "Error: Mismatch in mask dimensions" << endl; 
-      return 1;
-    }
+   if ( !nodemean.value() ) {
     for(int t1=0;t1<=input_volume1.maxt();t1++)
-      input_volume1[t1] *= theMask;
+      input_volume1[t1] -= input_volume1[t1].mean(mask);
     for(int t2=0;t2<=input_volume2.maxt();t2++)
-      input_volume2[t2] *= theMask;
-  } 
-
+      input_volume2[t2] -= input_volume2[t2].mean(mask);
+   }
 
-  for(int t1=0;t1<input_volume1.tsize();t1++)
+  for(int t1=0;t1<=input_volume1.maxt();t1++)
   {
-    double ss1=sqrt(input_volume1.constantSubVolume(t1).sumsquares());  
-    for(int t2=0;t2<input_volume2.tsize();t2++)
+    double ss1=sqrt(input_volume1[t1].sumsquares(mask));  
+    for(int t2=0;t2<=input_volume2.maxt();t2++)
     {
-       double ss2=sqrt(input_volume2.constantSubVolume(t2).sumsquares());  
+       double ss2=sqrt(input_volume2[t2].sumsquares(mask));  
        double score=0;
-       for(int k=0;k<input_volume1.zsize();k++)
-         for(int j=0;j<input_volume1.ysize();j++)
-           for(int i=0;i<=input_volume1.xsize();i++)
-	     score+=(double)input_volume1(i,j,k,t1)*(double)input_volume2(i,j,k,t2); 
+       for(int k=0;k<=input_volume1.maxz();k++)
+         for(int j=0;j<=input_volume1.maxy();j++)
+           for(int i=0;i<=input_volume1.maxx();i++)
+	     if ( !fnmask.set() || mask(i,j,k)>0 ) 
+	       score+=(double)input_volume1(i,j,k,t1)*(double)input_volume2(i,j,k,t2); 
        if (!noabs.value())
 	 score=fabs(score);
        score/=(ss1*ss2);
@@ -87,7 +87,7 @@ int fmrib_main(int argc, char *argv[])
 
 int main(int argc,char *argv[])
 {
-  string title("fslcc");
+  string title("fslcc: Cross-correlate two time-series, timepoint by timepoint");
   string examples("fslcc [options] <first_input> <second_input> ");
   OptionParser options(title, examples);
 
@@ -99,7 +99,7 @@ int main(int argc,char *argv[])
   unsigned int done;
 
   try {
-    done=options.parse_command_line(argc, argv);
+    done=options.parse_command_line(argc, argv,0,true);
   }
   catch(X_OptionError& e) {
     options.usage();