Added GD mask code

fslcc.cc

@@ -11,7 +11,9 @@
 using namespace NEWIMAGE;
 using namespace Utilities;
 
-
+Option<string> fnmask(string("-m"), string(""),
+		string("mask file name "),
+		false, requires_argument);
 Option<bool> noabs(string("--noabs"), false, 
 		     string("\tDon't return absolute values (keep sign)"), 
 		     false, no_argument);
@@ -44,6 +46,22 @@ int fmrib_main(int argc, char *argv[])
     input_volume1-=input_volume1.mean();
     input_volume2-=input_volume2.mean();
    }
+
+
+  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;
+    }
+    for(int t1=0;t1<=input_volume1.maxt();t1++)
+      input_volume1[t1] *= theMask;
+    for(int t2=0;t2<=input_volume2.maxt();t2++)
+      input_volume2[t2] *= theMask;
+  } 
+
+
   for(int t1=0;t1<input_volume1.tsize();t1++)
   {
     double ss1=sqrt(input_volume1.constantSubVolume(t1).sumsquares());  
@@ -73,6 +91,7 @@ int main(int argc,char *argv[])
   string examples("fslcc [options] <first_input> <second_input> ");
   OptionParser options(title, examples);
 
+  options.add(fnmask);
   options.add(noabs);
   options.add(nodemean);
   options.add(thresh);