more modifications

fsl_glm.cc

@@ -26,7 +26,7 @@ using namespace std;
 		string("\nCopyright(c) 2004-2009, University of Oxford (Christian F. Beckmann)\n")+
 		string(" \n Simple GLM usign ordinary least-squares (OLS) regression on\n")+
 		string(" time courses and/or 3D/4D imges against time courses \n")+
-		string(" or 3D/4D images\n\n");
+		string(" or 3D/4D images");
   string examples="fsl_glm -i <input> -d <design> -o <output> [options]";
 
 //Command line Options {
@@ -35,10 +35,10 @@ using namespace std;
 		true, requires_argument);
   Option<string> fnout(string("-o,--out"), string(""),
 		string("output file name for GLM parameter estimates (GLM betas)"),
-		true, requires_argument);
+		false, requires_argument);
   Option<string> fndesign(string("-d,--design"), string(""),
 		string("file name of the GLM design matrix (time courses or spatial maps)"),
-		true, requires_argument);
+		false, requires_argument);
   Option<string> fnmask(string("-m,--mask"), string(""),
 		string("mask image file name if input is image"),
 		false, requires_argument);
@@ -66,6 +66,9 @@ using namespace std;
 	Option<int> help(string("-h,--help"), 0,
 		string("display this help text"),
 		false,no_argument);
+	Option<bool> debug(string("--debug"), FALSE,
+		string("display debug information"),
+		false,no_argument,false);
 	// Output options	
 	Option<string> outcope(string("--out_cope"),string(""),
 		string("output file name for COPEs (either as text file or image)"),
@@ -103,7 +106,7 @@ using namespace std;
 		/*
 }
 */
-//Globals {
+//Globals 
 	Melodic::basicGLM glm;
 	int voxels = 0;
 	Matrix data;
@@ -112,9 +115,8 @@ using namespace std;
 	Matrix fcontrasts;
 	Matrix meanR;
 	RowVector vnscales;
-	volume<float> mask;  /*
-}
-*/
+	volume<float> mask;  
+
 ////////////////////////////////////////////////////////////////////////////
 
 // Local functions
@@ -159,22 +161,21 @@ int setup(){
 				return 1;
 			};
 		}else{
-			mask = tmpdata[0]*0.0+1.0;	
-		}
-		
+			mask=tmpdata[0]*0.0+1.0;
+			data=tmpdata.matrix(mask);
+			Melodic::update_mask(mask,data);
+		}	
 		data = tmpdata.matrix(mask);
 		voxels = data.Ncols();
+			
+		if(perfvn.value()){
+			data = remmean(data,1);
+			vnscales = Melodic::varnorm(data);		
+		}
 	}
 	else
 		data = read_ascii_matrix(fnin.value());	
 
-	if(perf_demean.value())
-		data = remmean(data,1);
-	if(perfvn.value())
-		vnscales = Melodic::varnorm(data);
-	if(normdat.value())
-		data =  SP(data,ones(data.Nrows(),1)*pow(stdev(data,1),-1));
-
 	if(fsl_imageexists(fndesign.value())){//read design
 		volume4D<float> tmpdata;
 		read_volume4D(tmpdata,fndesign.value());
@@ -188,11 +189,16 @@ int setup(){
 		design = read_ascii_matrix(fndesign.value());
 	}
 
+	if(perf_demean.value())
+		data = remmean(data,1);
+	if(normdat.value())
+		data =  SP(data,ones(data.Nrows(),1)*pow(stdev(data,1),-1));
+
 	meanR=mean(data,1);
-	if(perf_demean.value()){	
+	if(perf_demean.value())	
+		design = remmean(design,1);
 	if(normdes.value())
 		design =  SP(design,ones(design.Nrows(),1)*pow(stdev(design,1),-1));
-
 	if(fncontrasts.value()>""){//read contrast		
 		contrasts = read_ascii_matrix(fncontrasts.value());
 		if(!(contrasts.Ncols()==design.Ncols())){