*** empty log message ***

fsl_regfilt.cc

@@ -44,9 +44,12 @@ using namespace std;
 	Option<string> filter(string("-f,--filter"),string(""),
 		string("filter out part of the regression model, e.g. -f \"1,2,3\""),
 		true, requires_argument);
+	Option<bool> verbose(string("-v"),FALSE,
+		string("        switch on diagnostic messages"),
+		false, no_argument);
 	Option<bool> perfvn(string("--vn"),FALSE,
 		string("        perfrom variance-normalisation on data"),
-		false, requires_argument);
+		false, no_argument);
 	Option<int> help(string("-h,--help"), 0,
 		string("display this help text"),
 		false,no_argument);
@@ -67,6 +70,7 @@ using namespace std;
 	Matrix meanR;
 	RowVector vnscales;
 	volume<float> mask;
+	volume<float> Mean;
 	volumeinfo volinf;  /*
 }
 */
@@ -103,7 +107,9 @@ int dofilter(){
 		cerr << "ERROR: need to specify 4D input to use filtering" << endl;
 		return 1;
 	}
-  Matrix unmixMatrix = pinv(design);
+	if(verbose.value())
+		cout << "  Calculating maps " << endl;  
+	Matrix unmixMatrix = pinv(design);
   Matrix maps = unmixMatrix * data;
 
   Matrix noisedes;
@@ -133,7 +139,9 @@ int dofilter(){
     }
   }while(p);
   Matrix newData;
-  newData = data - noisedes * noisemaps.t();
+	if(verbose.value())
+		cout << "  Calculating filtered data " << endl;
+ 	newData = data - noisedes * noisemaps.t();
   newData = newData + ones(newData.Nrows(),1)*meanR;
   
 	save4D(newData,fnout.value());
@@ -154,11 +162,19 @@ int setup(){
 				return 1;
 			};
 		}else{
-			mask = tmpdata[0]*0.0+1.0;	
+			if(verbose.value())
+				cout << "  Creating mask image "  << endl;
+			Mean = meanvol(tmpdata);
+			float Mmin, Mmax;
+			Mmin = Mean.min(); Mmax = Mean.max();
+			mask = binarise(Mean,float(Mmin + 0.01* (Mmax-Mmin)),Mmax);
 		}
 		
 		data = tmpdata.matrix(mask);
 		voxels = data.Ncols();
+		if(verbose.value())
+			cout << " Data matrix size : " << data.Nrows() << " x " << voxels << endl;
+		
 	}else{
 		cerr << "ERROR: cannot read input image " << fnin.value()<<endl;
 		return 1;
@@ -205,6 +221,7 @@ int main(int argc,char *argv[]){
 			options.add(fnmask);
 			options.add(filter);
 			options.add(perfvn);
+			options.add(verbose);
 			options.add(help);
 			options.add(outdata);
 			options.add(outvnscales);
@@ -226,5 +243,5 @@ int main(int argc,char *argv[]){
 	  }catch(std::exception &e) {
 	    cerr << e.what() << endl;
 	  } 
-	}
+}
 

meldata.cc

@@ -526,7 +526,6 @@ namespace Melodic{
 		if(meanR.Storage()>0)
     	newData = newData + ones(newData.Nrows(),1)*meanR;
     
-		cerr << " HERE REMOVE " << endl;
     volume4D<float> tmp;
     read_volume4D(tmp,opts.inputfname.value().at(0)); 
     tmp.setmatrix(newData,Mask);

melgmix.cc

@@ -239,9 +239,7 @@ namespace Melodic{
 				SortAscending(tmp);
 				RowVector newcdf(tmp);
 	  		newcdf << normcdf(tmp,means(1),vars(1));
-				write_ascii_matrix(dat,"dat");
-				write_ascii_matrix(newcdf,"newcdf");
-				write_ascii_matrix(tmp,"tmpmat");
+
 				float thrp = tmp(tmp.Ncols())+0.01;
 				float thrn = tmp(1)-0.01;
 				int ctr=tmp.Ncols();

meloptions.h

@@ -168,7 +168,7 @@ class MelodicOptions {
    perf_bet(string("--nobet"), true,
 	   string("\tswitch off BET"), 
 	   false, no_argument),
-   threshold(string("--bgthreshold"),  0.00000001,
+   threshold(string("--bgthreshold"),  0.01,
 	   string("brain / non-brain threshold (only if --nobet selected)\n"), 
 	   false, requires_argument),
    pca_dim(string("-d,--dim"), 0,

melreport.h

@@ -80,7 +80,7 @@ namespace Melodic{
 				   		report <<"<OBJECT data="<<opts.guireport.value()<< "></OBJECT>"<< endl;
 							loghtml <<"<OBJECT data="<<opts.guireport.value()<< "></OBJECT>"<< endl;
 						}
-						report << "<IFRAME  height=100px width=100% src=nav.html frameborder=0></IFRAME><p>"<< endl;		
+						report << "<IFRAME  height=80px width=100% src=nav.html frameborder=0></IFRAME><p>"<< endl;		
 						loghtml << "<IFRAME  height=100px width=100% src=nav.html frameborder=0></IFRAME><p>"
 							<<"<pre>../melodic.log</pre>" <<endl;		
 						navigator <<"<CENTER><TABLE BORDER=0><TR>" << endl