*** empty log message ***

meloptions.h

@@ -81,7 +81,8 @@ class MelodicOptions {
 		Option<string> bgimage;
   	Option<float>  tr;
   	Option<bool>   logPower;
-		Option<bool>  addsigchng;
+		Option<bool>   addsigchng;
+		Option<bool>   varplots;
 
 		Option<string> fn_Tdesign;
 		Option<string> fn_Tcon;
@@ -256,6 +257,9 @@ class MelodicOptions {
 	 addsigchng(string("--sigchng"),  false,
 		 string("add signal change estimates to report pages\n"), 
 		 false, no_argument, false),
+	 varplots(string("--varplots"),  false,
+			 string("add std error envelopes to time course plots\n"), 
+			 false, no_argument, false),
 	 fn_Tdesign(string("--Tdes"), string(""),
 	   string("        design matrix across time-domain"),
 		 false, requires_argument),
@@ -387,6 +391,7 @@ class MelodicOptions {
 	    options.add(tr);
 	    options.add(logPower);
 	    options.add(addsigchng);
+	    options.add(varplots);
 			options.add(fn_Tdesign);
 			options.add(fn_Tcon);
 			options.add(fn_TconF);

melreport.cc

@@ -124,7 +124,7 @@ namespace Melodic{
 			}
 
 			//add deviation around time course
-			if(melodat.get_Tmodes(cnum-1).Ncols()>1){
+			if(melodat.get_Tmodes(cnum-1).Ncols()>1 && opts.varplots.value()){
 				Matrix tmp = stdev(melodat.get_Tmodes(cnum-1).Columns(2,melodat.get_Tmodes(cnum-1).Ncols()).t(),1);
 				tmptc &= melodat.get_Tmodes(cnum-1).Column(1).t()+tmp;
 				tmptc &= melodat.get_Tmodes(cnum-1).Column(1).t()-tmp;
@@ -140,8 +140,9 @@ namespace Melodic{
 		  	newplot.add_xlabel(string("Time (TRs)"));
 			
 			newplot.add_ylabel("Normalised Response");
-			newplot.set_yrange(tmptc.Minimum()-0.05*(tmptc.Maximum()-tmptc.Minimum()),
-				tmptc.Maximum()+0.05*(tmptc.Maximum()-tmptc.Minimum()));
+			newplot.set_yrange(tmptc.Row(1).Minimum()-0.05*(tmptc.Row(1).Maximum() - 
+				tmptc.Row(1).Minimum()),tmptc.Row(1).Maximum()+
+				0.05*(tmptc.Row(1).Maximum()-tmptc.Row(1).Minimum()));
 			newplot.grid_swapdefault();
 	    newplot.timeseries(tmptc,
 			  report.appendDir(string("t")+num2str(cnum)+".png"),