steve\'s complaining again

melodic.cc

@@ -123,7 +123,7 @@ int main(int argc, char *argv[]){
 	    			}
 	    			if(!leaveloop){
 					if(opts.paradigmfname.value().length()>0)
-						opts.pca_dim.set_T(std::max(opts.pca_dim.value(),melodat.get_param().Ncols()+3*opts.retrystep-1);
+						opts.pca_dim.set_T(std::max(opts.pca_dim.value(),melodat.get_param().Ncols()+3*opts.retrystep-1));
 	      			message(endl << "Restarting MELODIC using -d " 
 		      			<< opts.pca_dim.value() 
 		      			<< endl << endl);

meloptions.h

@@ -111,6 +111,7 @@ class MelodicOptions {
 
   	Option<string> guessfname;
   	Option<string> paradigmfname;
+  	Option<string> axials_str;
 
   	Option<int>   dummy;
   	Option<int>   repeats;
@@ -337,6 +338,9 @@ class MelodicOptions {
    paradigmfname(string("--init_pca"),  string(""),
 	   string("file name of FEAT paradigm file (design.mat) for PCA initialisation"), 
 	   false, requires_argument, false),
+   axials_str(string("--report_maps"),  string(" -s 2 -A 950 "),
+		   string("control string for spatial map images (see slicer)"), 
+		   false, requires_argument),
    dummy(string("--dummy"),  0,
 	   string("number of dummy volumes"), 
 	   false, requires_argument,false),
@@ -437,6 +441,7 @@ class MelodicOptions {
 	   
 	    options.add(guessfname);
 	    options.add(paradigmfname); 
+	    options.add(axials_str); 
 	    options.add(dummy);
 	    options.add(repeats);
 	    options.add(nlconst1);

melreport.cc

@@ -92,8 +92,7 @@ namespace Melodic{
 	  		//save_volume(newvol,report.appendDir(mmodel.get_prefix()+"rendered"),
 	  		//      melodat.tempInfo);
 				sprintf(instr," ");
-				strcat(instr," -s 2");
-				strcat(instr," -A 950 ");
+				strcat(instr,axials_instr.c_str());
 				strcat(instr,string(report.appendDir(mmodel.get_prefix()+
 					     	"_thresh.png")).c_str());
 				newpic.set_title(string("Component No. "+num2str(cnum)+
@@ -390,8 +389,7 @@ namespace Melodic{
 	    	//save_volume(newvol,report.appendDir(mmodel.get_prefix()+"rendered"),
 	    	//      melodat.tempInfo);
 	    	sprintf(instr," ");
-	    	strcat(instr," -s 2");
-	    	strcat(instr," -A 950 ");
+	    	strcat(instr,axials_instr.c_str());
 	    	strcat(instr,string(report.appendDir(mmodel.get_prefix()+"_thresh"+
 						 	num2str(tctr)+".png")).c_str());
 	    	newpic.set_title(string("Component No. "+num2str(cnum)+
@@ -487,8 +485,7 @@ namespace Melodic{
 	  		//save_volume(newvol,report.appendDir(mmodel.get_prefix()+"rendered"),
 	  		//      melodat.tempInfo);
 	  		sprintf(instr," ");
-	  		strcat(instr," -s 2");
-	  		strcat(instr," -A 950 ");
+	  		strcat(instr,axials_instr.c_str());
 	  		strcat(instr,string(report.appendDir(mmodel.get_prefix()+
 		 			".png")).c_str());
 	  		newpic.set_title(string("Component No. "+num2str(cnum)+
@@ -522,8 +519,8 @@ namespace Melodic{
 	  		char instr[10000];
 
 	  		sprintf(instr," ");
-	  		strcat(instr,"-l render1 -s 2");
-	  		strcat(instr," -A 950 ");
+	  		strcat(instr,"-l render1 ");
+	  		strcat(instr,axials_instr.c_str());
 	  		strcat(instr,string(report.appendDir(mmodel.get_prefix()+
 					"_prob.png")).c_str());      
 	  		newpic.set_title(string("Component No. "+num2str(cnum)+
@@ -660,8 +657,7 @@ namespace Melodic{
 	  		//save_volume(newvol,report.appendDir(prefix+"rendered"),
 	  		//      melodat.tempInfo);
 	  		sprintf(instr," ");
-	  		strcat(instr," -s 2");
-	  		strcat(instr," -A 950 ");
+	  		strcat(instr,axials_instr.c_str());
 	  		strcat(instr,string(report.appendDir(prefix+
 					".png")).c_str());
 	  		newpic.set_title(string("Component No. "+num2str(cnum)+

melreport.h

@@ -90,6 +90,7 @@ namespace Melodic{
 							navigator << "<A HREF=\"log.html\" target=\"_top\">Log</A>&nbsp;-&nbsp;";
 						navigator	<<"Components: ";
 						navigator.flush();
+						axials_instr = opts.axials_str.value();
 	  			}
 				}
 
@@ -301,7 +302,8 @@ namespace Melodic{
 
       Log IChtml;
       Log IChtml2;
-
+      string axials_instr;
+	
       void IC_rep_det(MelGMix &mmodel, int cnum, int dim);
       
       string int2str(int n){