diff --git a/ptx_nmasks.cc b/ptx_nmasks.cc
index 929bc21e82249d42f57e0497466e266178e77c73..c36f4d0cd18ec49d3745059a48c1e51831fd34c9 100644
--- a/ptx_nmasks.cc
+++ b/ptx_nmasks.cc
@@ -42,8 +42,7 @@ void nmasks()
   Seedmanager seedmanager(counter);
 
   for(unsigned int i=0;i<seeds.size();i++){
-    if(i>0)
-      stline.pop_waymasks();
+    stline.clear_waymasks();
     for(unsigned int j=0;j<seeds.size();j++){
       if(j!=i)
 	stline.add_waymask(seeds[j]);
diff --git a/ptx_seedmask.cc b/ptx_seedmask.cc
index c66f0348adc5f9bc38f1b54f29f6771d5e9cf573..d77365d61a01f7efc9328e94b53f2fd6a2d661c0 100644
--- a/ptx_seedmask.cc
+++ b/ptx_seedmask.cc
@@ -30,19 +30,22 @@ void seedmask()
   seeds=NEWIMAGE::abs(seeds);
   seeds.binarise(0,seeds.max()+1,exclusive);
 
+  int keeptotal=0;
   for(int z=0;z<seeds.zsize();z++){
     cout <<"sl "<<z<<endl;
     for(int y=0;y<seeds.ysize();y++){
       for(int x=0;x<seeds.xsize();x++){
 	if(seeds(x,y,z)>0){
 	  cout <<"run"<<endl;
-	  seedmanager.run(x,y,z); 
+	  keeptotal += seedmanager.run(x,y,z); 
 	}
       }
     }
   }
-  
+
+  counter.save_total(keeptotal);  
   counter.save();
+
   cout<<"finished"<<endl;
 }
 
diff --git a/streamlines.cc b/streamlines.cc
index 341aa7e5b87c21fa4eee402cee347155b28d2635..71ea3b74cb6c68ee4b046a2192247ed2986e4e86 100644
--- a/streamlines.cc
+++ b/streamlines.cc
@@ -214,6 +214,7 @@ namespace TRACT{
     }   
     if(rubbish_passed)
       accept_path=false;
+
     return accept_path;
   }
   
@@ -548,6 +549,15 @@ namespace TRACT{
     
   }
 
+  void Counter::save_total(const int& keeptotal){
+    
+    // save total number of particles that made it through the streamlining
+    ColumnVector keeptotvec(1);
+    keeptotvec(1)=keeptotal;
+    write_ascii_matrix(keeptotvec,logger.appendDir("waytotal"));
+
+  }
+
   void Counter::save(){
     if(opts.simpleout.value()){
       save_pathdist();
@@ -612,7 +622,8 @@ namespace TRACT{
   
   }
   
-  void Seedmanager::run(const float& x,const float& y,const float& z,bool onewayonly, int fibst){
+  // this function now returns the total number of pathways that survived a streamlining (SJ)
+  int Seedmanager::run(const float& x,const float& y,const float& z,bool onewayonly, int fibst){
     //onewayonly for mesh things..
     cout <<x<<" "<<y<<" "<<z<<endl;
     if(fibst == -1){
@@ -626,6 +637,7 @@ namespace TRACT{
 	fibst=1;// fix this for > 2 fibres
     }
     
+    int nlines=0;
     for(int p=0;p<opts.nparticles.value();p++){
       if(opts.verbose.value()>1)
 	logger.setLogFile("particle"+num2str(p));
@@ -637,23 +649,25 @@ namespace TRACT{
 	  forwardflag=true;
 	  m_counter.store_path();
 	  m_counter.count_streamline();
+	  nlines++;
 	}
 	m_stline.reverse();
       }
       if(m_stline.streamline(x,y,z,m_seeddims,fibst)){
 	backwardflag=true;
 	m_counter.count_streamline();
+	//nlines++; //count twice ?
       }
      
       m_counter.clear_streamline(forwardflag,backwardflag); 
     }
     m_counter.count_seed();
     
+    return nlines;
     
   }
 
 
-
 }
   
   
diff --git a/streamlines.h b/streamlines.h
index af95f0ab0dbc2dc5e6a3b50f88332d8e384f641b..050937f4d423a2c838dc36f934f378f0cb6d6a8c 100644
--- a/streamlines.h
+++ b/streamlines.h
@@ -63,6 +63,11 @@ namespace TRACT{
       m_own_waymasks.pop_back();
       
     }
+    void clear_waymasks(){
+      // clear all waymasks
+      for(unsigned int i=0;i<m_waymasks.size();i++)
+	pop_waymasks();
+    }
     
     inline const float get_x_seed() const {return m_x_s_init;}
     inline const float get_y_seed() const {return m_y_s_init;}
@@ -165,6 +170,7 @@ namespace TRACT{
   
     void update_maskmatrix(){} //not written yet
     
+    void save_total(const int& keeptotal);
     void save();
     void save_pathdist();
     void save_pathdist(string add);
@@ -197,7 +203,7 @@ namespace TRACT{
       m_seeddims.ReSize(3);
       m_seeddims<<m_seeds.xdim()<<m_seeds.ydim()<<m_seeds.zdim();
     }
-    void run(const float& x,const float& y,const float& z,bool onewayonly=false, int fibst=-1);
+    int run(const float& x,const float& y,const float& z,bool onewayonly=false, int fibst=-1);
   };
 
 }