target masks memory saving

ptx_meshmask.cc

@@ -34,27 +34,13 @@ void meshmask()
   seeds=0;
 
 
-  ////////////////////////////////
-  //  Log& logger = LogSingleton::getInstance();
-  Streamliner stline(seeds);
-  Counter counter(seeds,stline);
-  counter.initialise();
-  Seedmanager seedmanager(counter);
-
+  
   Matrix mm_to_vox(4,4);
   mm_to_vox << -1 << 0 << 0 <<  (seeds.xsize())/2
  	    <<  0 << 0 << -1 << (seeds.zsize())/2
  	    <<  0 << 1 << 0 <<  (seeds.ysize())/2
  	    <<  0 << 0 << 0 << 1;
 
-//   mm_to_vox <<  1 << 0 << 0 <<  (seeds.xsize()-1)/2
-// 	    <<  0 << 1 << 1 << (seeds.zsize()-1)/2
-// 	    <<  0 << 0 << 1 <<  (seeds.ysize()-1)/2
-// 	    <<  0 << 0 << 0 << 1;
-
-
-//  ColumnVector mni_orig(4);
-//  mni_orig << 92 << 128 << 74 << 0;
 
 
   ColumnVector fs_coord_mm(4),xyz_vox,seeddim(3);
@@ -62,6 +48,32 @@ void meshmask()
   ColumnVector dir(3);
   int keeptotal=0;
 
+  // first fill seed with ones
+  seeds = 0;
+  for(vector<Mpoint*>::iterator i = mseeds._points.begin();i!=mseeds._points.end();i++){
+    if((*i)->get_value() > 0){
+    
+      fs_coord_mm<<(*i)->get_coord().X<<(*i)->get_coord().Y<<(*i)->get_coord().Z << 1.0; 
+      xyz_vox = mm_to_vox*fs_coord_mm;
+      
+      float x=xyz_vox(1);float y=xyz_vox(2);float z=xyz_vox(3);
+      Pt newPt(x,y,z);
+      (*i)->_update_coord = newPt;
+
+      seeds(int(round(x)),int(round(y)),int(round(z))) = 1;
+	
+    }
+  }
+
+  
+  ////////////////////////////////
+  //  Log& logger = LogSingleton::getInstance();
+  Streamliner stline(seeds);
+  Counter counter(seeds,stline);
+  counter.initialise();
+  Seedmanager seedmanager(counter);
+
+
   for(vector<Mpoint*>::iterator i = mseeds._points.begin();i!=mseeds._points.end();i++){
     if((*i)->get_value() > 0){
     

ptx_nmasks.cc

@@ -31,6 +31,11 @@ void nmasks()
   else
     read_masks(masknames,opts.seedfile.value());
 
+  if(opts.s2tout.value()){
+    cerr << "Seed_to_target not available in multiple seed tractography" << endl;
+    exit(0);
+  }
+
   for(unsigned int m=0;m<masknames.size();m++){
     read_volume(tmpvol,masknames[m]);
     tmpvol=NEWIMAGE::abs(tmpvol);