Current Version Jan 15

fslsmoothfill.cc

@@ -465,8 +465,15 @@ int do_work()
 {
   // read in images
   volume<float> invol;
-  read_volume(invol,inputname.value());
-  
+
+  try {
+    read_volume(invol,inputname.value());
+  }
+  catch(...) {
+    cerr << "smoothfill: Problem reading input image " << inputname.value() << endl;
+    exit(EXIT_FAILURE);
+  }
+
   // read reference volume and set size of invol
   read_volume(global_mask,maskname.value());
 
@@ -478,7 +485,7 @@ int do_work()
   volume<float> mask;
   mask=global_mask;
   dilall_extra(invol,mask);
-  save_volume(invol,fslbasename(outname.value())+"_init");
+  save_volume(invol,make_basename(outname.value())+"_init");
   float cost = calc_cost(invol);
   cout << "Cost is " << cost << endl;
   // generate subsampled versions of the dilated volume for spatial blurring (distance dependent)
@@ -489,8 +496,8 @@ int do_work()
   vol8 = subsample_by_2(vol4,true);
   vol16 = subsample_by_2(vol8,true);
   vol32 = subsample_by_2(vol16,true);
-  save_volume(vol2,fslbasename(outname.value())+"_vol2");
-  save_volume(vol32,fslbasename(outname.value())+"_vol32");
+  save_volume(vol2,make_basename(outname.value())+"_vol2");
+  save_volume(vol32,make_basename(outname.value())+"_vol32");
   for (int z=0; z<=invol.maxz(); z++) {
     for (int y=0; y<=invol.maxy(); y++) {
       for (int x=0; x<=invol.maxx(); x++) {
@@ -518,7 +525,7 @@ int do_work()
   if (verbose.value()) { cout << "After gradient descent" << endl; }
   
   save_volume(invol,outname.value());
-  save_volume(mask,fslbasename(outname.value())+"_idxmask");
+  save_volume(mask,make_basename(outname.value())+"_idxmask");
   
   return(EXIT_SUCCESS);
 }
@@ -563,15 +570,6 @@ int main(int argc, char *argv[])
     cerr << e.what() << endl;
   } 
 
-  volume<float>   invol;
-  try {
-    read_volume_hdr_only(invol,inputname.value());
-  }
-  catch(...) {
-    cerr << "smoothfill: Problem reading input image " << inputname.value() << endl;
-    exit(EXIT_FAILURE);
-  }
-
   return do_work();
 }
 

fslsplit.cc

@@ -50,9 +50,6 @@ int fmrib_main(int argc, char *argv[])
 
 int main(int argc,char *argv[])
 {
-
-  Tracer tr("main");
-
   string progname=argv[0];
   if (argc <= 1 || argc >= 5) 
   {