diff --git a/Makefile b/Makefile
index f7c2593f4a03fd59bec876aa56331eb8d51f23af..990faa5da2220f920a23f87fbcff896d2760fc6c 100644
--- a/Makefile
+++ b/Makefile
@@ -50,7 +50,7 @@ VECREGOBJS=vecreg.o
 SGEBEDPOST = bedpost bedpost_datacheck
 SGEBEDPOSTX = bedpostX bedpostX_postproc.sh bedpostX_preproc.sh bedpostX_single_slice.sh
 
-SCRIPTS = eddy_correct zeropad ${SGEBEDPOST} ${SGEBEDPOSTX}
+SCRIPTS = eddy_correct zeropad maskdyads ${SGEBEDPOST} ${SGEBEDPOSTX}
 FSCRIPTS = correct_and_average ocmr_preproc
 
 XFILES = dtifit ccops probtrack find_the_biggest medianfilter diff_pvm make_dyadic_vectors proj_thresh vecreg xfibres
diff --git a/maskdyads b/maskdyads
index de80def5dfd32e9f286903190bad1630d6ed10d2..d2dd2d0b8caa7ed4e7e19ed2bc9808efb22ade2b 100755
--- a/maskdyads
+++ b/maskdyads
@@ -22,7 +22,7 @@ if [ "$3" != "" ] ; then
 fi
 
 
-$FSLDIR/bin/avwmaths++ $f -thr $t -bin /tmp/grot
-$FSLDIR/bin/avwmaths++ $d -mul /tmp/grot ${d}_thr$t
+$FSLDIR/bin/fslmaths $f -thr $t -bin /tmp/grot
+$FSLDIR/bin/fslmaths $d -mul /tmp/grot ${d}_thr$t
 $FSLDIR/bin/imrm /tmp/grot
 
diff --git a/probtrackx.cc b/probtrackx.cc
index 4150d57d0e5ac134cef21c76ab0bd90bec94e390..816381a2d6f7f1a9ea3764c7a3e691db7d4d7238 100644
--- a/probtrackx.cc
+++ b/probtrackx.cc
@@ -32,8 +32,11 @@ int main ( int argc, char **argv ){
   if(opts.verbose.value()>0){
     opts.status();
   }
-  if(opts.mode.value()=="simple")
+  if(opts.mode.value()=="simple"){
     track();
+    return 0;
+  }
+
   string tmpin=opts.seedfile.value();
   if(fsl_imageexists(opts.seedfile.value())){ 
     if(fsl_imageexists(opts.mask2.value())){ twomasks();}
diff --git a/pt_simple.cc b/pt_simple.cc
index 8ba98583b70ff8f82a9bb9c9901f780ad18243e6..ea90070fe0ba430ee246110f62e94ed419890cef 100644
--- a/pt_simple.cc
+++ b/pt_simple.cc
@@ -201,7 +201,9 @@ void track(){
       
     } // Close Particle Number Loop    
     string thisout=opts.outfile.value()+num2str(Seeds(SN,1))+(string)"_"+num2str(Seeds(SN,2))+(string)"_"+num2str(Seeds(SN,3));
-    save_volume(prob,logger.appendDir(thisout));
-    //save_volume(prob,thisout);
+
+    save_volume(prob,thisout);
+  
   } //Close Seed number Loop
+
 }
diff --git a/ptx_simple.cc b/ptx_simple.cc
index 418c252041312119afb5d4d71545660ff3079e35..8c79bfb1d890c014d11c669af0061261b3083d9b 100644
--- a/ptx_simple.cc
+++ b/ptx_simple.cc
@@ -50,5 +50,4 @@ void track(){
     counter.reset_prob();
   } //Close Seed number Loop
 
-  //counter.save_total(keeptot);
 }
diff --git a/streamlines.h b/streamlines.h
index e908d20edad34cc296dab56238ea7b18c4dbc86f..050937f4d423a2c838dc36f934f378f0cb6d6a8c 100644
--- a/streamlines.h
+++ b/streamlines.h
@@ -93,7 +93,7 @@ namespace TRACT{
     Matrix m_I;
     vector<ColumnVector> m_path;
     
-    vector<volume<float> > m_seedcounts;
+    vector<volume<int> > m_seedcounts;
     vector<volume<int> > m_targetmasks;
     vector<string> m_targetmasknames;
     vector<int> m_targflags;
diff --git a/vecreg.cc b/vecreg.cc
index 5dd4ae6b20a3947ab703a93cc6a38f889d89083a..7507fc32b34bd708db6bf99064a063a2ee6c1a9e 100755
--- a/vecreg.cc
+++ b/vecreg.cc
@@ -11,8 +11,8 @@
 
 using namespace Utilities;
 
-string title="vector_flirt (Version 1.0)\nVector Affine/non linear Tranformation with Orientation Preservation";
-string examples="vector_flirt -i <input4Dvector> -o <output4D> -t <transformation>";
+string title="vecreg (Version 1.0)\nVector Affine/non linear Tranformation with Orientation Preservation";
+string examples="vecreg -i <input4Dvector> -o <output4D> -t <transformation>";
 
 Option<bool> verbose(string("-v,--verbose"),false,
 		       string("switch on diagnostic messages"),