diff --git a/common/CMakeLists.txt b/common/CMakeLists.txt
index e17c4dc3..c2d5c8f5 100644
--- a/common/CMakeLists.txt
+++ b/common/CMakeLists.txt
@@ -72,6 +72,25 @@ endif()
 #=========================================================
 
 target_link_libraries(clitkCommon ${VTK_LIBRARIES} ${ITK_LIBRARIES})
+# I have some linking problems on linux if VTK 7.1.1 (at least) is built statically - It asks for Qt5::X11Extras - I do not know why
+# First workaround - link clitkCommon with Qt5::X11Extras - Qt5::X11Extras is not necessary if VTK is built dynamically
+# Second workaround - oblige the user to recompile VTK as a dynamic library (better solution)
+if(UNIX AND NOT APPLE)
+    if(vv_QT_VERSION VERSION_EQUAL "5") #5
+        if(VTK_VERSION VERSION_EQUAL "7.1.1") #7.1.1
+            #message(${VTK_DIR})
+            list(GET VTK_LIBRARIES 0 FIRST_VTK_ELEMENT)
+            #message(${FIRST_VTK_ELEMENT})
+            file(GLOB FIRST_VTK_LIB ${VTK_DIR}/../../*${FIRST_VTK_ELEMENT}*.a)
+            #message(${FIRST_VTK_LIB})
+            if(EXISTS ${FIRST_VTK_LIB})
+                message(FATAL_ERROR "VTK is built as a statically library - you need to recompile VTK and/or ITK as dynamic libraries")
+                #find_package(Qt5X11Extras REQUIRED)
+                #target_link_libraries(clitkCommon Qt5::X11Extras)
+            endif()
+        endif()
+    endif()
+endif()
 
 add_library(clitkDicomRTStruct STATIC
   clitkDicomRT_Contour.cxx
diff --git a/common/clitkCommon.h b/common/clitkCommon.h
index 37295846..7e9985db 100644
--- a/common/clitkCommon.h
+++ b/common/clitkCommon.h
@@ -76,7 +76,7 @@ namespace clitk {
   //--------------------------------------------------------------------
   // when everything goes wrong
 #define WHEREAMI "[ " << __FILE__  << " ] line " << __LINE__
-#define FATAL(a) { std::cerr << "ERROR in " << WHEREAMI << ": " << a; exit(0); }
+#define FATAL(a) { std::cerr << "ERROR in " << WHEREAMI << ": " << a << std::endl; exit(0); }
 
   //--------------------------------------------------------------------
   // GGO with modified struct name
diff --git a/common/clitkDicomRTStruct2ImageFilter.cxx b/common/clitkDicomRTStruct2ImageFilter.cxx
index 2e11fdc4..65ef9034 100644
--- a/common/clitkDicomRTStruct2ImageFilter.cxx
+++ b/common/clitkDicomRTStruct2ImageFilter.cxx
@@ -23,6 +23,7 @@
 // clitk
 #include "clitkDicomRTStruct2ImageFilter.h"
 #include "clitkImageCommon.h"
+#include "vvImageWriter.h"
 
 // vtk
 #include <vtkVersion.h>
@@ -32,6 +33,7 @@
 #include <vtkLinearExtrusionFilter.h>
 #include <vtkMetaImageWriter.h>
 #include <vtkXMLPolyDataWriter.h>
+#include <vtkTransformPolyDataFilter.h>
 
 
 //--------------------------------------------------------------------
@@ -107,13 +109,19 @@ void clitk::DicomRTStruct2ImageFilter::SetImage(vvImage::Pointer image)
 {
   if (image->GetNumberOfDimensions() != 3) {
     std::cerr << "Error. Please provide a 3D image." << std::endl;
-    exit(0);
+    exit(EXIT_FAILURE);
   }
   mSpacing.resize(3);
   mOrigin.resize(3);
   mSize.resize(3);
   mDirection.resize(3);
-  mTransformMatrix = image->GetTransform()[0]->GetMatrix();
+  //mTransformMatrix = image->GetTransform()[0]->GetMatrix();
+  mTransformMatrix = vtkSmartPointer<vtkMatrix4x4>::New();
+  for(unsigned int i=0;i<4;i++) {
+      for(unsigned int j=0;j<4;j++) {
+          mTransformMatrix->SetElement(i,j,image->GetTransform()[0]->GetMatrix()->GetElement(i,j));
+      }
+  }
   for(unsigned int i=0; i<3; i++) {
     mSpacing[i] = image->GetSpacing()[i];
     mOrigin[i] = image->GetOrigin()[i];
@@ -132,7 +140,7 @@ void clitk::DicomRTStruct2ImageFilter::SetImageFilename(std::string f)
   itk::ImageIOBase::Pointer header = clitk::readImageHeader(f);
   if (header->GetNumberOfDimensions() < 3) {
     std::cerr << "Error. Please provide a 3D image instead of " << f << std::endl;
-    exit(0);
+    exit(EXIT_FAILURE);
   }
   if (header->GetNumberOfDimensions() > 3) {
     std::cerr << "Warning dimension > 3 are ignored" << std::endl;
@@ -149,6 +157,18 @@ void clitk::DicomRTStruct2ImageFilter::SetImageFilename(std::string f)
     for(unsigned int j=0; j<3; j++)
       mDirection[i][j] = header->GetDirection(i)[j];
   }
+  //cf. AddItkImage function in vvImage.txx
+  mTransformMatrix = vtkSmartPointer<vtkMatrix4x4>::New();
+  mTransformMatrix->Identity();
+  for(unsigned int i=0; i<3; i++) {
+      double tmp = 0;
+      for(unsigned int j=0; j<3; j++) {
+          mTransformMatrix->SetElement(i,j,mDirection[i][j]);
+          tmp -= mDirection[i][j] * mOrigin[j];
+      }
+      tmp += mOrigin[i];
+      mTransformMatrix->SetElement(i,3,tmp);
+  }
 }
 //--------------------------------------------------------------------
 
@@ -182,11 +202,11 @@ void clitk::DicomRTStruct2ImageFilter::Update()
 {
   if (!mROI) {
     std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
-    exit(0);
+    exit(EXIT_FAILURE);
   }
   if (!ImageInfoIsSet()) {
     std::cerr << "Error. Please provide image info (spacing/origin) with SetImageFilename" << std::endl;
-    exit(0);
+    exit(EXIT_FAILURE);
   }
 
   // Get Mesh
@@ -206,7 +226,7 @@ void clitk::DicomRTStruct2ImageFilter::Update()
 
   // Get bounds
   double *bounds=mesh->GetBounds();
-
+  /*
   //Change mOrigin, mSize and mSpacing with respect to the directions
   // Spacing is influenced by input direction
   std::vector<double> tempSpacing;
@@ -238,7 +258,7 @@ void clitk::DicomRTStruct2ImageFilter::Update()
     }
     mSize[i] = lrint(tempSize[i]);
   }
-
+  */
   // Compute origin
   std::vector<double> origin;
   origin.resize(3);
@@ -259,7 +279,18 @@ void clitk::DicomRTStruct2ImageFilter::Update()
       extend[i] = mSize[i]-1;
     }
   }
-
+  //Apply the transform to the mesh
+  vtkSmartPointer<vtkTransform> outputLabelmapGeometryTransform = vtkSmartPointer<vtkTransform>::New();
+  outputLabelmapGeometryTransform->SetMatrix(mTransformMatrix);
+  // Apparently the inverse is wrong...
+  //outputLabelmapGeometryTransform->Inverse();
+  vtkSmartPointer<vtkTransformPolyDataFilter> transformPolyDataFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
+#if VTK_MAJOR_VERSION <= 5
+  transformPolyDataFilter->SetInput(mesh);
+#else
+  transformPolyDataFilter->SetInputData(mesh);
+#endif
+  transformPolyDataFilter->SetTransform(outputLabelmapGeometryTransform);
   // Create new output image
   mBinaryImage = vtkSmartPointer<vtkImageData>::New();
 #if VTK_MAJOR_VERSION <= 5
@@ -281,11 +312,7 @@ void clitk::DicomRTStruct2ImageFilter::Update()
 
   // Extrude
   vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
-#if VTK_MAJOR_VERSION <= 5
-  extrude->SetInput(mesh);
-#else
-  extrude->SetInputData(mesh);
-#endif
+  extrude->SetInputConnection(transformPolyDataFilter->GetOutputPort());
   ///We extrude in the -slice_spacing direction to respect the FOCAL convention (NEEDED !)
   extrude->SetVector(0, 0, -mSpacing[2]);
 
@@ -295,11 +322,7 @@ void clitk::DicomRTStruct2ImageFilter::Update()
   //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
   sts->SetTolerance(0);
   sts->SetInformationInput(mBinaryImage);
-#if VTK_MAJOR_VERSION <= 5
-  sts->SetInput(extrude->GetOutput());
-#else
   sts->SetInputConnection(extrude->GetOutputPort(0));
-#endif
   //sts->SetInput(mesh);
 
   vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
@@ -316,22 +339,26 @@ void clitk::DicomRTStruct2ImageFilter::Update()
   stencil->ReverseStencilOn();
   stencil->Update();
 
-  /*
-  vtkSmartPointer<vtkMetaImageWriter> w = vtkSmartPointer<vtkMetaImageWriter>::New();
-  w->SetInput(stencil->GetOutput());
-  w->SetFileName("binary2.mhd");
-  w->Write();
-  */
-
   mBinaryImage->ShallowCopy(stencil->GetOutput());
 
+  vvImage::Pointer vvBinaryImage = vvImage::New();
+  vtkSmartPointer<vtkTransform> vvBinaryImageT = vtkSmartPointer<vtkTransform>::New();
+  vvBinaryImageT->SetMatrix(mTransformMatrix);
+  vvBinaryImage->AddVtkImage(mBinaryImage, vvBinaryImageT);
+
   if (mWriteOutput) {
-    typedef itk::Image<unsigned char, 3> ImageType;
-    typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
-    ConnectorType::Pointer connector = ConnectorType::New();
-    connector->SetInput(GetOutput());
-    connector->Update();
-    clitk::writeImage<ImageType>(connector->GetOutput(), mOutputFilename);
+    //typedef itk::Image<unsigned char, 3> ImageType;
+    //typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
+    //ConnectorType::Pointer connector = ConnectorType::New();
+    //connector->SetInput(GetOutput());
+    //connector->Update();
+    //clitk::writeImage<ImageType>(connector->GetOutput(), mOutputFilename);
+    vvImageWriter::Pointer writer = vvImageWriter::New();
+    writer->SetInput(vvBinaryImage);
+    if (!vvBinaryImage->GetTransform().empty())
+        writer->SetSaveTransform(true);
+    writer->SetOutputFileName(mOutputFilename);
+    writer->Update();
   }
 }
 //--------------------------------------------------------------------
@@ -341,7 +368,10 @@ void clitk::DicomRTStruct2ImageFilter::Update()
 //--------------------------------------------------------------------
 vtkImageData * clitk::DicomRTStruct2ImageFilter::GetOutput()
 {
-  assert(mBinaryImage);
+  //assert(mBinaryImage);
+  if (mBinaryImage == NULL) {
+      FATAL("The binary RTStruct image is NULL");
+  }
   return mBinaryImage;
 }
 //--------------------------------------------------------------------
diff --git a/common/clitkDicomRTStruct2ImageFilter.h b/common/clitkDicomRTStruct2ImageFilter.h
index f93cbb29..9ba08453 100644
--- a/common/clitkDicomRTStruct2ImageFilter.h
+++ b/common/clitkDicomRTStruct2ImageFilter.h
@@ -72,17 +72,17 @@ namespace clitk {
 
 //--------------------------------------------------------------------
 
-template <int Dimension> 
-typename itk::Image<unsigned char,Dimension>::ConstPointer clitk::DicomRTStruct2ImageFilter::GetITKOutput()
-{
-  assert(mBinaryImage);
-  typedef itk::Image<unsigned char,Dimension> ConnectorImageType;
-  typedef itk::VTKImageToImageFilter <ConnectorImageType> ConnectorType;
-  typename ConnectorType::Pointer connector = ConnectorType::New();
-  connector->SetInput(mBinaryImage);
-  connector->Update();
-  return connector->GetOutput();
-}
+//template <int Dimension>
+//typename itk::Image<unsigned char,Dimension>::ConstPointer clitk::DicomRTStruct2ImageFilter::GetITKOutput()
+//{
+//  assert(mBinaryImage);
+//  typedef itk::Image<unsigned char,Dimension> ConnectorImageType;
+//  typedef itk::VTKImageToImageFilter <ConnectorImageType> ConnectorType;
+//  typename ConnectorType::Pointer connector = ConnectorType::New();
+//  connector->SetInput(mBinaryImage);
+//  connector->Update();
+//  return connector->GetOutput();
+//}
 //--------------------------------------------------------------------
 #endif // CLITKDICOMRT_TRUCT2IMAGEFILTER_H
 
diff --git a/common/clitkDicomRT_Contour.cxx b/common/clitkDicomRT_Contour.cxx
index 9a5042be..89ff7755 100644
--- a/common/clitkDicomRT_Contour.cxx
+++ b/common/clitkDicomRT_Contour.cxx
@@ -82,11 +82,7 @@ void clitk::DicomRT_Contour::UpdateDicomItem()
     double * p = mData->GetPoint(i);
     points[i*3] = p[0];
     points[i*3+1] = p[1];
-#if VTK_MAJOR_VERSION <= 5
-    points[i*3+1] = p[2];
-#else
     points[i*3+1] = p[2]-0.5;
-#endif
   }
 
   // Get attribute
@@ -96,7 +92,7 @@ void clitk::DicomRT_Contour::UpdateDicomItem()
   at.SetFromDataElement( contourdata );
 
   // Set attribute
-  at.SetValues(&points[0], points.size(), false);
+  at.SetValues(&points[0], points.size());
   DD(at.GetValues()[0]);
   
   DD("replace");
@@ -151,7 +147,10 @@ bool clitk::DicomRT_Contour::Read(gdcm::Item * item)
   at.SetFromDataElement( contourdata );
   const double* points = at.GetValues();
   //  unsigned int npts = at.GetNumberOfValues() / 3;
-  assert(at.GetNumberOfValues() == static_cast<unsigned int>(mNbOfPoints)*3);
+  //assert(at.GetNumberOfValues() == static_cast<unsigned int>(mNbOfPoints)*3);
+  if (at.GetNumberOfValues() != static_cast<unsigned int>(mNbOfPoints)*3) {
+      FATAL("The number of contour points is inconsistent with the number of triplets defining the contour");
+  }
 
   // Organize values
   mData = vtkSmartPointer<vtkPoints>::New();
@@ -161,19 +160,16 @@ bool clitk::DicomRT_Contour::Read(gdcm::Item * item)
     double p[3];
     p[0] = points[i*3];
     p[1] = points[i*3+1];
-#if VTK_MAJOR_VERSION <= 5
-    p[2] = points[i*3+2];
-#else
     p[2] = points[i*3+2]+0.5;
-#endif
     mData->SetPoint(i, p);
     if (mZ == -1) mZ = p[2];
-    if (p[2] != mZ) {
+    if (std::fabs(p[2] - mZ) > mTolerance) {
       DD(i);
       DD(p[2]);
       DD(mZ);
-      std::cout << "ERROR ! contour not in the same slice" << std::endl;
-      assert(p[2] == mZ);
+      //std::cout << "ERROR ! contour not in the same slice" << std::endl;
+      //assert(p[2] == mZ);
+      FATAL("ERROR ! contour not in the same slice");
     }
   }
 
@@ -202,7 +198,10 @@ bool clitk::DicomRT_Contour::Read(gdcm::SQItem * item)
 
   // Read values [Contour Data]
   std::vector<float> points = parse_string<float>(item->GetEntryValue(0x3006,0x0050),'\\');
-  assert(points.size() == static_cast<unsigned int>(mNbOfPoints)*3);
+  //assert(points.size() == static_cast<unsigned int>(mNbOfPoints)*3);
+  if (points.size() != static_cast<unsigned int>(mNbOfPoints)*3) {
+      FATAL("The number of contour points is inconsistent with the number of triplets defining the contour");
+  }
 
   // Organize values
   mData = vtkSmartPointer<vtkPoints>::New();
@@ -212,19 +211,16 @@ bool clitk::DicomRT_Contour::Read(gdcm::SQItem * item)
     double p[3];
     p[0] = points[i*3];
     p[1] = points[i*3+1];
-#if VTK_MAJOR_VERSION <= 5
-    p[2] = points[i*3+2];
-#else
     p[2] = points[i*3+2]+0.5;
-#endif
     mData->SetPoint(i, p);
     if (mZ == -1) mZ = p[2];
-    if (p[2] != mZ) {
+    if (std::fabs(p[2] - mZ) > mTolerance) {
       DD(i);
       DD(p[2]);
       DD(mZ);
-      std::cout << "ERROR ! contour not in the same slice" << std::endl;
-      assert(p[2] == mZ);
+      //std::cout << "ERROR ! contour not in the same slice" << std::endl;
+      //assert(p[2] == mZ);
+      FATAL("ERROR ! contour not in the same slice");
     }
   }
 
@@ -259,8 +255,17 @@ void clitk::DicomRT_Contour::SetTransformMatrix(vtkMatrix4x4* matrix)
   mTransformMatrix = matrix;
 }
 //--------------------------------------------------------------------
-
-
+//--------------------------------------------------------------------
+double clitk::DicomRT_Contour::GetTolerance()
+{
+  return mTolerance;
+}
+//--------------------------------------------------------------------
+void clitk::DicomRT_Contour::SetTolerance(double tol)
+{
+  mTolerance = tol;
+}
+//--------------------------------------------------------------------
 //--------------------------------------------------------------------
 void clitk::DicomRT_Contour::ComputeMeshFromDataPoints()
 {
@@ -271,10 +276,10 @@ void clitk::DicomRT_Contour::ComputeMeshFromDataPoints()
   mMesh->SetPoints(mPoints);
   vtkIdType ids[2];
   for (unsigned int idx=0 ; idx<mNbOfPoints ; idx++) {
-    double pointIn[4];
-    for (unsigned int j=0 ; j<3; ++j)
-      pointIn[j] = mData->GetPoint(idx)[j];
-    pointIn[3] = 1.0;
+    //double pointIn[4];
+    //for (unsigned int j=0 ; j<3; ++j)
+    //  pointIn[j] = mData->GetPoint(idx)[j];
+    //pointIn[3] = 1.0;
     /*double pointOut[4];
     mTransformMatrix->MultiplyPoint(pointIn, pointOut);
     std::cout << pointOut[0] << " " << pointOut[1] << " " << pointOut[2] << " " << pointOut[3] << std::endl;
diff --git a/common/clitkDicomRT_Contour.h b/common/clitkDicomRT_Contour.h
index ab6db0d2..389bbdd8 100644
--- a/common/clitkDicomRT_Contour.h
+++ b/common/clitkDicomRT_Contour.h
@@ -56,6 +56,8 @@ class DicomRT_Contour : public itk::LightObject{
   vtkPoints * GetPoints() {return mData;}
   double GetZ() const {return mZ;}
   void SetTransformMatrix(vtkMatrix4x4* matrix);
+  double GetTolerance();
+  void SetTolerance(double tol);
   
   
 protected:
@@ -70,6 +72,7 @@ class DicomRT_Contour : public itk::LightObject{
   bool mMeshIsUpToDate;
   ///Z location of the contour
   double mZ;
+  double mTolerance;
   
 #if GDCM_MAJOR_VERSION >= 2
   gdcm::Item * mItem;
diff --git a/common/clitkDicomRT_ROI.cxx b/common/clitkDicomRT_ROI.cxx
index af8bee67..bc2a1c54 100644
--- a/common/clitkDicomRT_ROI.cxx
+++ b/common/clitkDicomRT_ROI.cxx
@@ -149,7 +149,7 @@ double clitk::DicomRT_ROI::GetForegroundValueLabelImage() const
 
 //--------------------------------------------------------------------
 #if GDCM_MAJOR_VERSION >= 2
-bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
+bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour, double tol)
 {
   //FATAL("Error : compile vv with itk4 + external gdcm");
   // Keep dicom item
@@ -186,7 +186,10 @@ bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
   // ROI Color [ROI Display Color]
   gdcm::Attribute<0x3006,0x002a> color = {};
   color.SetFromDataSet( nestedds );
-  assert( color.GetNumberOfValues() == 3 );
+  //assert( color.GetNumberOfValues() == 3 );
+  if (color.GetNumberOfValues() != 3) {
+      FATAL("The RGB triplet color representation for ROI is not a triplet");
+  }
   mColor[0] = color.GetValue(0);
   mColor[1] = color.GetValue(1);
   mColor[2] = color.GetValue(2);
@@ -212,6 +215,7 @@ bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
     {
       gdcm::Item & j = sqi2->GetItem(i+1); // Item start at #1
       DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+      c->SetTolerance(tol);
       c->SetTransformMatrix(mTransformMatrix);
       bool b = c->Read(&j);
       if (b) {
@@ -222,7 +226,7 @@ bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
   return true;
 }
 #else
-void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem * item)
+void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem * item, double tol)
 {
   // ROI number [Referenced ROI Number]
   mNumber = atoi(item->GetEntryValue(0x3006,0x0084).c_str());
@@ -239,6 +243,7 @@ void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem *
     int i=0;
     for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) {
       DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+      c->SetTolerance(tol);
       c->SetTransformMatrix(mTransformMatrix);
       bool b = c->Read(j);
       if (b) {
@@ -506,7 +511,7 @@ void clitk::DicomRT_ROI::ComputeContoursFromImage()
 
 //--------------------------------------------------------------------
 #if CLITK_USE_SYSTEM_GDCM == 1
-void clitk::DicomRT_ROI::Read(vtkSmartPointer<vtkGDCMPolyDataReader> & reader, int roiindex)
+void clitk::DicomRT_ROI::Read(vtkSmartPointer<vtkGDCMPolyDataReader> & reader, int roiindex, double tol)
 {
   vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
   
@@ -529,6 +534,7 @@ void clitk::DicomRT_ROI::Read(vtkSmartPointer<vtkGDCMPolyDataReader> & reader, i
   // Get the contour
   mMesh =  reader->GetOutput(roiindex);  
   DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+  c->SetTolerance(tol);
   c->SetTransformMatrix(mTransformMatrix);
   c->SetMesh(mMesh); // FIXME no GetZ, not GetPoints  
   mMeshIsUpToDate = true;
diff --git a/common/clitkDicomRT_ROI.h b/common/clitkDicomRT_ROI.h
index b4179332..d7c5a981 100644
--- a/common/clitkDicomRT_ROI.h
+++ b/common/clitkDicomRT_ROI.h
@@ -80,14 +80,14 @@ class DicomRT_ROI : public itk::LightObject
 
   // Read from DICOM RT STRUCT
 #if GDCM_MAJOR_VERSION >= 2
-  bool Read(gdcm::Item * itemInfo, gdcm::Item * itemContour);
+  bool Read(gdcm::Item * itemInfo, gdcm::Item * itemContour, double tol);
   void UpdateDicomItem();
 #else
-  void Read(std::map<int, std::string> & rois, gdcm::SQItem * item);
+  void Read(std::map<int, std::string> & rois, gdcm::SQItem * item, double tol);
 #endif
 
 #if CLITK_USE_SYSTEM_GDCM == 1
-  void Read(vtkSmartPointer<vtkGDCMPolyDataReader> & reader, int roiindex);
+  void Read(vtkSmartPointer<vtkGDCMPolyDataReader> & reader, int roiindex, double tol);
 #endif
 
 protected:
diff --git a/common/clitkDicomRT_StructureSet.cxx b/common/clitkDicomRT_StructureSet.cxx
index a845ef55..68a5c216 100644
--- a/common/clitkDicomRT_StructureSet.cxx
+++ b/common/clitkDicomRT_StructureSet.cxx
@@ -317,7 +317,7 @@ void clitk::DicomRT_StructureSet::Write(const std::string & filename)
 
 
 //--------------------------------------------------------------------
-void clitk::DicomRT_StructureSet::Read(const std::string & filename)
+void clitk::DicomRT_StructureSet::Read(const std::string & filename, double tol)
 {
 
 //Try to avoid to use extern GDCM library
@@ -397,7 +397,10 @@ void clitk::DicomRT_StructureSet::Read(const std::string & filename)
   //const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
   mROIInfoSequenceOfItems = ssroisq.GetValueAsSQ();
   gdcm::SmartPointer<gdcm::SequenceOfItems> & roi_seq = mROIInfoSequenceOfItems;
-  assert(roi_seq); // TODO error message
+  //assert(roi_seq); // TODO error message
+  if (roi_seq == NULL) {
+      FATAL("The Structure Set ROI Sequence tag does not contain any value");
+  }
   for(unsigned int ridx = 0; ridx < roi_seq->GetNumberOfItems(); ++ridx)
     {
     gdcm::Item & item = roi_seq->GetItem( ridx + 1); // Item starts at 1
@@ -429,7 +432,10 @@ void clitk::DicomRT_StructureSet::Read(const std::string & filename)
   //const gdcm::DataElement &roicsq = ds.GetDataElement( troicsq );
   gdcm::SmartPointer<gdcm::SequenceOfItems> roi_contour_seq = roicsq.GetValueAsSQ();
   mROIContoursSequenceOfItems = roi_contour_seq;
-  assert(roi_contour_seq); // TODO error message
+  //assert(roi_contour_seq); // TODO error message
+  if (roi_contour_seq == NULL) {
+      FATAL("The ROI Contour Sequence tag does not contain any value");
+  }
   for(unsigned int ridx = 0; ridx < roi_contour_seq->GetNumberOfItems(); ++ridx) {
     gdcm::Item & item = roi_contour_seq->GetItem( ridx + 1); // Item starts at 1
     // ROI number [Referenced ROI Number]
@@ -448,7 +454,7 @@ void clitk::DicomRT_StructureSet::Read(const std::string & filename)
     // Create the roi
     mROIs[nb] = DicomRT_ROI::New();
     mROIs[nb]->SetTransformMatrix(mTransformMatrix);
-    mROIs[nb]->Read(mMapOfROIInfo[nb], mMapOfROIContours[nb]);
+    mROIs[nb]->Read(mMapOfROIInfo[nb], mMapOfROIContours[nb], tol);
   }
     
   return;
@@ -534,5 +540,60 @@ int clitk::DicomRT_StructureSet::AddBinaryImageAsNewROI(vvImage * im, std::strin
   return max;
 }
 //--------------------------------------------------------------------
-
-
+void clitk::DicomRT_StructureSet::Anon(const std::string & filename, const std::string & outputfilename, const std::string newPID)
+{
+    bool isDRTStruct = this->IsDicomRTStruct(filename);
+    if(isDRTStruct == false) {
+        std::cerr << "Your file is not a proper RTStruct" << std::endl;
+        return;
+    }
+#if GDCM_MAJOR_VERSION >= 2
+    gdcm::DataSet & ds = mFile->GetDataSet();
+    //Patient name = 0010,0010
+    gdcm::Attribute<0x0010,0x0010> patientNameA;
+    patientNameA.SetFromDataSet(ds);
+    std::string patientName = patientNameA.GetValue();
+    std::cout<<"Patient name="<< patientName <<std::endl;
+    std::string delimiter = "^";
+    std::string newPatientName;
+    newPatientName = patientName.substr(0,1) + patientName.substr(patientName.find(delimiter)+1,1);
+    std::cout<<"New patient name="<< newPatientName <<std::endl;
+    patientNameA.SetValue(newPatientName);
+    ds.Replace(patientNameA.GetAsDataElement());
+    //Patient birthdate = 0010,0030
+    gdcm::Attribute<0x0010,0x0030> patientBirthdateA;
+    patientBirthdateA.SetFromDataSet(ds);
+    std::string patientBirthdate = patientBirthdateA.GetValue();
+    std::cout<<"Patient birthday="<< patientBirthdate <<std::endl;
+    std::string newPatientBirthdate;
+    newPatientBirthdate = patientBirthdate.substr(0, patientBirthdate.length()-2);
+    std::cout<<"New patient birthday="<< newPatientBirthdate <<std::endl;
+    patientBirthdateA.SetValue(newPatientBirthdate);
+    ds.Replace(patientBirthdateA.GetAsDataElement());
+    //Patient id = 0010,0020
+    gdcm::Attribute<0x0010,0x0020> patientIDA;
+    patientIDA.SetFromDataSet(ds);
+    std::string patientID = patientIDA.GetValue();
+    std::cout<<"Patient ID="<< patientID <<std::endl;
+    std::cout<<"New patient id="<< newPID <<std::endl;
+    patientIDA.SetValue(newPID);
+    ds.Replace(patientIDA.GetAsDataElement());
+    //Patient address = 0010,1040
+    gdcm::Attribute<0x0010,0x1040> patientAddressA;
+    patientAddressA.SetFromDataSet(ds);
+    std::string patientAddress = patientAddressA.GetValue();
+    std::cout<<"Patient address="<< patientAddress <<std::endl;
+    std::cout<<"New patient address="<< "" <<std::endl;
+    patientAddressA.SetValue("");
+    ds.Replace(patientAddressA.GetAsDataElement());
+    // Write dicom
+    gdcm::Writer writer;
+    //writer.CheckFileMetaInformationOff();
+    writer.SetFileName(outputfilename.c_str());
+    writer.SetFile(*mFile);
+    writer.Write();
+#else
+    FATAL("Sorry not compatible with GDCM1, use GDCM2");
+#endif
+}
+//--------------------------------------------------------------------
diff --git a/common/clitkDicomRT_StructureSet.h b/common/clitkDicomRT_StructureSet.h
index dff4d752..2bccf593 100644
--- a/common/clitkDicomRT_StructureSet.h
+++ b/common/clitkDicomRT_StructureSet.h
@@ -60,10 +60,13 @@ class DicomRT_StructureSet : public itk::LightObject{
   typedef ROIMapContainer::const_iterator ROIConstIteratorType;
 
   void Print(std::ostream & os = std::cout) const;
-  void Read(const std::string & filename);
+  void Read(const std::string & filename, double tol);
   void SetTransformMatrix(vtkMatrix4x4* matrix);
   bool IsDicomRTStruct(const std::string & filename);
   void Write(const std::string & filename);
+  void Anon(const std::string & filename,
+            const std::string & outputfilename,
+            const std::string newPID);
 
   clitk::DicomRT_ROI * GetROIFromROINumber(int n);
   clitk::DicomRT_ROI* GetROIFromROIName(const std::string& name);
diff --git a/common/clitkImageCommon.h b/common/clitkImageCommon.h
index 32bba491..a849650a 100644
--- a/common/clitkImageCommon.h
+++ b/common/clitkImageCommon.h
@@ -90,6 +90,14 @@ void ComputeWeightsOfEachClasses(const typename InputImageType::Pointer & input,
 
 //--------------------------------------------------------------------
 template<class ImageType1, class ImageType2>
+bool HaveSameOrigin(typename ImageType1::ConstPointer A,
+                     typename ImageType2::ConstPointer B);
+
+template<class ImageType1, class ImageType2>
+bool HaveSameOrigin(typename ImageType1::Pointer A,
+                     typename ImageType2::Pointer B);
+//--------------------------------------------------------------------
+template<class ImageType1, class ImageType2>
 bool HaveSameSpacing(typename ImageType1::ConstPointer A,
                      typename ImageType2::ConstPointer B);
 
diff --git a/common/clitkImageCommon.txx b/common/clitkImageCommon.txx
index a07c66f0..56e1ed81 100644
--- a/common/clitkImageCommon.txx
+++ b/common/clitkImageCommon.txx
@@ -308,6 +308,28 @@ void ComputeWeightsOfEachClasses(const typename InputImageType::Pointer & input,
 }
 //--------------------------------------------------------------------
 
+//--------------------------------------------------------------------
+template<class ImageType1, class ImageType2>
+bool HaveSameOrigin(typename ImageType1::ConstPointer A,
+                    typename ImageType2::ConstPointer B)
+{
+  if (A->GetImageDimension() != B->GetImageDimension()) return false;
+  for(unsigned int i=0; i<A->GetImageDimension(); i++) {
+    if (A->GetOrigin()[i] != B->GetOrigin()[i]) return false;
+  }
+  return true;
+}
+template<class ImageType1, class ImageType2>
+bool HaveSameOrigin(typename ImageType1::Pointer A,
+                    typename ImageType2::Pointer B)
+{
+  if (A->GetImageDimension() != B->GetImageDimension()) return false;
+  for(unsigned int i=0; i<A->GetImageDimension(); i++) {
+    if (A->GetOrigin()[i] != B->GetOrigin()[i]) return false;
+  }
+  return true;
+}
+//--------------------------------------------------------------------
 
 //--------------------------------------------------------------------
 template<class ImageType1, class ImageType2>
diff --git a/common/clitkTransformUtilities.cxx b/common/clitkTransformUtilities.cxx
index 832d5983..433111bc 100644
--- a/common/clitkTransformUtilities.cxx
+++ b/common/clitkTransformUtilities.cxx
@@ -37,6 +37,23 @@ GetForwardAffineMatrix<3>(itk::Array<double> transformParameters)
   return GetForwardAffineMatrix3D(transformParameters);
 }
 
+//--------------------------------------------------------------------
+template < >
+itk::Matrix<double, 5, 5>
+GetForwardAffineMatrix<4>(itk::Array<double> transformParameters)
+{
+  itk::Matrix<double, 5, 5> matrix;
+  matrix.SetIdentity();
+  itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
+  for (unsigned int i = 0; i < 3; ++i)
+    for (unsigned int j = 0; j < 3; ++j)
+      matrix[i][j] = tmp[i][j];
+  for (unsigned int i = 0; i < 3; ++i)
+    matrix[i][4] = tmp[i][3];
+  //
+  return matrix;
+}
+
 //--------------------------------------------------------------------
 template < >
 itk::Matrix<double, 3, 3>
diff --git a/common/vvImage.cxx b/common/vvImage.cxx
index f75d3212..3fe5df2d 100644
--- a/common/vvImage.cxx
+++ b/common/vvImage.cxx
@@ -70,7 +70,7 @@ void vvImage::Reset()
 //--------------------------------------------------------------------
 
 //--------------------------------------------------------------------
-void vvImage::AddVtkImage(vtkImageData* input)
+void vvImage::AddVtkImage(vtkImageData* input, vtkSmartPointer<vtkTransform> transform)
 {
   // RP: 20/12/2011
   // Note that we're simply adding a new image to the vector.
@@ -90,6 +90,7 @@ void vvImage::AddVtkImage(vtkImageData* input)
     mImageDimension = 1;
   
   mVtkImages.push_back(input);
+  mTransform.push_back(transform);
 }
 
 //--------------------------------------------------------------------
diff --git a/common/vvImage.h b/common/vvImage.h
index cbb0284c..81c2219b 100644
--- a/common/vvImage.h
+++ b/common/vvImage.h
@@ -47,7 +47,7 @@ public :
   void Init();
   void Reset();
   template<class TItkImageType> void AddItkImage(TItkImageType *input);
-  void AddVtkImage(vtkImageData* input);
+  void AddVtkImage(vtkImageData* input, vtkSmartPointer<vtkTransform> transform);
   const std::vector<vtkImageData*>& GetVTKImages();
   vtkImageData* GetFirstVTKImageData();
   int GetNumberOfDimensions() const;
diff --git a/common/vvImageReader.txx b/common/vvImageReader.txx
index 2eba11c8..20fe59b8 100644
--- a/common/vvImageReader.txx
+++ b/common/vvImageReader.txx
@@ -200,10 +200,10 @@ void vvImageReader::UpdateWithDimAndInputPixelType()
       }
     }
 
-/*    if (VImageDimension == 4)
-      mType == VECTORPIXELIMAGEWITHTIME;
+    if (VImageDimension == 4)
+      mType = VECTORPIXELIMAGEWITHTIME;
     else
-      mType == VECTORPIXELIMAGE;*/
+      mType = VECTORPIXELIMAGE;
 
     try {
       mImage = vvImageFromITK<VImageDimension,InputPixelType>(output, mType == VECTORPIXELIMAGEWITHTIME);
@@ -316,4 +316,3 @@ void vvImageReader::UpdateWithDimAndInputVectorPixelType()
 //----------------------------------------------------------------------------
 
 #endif /* end #define vvImageReader_TXX */
-
diff --git a/itk/clitkCropLikeImageFilter.txx b/itk/clitkCropLikeImageFilter.txx
index e7e342fc..184e669a 100644
--- a/itk/clitkCropLikeImageFilter.txx
+++ b/itk/clitkCropLikeImageFilter.txx
@@ -101,11 +101,11 @@ GenerateOutputInformation() {
   // Get input info
   typename ImageType::SizeType likeSize;
   typename ImageType::IndexType likeStart;
-  typename ImageType::PointType likeOrigin;  
-  typename ImageType::SpacingType likeSpacing;  
+  typename ImageType::PointType likeOrigin;
+  typename ImageType::SpacingType likeSpacing;
   typename ImageType::DirectionType likeDirection;
   typename ImageType::DirectionType like_invDirection;
-  if (m_LikeImage) {   
+  if (m_LikeImage) {
     likeSize = m_LikeImage->GetLargestPossibleRegion().GetSize();
     likeStart = m_LikeImage->GetLargestPossibleRegion().GetIndex();
     likeOrigin = m_LikeImage->GetOrigin();
@@ -126,10 +126,10 @@ GenerateOutputInformation() {
         likeSpacing[i] = header->GetSpacing(i);
         for(unsigned int j=0; j<ImageType::ImageDimension; j++)
             likeDirection[i][j] = header->GetDirection(i)[j];
-       }
+      }
       //I don't know really why I need the inverse...
       like_invDirection = likeDirection.GetInverse();
-      }
+    }
     else {
       clitkExceptionMacro("You should provide SetCropLikeFilename or SetCropLike to CropLikeImageFilter");
     }
@@ -159,7 +159,7 @@ GenerateOutputInformation() {
   output->SetRegions(m_OutputRegion);
   output->SetRequestedRegion(m_OutputRegion);
   output->SetBufferedRegion(m_OutputRegion);
-  output->SetSpacing(likeSpacing);  
+  output->SetSpacing(likeSpacing);
   output->SetOrigin(likeOrigin);
   output->SetDirection(like_invDirection);
   output->Allocate(); // Needed ?
diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index 75e5ef35..432b9c32 100644
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -1430,8 +1430,9 @@ namespace clitk {
     typename InfoFilterType::Pointer indexChangeFilter = InfoFilterType::New(); 
     indexChangeFilter->ChangeRegionOn(); 
     // The next line is commented because not exist in itk 3
-    // typename InfoFilterType::OutputImageOffsetValueType indexShift[3];
-    long indexShift[3];
+    typename InfoFilterType::OutputImageOffsetValueType indexShift[3];
+    // does not compile on windows - uncomment the previous line
+    // long indexShift[3];
     typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
     for(uint i=0;i<ImageType::ImageDimension; i++)
       indexShift[i] = (index[i]<0 ? -index[i]:0);
diff --git a/registration/CMakeLists.txt b/registration/CMakeLists.txt
index 91f1e261..aaad5c67 100644
--- a/registration/CMakeLists.txt
+++ b/registration/CMakeLists.txt
@@ -8,6 +8,10 @@ if(CLITK_BUILD_REGISTRATION)
                 ${clitkAffineRegistration_GGO_C}
                 clitkLBFGSBOptimizer.cxx
                 clitkGenericAffineTransform.cxx)
+    set_target_properties(clitkAffineRegistrationLib PROPERTIES
+                          CXX_STANDARD 11
+                          CXX_STANDARD_REQUIRED ON
+                          CXX_EXTENSIONS OFF)
 
 #=========================================================
 
@@ -25,6 +29,10 @@ if(CLITK_BUILD_REGISTRATION)
     add_executable(clitkBLUTDIR  clitkBLUTDIR.cxx clitkBLUTDIRGenericFilter.cxx ${clitkBLUTDIR_GGO_C} clitkLBFGSBOptimizer.cxx )
     target_link_libraries(clitkBLUTDIR clitkCommon)
     set(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkBLUTDIR)
+    set_target_properties(clitkBLUTDIR PROPERTIES
+                          CXX_STANDARD 11
+                          CXX_STANDARD_REQUIRED ON
+                          CXX_EXTENSIONS OFF)
 
 
     ############################## registration-related tools to process points, bsplines, vf and image pyramids
diff --git a/registration/clitkCorrelationRatioImageToImageMetric.txx b/registration/clitkCorrelationRatioImageToImageMetric.txx
index d76f020e..d554cba7 100644
--- a/registration/clitkCorrelationRatioImageToImageMetric.txx
+++ b/registration/clitkCorrelationRatioImageToImageMetric.txx
@@ -33,6 +33,7 @@
 #include "itkImageRegionConstIteratorWithIndex.h"
 #include "itkImageRegionConstIterator.h"
 #include "itkImageRegionIterator.h"
+#include <cmath>
 
 namespace clitk
 {
diff --git a/registration/clitkOptNormalizedCorrelationImageToImageMetric.h b/registration/clitkOptNormalizedCorrelationImageToImageMetric.h
index ea065716..7da08a81 100644
--- a/registration/clitkOptNormalizedCorrelationImageToImageMetric.h
+++ b/registration/clitkOptNormalizedCorrelationImageToImageMetric.h
@@ -128,14 +128,14 @@ class ITK_EXPORT NormalizedCorrelationImageToImageMetric :
   MeasureType ComputeSums( const ParametersType & parameters ) const;
 
 
-  inline bool GetValueThreadProcessSample( unsigned int threadID,
-      unsigned long fixedImageSample,
+  inline bool GetValueThreadProcessSample( itk::ThreadIdType threadID,
+      itk::SizeValueType fixedImageSample,
       const MovingImagePointType & mappedPoint,
       double movingImageValue ) const ITK_OVERRIDE;
 
 
-  inline bool GetValueAndDerivativeThreadProcessSample( unsigned int threadID,
-      unsigned long fixedImageSample,
+  inline bool GetValueAndDerivativeThreadProcessSample( itk::ThreadIdType threadID,
+      itk::SizeValueType fixedImageSample,
       const MovingImagePointType & mappedPoint,
       double movingImageValue,
       const ImageDerivativesType &
diff --git a/registration/clitkOptNormalizedCorrelationImageToImageMetric.txx b/registration/clitkOptNormalizedCorrelationImageToImageMetric.txx
index fbb52ca4..061ed011 100644
--- a/registration/clitkOptNormalizedCorrelationImageToImageMetric.txx
+++ b/registration/clitkOptNormalizedCorrelationImageToImageMetric.txx
@@ -211,8 +211,8 @@ template < class TFixedImage, class TMovingImage  >
 inline bool
 NormalizedCorrelationImageToImageMetric<TFixedImage,TMovingImage>
 ::GetValueThreadProcessSample(
-  unsigned int threadID,
-  unsigned long fixedImageSample,
+  itk::ThreadIdType threadID,
+  itk::SizeValueType fixedImageSample,
   const MovingImagePointType & itkNotUsed(mappedPoint),
   double movingImageValue) const
 {
@@ -416,8 +416,8 @@ template < class TFixedImage, class TMovingImage  >
 inline bool
 NormalizedCorrelationImageToImageMetric<TFixedImage,TMovingImage>
 ::GetValueAndDerivativeThreadProcessSample(
-  unsigned int threadID,
-  unsigned long fixedImageSample,
+  itk::ThreadIdType threadID,
+  itk::SizeValueType fixedImageSample,
   const MovingImagePointType & itkNotUsed(mappedPoint),
   double movingImageValue,
   const ImageDerivativesType &
diff --git a/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h b/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h
index 3afd1b6b..559dd778 100644
--- a/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h
+++ b/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h
@@ -128,14 +128,14 @@ class ITK_EXPORT NormalizedCorrelationImageToImageMetricFor3DBLUTFFD :
   MeasureType ComputeSums( const ParametersType & parameters ) const;
 
 
-  inline bool GetValueThreadProcessSample( unsigned int threadID,
-      unsigned long fixedImageSample,
+  inline bool GetValueThreadProcessSample( itk::ThreadIdType threadID,
+      itk::SizeValueType fixedImageSample,
       const MovingImagePointType & mappedPoint,
       double movingImageValue ) const ITK_OVERRIDE;
 
 
-  inline bool GetValueAndDerivativeThreadProcessSample( unsigned int threadID,
-      unsigned long fixedImageSample,
+  inline bool GetValueAndDerivativeThreadProcessSample( itk::ThreadIdType threadID,
+      itk::SizeValueType fixedImageSample,
       const MovingImagePointType & mappedPoint,
       double movingImageValue,
       const ImageDerivativesType &
diff --git a/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx b/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx
index 494c61a5..632ce5fc 100644
--- a/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx
+++ b/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx
@@ -211,8 +211,8 @@ template < class TFixedImage, class TMovingImage  >
 inline bool
 NormalizedCorrelationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
 ::GetValueThreadProcessSample(
-  unsigned int threadID,
-  unsigned long fixedImageSample,
+  itk::ThreadIdType threadID,
+  itk::SizeValueType fixedImageSample,
   const MovingImagePointType & itkNotUsed(mappedPoint),
   double movingImageValue) const
 {
@@ -416,8 +416,8 @@ template < class TFixedImage, class TMovingImage  >
 inline bool
 NormalizedCorrelationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
 ::GetValueAndDerivativeThreadProcessSample(
-  unsigned int threadID,
-  unsigned long fixedImageSample,
+  itk::ThreadIdType threadID,
+  itk::SizeValueType fixedImageSample,
   const MovingImagePointType & itkNotUsed(mappedPoint),
   double movingImageValue,
   const ImageDerivativesType &
diff --git a/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h b/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h
index 79bd1c17..3ba1d252 100644
--- a/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h
+++ b/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h
@@ -333,8 +333,8 @@ class ITK_EXPORT MattesMutualInformationImageToImageMetricFor3DBLUTFFD :
 
   virtual inline void GetValueThreadPreProcess( unsigned int threadID,
       bool withinSampleThread ) const ITK_OVERRIDE;
-  virtual inline bool GetValueThreadProcessSample( unsigned int threadID,
-      unsigned long fixedImageSample,
+  virtual inline bool GetValueThreadProcessSample( itk::ThreadIdType threadID,
+      itk::SizeValueType fixedImageSample,
       const MovingImagePointType & mappedPoint,
       double movingImageValue ) const ITK_OVERRIDE;
   virtual inline void GetValueThreadPostProcess( unsigned int threadID,
@@ -343,8 +343,8 @@ class ITK_EXPORT MattesMutualInformationImageToImageMetricFor3DBLUTFFD :
   virtual inline void GetValueAndDerivativeThreadPreProcess(
     unsigned int threadID,
     bool withinSampleThread ) const ITK_OVERRIDE;
-  virtual inline bool GetValueAndDerivativeThreadProcessSample( unsigned int threadID,
-      unsigned long fixedImageSample,
+  virtual inline bool GetValueAndDerivativeThreadProcessSample( itk::ThreadIdType threadID,
+      itk::SizeValueType fixedImageSample,
       const MovingImagePointType & mappedPoint,
       double movingImageValue,
       const ImageDerivativesType &
diff --git a/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx b/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx
index 9f717668..4bce2829 100644
--- a/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx
+++ b/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx
@@ -559,8 +559,8 @@ MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
 template < class TFixedImage, class TMovingImage  >
 inline bool
 MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::GetValueThreadProcessSample( unsigned int threadID,
-                               unsigned long fixedImageSample,
+::GetValueThreadProcessSample( itk::ThreadIdType threadID,
+                               itk::SizeValueType fixedImageSample,
                                const MovingImagePointType & itkNotUsed(mappedPoint),
                                double movingImageValue) const
 {
@@ -822,8 +822,8 @@ MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
 template < class TFixedImage, class TMovingImage  >
 inline bool
 MattesMutualInformationImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::GetValueAndDerivativeThreadProcessSample( unsigned int threadID,
-    unsigned long fixedImageSample,
+::GetValueAndDerivativeThreadProcessSample( itk::ThreadIdType threadID,
+    itk::SizeValueType fixedImageSample,
     const MovingImagePointType & itkNotUsed(mappedPoint),
     double movingImageValue,
     const ImageDerivativesType &
diff --git a/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.h b/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.h
index d23a9cd6..8bdc0276 100644
--- a/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.h
+++ b/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.h
@@ -127,13 +127,13 @@ class ITK_EXPORT MeanSquaresImageToImageMetricFor3DBLUTFFD :
   //purposely not implemented
   void operator=(const Self &);
 
-  inline bool GetValueThreadProcessSample( unsigned int threadID,
-      unsigned long fixedImageSample,
+  inline bool GetValueThreadProcessSample( itk::ThreadIdType threadID,
+      itk::SizeValueType fixedImageSample,
       const MovingImagePointType & mappedPoint,
       double movingImageValue ) const ITK_OVERRIDE;
 
-  inline bool GetValueAndDerivativeThreadProcessSample( unsigned int threadID,
-      unsigned long fixedImageSample,
+  inline bool GetValueAndDerivativeThreadProcessSample( itk::ThreadIdType threadID,
+      itk::SizeValueType fixedImageSample,
       const MovingImagePointType & mappedPoint,
       double movingImageValue,
       const ImageDerivativesType &
diff --git a/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.txx b/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.txx
index 02427a39..ed9c41b0 100644
--- a/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.txx
+++ b/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.txx
@@ -136,8 +136,8 @@ MeanSquaresImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
 template < class TFixedImage, class TMovingImage  >
 inline bool
 MeanSquaresImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::GetValueThreadProcessSample( unsigned int threadID,
-                               unsigned long fixedImageSample,
+::GetValueThreadProcessSample( itk::ThreadIdType threadID,
+                               itk::SizeValueType fixedImageSample,
                                const MovingImagePointType & itkNotUsed(mappedPoint),
                                double movingImageValue) const
 {
@@ -202,8 +202,8 @@ MeanSquaresImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
 template < class TFixedImage, class TMovingImage  >
 inline bool
 MeanSquaresImageToImageMetricFor3DBLUTFFD<TFixedImage,TMovingImage>
-::GetValueAndDerivativeThreadProcessSample( unsigned int threadID,
-    unsigned long fixedImageSample,
+::GetValueAndDerivativeThreadProcessSample( itk::ThreadIdType threadID,
+    itk::SizeValueType fixedImageSample,
     const MovingImagePointType & itkNotUsed(mappedPoint),
     double movingImageValue,
     const ImageDerivativesType &
diff --git a/tools/clitkAffineTransformGenericFilter.txx b/tools/clitkAffineTransformGenericFilter.txx
index c1fe88a4..ce202d32 100644
--- a/tools/clitkAffineTransformGenericFilter.txx
+++ b/tools/clitkAffineTransformGenericFilter.txx
@@ -53,11 +53,13 @@ namespace clitk
     ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
 
     // Call UpdateWithDim
-    if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
-    else 
-      if(Dimension==3) UpdateWithDim<3>(PixelType, Components);
-      else if (Dimension==4)UpdateWithDim<4>(PixelType, Components);
-      else {
+    if (Dimension==2)
+        UpdateWithDim<2>(PixelType, Components);
+    else if (Dimension==3)
+        UpdateWithDim<3>(PixelType, Components);
+    else if (Dimension==4)
+        UpdateWithDim<4>(PixelType, Components);
+    else {
         std::cout<<"Error, Only for 2, 3 or 4  Dimensions!!!"<<std::endl ;
         return;
       }
@@ -397,63 +399,47 @@ namespace clitk
 
     // Matrix
     typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
-    if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
-      {
-        if (m_ArgsInfo.matrix_given)
-          {
+    if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given) {
+        if (m_ArgsInfo.matrix_given) {
             std::cerr << "You must use either rotate/translate or matrix options" << std::endl;
             return;
-          }
+        }
         itk::Array<double> transformParameters(2 * Dimension);
         transformParameters.Fill(0.0);
-        if (m_ArgsInfo.rotate_given)
-          {
+        if (m_ArgsInfo.rotate_given) {
             if (Dimension == 2)
-              transformParameters[0] = m_ArgsInfo.rotate_arg[0];
+                transformParameters[0] = m_ArgsInfo.rotate_arg[0];
             else
-              for (unsigned int i = 0; i < 3; i++)
-                transformParameters[i] = m_ArgsInfo.rotate_arg[i];
-          }
-        if (m_ArgsInfo.translate_given)
-          {
+                for (unsigned int i = 0; i < 3; i++)
+                    transformParameters[i] = m_ArgsInfo.rotate_arg[i];
+        }
+        if (m_ArgsInfo.translate_given) {
             int pos = 3;
             if (Dimension == 2)
               pos = 1;
             for (unsigned int i = 0; i < Dimension && i < 3; i++)
               transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
-          }
-        if (Dimension == 4)
-          {
-            matrix.SetIdentity();
-            itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
-            for (unsigned int i = 0; i < 3; ++i)
-              for (unsigned int j = 0; j < 3; ++j)
-                matrix[i][j] = tmp[i][j];
-            for (unsigned int i = 0; i < 3; ++i)
-              matrix[i][4] = tmp[i][3];
-          }
-        else
-          matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
-      }
-    else
-      {
-        if (m_ArgsInfo.matrix_given)
-          {
+        }
+        matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
+    }
+    else {
+        if (m_ArgsInfo.matrix_given) {
             matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
-            if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
-          }
+            if (m_Verbose)
+                std::cout << "Reading the matrix..." << std::endl;
+        }
         else {
           if (m_ArgsInfo.elastix_given) {
             std::string filename(m_ArgsInfo.elastix_arg);
             matrix = createMatrixFromElastixFile<Dimension>(filename, m_Verbose);
           }
-          else 
-            matrix.SetIdentity();
+          else
+              matrix.SetIdentity();
         }
-      }
+    }
     if (m_Verbose)
-      std::cout << "Using the following matrix:" << std::endl
-                << matrix << std::endl;
+        std::cout << "Using the following matrix:" << std::endl
+                  << matrix << std::endl;
     typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
     typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
 
@@ -720,54 +706,38 @@ namespace clitk
 
     // Matrix
     typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
-    if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
-      {
-        if (m_ArgsInfo.matrix_given)
-          {
+    if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given) {
+        if (m_ArgsInfo.matrix_given) {
             std::cerr << "You must use either rotate/translate or matrix options" << std::endl;
             return;
-          }
+        }
         itk::Array<double> transformParameters(2 * Dimension);
         transformParameters.Fill(0.0);
-        if (m_ArgsInfo.rotate_given)
-          {
+        if (m_ArgsInfo.rotate_given) {
             if (Dimension == 2)
               transformParameters[0] = m_ArgsInfo.rotate_arg[0];
             else
               for (unsigned int i = 0; i < 3; i++)
                 transformParameters[i] = m_ArgsInfo.rotate_arg[i];
-          }
-        if (m_ArgsInfo.translate_given)
-          {
+        }
+        if (m_ArgsInfo.translate_given) {
             int pos = 3;
             if (Dimension == 2)
               pos = 1;
             for (unsigned int i = 0; i < Dimension && i < 3; i++)
               transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
-          }
-        if (Dimension == 4)
-          {
-            matrix.SetIdentity();
-            itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
-            for (unsigned int i = 0; i < 3; ++i)
-              for (unsigned int j = 0; j < 3; ++j)
-                matrix[i][j] = tmp[i][j];
-            for (unsigned int i = 0; i < 3; ++i)
-              matrix[i][4] = tmp[i][3];
-          }
-        else
-          matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
-      }
-    else
-      {
-        if (m_ArgsInfo.matrix_given)
-          {
+        }
+        matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
+    }
+    else {
+        if (m_ArgsInfo.matrix_given) {
             matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
-            if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
-          }
+            if (m_Verbose)
+                std::cout << "Reading the matrix..." << std::endl;
+        }
         else
-          matrix.SetIdentity();
-      }
+            matrix.SetIdentity();
+    }
     if (m_Verbose)
       std::cout << "Using the following matrix:" << std::endl
                 << matrix << std::endl;
diff --git a/tools/clitkBlurImageGenericFilter.txx b/tools/clitkBlurImageGenericFilter.txx
index ac0a459b..95a25eed 100644
--- a/tools/clitkBlurImageGenericFilter.txx
+++ b/tools/clitkBlurImageGenericFilter.txx
@@ -30,6 +30,7 @@
 // itk include
 #include "itkDiscreteGaussianImageFilter.h"
 #include <clitkCommon.h>
+#include <typeinfo>
 
 namespace clitk
 {
@@ -110,21 +111,42 @@ BlurImageGenericFilter<args_info_type>::UpdateWithInputImageType()
   typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
 
   // Main filter
-  typedef typename InputImageType::PixelType PixelType;
+  typedef typename InputImageType::PixelType InputPixelType;
   typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
+  typedef itk::Image<double, InputImageType::ImageDimension> DoubleOutputImageType;
 
   // Filter
-  typedef itk::DiscreteGaussianImageFilter<InputImageType, OutputImageType> DiscreteGaussianImageFilterType;
-  typename DiscreteGaussianImageFilterType::Pointer gaussianFilter=DiscreteGaussianImageFilterType::New();
-  gaussianFilter->SetInput(input);
-  gaussianFilter->SetVariance(varianceArray);
-  gaussianFilter->SetUseImageSpacing(true);
-  gaussianFilter->Update();
+  if(typeid(InputPixelType) != typeid(double)) {
+      if(mArgsInfo.verbose_flag) {
+          std::cout<<"OutputPixelType is set to float"<<std::endl;
+      }
+      typedef itk::DiscreteGaussianImageFilter<InputImageType, OutputImageType> DiscreteGaussianImageFilterType;
+      typename DiscreteGaussianImageFilterType::Pointer gaussianFilter=DiscreteGaussianImageFilterType::New();
+      gaussianFilter->SetInput(input);
+      gaussianFilter->SetVariance(varianceArray);
+      gaussianFilter->SetUseImageSpacing(true);
+      gaussianFilter->Update();
+
+      //std::cout<<"variance value="<<gaussianFilter->GetVariance()<<std::endl;
+
+      // Write/Save results
+      this->template SetNextOutput<OutputImageType>(gaussianFilter->GetOutput());
+  } else {
+      if(mArgsInfo.verbose_flag) {
+          std::cout<<"OutputPixelType is set to double"<<std::endl;
+      }
+      typedef itk::DiscreteGaussianImageFilter<InputImageType, DoubleOutputImageType> DiscreteGaussianImageFilterType;
+      typename DiscreteGaussianImageFilterType::Pointer gaussianFilter=DiscreteGaussianImageFilterType::New();
+      gaussianFilter->SetInput(input);
+      gaussianFilter->SetVariance(varianceArray);
+      gaussianFilter->SetUseImageSpacing(true);
+      gaussianFilter->Update();
 
-  //std::cout<<"variance value="<<gaussianFilter->GetVariance()<<std::endl;
+      //std::cout<<"variance value="<<gaussianFilter->GetVariance()<<std::endl;
 
-  // Write/Save results
-  this->template SetNextOutput<OutputImageType>(gaussianFilter->GetOutput());
+      // Write/Save results
+      this->template SetNextOutput<DoubleOutputImageType>(gaussianFilter->GetOutput());
+  }
 }
 //--------------------------------------------------------------------
 
diff --git a/tools/clitkDicom2Image.cxx b/tools/clitkDicom2Image.cxx
index 614c5d96..c2253d77 100644
--- a/tools/clitkDicom2Image.cxx
+++ b/tools/clitkDicom2Image.cxx
@@ -62,7 +62,11 @@ int main(int argc, char * argv[])
   NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
   nameGenerator->SetUseSeriesDetails(false);
   std::string folderName=".";
+#ifdef _WIN32
+  const size_t last_slash_idx = input_files[0].rfind('\\');
+#else
   const size_t last_slash_idx = input_files[0].rfind('/');
+#endif
   if (std::string::npos != last_slash_idx)
     folderName = input_files[0].substr(0, last_slash_idx);
   nameGenerator->SetInputDirectory(folderName);
@@ -87,7 +91,7 @@ int main(int argc, char * argv[])
 #endif
   for(unsigned int i=0; i<args_info.inputs_num; i++) {
     if (args_info.verbose_flag)
-        std::cout << "Reading <" << input_files[i] << std::endl;
+        std::cout << "Reading < " << input_files[i] << std::endl;
 #if GDCM_MAJOR_VERSION >= 2
     gdcm::Reader hreader;
     hreader.SetFileName(input_files[i].c_str());
@@ -161,6 +165,16 @@ int main(int argc, char * argv[])
     std::vector<double> origin = theorigin[*sn];
     std::vector<double> instanceNumberSerie = instanceNumber[*sn];
     std::vector<std::string> files = seriesFiles[*sn];
+    //Let's process the filenames -- it is mandatory for the line "if (tempFilename == files[i])"
+    for(unsigned int i=0; i<files.size(); i++) {
+#ifdef _WIN32
+        const size_t first_slash_idx_fn = files[i].find('\\');
+#else
+        const size_t first_slash_idx_fn = files[i].find('/');
+#endif
+        if (std::string::npos != first_slash_idx_fn && first_slash_idx_fn == 1 && files[i][0] == '.')
+          files[i] = files[i].substr(first_slash_idx_fn+1);
+    }
     std::vector<int> sliceIndex(files.size());
     //clitk::GetSortedIndex(locs, sliceIndex);
     //Look for files into GDCMSeriesFileNames, because it sorts files correctly and take the order
@@ -169,10 +183,18 @@ int main(int argc, char * argv[])
       int j(0);
       bool found(false);
       while (!found && j<temp.size()) {
-        const size_t last_slash_idx2 = temp[j].rfind('/');
         std::string tempFilename(temp[j]);
-        if (temp[j][0] == '.' && temp[j][1] == '/')
-          tempFilename = temp[j].substr(2, temp[j].size()-1);
+#ifdef _WIN32
+        // There is a bug on Windows, the last \ is a /...
+        // Let's substitute it
+        const size_t last_slash_idx_win = tempFilename.rfind('/');
+        tempFilename[last_slash_idx_win] = '\\';
+        const size_t first_slash_idx = tempFilename.find('\\');
+#else
+        const size_t first_slash_idx = tempFilename.find('/');
+#endif
+        if (std::string::npos != first_slash_idx && first_slash_idx == 1 && tempFilename[0] == '.')
+          tempFilename = tempFilename.substr(first_slash_idx+1);
         if (tempFilename == files[i]) {
           sliceIndex[j] = i;
           found = true;
@@ -278,7 +300,7 @@ int main(int argc, char * argv[])
       modifier->SetOutputOrigin(origin[0], origin[1], locs[sliceIndex[0]]);
       modifier->Update();
       vvImage::Pointer focal_image = vvImage::New();
-      focal_image->AddVtkImage(modifier->GetOutput());
+      focal_image->AddVtkImage(modifier->GetOutput(), image->GetTransform()[0]);
       image = focal_image;
     }
 
@@ -289,7 +311,11 @@ int main(int argc, char * argv[])
       std::ostringstream name;
       std::vector<std::string> directory = clitk::SplitFilename(args_info.output_arg);
       if (directory.size() == 2)
+#ifdef _WIN32
+        name << directory[0] << "\\" << *sn << "_" << directory[1];
+#else
         name << directory[0] << "/" << *sn << "_" << directory[1];
+#endif
       else
         name << *sn << "_" << args_info.output_arg;
       outfile = name.str();
diff --git a/tools/clitkDicomRTStruct2Image.cxx b/tools/clitkDicomRTStruct2Image.cxx
index 3790ab7b..a62cee06 100644
--- a/tools/clitkDicomRTStruct2Image.cxx
+++ b/tools/clitkDicomRTStruct2Image.cxx
@@ -22,6 +22,31 @@
 #include "clitkDicomRTStruct2Image_ggo.h"
 #include "clitkIO.h"
 
+//--------------------------------------------------------------------
+std::string outputFileName(clitk::DicomRT_ROI::Pointer roi, const args_info_clitkDicomRTStruct2Image& args_info)
+{
+  std::string name = roi->GetName();
+  int num = roi->GetROINumber();
+  name.erase(remove_if(name.begin(), name.end(), isspace), name.end());
+  std::string n;
+  n = std::string(args_info.output_arg).append(clitk::toString(num)).append("_").append(name);
+  if (args_info.mha_flag) {
+    n=n.append(".mha");
+  }
+  else if (args_info.nii_flag) {
+    n=n.append(".nii");
+  }
+  else if (args_info.niigz_flag) {
+    n=n.append(".nii.gz");
+  }
+  else {
+    n=n.append(".mhd");
+  }
+  if (args_info.verbose_flag) {
+    std::cout << num << " " << roi->GetName() << " num=" << num << " : " << n << std::endl;
+  }
+  return n;
+}
 //--------------------------------------------------------------------
 int main(int argc, char * argv[]) {
 
@@ -31,27 +56,33 @@ int main(int argc, char * argv[]) {
 
   // Read and display information
   clitk::DicomRT_StructureSet::Pointer s = clitk::DicomRT_StructureSet::New();
-  s->Read(args_info.input_arg);
+  s->Read(args_info.input_arg, args_info.tolerance_arg);
   if (args_info.verboseFile_flag) {
     s->Print(std::cout);
   }
-  
-  // New filter to convert to binary image
-  clitk::DicomRTStruct2ImageFilter filter;
-  filter.SetCropMaskEnabled(args_info.crop_flag);
-  filter.SetImageFilename(args_info.image_arg);  // Used to get spacing + origin
-  if (args_info.vtk_flag) {
-    filter.SetWriteMesh(true);
-  }
-  if (args_info.roiName_given) {
-    filter.SetROI(s->GetROIFromROIName(args_info.roiName_arg)); 
-    filter.SetOutputImageFilename(args_info.output_arg);
-    filter.Update();  
-  }
-  else if (args_info.roi_given && args_info.roi_arg != -1) {
-    filter.SetROI(s->GetROIFromROINumber(args_info.roi_arg)); 
-    filter.SetOutputImageFilename(args_info.output_arg);
-    filter.Update();  
+  if (args_info.roiName_given || (args_info.roi_given && args_info.roi_arg != -1)) {
+    clitk::DicomRT_ROI::Pointer roi;
+    if (args_info.roiName_given) {
+      roi = s->GetROIFromROIName(args_info.roiName_arg);
+    }
+    else if (args_info.roi_given && args_info.roi_arg != -1) {
+        roi = s->GetROIFromROINumber(args_info.roi_arg);
+    }
+    if (roi) {
+      // New filter to convert to binary image
+      clitk::DicomRTStruct2ImageFilter filter;
+      filter.SetCropMaskEnabled(args_info.crop_flag);
+      filter.SetImageFilename(args_info.image_arg);  // Used to get spacing + origin
+      if (args_info.vtk_flag) {
+        filter.SetWriteMesh(true);
+      }
+      filter.SetROI(roi);
+      filter.SetOutputImageFilename(outputFileName(roi, args_info));
+      filter.Update();
+      } else {
+        std::cerr<<"No ROI with this name/id"<<std::endl;
+          return EXIT_FAILURE;
+      }
   }
   else {
     clitk::DicomRT_StructureSet::ROIMapContainer* rois;
@@ -65,36 +96,18 @@ int main(int argc, char * argv[]) {
       for(iter = rois->begin(); iter != rois->end(); iter++) {
         clitk::DicomRT_ROI::Pointer roi = iter->second;
         clitk::DicomRTStruct2ImageFilter filter;
-        std::string name = roi->GetName();
-        int num = roi->GetROINumber();
-        filter.SetROI(roi); 
         filter.SetCropMaskEnabled(args_info.crop_flag);
         filter.SetImageFilename(args_info.image_arg);  // Used to get spacing + origin
         if (args_info.vtk_flag) {
           filter.SetWriteMesh(true);
         }
-        name.erase(remove_if(name.begin(), name.end(), isspace), name.end());
-        std::string n;
-        if (args_info.mha_flag) {
-          n = std::string(args_info.output_arg).append
-            (clitk::toString(num)).append
-            ("_").append
-            (name).append
-            (".mha");
-        }
-        else {
-          n = std::string(args_info.output_arg).append
-            (clitk::toString(num)).append
-            ("_").append
-            (name).append
-            (".mhd");
-        }
-        if (args_info.verbose_flag) {
-          std::cout << num << " " << roi->GetName() << " num=" << num << " : " << n << std::endl;
-        }
-        filter.SetOutputImageFilename(n);
-        filter.Update();  
+        filter.SetROI(roi);
+        filter.SetOutputImageFilename(outputFileName(roi, args_info));
+        filter.Update();
       }
+    } else {
+        std::cerr<<"No ROIs with this substring of ROI name"<<std::endl;
+        return EXIT_FAILURE;
     }
   }
 //   else {
@@ -144,5 +157,5 @@ int main(int argc, char * argv[]) {
   //}
 
   // This is the end my friend 
-  return 0;
+  return EXIT_SUCCESS;
 }
diff --git a/tools/clitkDicomRTStruct2Image.ggo b/tools/clitkDicomRTStruct2Image.ggo
index 8e6159a1..81c7e7d0 100644
--- a/tools/clitkDicomRTStruct2Image.ggo
+++ b/tools/clitkDicomRTStruct2Image.ggo
@@ -9,13 +9,16 @@ option "verboseFile"  - "Verbose file content"
 option "input"        i "Input Dicom file"                                                      string  yes
 option "image"        j "Used to read image info (spacing, origin)"                             string  yes
 option "output"       o "Output image base filename (roi number and extension will be append)"  string  yes
+option "tolerance"    t "Tolerance for slice position"                                          double  no  default="0"
 
-defgroup "ROIoption" groupdesc="an option of this group is required" 
-groupoption "roi"           r "ROI to binarize (if -1 = all roi)"                                                             int     no default="-1" group="ROIoption"
-groupoption "roiName"       n "ROI name to binarize (be wary of spaces in ROI names; if blank, use given 'roi' value)"        string  no default=""   group="ROIoption"
-groupoption "roiNameSubstr" s "Substring of ROI name to binarize (reuturns all matches; if blank, use given 'roiName' value)" string  no default=""   group="ROIoption"
-
+text "\nOutput options - the default output format is mhd"
 option "crop"         c "Crop binary mask"                                                      flag off
 option "mha"          - "Write the RTStruct as a mha image to avoid special character problems" flag off
 option "vtk"          - "Write the vtk Mesh as a vtk file"                                      flag off
+option "nii"          - "Write the RTStruct as a nii image"                                     flag off
+option "niigz"        - "Write the RTStruct as a gzipped nii image"                             flag off
 
+defgroup "ROI option" groupdesc="an option of this group is required"
+groupoption "roi"           r "ROI number to binarize (if -1 = all roi)"                                                      int     no default="-1" group="ROI option"
+groupoption "roiName"       n "ROI name to binarize (be wary of spaces in ROI names; if blank, use given 'roi' value)"        string  no default=""   group="ROI option"
+groupoption "roiNameSubstr" s "Substring of ROI name to binarize (returns all matches; if blank, use given 'roiName' value)"  string  no default=""   group="ROI option"
diff --git a/tools/clitkImageArithmGenericFilter.h b/tools/clitkImageArithmGenericFilter.h
index 3c3579f8..6cba07b0 100644
--- a/tools/clitkImageArithmGenericFilter.h
+++ b/tools/clitkImageArithmGenericFilter.h
@@ -79,7 +79,16 @@ namespace clitk {
 
   protected:  
     template<unsigned int Dim> void InitializeImageType();
-    bool mIsOperationUseASecondImage;
+    bool mIsOperationUseASecondImage;//if yes then - need to define more variables
+    std::string mFirstImageFileName;
+    int mFirstImageDimension;
+    std::string mFirstImagePixelType;
+    int mFirstImageComponents;
+    std::string mSecondImageFileName;
+    int mSecondImageDimension;
+    std::string mSecondImagePixelType;
+    int mSecondImageComponents;
+
     double mScalar;
     double mDefaultPixelValue;
     int mTypeOfOperation;  
diff --git a/tools/clitkImageArithmGenericFilter.txx b/tools/clitkImageArithmGenericFilter.txx
index 6bf79d51..a941b777 100644
--- a/tools/clitkImageArithmGenericFilter.txx
+++ b/tools/clitkImageArithmGenericFilter.txx
@@ -77,6 +77,40 @@ void ImageArithmGenericFilter<args_info_type>::SetArgsInfo(const args_info_type
   if (mArgsInfo.input2_given) {
     mIsOperationUseASecondImage = true;
     this->AddInputFilename(mArgsInfo.input2_arg);
+    mFirstImageFileName = mArgsInfo.input1_arg;
+    mFirstImageDimension = 0;
+    mFirstImagePixelType = "";
+    mFirstImageComponents = 0;
+    clitk::ReadImageDimensionAndPixelType(mFirstImageFileName,
+                                          mFirstImageDimension,
+                                          mFirstImagePixelType,
+                                          mFirstImageComponents);
+    mSecondImageFileName = mArgsInfo.input2_arg;
+    mSecondImageDimension = 0;
+    mSecondImagePixelType = "";
+    mSecondImageComponents = 0;
+    clitk::ReadImageDimensionAndPixelType(mSecondImageFileName,
+                                          mSecondImageDimension,
+                                          mSecondImagePixelType,
+                                          mSecondImageComponents);
+    if(mSecondImageDimension != mFirstImageDimension) {
+        std::cerr << "ERROR : input and input2 must have the same dimensions" << std::endl;
+        std::cerr << "input is "<< mFirstImageDimension <<"D" << std::endl;
+        std::cerr << "input2 is "<< mSecondImageDimension <<"D" << std::endl;
+        exit(-1);
+    }
+    if(mSecondImageComponents != mFirstImageComponents) {
+        std::cerr << "ERROR : input and input2 must have the same number of components" << std::endl;
+        std::cerr << "input is "<< mFirstImageComponents << std::endl;
+        std::cerr << "input2 is "<< mSecondImageComponents << std::endl;
+        exit(-1);
+    }
+    //if(mSecondImagePixelType.compare(mFirstImagePixelType) != 0) {
+    //    std::cerr << "ERROR : input and input2 must have the same pixel type" << std::endl;
+    //    std::cerr << "input is "<< mFirstImagePixelType << std::endl;
+    //    std::cerr << "input2 is "<< mSecondImagePixelType << std::endl;
+    //    exit(-1);
+    //}
   }
 
   if (mArgsInfo.output_given) this->SetOutputFilename(mArgsInfo.output_arg);
@@ -135,6 +169,10 @@ void ImageArithmGenericFilter<args_info_type>::UpdateWithInputImageType()
         itkWarningMacro(<< "The images (input and input2) do not have the same spacing. "
                         << "Using first input's information.");
       }
+      if(!clitk::HaveSameOrigin<ImageType, ImageType>(input1, input2)) {
+        itkWarningMacro(<< "The images (input and input2) do not have the same origin. "
+                        << "Using first input's information.");
+      }
   }
 
   // Check if overwrite and outputisfloat and pixeltype is not float -> do not overwrite
diff --git a/tools/clitkImageStatisticsGenericFilter.txx b/tools/clitkImageStatisticsGenericFilter.txx
index 82a11ab5..57bf5fa2 100644
--- a/tools/clitkImageStatisticsGenericFilter.txx
+++ b/tools/clitkImageStatisticsGenericFilter.txx
@@ -248,13 +248,48 @@ namespace clitk
 
         // Output
         if (m_Verbose) std::cout<<"N° of pixels: ";
-        std::cout<<statisticsFilter->GetCount(label)<<std::endl;
+        unsigned int nbPixels = statisticsFilter->GetCount(label);
+        std::cout<<nbPixels<<std::endl;
         if (m_Verbose) std::cout<<"Mean: ";
-        std::cout<<statisticsFilter->GetMean(label)<<std::endl;
-        if (m_Verbose) std::cout<<"SD: ";
+        double mean = statisticsFilter->GetMean(label);
+        std::cout<<mean<<std::endl;
+        if (m_Verbose) std::cout<<"SD_N-1: ";
         std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
-        if (m_Verbose) std::cout<<"Variance: ";
+        if (m_Verbose) std::cout<<"Variance_N-1: ";
         std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
+        //
+        double sigma = 0.0;
+        double skewness = 0.0;
+        double kurtosis = 0.0;
+        itk::ImageRegionIterator<InputImageAdaptorType> ItI(input_adaptor, input_adaptor->GetLargestPossibleRegion());
+        itk::ImageRegionIterator<LabelImageType> ItM(labelImage, labelImage->GetLargestPossibleRegion());
+        for ( ItI.GoToBegin(), ItM.GoToBegin(); !ItI.IsAtEnd(); ++ItI, ++ItM ) {
+            if ( ItM.Get() == label ) {
+              PixelType value = ItI.Get();
+              sigma+=(value-mean)*(value-mean)/nbPixels;
+              double diff = value - mean;
+              skewness += ( diff * diff * diff ) /nbPixels;
+              kurtosis += ( diff * diff * diff * diff ) /nbPixels;
+            }
+        }
+        sigma=std::sqrt(sigma);
+        if(sigma == 0) {
+            skewness=0;
+            kurtosis=3;
+        } else {
+            skewness/=(sigma*sigma*sigma);
+            kurtosis/=(sigma*sigma*sigma*sigma);
+        }
+        //Show results
+        if (m_Verbose) std::cout<<"SD_N: ";
+        std::cout<<sigma<<std::endl;
+        if (m_Verbose) std::cout<<"Variance_N: ";
+        std::cout<<sigma*sigma<<std::endl;
+        if (m_Verbose) std::cout<<"Skewness: ";
+        std::cout<<skewness<<std::endl;
+        if (m_Verbose) std::cout<<"Kurtosis: ";
+        std::cout<<kurtosis<<std::endl;
+        //
         if (m_Verbose) std::cout<<"Min: ";
         std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
         if (m_Verbose && m_Localize) {
@@ -288,14 +323,67 @@ namespace clitk
           if (m_Verbose) std::cout<<"Histogram: "<<std::endl;
             std::cout<<"# MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
           for( int i =0; i <m_ArgsInfo.bins_arg; i++)
-            std::cout<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
+            std::cout<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<double (histogram->GetFrequency(i))/ double (histogram->GetTotalFrequency())<<std::endl;
 
           // Add to the file
           std::ofstream histogramFile(m_ArgsInfo.histogram_arg);
           histogramFile<<"#Histogram: "<<std::endl;
           histogramFile<<"#MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
           for( int i =0; i <m_ArgsInfo.bins_arg; i++)
-            histogramFile<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
+            histogramFile<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<double (histogram->GetFrequency(i))/ double (histogram->GetTotalFrequency())<<std::endl;
+
+          //mean + sigma + kurtosis + skewness - calculated from the histogram
+          double mean = 0.0;
+          double sigma = 0.0;
+          double skewness = 0.0;
+          double kurtosis = 0.0;
+          double totalFreq = histogram->GetTotalFrequency();
+
+          for( int i =0; i <m_ArgsInfo.bins_arg; i++) {
+            double binVal = histogram->GetMeasurement(i,0);
+            unsigned int freqVal = histogram->GetFrequency(i);
+            mean+=binVal*freqVal/totalFreq;
+          }
+          for( int i =0; i <m_ArgsInfo.bins_arg; i++) {
+            double binVal = histogram->GetMeasurement(i,0);
+            unsigned int freqVal = histogram->GetFrequency(i);
+            sigma+=(binVal-mean)*(binVal-mean)*freqVal/totalFreq;
+            skewness+=(binVal-mean)*
+                    (binVal-mean)*
+                    (binVal-mean)*
+                    freqVal/totalFreq;
+            kurtosis+=(binVal-mean)*
+                    (binVal-mean)*
+                    (binVal-mean)*
+                    (binVal-mean)*
+                    freqVal/totalFreq;
+          }
+          sigma=std::sqrt(sigma);
+          if(sigma == 0) {
+              skewness=0;
+              kurtosis=3;
+          } else {
+              skewness/=(sigma*sigma*sigma);
+              kurtosis/=(sigma*sigma*sigma*sigma);
+          }
+
+          std::cout<<"Histogram statistics"<<std::endl;
+          if (m_Verbose) {
+              std::cout<<"HMean: ";
+          }
+          std::cout<<mean<<std::endl;
+          if (m_Verbose) {
+              std::cout<<"HSTD: ";
+          }
+          std::cout<<sigma<<std::endl;
+          if (m_Verbose) {
+              std::cout<<"HSkewness: ";
+          }
+          std::cout<<skewness<<std::endl;
+          if (m_Verbose) {
+              std::cout<<"HKurtosis: ";
+          }
+          std::cout<<kurtosis<<std::endl;
         }
 
         // DVH
diff --git a/tools/clitkPadImageGenericFilter.cxx b/tools/clitkPadImageGenericFilter.cxx
index 8477a35d..d553e51b 100644
--- a/tools/clitkPadImageGenericFilter.cxx
+++ b/tools/clitkPadImageGenericFilter.cxx
@@ -152,10 +152,13 @@ namespace clitk
     if (mArgsInfo.verbose_flag)
       std::cout << "Calculating padding." << std::endl;
     
-    SpacingType spacing = input->GetSpacing(), like_spacing = like_image->GetSpacing(); 
-    if (spacing != like_spacing) {
-      std::cerr << "Like-image must have same spacing as input: " << spacing << " " << like_spacing << std::endl;
-      return PAD_ERR_NOT_SAME_SPACING;
+    SpacingType spacing = input->GetSpacing(), like_spacing = like_image->GetSpacing();
+    for (unsigned int i = 0; i < dim; i++) {
+        double diff_spacing = std::fabs((double) spacing[i] - (double) like_spacing[i]);
+        if (diff_spacing > 1e-6) {
+          std::cerr << "Like-image must have same spacing as input: " << spacing << " " << like_spacing << std::endl;
+          return PAD_ERR_NOT_SAME_SPACING;
+        }
     }
     
     SizeType size = input->GetLargestPossibleRegion().GetSize(), like_size = like_image->GetLargestPossibleRegion().GetSize();
diff --git a/tools/clitkSplitImage.cxx b/tools/clitkSplitImage.cxx
index 260e220a..56f6ed4e 100644
--- a/tools/clitkSplitImage.cxx
+++ b/tools/clitkSplitImage.cxx
@@ -39,7 +39,7 @@ int main(int argc, char * argv[])
   itk::ImageIOBase::Pointer header = clitk::readImageHeader(args_info.input_arg);
   if (header.IsNull()) {
     std::cerr << "Unable to read image file " << args_info.input_arg << std::endl;
-    std::exit(1);
+    std::exit(EXIT_FAILURE);
   }
   unsigned int dim = header->GetNumberOfDimensions();
 
@@ -55,9 +55,12 @@ int main(int argc, char * argv[])
   filter.SetSplitDimension(args_info.dimension_arg);
   filter.SetPng(args_info.png_flag);
   filter.SetWindowLevel(args_info.window_arg, args_info.level_arg);
+  filter.SetMha(args_info.mha_flag);
+  filter.SetNii(args_info.nii_flag);
+  filter.SetNiigz(args_info.niigz_flag);
   filter.SetVerbose(args_info.verbose_flag);
   filter.Update();
 
   // this is the end my friend
-  return 0;
+  return EXIT_SUCCESS;
 } // end main
diff --git a/tools/clitkSplitImage.ggo b/tools/clitkSplitImage.ggo
index 5d427eb7..62b0e5f1 100644
--- a/tools/clitkSplitImage.ggo
+++ b/tools/clitkSplitImage.ggo
@@ -10,6 +10,11 @@ option "output"     o  "Output image base filename" string  yes
 option "verbose"    v  "Verbose"                    flag    off
 
 option "dimension"  d  "Dimension to split on"      int     yes
-option "png"        p  "Png file format"            flag    off
+
+text "\nOutput options - the default output format is mhd"
+option "png"        p  "png file format"            flag    off
 option "window"     w  "Window"                     double  no
 option "level"      l  "Level"                      double  no
+option "mha"        -  "mha file format"            flag    off
+option "nii"        -  "nii file format"            flag    off
+option "niigz"      -  "nii.gz file format"         flag    off
diff --git a/tools/clitkSplitImageGenericFilter.cxx b/tools/clitkSplitImageGenericFilter.cxx
index 58732ab2..ab1cd12d 100644
--- a/tools/clitkSplitImageGenericFilter.cxx
+++ b/tools/clitkSplitImageGenericFilter.cxx
@@ -142,6 +142,18 @@ void clitk::SplitImageGenericFilter::UpdateWithInputImageType()
         output = png.Do(this->m_Window, this->m_Level, informationFilter->GetOutput());
         this->template SetNextOutput<typename PngConversion<OutputImageType>::OutputPngImageType>(output);
       }
+      else if(this->m_mha){
+          SetOutputFilename(base_filename+"_"+ss.str()+".mha");
+          SetNextOutput<OutputImageType>(informationFilter->GetOutput());
+      }
+      else if(this->m_nii){
+          SetOutputFilename(base_filename+"_"+ss.str()+".nii");
+          SetNextOutput<OutputImageType>(informationFilter->GetOutput());
+      }
+      else if(this->m_niigz){
+          SetOutputFilename(base_filename+"_"+ss.str()+".nii.gz");
+          SetNextOutput<OutputImageType>(informationFilter->GetOutput());
+      }
       else {
         SetOutputFilename(base_filename+"_"+ss.str()+".mhd");
         SetNextOutput<OutputImageType>(informationFilter->GetOutput());
@@ -156,6 +168,18 @@ void clitk::SplitImageGenericFilter::UpdateWithInputImageType()
         output = png.Do(this->m_Window, this->m_Level, filter->GetOutput());
         this->template SetNextOutput<typename PngConversion<OutputImageType>::OutputPngImageType>(output);
       }
+      else if(this->m_mha){
+          SetOutputFilename(base_filename+"_"+ss.str()+".mha");
+          SetNextOutput<OutputImageType>(filter->GetOutput());
+      }
+      else if(this->m_nii){
+          SetOutputFilename(base_filename+"_"+ss.str()+".nii");
+          SetNextOutput<OutputImageType>(filter->GetOutput());
+      }
+      else if(this->m_niigz){
+          SetOutputFilename(base_filename+"_"+ss.str()+".nii.gz");
+          SetNextOutput<OutputImageType>(filter->GetOutput());
+      }
       else {
         SetOutputFilename(base_filename+"_"+ss.str()+".mhd");
         SetNextOutput<OutputImageType>(filter->GetOutput());
diff --git a/tools/clitkSplitImageGenericFilter.h b/tools/clitkSplitImageGenericFilter.h
index 4b6d6762..9fc987fe 100644
--- a/tools/clitkSplitImageGenericFilter.h
+++ b/tools/clitkSplitImageGenericFilter.h
@@ -60,6 +60,9 @@ namespace clitk {
     void SetVerbose (const bool v) { m_Verbose = v; }
     void SetPng (const bool v) { m_Png = v; }
     void SetWindowLevel(const double w, const double l){ m_Window = w; m_Level = l;}
+    void SetMha (const bool v) { m_mha = v; }
+    void SetNii (const bool v) { m_nii = v; }
+    void SetNiigz (const bool v) { m_niigz = v; }
 
    //--------------------------------------------------------------------
     // Main function called each time the filter is updated
@@ -89,6 +92,9 @@ namespace clitk {
     bool m_Verbose;
     bool m_Png;
     double m_Window, m_Level;
+    bool m_mha;
+    bool m_nii;
+    bool m_niigz;
 
   }; // end class SplitImageGenericFilter
 //--------------------------------------------------------------------
diff --git a/vv/vvIntensityValueSlider.h b/vv/vvIntensityValueSlider.h
index b123f404..08ddbe39 100644
--- a/vv/vvIntensityValueSlider.h
+++ b/vv/vvIntensityValueSlider.h
@@ -20,11 +20,11 @@
 
 // qt
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 #include <QDialog>
 
 // clitk 
diff --git a/vv/vvLabelImageLoaderWidget.h b/vv/vvLabelImageLoaderWidget.h
index 178acb2a..c1a81aba 100644
--- a/vv/vvLabelImageLoaderWidget.h
+++ b/vv/vvLabelImageLoaderWidget.h
@@ -24,11 +24,11 @@
 
 // qt
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 #include <QDialog>
 #include "ui_vvLabelImageLoaderWidget.h"
 
diff --git a/vv/vvSegmentationDialog.h b/vv/vvSegmentationDialog.h
index 277abc17..400c8fea 100644
--- a/vv/vvSegmentationDialog.h
+++ b/vv/vvSegmentationDialog.h
@@ -37,11 +37,11 @@
 #include "vtkPolyData.h"
 #include <vtkPolyDataMapper.h>
 
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 #include <QTreeWidget>
 
 //====================================================================
diff --git a/vv/vvSurfaceViewerDialog.h b/vv/vvSurfaceViewerDialog.h
index 9601e9af..e7b8a19f 100644
--- a/vv/vvSurfaceViewerDialog.h
+++ b/vv/vvSurfaceViewerDialog.h
@@ -28,11 +28,11 @@ class vtkPolyDataMapper;
 class vtkActor;
 class vtkOBJReader;
 
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 #include <QTreeWidget>
 
 //====================================================================
diff --git a/vv/vvToolBinarize.h b/vv/vvToolBinarize.h
index 4cdaa851..72448255 100644
--- a/vv/vvToolBinarize.h
+++ b/vv/vvToolBinarize.h
@@ -19,11 +19,11 @@
 #define VVTOOLBINARIZE_H
 
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 
 #include "vvToolBase.h"
 #include "vvToolWidgetBase.h"
diff --git a/vv/vvToolCropImage.h b/vv/vvToolCropImage.h
index c5d8ce15..85440bd7 100644
--- a/vv/vvToolCropImage.h
+++ b/vv/vvToolCropImage.h
@@ -20,11 +20,11 @@
 
 //qt
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 #include <QDialog>
 #include <QSlider>
 // vv
diff --git a/vv/vvToolHistogram.h b/vv/vvToolHistogram.h
index 84813782..f75d8431 100644
--- a/vv/vvToolHistogram.h
+++ b/vv/vvToolHistogram.h
@@ -19,11 +19,11 @@
 #define VVTOOLHISTOGRAM_H
 
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 
 #include "vvToolBase.h"
 #include "vvToolWidgetBase.h"
diff --git a/vv/vvToolImageArithm.h b/vv/vvToolImageArithm.h
index 964b9c81..5dbdb6d4 100644
--- a/vv/vvToolImageArithm.h
+++ b/vv/vvToolImageArithm.h
@@ -19,11 +19,11 @@
 #define VVTOOLImageArithm_H
 
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 
 #include "vvToolBase.h"
 #include "vvToolWidgetBase.h"
diff --git a/vv/vvToolInputSelectorWidget.h b/vv/vvToolInputSelectorWidget.h
index 76e0c34f..3879e007 100644
--- a/vv/vvToolInputSelectorWidget.h
+++ b/vv/vvToolInputSelectorWidget.h
@@ -20,11 +20,11 @@
 
 // qt
 #include <QObject>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 #include <QDialog>
 
 // vv
diff --git a/vv/vvToolMIP.h b/vv/vvToolMIP.h
index e915525c..b40564fb 100644
--- a/vv/vvToolMIP.h
+++ b/vv/vvToolMIP.h
@@ -48,11 +48,11 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <vvImage.h>
 
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 #include "vvToolBase.h"
 #include "QWidget"
 #include "vvToolWidgetBase.h"
diff --git a/vv/vvToolMedianFilter.h b/vv/vvToolMedianFilter.h
index b075ac17..abb43bf1 100644
--- a/vv/vvToolMedianFilter.h
+++ b/vv/vvToolMedianFilter.h
@@ -46,11 +46,11 @@
   #define VVTOOLMedianFilter_H
 
   #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-  #include <QtUiPlugin/QDesignerExportWidget>
-#else
-  #include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//  #include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//  #include <QtDesigner/QDesignerExportWidget>
+//#endif
   #include "vvToolBase.h"
   #include "QWidget"
   #include "vvToolWidgetBase.h"
diff --git a/vv/vvToolProfile.h b/vv/vvToolProfile.h
index 8297a90d..fe8ed83f 100644
--- a/vv/vvToolProfile.h
+++ b/vv/vvToolProfile.h
@@ -19,11 +19,11 @@
 #define VVTOOLPROFILE_H
 
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 
 #include "vvToolBase.h"
 #include "vvToolWidgetBase.h"
diff --git a/vv/vvToolROIManager.cxx b/vv/vvToolROIManager.cxx
index 00eff1df..1eb7d481 100644
--- a/vv/vvToolROIManager.cxx
+++ b/vv/vvToolROIManager.cxx
@@ -330,7 +330,7 @@ void vvToolROIManager::SelectedImageHasChanged(vvSlicerManager * m)
 void vvToolROIManager::Open()
 {
   // Open images
-  QString Extensions = "Images or Dicom-Struct files ( *.mha *.mhd *.hdr *.his *.dcm RS*)";
+  QString Extensions = "Images or Dicom-Struct files (*.nii *.nii.gz *.mha *.mhd *.hdr *.his *.dcm RS*)";
   Extensions += ";;All Files (*)";
   QStringList filename =
     QFileDialog::getOpenFileNames(this,tr("Open binary image or DICOM RT Struct"),
@@ -392,7 +392,7 @@ void vvToolROIManager::OpenBinaryImage(QStringList & filename)
 
 
 //------------------------------------------------------------------------------
-void vvToolROIManager::OpenDicomImage(std::string filename)
+void vvToolROIManager::OpenDicomImage(std::string filename, double tol)
 {
   // GUI selector of roi
   vvMeshReader reader;
@@ -412,7 +412,7 @@ void vvToolROIManager::OpenDicomImage(std::string filename)
     vtkSmartPointer<vtkMatrix4x4> transformMatrix = vtkSmartPointer<vtkMatrix4x4>::New();
     transformMatrix = mCurrentImage->GetTransform()[0]->GetMatrix();
     s->SetTransformMatrix(transformMatrix);
-    s->Read(filename);
+    s->Read(filename, tol);
 
     // Loop on selected struct
     std::vector<int> list = selector.getSelectedItems();
@@ -428,7 +428,7 @@ void vvToolROIManager::OpenDicomImage(std::string filename)
 
       // Get image
       vvImage::Pointer binaryImage = vvImage::New();
-      binaryImage->AddVtkImage(filter.GetOutput());
+      binaryImage->AddVtkImage(filter.GetOutput(), mCurrentImage->GetTransform()[0]);
 
       // Add to gui
       AddImage(binaryImage, s->GetROIFromROINumber(list[i])->GetName(), "", 0, true); // "" = no filename
diff --git a/vv/vvToolROIManager.h b/vv/vvToolROIManager.h
index db630c64..4879ccd5 100644
--- a/vv/vvToolROIManager.h
+++ b/vv/vvToolROIManager.h
@@ -20,11 +20,11 @@
 #define VVTOOLROIMANAGER_H
 
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 #include <QSharedPointer>
 
 #include "vvToolBase.h"
@@ -63,7 +63,7 @@ class vvToolROIManager:
   void SelectedImageHasChanged(vvSlicerManager *);
   void Open();
   void OpenBinaryImage(QStringList & filenames);
-  void OpenDicomImage(std::string filaneme);
+  void OpenDicomImage(std::string filaneme, double tol=0);
   void SelectedItemChangedInTree();
   void VisibleROIToggled(bool b);
   void VisibleContourROIToggled(bool b);
diff --git a/vv/vvToolSegmentation.h b/vv/vvToolSegmentation.h
index 7e49dc46..1250b7d5 100644
--- a/vv/vvToolSegmentation.h
+++ b/vv/vvToolSegmentation.h
@@ -19,11 +19,11 @@
 #define VVTOOLSEGMENTATION_H
 
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 
 #include "vvToolBase.h"
 #include "vvToolWidgetBase.h"
diff --git a/vv/vvToolSimpleInputSelectorWidget.h b/vv/vvToolSimpleInputSelectorWidget.h
index 4b8028fa..d3276d07 100644
--- a/vv/vvToolSimpleInputSelectorWidget.h
+++ b/vv/vvToolSimpleInputSelectorWidget.h
@@ -19,11 +19,11 @@
 #define VVTOOLSIMPLEINPUTSELECTORWIDGET_H
 
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 #include <QDialog>
 #include "ui_vvToolSimpleInputSelectorWidget.h"
 
diff --git a/vv/vvToolWidgetBase.h b/vv/vvToolWidgetBase.h
index 7a3a5dfd..2c9af33c 100644
--- a/vv/vvToolWidgetBase.h
+++ b/vv/vvToolWidgetBase.h
@@ -20,11 +20,11 @@
 #define VVTOOLWIDGETBASE_H
 
 #include <QtGlobal>
-#if QT_VERSION >= 0x050000
-#include <QtUiPlugin/QDesignerExportWidget>
-#else
-#include <QtDesigner/QDesignerExportWidget>
-#endif
+//#if QT_VERSION >= 0x050000
+//#include <QtUiPlugin/QDesignerExportWidget>
+//#else
+//#include <QtDesigner/QDesignerExportWidget>
+//#endif
 #include "ui_vvToolWidgetBase.h"
 #include "clitkImageToImageGenericFilter.h"