diff --git a/Applications/FlowBench/MitkFlowBench.cpp b/Applications/FlowBench/MitkFlowBench.cpp
index 68f548deb5..55cc928c43 100644
--- a/Applications/FlowBench/MitkFlowBench.cpp
+++ b/Applications/FlowBench/MitkFlowBench.cpp
@@ -1,42 +1,77 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center,
 Division of Medical and Biological Informatics.
 All rights reserved.
 
 This software is distributed WITHOUT ANY WARRANTY; without
 even the implied warranty of MERCHANTABILITY or FITNESS FOR
 A PARTICULAR PURPOSE.
 
 See LICENSE.txt or http://www.mitk.org for details.
 
 ===================================================================*/
 
 #include <mitkBaseApplication.h>
 
 #include <QVariant>
 
+
+class FlowApplication : public mitk::BaseApplication
+{
+public:
+  static const QString ARG_OUTPUTDIR;
+  static const QString ARG_OUTPUTFORMAT;
+
+  FlowApplication(int argc, char **argv) : mitk::BaseApplication(argc, argv)
+  {
+  };
+
+  ~FlowApplication() = default;
+
+protected:
+  /**
+  * Define command line arguments
+  * @param options
+  */
+  void defineOptions(Poco::Util::OptionSet &options) override
+  {
+    Poco::Util::Option outputDirOption(ARG_OUTPUTDIR.toStdString(), "", "the location for storing persistent application data");
+    outputDirOption.argument("<dir>").binding(ARG_OUTPUTDIR.toStdString());
+    options.addOption(outputDirOption);
+
+    Poco::Util::Option outputFormatOption(ARG_OUTPUTFORMAT.toStdString(), "", "the location for storing persistent application data");
+    outputFormatOption.argument("<format>").binding(ARG_OUTPUTFORMAT.toStdString());
+    options.addOption(outputFormatOption);
+
+    mitk::BaseApplication::defineOptions(options);
+  };
+};
+
+const QString FlowApplication::ARG_OUTPUTDIR = "flow.outputdir";
+const QString FlowApplication::ARG_OUTPUTFORMAT = "flow.outputformat";
+
 int main(int argc, char **argv)
 {
-  mitk::BaseApplication app(argc, argv);
+  FlowApplication app(argc, argv);
 
   app.setSingleMode(true);
   app.setApplicationName("MITK FlowBench");
   app.setOrganizationName("DKFZ");
 
   // Preload the org.mitk.gui.qt.application plug-in to speed
   // up a clean-cache start. This also works around bugs in older gcc and glibc implementations,
   // which have difficulties with multiple dynamic opening and closing of shared libraries with
   // many global static initializers. It also helps if dependent libraries have weird static
   // initialization methods and/or missing de-initialization code.
   QStringList preloadLibs;
   preloadLibs << "org_mitk_gui_qt_application";
   app.setPreloadLibraries(preloadLibs);
 
   app.setProperty(mitk::BaseApplication::PROP_PRODUCT, "org.mitk.gui.qt.flowapplication.workbench");
 
   // Run the workbench.
   return app.run();
 }
diff --git a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.cpp b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.cpp
index fd2d75d944..11e344c603 100644
--- a/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.cpp
+++ b/Plugins/org.mitk.gui.qt.flow.segmentation/src/internal/QmitkSegmentationFlowControlView.cpp
@@ -1,126 +1,129 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center,
 Division of Medical and Biological Informatics.
 All rights reserved.
 
 This software is distributed WITHOUT ANY WARRANTY; without
 even the implied warranty of MERCHANTABILITY or FITNESS FOR
 A PARTICULAR PURPOSE.
 
 See LICENSE.txt or http://www.mitk.org for details.
 
 ===================================================================*/
 
 #include "org_mitk_gui_qt_flow_segmentation_Activator.h"
 
 // Blueberry
 #include <berryISelectionService.h>
 #include <berryIWorkbenchWindow.h>
+#include <berryPlatform.h>
 
 #include <itksys/SystemTools.hxx>
 
 //MITK
 #include "mitkLabelSetImage.h"
 #include "mitkNodePredicateAnd.h"
 #include "mitkNodePredicateNot.h"
 #include "mitkNodePredicateProperty.h"
 #include "mitkNodePredicateDataType.h"
 #include "mitkIOUtil.h"
 
 // Qmitk
 #include "QmitkSegmentationFlowControlView.h"
 
 // Qt
 #include <QMessageBox>
 
 const std::string QmitkSegmentationFlowControlView::VIEW_ID = "org.mitk.views.flow.control";
 
 QmitkSegmentationFlowControlView::QmitkSegmentationFlowControlView()
     : m_Parent(nullptr)
 {
   auto nodePredicate = mitk::NodePredicateAnd::New();
   nodePredicate->AddPredicate(mitk::TNodePredicateDataType<mitk::LabelSetImage>::New());
   nodePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")));
   m_SegmentationPredicate = nodePredicate;
 
   m_OutputDir = itksys::SystemTools::GetCurrentWorkingDirectory();
   m_FileExtension = "nrrd";
 }
 
 void QmitkSegmentationFlowControlView::SetFocus()
 {
     m_Controls.btnStoreAndAccept->setFocus();
 }
 
 void QmitkSegmentationFlowControlView::CreateQtPartControl(QWidget* parent)
 {
     // create GUI widgets from the Qt Designer's .ui file
     m_Controls.setupUi(parent);
 
     m_Parent = parent;
 
     connect(m_Controls.btnStoreAndAccept, SIGNAL(clicked()), this, SLOT(OnAcceptButtonPushed()));
 
     m_Controls.labelStored->setVisible(false);
     UpdateControls();
 
 
     auto arguments = QCoreApplication::arguments();
+
     bool isFlagFound = false;
     for (auto arg : arguments)
     {
+      std::cout << "arg: " << arg << std::endl;
       if (isFlagFound)
       {
         m_OutputDir = arg.toStdString();
         break;
       }
       isFlagFound = arg.startsWith("--flow.outputdir");
     }
     isFlagFound = false;
     for (auto arg : arguments)
     {
       if (isFlagFound)
       {
         m_FileExtension = arg.toStdString();
         break;
       }
       isFlagFound = arg.startsWith("--flow.outputformat");
     }
 }
 
 void QmitkSegmentationFlowControlView::OnAcceptButtonPushed()
 {
   auto nodes = this->GetDataStorage()->GetSubset(m_SegmentationPredicate);
 
   for (auto node : *nodes)
   {
     std::string outputpath = m_OutputDir + "\\" + node->GetName() + "." + m_FileExtension;
     mitk::IOUtil::Save(node->GetData(), outputpath);
   }
 
   m_Controls.labelStored->setVisible(true);
 }
 
 void QmitkSegmentationFlowControlView::UpdateControls()
 {
   auto nodes = this->GetDataStorage()->GetSubset(m_SegmentationPredicate);
   m_Controls.btnStoreAndAccept->setEnabled(!nodes->empty());
 };
 
 void QmitkSegmentationFlowControlView::NodeAdded(const mitk::DataNode* /*node*/)
 {
   UpdateControls();
 };
 
 void QmitkSegmentationFlowControlView::NodeChanged(const mitk::DataNode* /*node*/)
 {
   UpdateControls();
 };
 
 void QmitkSegmentationFlowControlView::NodeRemoved(const mitk::DataNode* /*node*/)
 {
   UpdateControls();
 };