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 4027f2b176..bc674b04d4 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 +1,104 @@
 /*============================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center (DKFZ)
 All rights reserved.
 
 Use of this source code is governed by a 3-clause BSD license that can be
 found in the LICENSE file.
 
 ============================================================================*/
 
 #include "org_mitk_gui_qt_flow_segmentation_Activator.h"
 
 // Blueberry
 #include <berryISelectionService.h>
 #include <berryIWorkbenchWindow.h>
 
 #include <itksys/SystemTools.hxx>
 
 //MITK
-#include "mitkLabelSetImage.h"
-#include "mitkNodePredicateAnd.h"
-#include "mitkNodePredicateNot.h"
-#include "mitkNodePredicateProperty.h"
-#include "mitkNodePredicateDataType.h"
-#include "mitkIOUtil.h"
+#include <mitkBaseApplication.h>
+#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>
 #include <QDir>
 
 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 = QString::fromStdString(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)
-    {
-      if (isFlagFound)
-      {
-        m_OutputDir = arg;
-        break;
-      }
-      isFlagFound = arg.startsWith("--flow.outputdir");
-    }
-    isFlagFound = false;
-    for (auto arg : arguments)
-    {
-      if (isFlagFound)
-      {
-        m_FileExtension = arg;
-        break;
-      }
-      isFlagFound = arg.startsWith("--flow.outputextension");
-    }
-
-    m_OutputDir = QDir::fromNativeSeparators(m_OutputDir);
+  // 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();
+
+  m_OutputDir = QString::fromStdString(mitk::BaseApplication::instance().config().getString("flow.outputdir", itksys::SystemTools::GetCurrentWorkingDirectory()));
+  m_OutputDir = QDir::fromNativeSeparators(m_OutputDir);
+
+  m_FileExtension = QString::fromStdString(mitk::BaseApplication::instance().config().getString("flow.outputextension", "nrrd"));
 }
 
 void QmitkSegmentationFlowControlView::OnAcceptButtonPushed()
 {
   auto nodes = this->GetDataStorage()->GetSubset(m_SegmentationPredicate);
 
   for (auto node : *nodes)
   {
     QString outputpath = m_OutputDir + "/" + QString::fromStdString(node->GetName()) + "." + m_FileExtension;
     outputpath = QDir::toNativeSeparators(QDir::cleanPath(outputpath));
     mitk::IOUtil::Save(node->GetData(), outputpath.toStdString());
   }
 
   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();
 };