diff --git a/Plugins/org.mitk.gui.qt.cli/src/internal/QmitkCmdLineModuleProgressWidget.cpp b/Plugins/org.mitk.gui.qt.cli/src/internal/QmitkCmdLineModuleProgressWidget.cpp
index 94c077ffd3..f56d4389c8 100644
--- a/Plugins/org.mitk.gui.qt.cli/src/internal/QmitkCmdLineModuleProgressWidget.cpp
+++ b/Plugins/org.mitk.gui.qt.cli/src/internal/QmitkCmdLineModuleProgressWidget.cpp
@@ -1,595 +1,603 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) University College London (UCL).
 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 "QmitkCmdLineModuleProgressWidget.h"
 #include "ui_QmitkCmdLineModuleProgressWidget.h"
 
 // Qt
 #include <QFile>
 #include <QVBoxLayout>
 #include <QLayoutItem>
 #include <QTextBrowser>
 
 // CTK
 #include <ctkCmdLineModuleFuture.h>
 #include <ctkCmdLineModuleManager.h>
 #include <ctkCmdLineModuleFrontend.h>
 #include <ctkCmdLineModuleDescription.h>
 #include <ctkCmdLineModuleParameter.h>
 
 // MITK
 #include <mitkIOUtil.h>
 #include <mitkDataStorage.h>
 #include <mitkDataNode.h>
 #include <QmitkCommonFunctionality.h>
 #include <QmitkCustomVariants.h>
 #include "QmitkCmdLineModuleFactoryGui.h"
 
 //-----------------------------------------------------------------------------
 QmitkCmdLineModuleProgressWidget::QmitkCmdLineModuleProgressWidget(QWidget *parent)
   : QWidget(parent)
 , m_ModuleManager(NULL)
 , m_DataStorage(NULL)
 , m_TemporaryDirectoryName("")
 , m_UI(new Ui::QmitkCmdLineModuleProgressWidget)
 , m_ModuleFrontEnd(NULL)
 , m_FutureWatcher(NULL)
 {
   m_UI->setupUi(this);
   m_UI->m_RemoveButton->setIcon(QApplication::style()->standardIcon(QStyle::SP_TitleBarCloseButton));
 
   m_Layout = new QVBoxLayout();
   m_UI->m_ParametersGroupBox->setLayout(m_Layout);
 
   qRegisterMetaType<mitk::DataNode::Pointer>();
   qRegisterMetaType<ctkCmdLineModuleReference>();
 
   // Due to Qt bug 12152, we cannot listen to the "paused" signal because it is
   // not emitted directly when the QFuture is paused. Instead, it is emitted after
   // resuming the future, after the "resume" signal has been emitted... we use
   // a polling approach instead.
   m_PollPauseTimer.setInterval(300);
   connect(&m_PollPauseTimer, SIGNAL(timeout()), SLOT(OnCheckModulePaused()));
 
   connect(m_UI->m_RemoveButton, SIGNAL(clicked()), this, SLOT(OnRemoveButtonClicked()));
 
   m_PollPauseTimer.start();
 }
 
 
 //-----------------------------------------------------------------------------
 QmitkCmdLineModuleProgressWidget::~QmitkCmdLineModuleProgressWidget()
 {
   if (m_ModuleFrontEnd != NULL)
   {
     delete m_ModuleFrontEnd;
   }
 
   this->ClearUpTemporaryFiles();
 
   delete m_UI;
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::SetManager(ctkCmdLineModuleManager* manager)
 {
   this->m_ModuleManager = manager;
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::SetDataStorage(mitk::DataStorage* dataStorage)
 {
   this->m_DataStorage = dataStorage;
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::SetTemporaryDirectory(const QString& directoryName)
 {
   this->m_TemporaryDirectoryName = directoryName;
 }
 
 
 //-----------------------------------------------------------------------------
 QString QmitkCmdLineModuleProgressWidget::GetTitle()
 {
   assert(m_ModuleFrontEnd);
 
   ctkCmdLineModuleReference reference = m_ModuleFrontEnd->moduleReference();
   ctkCmdLineModuleDescription description = reference.description();
 
   return description.title();
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::OnCheckModulePaused()
 {
   if (!this->IsStarted())
   {
     return;
   }
 
   if (this->m_FutureWatcher->future().isPaused())
   {
     if (!m_UI->m_PauseButton->isChecked())
     {
       m_UI->m_PauseButton->setChecked(true);
     }
   }
   else
   {
     if (m_UI->m_PauseButton->isChecked())
     {
       m_UI->m_PauseButton->setChecked(false);
     }
   }
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::OnPauseButtonToggled(bool toggled)
 {
   this->m_FutureWatcher->setPaused(toggled);
 
   if (toggled)
   {
     this->m_UI->m_ProgressTitle->setText(this->GetTitle() + ": paused");
   }
   else
   {
     this->m_UI->m_ProgressTitle->setText(this->GetTitle() + ": resumed");
   }
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::OnRemoveButtonClicked()
 {
   this->deleteLater();
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::OnModuleStarted()
 {
   this->m_UI->m_ProgressBar->setMaximum(0);
 
   QString message = "started.";
   this->PublishMessage(message);
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::OnModuleCanceled()
 {
+  QString message = "cancelling.";
+  this->PublishMessage(message);
+
   this->m_UI->m_PauseButton->setEnabled(false);
   this->m_UI->m_PauseButton->setChecked(false);
   this->m_UI->m_CancelButton->setEnabled(false);
   this->m_UI->m_RemoveButton->setEnabled(true);
 
   this->m_UI->m_ParametersGroupBox->setCollapsed(true);
   this->m_UI->m_ConsoleGroupBox->setCollapsed(true);
   this->m_UI->m_ProgressTitle->setText(this->GetTitle() + ": cancelled");
+
+  message = "cancelled.";
+  this->PublishMessage(message);
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::OnModuleFinished()
 {
-  QString message = "finishing.";
-  this->PublishMessage(message);
-
   this->m_UI->m_PauseButton->setEnabled(false);
   this->m_UI->m_PauseButton->setChecked(false);
   this->m_UI->m_CancelButton->setEnabled(false);
   this->m_UI->m_RemoveButton->setEnabled(true);
-  this->m_UI->m_ProgressTitle->setText(this->GetTitle() + ": finished");
 
   if (!this->m_FutureWatcher->isCanceled())
   {
+    QString message = "finishing.";
+    this->PublishMessage(message);
+
+    this->m_UI->m_ProgressTitle->setText(this->GetTitle() + ": finished");
+
     this->LoadOutputData();
     this->ClearUpTemporaryFiles();
-  }
 
-  message = "finished.";
-  this->PublishMessage(message);
+    message = "finished.";
+    this->PublishMessage(message);
+
+  }
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::OnModuleResumed()
 {
   this->m_UI->m_PauseButton->setChecked(false);
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::OnModuleProgressRangeChanged(int progressMin, int progressMax)
 {
   this->m_UI->m_ProgressBar->setMinimum(progressMin);
   this->m_UI->m_ProgressBar->setMaximum(progressMax);
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::OnModuleProgressTextChanged(const QString& progressText)
 {
   this->m_UI->m_Console->appendPlainText(progressText);
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::OnModuleProgressValueChanged(int progressValue)
 {
   this->m_UI->m_ProgressBar->setValue(progressValue);
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::PublishMessage(const QString& message)
 {
   QString prefix = ""; // Can put additional prefix here if needed.
   QString outputMessage = prefix + message;
 
   qDebug() << outputMessage;
   this->m_UI->m_Console->appendPlainText(outputMessage);
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::ClearUpTemporaryFiles()
 {
   QString message;
   QString fileName;
 
   foreach (fileName, m_TemporaryFileNames)
   {
     QFile file(fileName);
     if (file.exists())
     {
       message = QObject::tr("removing %1").arg(fileName);
       this->PublishMessage(message);
 
       bool success = file.remove();
 
       message = QObject::tr("removed %1, successfully=%2").arg(fileName).arg(success);
       this->PublishMessage(message);
     }
   }
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::LoadOutputData()
 {
   assert(m_DataStorage);
 
   std::vector<std::string> fileNames;
 
   QString fileName;
   foreach (fileName, m_OutputDataToLoad)
   {
     QString message = QObject::tr("loading %1").arg(fileName);
     this->PublishMessage(message);
 
     fileNames.push_back(fileName.toStdString());
   }
 
   if (fileNames.size() > 0)
   {
     int numberLoaded = mitk::IOUtil::LoadFiles(fileNames, *(m_DataStorage));
 
     QString message = QObject::tr("loaded %1 files").arg(numberLoaded);
     this->PublishMessage(message);
   }
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::SetModule(const ctkCmdLineModuleReference& reference)
 {
 
   assert(m_ModuleManager);
   assert(m_DataStorage);
 
   // If a widget exists, remove it from the layout and delete.
   QLayoutItem *item = m_Layout->itemAt(0);
   if (item != NULL)
   {
      m_Layout->removeItem(item);
      delete item;
   }
 
   // Also make sure we delete the layout.
   if (m_Layout != NULL)
   {
     delete m_Layout;
   }
 
   // If the corresponding front end exists, destroy it.
   if (m_ModuleFrontEnd != NULL)
   {
     delete m_ModuleFrontEnd;
   }
 
   m_Layout = new QVBoxLayout();
   m_Layout->setContentsMargins(5,0,5,0);
   m_Layout->setSpacing(0);
 
   m_UI->m_ParametersGroupBox->setLayout(m_Layout);
 
   // This method is called when the user selects a new module to display.
   // Aim of this method is to create a default GUI, and attach it to this widget.
 
   QmitkCmdLineModuleFactoryGui factory(m_DataStorage);
   m_ModuleFrontEnd = factory.create(reference);
 
   if (!m_ModuleFrontEnd)
   {
     qDebug() << "QmitkCmdLineModuleProgressWidget: Failed to SetModule() for " << reference.description().title();
     return;
   }
 
   // Build up the GUI layout programmatically (manually).
 
   QTabWidget *documentationTabWidget = new QTabWidget();
   documentationTabWidget->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Preferred);
 
   QWidget *aboutWidget = new QWidget();
   QWidget *helpWidget = new QWidget();
 
   QTextBrowser *aboutBrowser = new QTextBrowser(aboutWidget);
   aboutBrowser->setReadOnly(true);
   aboutBrowser->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Preferred);
 
   QTextBrowser *helpBrowser = new QTextBrowser(helpWidget);
   helpBrowser->setReadOnly(true);
   helpBrowser->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Preferred);
 
   QHBoxLayout *aboutLayout = new QHBoxLayout(aboutWidget);
   aboutLayout->addWidget(aboutBrowser);
   aboutLayout->setContentsMargins(0,0,0,0);
   aboutLayout->setSpacing(0);
 
   QHBoxLayout *helpLayout = new QHBoxLayout(helpWidget);
   helpLayout->addWidget(helpBrowser);
   helpLayout->setContentsMargins(0,0,0,0);
   helpLayout->setSpacing(0);
 
   documentationTabWidget->addTab(aboutWidget, "About");
   documentationTabWidget->addTab(helpWidget, "Help");
 
   QObject* guiHandle = m_ModuleFrontEnd->guiHandle();
   QWidget* generatedGuiWidgets = qobject_cast<QWidget*>(guiHandle);
 
   QWidget *topLevelWidget = new QWidget();
   QGridLayout *topLevelLayout = new QGridLayout(topLevelWidget);
 
   topLevelLayout->setContentsMargins(0,0,0,0);
   topLevelLayout->setSpacing(0);
   topLevelLayout->addWidget(documentationTabWidget, 0, 0);
   topLevelLayout->setRowStretch(0, 1);
   topLevelLayout->addWidget(generatedGuiWidgets, 1, 0);
   topLevelLayout->setRowStretch(1, 10);
 
   ctkCmdLineModuleDescription description = reference.description();
 
   QString helpString = "";
 
   if (!description.title().isEmpty())
   {
     QString titleHtml = "<h1>" + description.title() + "</h1>";
     helpString += titleHtml;
   }
 
   if (!description.description().isEmpty())
   {
     QString descriptionHtml = "<p>" + description.description() + "</p>";
     helpString += descriptionHtml;
   }
 
   if (!description.documentationURL().isEmpty())
   {
     QString docUrlHtml = "<p>For more information please see <a href=\"" + description.documentationURL() \
                          + "\">the online documentation</a>.</p>";
     helpString += docUrlHtml;
   }
 
   QString aboutString = "";
 
   if (!description.title().isEmpty())
   {
     QString titleHtml = "<h1>" + description.title() + "</h1>";
     aboutString += titleHtml;
   }
 
   if (!description.contributor().isEmpty())
   {
     QString contributorHtml = "<h2>Contributed By</h2><p>" + description.contributor() + "</p>";
     aboutString += contributorHtml;
   }
 
   if (!description.license().isEmpty())
   {
     QString licenseHtml = "<h2>License</h2><p>" + description.license() + "</p>";
     aboutString += licenseHtml;
   }
 
   if (!description.acknowledgements().isEmpty())
   {
     QString acknowledgementsHtml = "<h2>Acknowledgements</h2><p>" + description.acknowledgements() + "</p>";
     aboutString += acknowledgementsHtml;
   }
 
   helpBrowser->clear();
   helpBrowser->setHtml(helpString);
   aboutBrowser->clear();
   aboutBrowser->setHtml(aboutString);
 
   // So, we put the new GUI into the layout.
   m_Layout->insertWidget(0, topLevelWidget);
 
   // And configure a few other niceties.
   m_UI->m_ProgressTitle->setText(description.title());
   m_UI->m_ConsoleGroupBox->setCollapsed(true);
   m_UI->m_ParametersGroupBox->setCollapsed(false);
 }
 
 
 //-----------------------------------------------------------------------------
 QString QmitkCmdLineModuleProgressWidget::GetFullName() const
 {
   assert(m_ModuleFrontEnd);
 
   ctkCmdLineModuleDescription description = m_ModuleFrontEnd->moduleReference().description();
   QString fullName = description.category() + "." + description.title();
 
   return fullName;
 }
 
 
 //-----------------------------------------------------------------------------
 bool QmitkCmdLineModuleProgressWidget::IsStarted() const
 {
   bool isStarted = false;
   if (m_FutureWatcher != NULL && m_FutureWatcher->isStarted())
   {
     isStarted = true;
   }
   return isStarted;
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::Reset()
 {
   assert(m_ModuleFrontEnd);
 
   m_ModuleFrontEnd->resetValues();
 }
 
 
 //-----------------------------------------------------------------------------
 void QmitkCmdLineModuleProgressWidget::Run()
 {
   assert(m_ModuleManager);
   assert(m_ModuleFrontEnd);
 
   m_OutputDataToLoad.clear();
 
   ctkCmdLineModuleReference reference = m_ModuleFrontEnd->moduleReference();
   ctkCmdLineModuleDescription description = reference.description();
 
   QString message = "Saving image data to temporary storage...";
   this->PublishMessage(message);
 
   // Sanity check we have actually specified some input:
   QString parameterName;
   QList<ctkCmdLineModuleParameter> parameters;
 
   // For each input image, write a temporary file as a Nifti image,
   // and then save the full path name back on the parameter.
   parameters = m_ModuleFrontEnd->parameters("image", ctkCmdLineModuleFrontend::Input);
   foreach (ctkCmdLineModuleParameter parameter, parameters)
   {
     parameterName = parameter.name();
 
     QVariant tmp = m_ModuleFrontEnd->value(parameterName, ctkCmdLineModuleFrontend::UserRole);
     mitk::DataNode::Pointer node = tmp.value<mitk::DataNode::Pointer>();
 
     if (node.IsNotNull())
     {
       mitk::Image* image = dynamic_cast<mitk::Image*>(node->GetData());
       if (image != NULL)
       {
         QString name = QString::fromStdString(node->GetName());
         int pid = QCoreApplication::applicationPid();
         int randomInt = qrand() % 1000000;
 
         QString fileName = m_TemporaryDirectoryName + "/" + name + QString::number(pid) + "." + QString::number(randomInt) + ".nii";
 
         message = "Saving " + fileName;
         this->PublishMessage(message);
 
         std::string tmpFN = CommonFunctionality::SaveImage(image, fileName.toStdString().c_str());
         QString temporaryStorageFileName = QString::fromStdString(tmpFN);
 
         m_TemporaryFileNames.push_back(temporaryStorageFileName);
         m_ModuleFrontEnd->setValue(parameterName, temporaryStorageFileName);
 
         message = "Saved " + temporaryStorageFileName;
         this->PublishMessage(message);
       } // end if image
     } // end if node
   } // end foreach input image
 
   // For each output image or file, store the filename, so we can auto-load it once the process finishes.
   parameters = m_ModuleFrontEnd->parameters("image", ctkCmdLineModuleFrontend::Output);
   parameters << m_ModuleFrontEnd->parameters("file", ctkCmdLineModuleFrontend::Output);
 
   foreach (ctkCmdLineModuleParameter parameter, parameters)
   {
     parameterName = parameter.name();
     QString outputFileName = m_ModuleFrontEnd->value(parameterName).toString();
 
     if (!outputFileName.isEmpty())
     {
       m_OutputDataToLoad.push_back(outputFileName);
 
       message = "Command Line Module ... Registered " + outputFileName + " to auto load upon completion.";
       this->PublishMessage(message);
     }
   }
 
   // Now we run stuff.
   message = "starting.";
   this->PublishMessage(message);
 
   if (m_FutureWatcher == NULL)
   {
     m_FutureWatcher = new ctkCmdLineModuleFutureWatcher();
 
     connect(m_FutureWatcher, SIGNAL(started()), SLOT(OnModuleStarted()));
     connect(m_FutureWatcher, SIGNAL(canceled()), SLOT(OnModuleCanceled()));
     connect(m_FutureWatcher, SIGNAL(finished()), SLOT(OnModuleFinished()));
     connect(m_FutureWatcher, SIGNAL(resumed()), SLOT(OnModuleResumed()));
     connect(m_FutureWatcher, SIGNAL(progressRangeChanged(int,int)), SLOT(OnModuleProgressRangeChanged(int,int)));
     connect(m_FutureWatcher, SIGNAL(progressTextChanged(QString)), SLOT(OnModuleProgressTextChanged(QString)));
     connect(m_FutureWatcher, SIGNAL(progressValueChanged(int)), SLOT(OnModuleProgressValueChanged(int)));
 
     connect(m_UI->m_CancelButton, SIGNAL(clicked()), m_FutureWatcher, SLOT(cancel()));
     connect(m_UI->m_PauseButton, SIGNAL(toggled(bool)), this, SLOT(OnPauseButtonToggled(bool)));
 
   }
   ctkCmdLineModuleFuture future = m_ModuleManager->run(m_ModuleFrontEnd);
   m_FutureWatcher->setFuture(future);
 
   m_UI->m_PauseButton->setEnabled(future.canPause());
   m_UI->m_CancelButton->setEnabled(future.canCancel());
   m_UI->m_RemoveButton->setEnabled(!future.isRunning());
 
   // Configure some other niceties.
   m_UI->m_ParametersGroupBox->setCollapsed(true);
   m_UI->m_ConsoleGroupBox->setCollapsed(true);
 
   // Lock parameters, as once the module is running the user can't change them.
   m_Layout->itemAt(0)->widget()->setEnabled(false);
 
   // Give some immediate indication that we are running.
   m_UI->m_ProgressTitle->setText(description.title() + ": running");
 }