diff --git a/Mainwindow.cpp b/Mainwindow.cpp
index 7013133..6778b11 100644
--- a/Mainwindow.cpp
+++ b/Mainwindow.cpp
@@ -40,8 +40,7 @@ MainWindow::MainWindow(QWidget *parent) :
     ui->lineEdit_licksToReward->setValidator(intValidator);
     ui->lineEdit_iti->setValidator(doubleValidator);
 
-
-    connect(this,SIGNAL(paused()), &smc, SIGNAL(pauseRequested()));
+    connect(&smc, SIGNAL(statusMessage(QString)), this, SLOT(onStatusMessage(QString)));
 
 }
 
@@ -88,39 +87,30 @@ void MainWindow::on_pushButton_Run_clicked()
     }
 
     qDebug()<< settings.itiSequence;
-
-
-
-    smc.runStateMachine(settings);
+    smc.startStateMachine(settings);
 }
 
 void MainWindow::on_pushButton_Pause_toggled(bool checked)
 {
+    smc.pauseStateMachine();
     if (checked) {
-        qDebug() << "Paused";
         ui->statusBar->showMessage("Paused");
         ui->pushButton_Pause->setText("Resume");
-        emit(paused());
-
-
     } else {
-        qDebug() << "Resumed";
         ui->statusBar->showMessage("Resumed");
         ui->pushButton_Pause->setText("Pause");
-        emit(resumed());
     }
-
 }
 
 void MainWindow::on_pushButton_Stop_clicked()
 {
-//    timerDialog->removeTimer();
-//    mainTimer->stop();
-//    stateMachine->stop();
+    smc.stopStateMachine();
     qDebug() << "Stopped and terminated";
     ui->statusBar->showMessage("Stopped and terminated");
     ui->pushButton_Run->setDisabled(false);
-    emit(stopped());
+    ui->pushButton_Pause->setChecked(false);
+    ui->pushButton_Pause->setText("Pause");
+
 }
 
 
@@ -223,6 +213,11 @@ void MainWindow::on_lineEdit_preImaq_editingFinished()
     updateIti();
 }
 
+void MainWindow::onStatusMessage(QString statusMessage)
+{
+    ui->statusBar->showMessage(statusMessage);
+}
+
 void MainWindow::updateIti()
 {
     double preImaq = ui->lineEdit_preImaq->text().toDouble();
diff --git a/Mainwindow.h b/Mainwindow.h
index 6840c46..c3ff71d 100644
--- a/Mainwindow.h
+++ b/Mainwindow.h
@@ -43,6 +43,8 @@ private slots:
     void on_lineEdit_iti_editingFinished();
     void on_lineEdit_preImaq_editingFinished();
 
+    void onStatusMessage(QString statusMessage);
+
 
 private:
     Ui::MainWindow *ui;
@@ -61,12 +63,6 @@ private slots:
     QString selectedDirectory;
     QString selectedPositiveFileName;
     QString selectedNegativeFileName;
-
-signals:
-    void paused();
-    void resumed();
-    void stopped();
-
 };
 
 #endif // MAINWINDOW_H
diff --git a/StateMachineController.cpp b/StateMachineController.cpp
index a83098a..341b584 100644
--- a/StateMachineController.cpp
+++ b/StateMachineController.cpp
@@ -29,8 +29,8 @@ StateMachineController::StateMachineController(QObject *parent)
      * of the object will be set to false/true.
      */
 
-    runningState->assignProperty(this, "paused", false);
-    pausedState->assignProperty(this, "paused", true);
+//    runningState->assignProperty(this, "paused", false);
+//    pausedState->assignProperty(this, "paused", true);
 
     state_preDelay->addTransition(mainTimer, SIGNAL(timeout()), state_iti);
     state_iti->addTransition(mainTimer, SIGNAL(timeout()), state_userReaction);
@@ -71,10 +71,15 @@ StateMachineController::StateMachineController(QObject *parent)
     //connect(state_sound, SIGNAL(entered()), mainTimer, SLOT(start()));
     connect(state_sound, SIGNAL(exited()), this, SLOT(onStateSoundExited()));
 
+
+    connect(pausedState, SIGNAL(entered()), this, SLOT(onStatePauseEntered()));
 }
 
-void StateMachineController::runStateMachine(audioGameSettings settings)
+void StateMachineController::startStateMachine(audioGameSettings settings)
 {
+    if(stateMachine->isRunning())
+        stateMachine->stop();
+
     this->settings = settings;
     trialsCurrent = 1; // set index for first trial (1-based)
     trialsTotal = settings.trialSequence.length();
@@ -104,6 +109,18 @@ void StateMachineController::runStateMachine(audioGameSettings settings)
 
 }
 
+void StateMachineController::pauseStateMachine()
+{
+    emit(pauseRequested());
+}
+
+void StateMachineController::stopStateMachine()
+{
+    timerDialog->removeTimer();
+    mainTimer->stop();
+    stateMachine->stop();
+}
+
 
 void StateMachineController::onStatePreDelayEntered()
 {
@@ -126,10 +143,10 @@ void StateMachineController::onStateItiEntered()
 
 void StateMachineController::onStateUserReactionEntered()
 {
-//    timerDialog->removeTimer(); // remove previous timer dialog
-//    timerDialog->setUpTimer(settings.userReaction);
-//    timerDialog->show();
-//    timerDialog->startTimer();
+    timerDialog->removeTimer(); // remove previous timer dialog
+    timerDialog->setUpTimer(settings.userReaction);
+    timerDialog->show();
+    timerDialog->startTimer();
 
     qDebug()<< "Starting user reaction";
     emit(statusMessage("Starting user reaction"));
@@ -198,22 +215,8 @@ void StateMachineController::onStateSoundExited()
     }
 }
 
-
-//timerDialog->removeTimer();
-//bool MainWindow::paused() const
-//{
-//    return false;//m_paused;
-//}
-
-//void MainWindow::setPaused(bool paused)
-//{
-////    if (m_paused != paused) {
-////        m_paused = paused;
-////        emit pausedChanged();
-////    }
-//}
-
-//void MainWindow::pause()
-//{
-//    //emit pauseRequested();
-//}
+void StateMachineController::onStatePauseEntered()
+{
+    qDebug()<<"Pause state entered";
+     timerDialog->removeTimer();
+}
diff --git a/StateMachineController.h b/StateMachineController.h
index 0400d45..e1926b7 100644
--- a/StateMachineController.h
+++ b/StateMachineController.h
@@ -22,7 +22,10 @@ class StateMachineController : public QObject
 public:
     explicit StateMachineController(QObject *parent = 0);
     audioGameSettings settings;
-    void runStateMachine(audioGameSettings);
+    void startStateMachine(audioGameSettings);
+    void pauseStateMachine();
+    void stopStateMachine();
+
 
 private:
     // state machine
@@ -52,16 +55,10 @@ public slots:
     void onStateAcquisitionBaselineEntered();
     void onStateSoundEntered();
     void onStateSoundExited();
+    void onStatePauseEntered();
 
 signals:
     void statusMessage(QString);
-//Q_SIGNALS:
-    // change notification signals for the state properties
-     void pausedChanged();
-    /**
-     * This signal is emitted when the pause() slot is invoked and is used
-     * by the internal state machine only.
-     */
     void pauseRequested();