diff --git a/applications/mne_scan/plugins/neuronalconnectivity/neuronalconnectivity.cpp b/applications/mne_scan/plugins/neuronalconnectivity/neuronalconnectivity.cpp
index 7a7838fd0da..8ad64117590 100644
--- a/applications/mne_scan/plugins/neuronalconnectivity/neuronalconnectivity.cpp
+++ b/applications/mne_scan/plugins/neuronalconnectivity/neuronalconnectivity.cpp
@@ -109,7 +109,7 @@ NeuronalConnectivity::NeuronalConnectivity()
 
 NeuronalConnectivity::~NeuronalConnectivity()
 {
-    if(this->isRunning()) {
+    if(m_bProcessOutput) {
         stop();
     }
 }
@@ -195,7 +195,8 @@ void NeuronalConnectivity::unload()
 bool NeuronalConnectivity::start()
 {
     //Start thread
-    QThread::start();
+    m_bProcessOutput = true;
+    m_OutputProcessingThread = std::thread(&NeuronalConnectivity::run, this);
 
     return true;
 }
@@ -206,8 +207,11 @@ bool NeuronalConnectivity::stop()
 {
     m_pRtConnectivity->restart();
 
-    requestInterruption();
-    wait(500);
+    m_bProcessOutput = false;
+
+    if(m_OutputProcessingThread.joinable()){
+        m_OutputProcessingThread.join();
+    }
 
     m_bPluginControlWidgetsInit = false;
 
@@ -510,13 +514,13 @@ void NeuronalConnectivity::run()
             break;
         }
         m_mutex.unlock();
-        msleep(100);
+        std::this_thread::sleep_for(std::chrono::milliseconds(100));
     }
 
     int skip_count = 0;
     Network network;
 
-    while(!isInterruptionRequested()) {
+    while(m_bProcessOutput) {
         //Do processing after skip count has reached limit
         if((skip_count % m_iDownSample) == 0) {
             if(m_pCircularBuffer->pop(network)) {
@@ -562,7 +566,7 @@ void NeuronalConnectivity::onMetricChanged(const QString& sMetric)
 
     m_sConnectivityMethods = QStringList() << sMetric;
     m_connectivitySettings.setConnectivityMethods(m_sConnectivityMethods);
-    if(m_pRtConnectivity && this->isRunning()) {
+    if(m_pRtConnectivity && m_bProcessOutput) {
         m_pRtConnectivity->restart();
         m_pRtConnectivity->append(m_connectivitySettings);
     }
diff --git a/applications/mne_scan/plugins/neuronalconnectivity/neuronalconnectivity.h b/applications/mne_scan/plugins/neuronalconnectivity/neuronalconnectivity.h
index 4d97e087ba0..a175a1904b0 100644
--- a/applications/mne_scan/plugins/neuronalconnectivity/neuronalconnectivity.h
+++ b/applications/mne_scan/plugins/neuronalconnectivity/neuronalconnectivity.h
@@ -49,6 +49,8 @@
 #include <connectivity/connectivitysettings.h>
 #include <connectivity/network/network.h>
 
+#include <thread>
+
 //=============================================================================================================
 // QT INCLUDES
 //=============================================================================================================
@@ -272,6 +274,9 @@ class NEURONALCONNECTIVITYSHARED_EXPORT NeuronalConnectivity : public SCSHAREDLI
     Eigen::RowVectorXi          m_vecPicks;                     /**< The picked data channels. */
 
     CONNECTIVITYLIB::Network    m_currentConnectivityResult;    /**< The current connectivity result.*/
+
+    std::thread             m_OutputProcessingThread;
+    std::atomic_bool        m_bProcessOutput;
 };
 } // NAMESPACE
 
diff --git a/applications/mne_scan/plugins/noisereduction/noisereduction.cpp b/applications/mne_scan/plugins/noisereduction/noisereduction.cpp
index e99b1a66443..026a27eac95 100644
--- a/applications/mne_scan/plugins/noisereduction/noisereduction.cpp
+++ b/applications/mne_scan/plugins/noisereduction/noisereduction.cpp
@@ -111,7 +111,7 @@ NoiseReduction::NoiseReduction()
 
 NoiseReduction::~NoiseReduction()
 {
-    if(this->isRunning()) {
+    if(m_bProcessOutput) {
         stop();
     }
 }
@@ -159,8 +159,11 @@ bool NoiseReduction::start()
 
 bool NoiseReduction::stop()
 {
-    requestInterruption();
-    wait(500);
+    m_bProcessOutput = false;
+
+    if(m_OutputProcessingThread.joinable()){
+        m_OutputProcessingThread.join();
+    }
 
     m_iMaxFilterTapSize = -1;
 
@@ -224,7 +227,8 @@ void NoiseReduction::update(SCMEASLIB::Measurement::SPtr pMeasurement)
             if(m_iMaxFilterTapSize == -1) {
                 m_iMaxFilterTapSize = pRTMSA->getMultiSampleArray().first().cols();
                 initPluginControlWidgets();
-                QThread::start();
+                m_bProcessOutput = true;
+                m_OutputProcessingThread = std::thread(&NoiseReduction::run, this);
             }
 
             for(unsigned char i = 0; i < pRTMSA->getMultiSampleArray().size(); ++i) {
@@ -345,7 +349,7 @@ void NoiseReduction::run()
     MatrixXd matData;
     QScopedPointer<RTPROCESSINGLIB::FilterOverlapAdd> pRtFilter(new RTPROCESSINGLIB::FilterOverlapAdd());
 
-    while(!isInterruptionRequested()) {
+    while(m_bProcessOutput) {
         // Get the current data
         if(m_pCircularBuffer->pop(matData)) {
             m_mutex.lock();
@@ -409,7 +413,7 @@ void NoiseReduction::run()
             m_mutex.unlock();
 
             //Send the data to the connected plugins and the display
-            if(!isInterruptionRequested()) {
+            if(m_bProcessOutput) {
                 m_pNoiseReductionOutput->measurementData()->setValue(matData);
             }
         }
diff --git a/applications/mne_scan/plugins/noisereduction/noisereduction.h b/applications/mne_scan/plugins/noisereduction/noisereduction.h
index 15bc4153396..6d45e8382f0 100644
--- a/applications/mne_scan/plugins/noisereduction/noisereduction.h
+++ b/applications/mne_scan/plugins/noisereduction/noisereduction.h
@@ -50,6 +50,8 @@
 
 #include <scShared/Plugins/abstractalgorithm.h>
 
+#include <thread>
+
 //=============================================================================================================
 // QT INCLUDES
 //=============================================================================================================
@@ -263,6 +265,8 @@ class NOISEREDUCTIONSHARED_EXPORT NoiseReduction : public SCSHAREDLIB::AbstractA
     SCSHAREDLIB::PluginInputData<SCMEASLIB::RealTimeMultiSampleArray>::SPtr      m_pNoiseReductionInput;      /**< The RealTimeMultiSampleArray of the NoiseReduction input.*/
     SCSHAREDLIB::PluginOutputData<SCMEASLIB::RealTimeMultiSampleArray>::SPtr     m_pNoiseReductionOutput;     /**< The RealTimeMultiSampleArray of the NoiseReduction output.*/
 
+    std::thread             m_OutputProcessingThread;
+    std::atomic_bool        m_bProcessOutput;
 signals:
 };
 } // NAMESPACE
diff --git a/applications/mne_scan/plugins/rtcmne/rtcmne.cpp b/applications/mne_scan/plugins/rtcmne/rtcmne.cpp
index 4101491b538..4eb0c8ae282 100644
--- a/applications/mne_scan/plugins/rtcmne/rtcmne.cpp
+++ b/applications/mne_scan/plugins/rtcmne/rtcmne.cpp
@@ -115,7 +115,7 @@ RtcMne::~RtcMne()
 {
     m_future.waitForFinished();
 
-    if(this->isRunning()) {
+    if(m_bProcessOutput) {
         stop();
     }
 }
@@ -313,7 +313,8 @@ bool RtcMne::calcFiffInfo()
 
 bool RtcMne::start()
 {
-    QThread::start();
+    m_bProcessOutput = true;
+    m_OutputProcessingThread = std::thread(&RtcMne::run, this);
     return true;
 }
 
@@ -321,8 +322,11 @@ bool RtcMne::start()
 
 bool RtcMne::stop()
 {
-    requestInterruption();
-    wait(500);
+    m_bProcessOutput = false;
+
+    if(m_OutputProcessingThread.joinable()){
+        m_OutputProcessingThread.join();
+    }
 
     m_qListCovChNames.clear();
     m_bEvokedInput = false;
@@ -369,7 +373,7 @@ void RtcMne::updateRTFS(SCMEASLIB::Measurement::SPtr pMeasurement)
             m_qMutex.unlock();
 
             // update inverse operator
-            if(this->isRunning() && m_pRtInvOp) {
+            if(m_bProcessOutput && m_pRtInvOp) {
                 m_pRtInvOp->setFwdSolution(m_pFwd);
                 m_pRtInvOp->append(*m_pNoiseCov);
             }
@@ -386,7 +390,7 @@ void RtcMne::updateRTMSA(SCMEASLIB::Measurement::SPtr pMeasurement)
     if(m_pFwd) {
         QSharedPointer<RealTimeMultiSampleArray> pRTMSA = pMeasurement.dynamicCast<RealTimeMultiSampleArray>();
 
-        if(pRTMSA && this->isRunning()) {
+        if(pRTMSA && m_bProcessOutput) {
             //Fiff Information of the RTMSA
             m_qMutex.lock();
             if(!m_pFiffInfoInput) {
@@ -400,7 +404,7 @@ void RtcMne::updateRTMSA(SCMEASLIB::Measurement::SPtr pMeasurement)
                 initPluginControlWidgets();
             }
 
-            if(this->isRunning()) {
+            if(m_bProcessOutput) {
                 // Check for artifacts
                 QMap<QString,double> mapReject;
                 mapReject.insert("eog", 150e-06);
@@ -433,7 +437,7 @@ void RtcMne::updateRTC(SCMEASLIB::Measurement::SPtr pMeasurement)
     if(m_pFwd) {
         QSharedPointer<RealTimeCov> pRTC = pMeasurement.dynamicCast<RealTimeCov>();
 
-        if(pRTC && this->isRunning()) {
+        if(pRTC && m_bProcessOutput) {
             // Init Real-Time inverse estimator
             if(!m_pRtInvOp && m_pFiffInfo && m_pFwd) {
                 m_pRtInvOp = RtInvOp::SPtr(new RtInvOp(m_pFiffInfo, m_pFwd));
@@ -446,7 +450,7 @@ void RtcMne::updateRTC(SCMEASLIB::Measurement::SPtr pMeasurement)
                 m_qListCovChNames = pRTC->getValue()->names;
             }
 
-            if(this->isRunning() && m_pRtInvOp){
+            if(m_bProcessOutput && m_pRtInvOp){
                 m_pNoiseCov = pRTC->getValue();
                 m_pRtInvOp->append(*m_pNoiseCov);
             }
@@ -467,7 +471,7 @@ void RtcMne::updateRTE(SCMEASLIB::Measurement::SPtr pMeasurement)
                 initPluginControlWidgets();
             }
 
-            if(!this->isRunning() || !lResponsibleTriggerTypes.contains(m_sAvrType)) {
+            if(!m_bProcessOutput || !lResponsibleTriggerTypes.contains(m_sAvrType)) {
                 return;
             }
 
@@ -491,7 +495,7 @@ void RtcMne::updateRTE(SCMEASLIB::Measurement::SPtr pMeasurement)
                 initPluginControlWidgets();
             }
 
-            if(this->isRunning()) {
+            if(m_bProcessOutput) {
                 for(int i = 0; i < pFiffEvokedSet->evoked.size(); ++i) {
                     if(pFiffEvokedSet->evoked.at(i).comment == m_sAvrType) {
                         // Store current evoked as member so we can dispatch it if the time pick by the user changed
@@ -551,7 +555,7 @@ void RtcMne::onTimePointValueChanged(int iTimePointMs)
         m_iTimePointSps = m_pFiffInfoInput->sfreq * (float)iTimePointMs * 0.001f;
         m_qMutex.unlock();
 
-        if(this->isRunning()) {
+        if(m_bProcessOutput) {
             while(!m_pCircularEvokedBuffer->push(m_currentEvoked)) {
                 //Do nothing until the circular buffer is ready to accept new data again
             }
@@ -565,7 +569,7 @@ void RtcMne::run()
 {
     // Wait for fiff info to arrive
     while(!calcFiffInfo()) {
-        msleep(200);
+        std::this_thread::sleep_for(std::chrono::milliseconds(200));
     }
 
     // Init parameters
@@ -588,7 +592,7 @@ void RtcMne::run()
     QStringList lChNamesInvOp;
 
     // Start processing data
-    while(!isInterruptionRequested()) {
+    while(m_bProcessOutput) {
         m_qMutex.lock();
         iTimePointSps = m_iTimePointSps;
         bEvokedInput = m_bEvokedInput;
diff --git a/applications/mne_scan/plugins/rtcmne/rtcmne.h b/applications/mne_scan/plugins/rtcmne/rtcmne.h
index 83c36037120..fa3c2cf0faf 100644
--- a/applications/mne_scan/plugins/rtcmne/rtcmne.h
+++ b/applications/mne_scan/plugins/rtcmne/rtcmne.h
@@ -50,6 +50,8 @@
 
 #include <mne/mne_inverse_operator.h>
 
+#include <thread>
+
 //=============================================================================================================
 // QT INCLUDES
 //=============================================================================================================
@@ -265,6 +267,9 @@ class RTCMNESHARED_EXPORT RtcMne : public SCSHAREDLIB::AbstractAlgorithm
 
     MNELIB::MNEInverseOperator      m_invOp;                    /**< The inverse operator. */
 
+    std::thread             m_OutputProcessingThread;
+    std::atomic_bool        m_bProcessOutput;
+
 signals:
     void responsibleTriggerTypesChanged(const QStringList& lResponsibleTriggerTypes);
 
diff --git a/applications/mne_scan/plugins/rtfwd/rtfwd.cpp b/applications/mne_scan/plugins/rtfwd/rtfwd.cpp
index b4384cc3841..711784b8f8e 100644
--- a/applications/mne_scan/plugins/rtfwd/rtfwd.cpp
+++ b/applications/mne_scan/plugins/rtfwd/rtfwd.cpp
@@ -115,7 +115,7 @@ RtFwd::~RtFwd()
 {
     m_future.waitForFinished();
 
-    if(this->isRunning()) {
+    if(m_bProcessOutput) {
         stop();
     }
 }
@@ -222,7 +222,8 @@ bool RtFwd::start()
     stream->close();
 
     //Start thread
-    QThread::start();
+    m_bProcessOutput = true;
+    m_OutputProcessingThread = std::thread(&RtFwd::run, this);
 
     return true;
 }
@@ -231,8 +232,11 @@ bool RtFwd::start()
 
 bool RtFwd::stop()
 {
-    requestInterruption();
-    wait(500);
+    m_bProcessOutput = false;
+
+    if(m_OutputProcessingThread.joinable()){
+        m_OutputProcessingThread.join();
+    }
 
     m_bPluginControlWidgetsInit = false;
 
@@ -400,7 +404,7 @@ void RtFwd::run()
             break;
         }
         m_mutex.unlock();
-        msleep(200);
+        std::this_thread::sleep_for(std::chrono::milliseconds(200));
     }
 
     m_mutex.lock();
@@ -429,7 +433,7 @@ void RtFwd::run()
     bool bDoFwdComputation = false;             // compute forward if requested
     bool bIsInit = false;                       // only recompute if initial fwd solulion is calculated
 
-    while(!isInterruptionRequested()) {
+    while(m_bProcessOutput) {
         m_mutex.lock();
         bDoFwdComputation = m_bDoFwdComputation;
         m_mutex.unlock();
diff --git a/applications/mne_scan/plugins/rtfwd/rtfwd.h b/applications/mne_scan/plugins/rtfwd/rtfwd.h
index 29078297177..ef7af2c3dbf 100644
--- a/applications/mne_scan/plugins/rtfwd/rtfwd.h
+++ b/applications/mne_scan/plugins/rtfwd/rtfwd.h
@@ -49,6 +49,8 @@
 
 #include <fiff/fiff_coord_trans.h>
 
+#include <thread>
+
 //=============================================================================================================
 // QT INCLUDES
 //=============================================================================================================
@@ -225,6 +227,9 @@ class RTFWDSHARED_EXPORT RtFwd : public SCSHAREDLIB::AbstractAlgorithm
 
     SCSHAREDLIB::PluginOutputData<SCMEASLIB::RealTimeFwdSolution>::SPtr         m_pRTFSOutput;          /**< The fwd solution.*/
 
+    std::thread             m_OutputProcessingThread;
+    std::atomic_bool        m_bProcessOutput;
+
 signals:
     //=========================================================================================================
     /**
diff --git a/applications/mne_scan/plugins/writetofile/writetofile.cpp b/applications/mne_scan/plugins/writetofile/writetofile.cpp
index 3b8f7f72b60..1ef213112c8 100644
--- a/applications/mne_scan/plugins/writetofile/writetofile.cpp
+++ b/applications/mne_scan/plugins/writetofile/writetofile.cpp
@@ -111,7 +111,7 @@ WriteToFile::WriteToFile()
 
 WriteToFile::~WriteToFile()
 {
-    if(this->isRunning()) {
+    if(m_bProcessOutput) {
         stop();
     }
 }
@@ -145,7 +145,8 @@ void WriteToFile::unload()
 
 bool WriteToFile::start()
 {
-    QThread::start();
+    m_bProcessOutput = true;
+    m_OutputProcessingThread = std::thread(&WriteToFile::run, this);
 
     return true;
 }
@@ -154,8 +155,11 @@ bool WriteToFile::start()
 
 bool WriteToFile::stop()
 {
-    requestInterruption();
-    wait();
+    m_bProcessOutput = false;
+
+    if(m_OutputProcessingThread.joinable()){
+        m_OutputProcessingThread.join();
+    }
 
     m_bPluginControlWidgetsInit = false;
 
@@ -293,7 +297,7 @@ void WriteToFile::run()
     MatrixXd matData;
     qint32 size = 0;
 
-    while(!isInterruptionRequested()) {
+    while(m_bProcessOutput) {
         if(m_pCircularBuffer) {
             //pop matrix
 
diff --git a/applications/mne_scan/plugins/writetofile/writetofile.h b/applications/mne_scan/plugins/writetofile/writetofile.h
index 1530c89d7b7..e849fe28230 100644
--- a/applications/mne_scan/plugins/writetofile/writetofile.h
+++ b/applications/mne_scan/plugins/writetofile/writetofile.h
@@ -46,6 +46,8 @@
 #include <scShared/Plugins/abstractalgorithm.h>
 #include <fiff/fifffilesharer.h>
 
+#include <thread>
+
 //=============================================================================================================
 // QT INCLUDES
 //=============================================================================================================
@@ -310,6 +312,9 @@ class WRITETOFILESHARED_EXPORT WriteToFile : public SCSHAREDLIB::AbstractAlgorit
     FIFFLIB::FiffFileSharer                 m_FileSharer;                   /**< Handles copying recording file and saving copy to shared directory. */
 
     QStringList                             m_lFileNames;                   /**< List of file names of latest recording */
+
+    std::thread             m_OutputProcessingThread;
+    std::atomic_bool        m_bProcessOutput;
 };
 } // NAMESPACE