diff --git a/mainScript.m b/mainScript.m
index 2f3fa11..9c69cd4 100644
--- a/mainScript.m
+++ b/mainScript.m
@@ -34,6 +34,7 @@
 
     % Prepare for the output logfiles with all
     logFile.extraColumns = cfg.extraColumns;
+    logFile = saveEventsFile('init', cfg, logFile);
     logFile = saveEventsFile('open', cfg, logFile);
 
     disp(cfg);
@@ -48,7 +49,8 @@
 
     eyeTracker('StartRecording', cfg);
 
-    cfg = getExperimentStart(cfg);
+    % Wait for Trigger from Scanner and add timestamp of experiment onset
+    cfg.experimentStart = waitForTrigger(cfg);
 
     getResponse('start', cfg.keyboard.responseBox);
 
@@ -67,10 +69,8 @@
 
             [thisEvent, thisFixation, cfg] = preTrialSetup(cfg, iBlock, iTrial);
 
-            % AVAILABLE IN A NEW RELEASE SOON
-            %
-            % eyeTracker('Message', cfg, ...
-            %     ['start_trial-', num2str(iTrial), '_', thisEvent.trial_type]);
+            eyeTracker('Message', cfg, ...
+                       ['start_trial-', num2str(iTrial), '_', thisEvent.trial_type]);
 
             % play the dots and collect onset and duraton of the event
             [onset, duration] = doTrial(cfg, thisEvent, thisFixation);
@@ -79,7 +79,8 @@
                                      thisEvent, ...
                                      iBlock, ...
                                      iTrial, ...
-                                     duration, onset, ...
+                                     duration, ...
+                                     onset, ...
                                      cfg, ...
                                      logFile);
 
@@ -89,19 +90,22 @@
             % saving in the tsv file
             responseEvents = getResponse('check', cfg.keyboard.responseBox, cfg);
 
+            responseEvents(1).isStim = logFile.isStim;
             responseEvents(1).fileID = logFile.fileID;
             responseEvents(1).extraColumns = logFile.extraColumns;
             saveEventsFile('save', cfg, responseEvents);
 
-            % AVAILABLE IN A NEW RELEASE SOON
-            %
-            % eyeTracker('Message', cfg, ...
-            %     ['end_trial-', num2str(iTrial), '_', thisEvent.trial_type]);
+            eyeTracker('Message', cfg, ...
+                       ['end_trial-', num2str(iTrial), '_', thisEvent.trial_type]);
 
             waitFor(cfg, cfg.timing.ISI);
 
         end
 
+        eyeTracker('Message', cfg, ['end_block-', num2str(iBlock)]);
+
+        waitFor(cfg, cfg.timing.IBI);
+
     end
 
     % End of the run for the BOLD to go down
diff --git a/setParameters.m b/setParameters.m
index 04dd784..24b0c79 100644
--- a/setParameters.m
+++ b/setParameters.m
@@ -7,11 +7,12 @@
     % Initialize the parameters and general configuration variables
     cfg = struct();
 
-    % by default the data will be stored in an output folder created where the
-    % setParamters.m file is
-    % change that if you want the data to be saved somewhere else
+    % By default the data will be stored in an output folder created one folder up where the
+    % setParamters.m file is. with CPP_BIDS 2.3.0 this will change.
+    % Change that if you want the data to be saved somewhere else,
+    % below will set it to save the output within the sxperiment folder
     cfg.dir.output = fullfile( ...
-                              fileparts(mfilename('fullpath')), '..', ...
+                              fileparts(mfilename('fullpath')), ...
                               'output');
 
     %% Debug mode settings
diff --git a/src/preSaveSetup.m b/src/preSaveSetup.m
index 59d2096..de5fa9a 100644
--- a/src/preSaveSetup.m
+++ b/src/preSaveSetup.m
@@ -16,6 +16,7 @@
 
     % Save the events txt logfile
     % we save event by event so we clear this variable every loop
+    thisEvent.isStim = logFile.isStim;
     thisEvent.fileID = logFile.fileID;
     thisEvent.extraColumns = logFile.extraColumns;