From eb48b6841231b7dc3f35a985a32ccdc2f3816703 Mon Sep 17 00:00:00 2001
From: marcobarilari <marcobarilr@gmail.com>
Date: Sun, 20 Nov 2022 11:53:02 +0100
Subject: [PATCH 1/6] add initialization of the log file and uncomment add
 message to eyetracker

---
 mainScript.m | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/mainScript.m b/mainScript.m
index 2f3fa11..e550d03 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);
@@ -67,10 +68,8 @@
 
             [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);
@@ -93,10 +92,8 @@
             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);
 

From 30dd67d8223a0a905f328b042c74cafbd684d1d6 Mon Sep 17 00:00:00 2001
From: marcobarilari <marcobarilr@gmail.com>
Date: Fri, 16 Dec 2022 15:18:46 +0100
Subject: [PATCH 2/6] add waitForTrigger and IBI and eyetracker message at end
 of the block

---
 mainScript.m | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/mainScript.m b/mainScript.m
index e550d03..e2b5a3d 100644
--- a/mainScript.m
+++ b/mainScript.m
@@ -49,7 +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);
 
@@ -78,7 +79,8 @@
                                      thisEvent, ...
                                      iBlock, ...
                                      iTrial, ...
-                                     duration, onset, ...
+                                     duration, ...
+                                     onset, ...
                                      cfg, ...
                                      logFile);
 
@@ -88,6 +90,7 @@
             % 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);
@@ -99,6 +102,10 @@
 
         end
 
+        eyeTracker('Message', cfg, ['end_block-', num2str(iBlock)]);
+
+        waitFor(cfg, cfg.timing.IBI);
+
     end
 
     % End of the run for the BOLD to go down

From 14e8d9394a0e809e89a7e3f99bc8842a6aa45cd8 Mon Sep 17 00:00:00 2001
From: marcobarilari <marcobarilr@gmail.com>
Date: Fri, 16 Dec 2022 15:19:14 +0100
Subject: [PATCH 3/6] fix bug

---
 src/preSaveSetup.m | 1 +
 1 file changed, 1 insertion(+)

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;
 

From 43b498e099d804b3c62a4fd4e7acbd41446ce76a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 16 Dec 2022 14:21:02 +0000
Subject: [PATCH 4/6] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 mainScript.m | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mainScript.m b/mainScript.m
index e2b5a3d..9c69cd4 100644
--- a/mainScript.m
+++ b/mainScript.m
@@ -70,7 +70,7 @@
             [thisEvent, thisFixation, cfg] = preTrialSetup(cfg, iBlock, iTrial);
 
             eyeTracker('Message', cfg, ...
-                ['start_trial-', num2str(iTrial), '_', thisEvent.trial_type]);
+                       ['start_trial-', num2str(iTrial), '_', thisEvent.trial_type]);
 
             % play the dots and collect onset and duraton of the event
             [onset, duration] = doTrial(cfg, thisEvent, thisFixation);
@@ -96,7 +96,7 @@
             saveEventsFile('save', cfg, responseEvents);
 
             eyeTracker('Message', cfg, ...
-                ['end_trial-', num2str(iTrial), '_', thisEvent.trial_type]);
+                       ['end_trial-', num2str(iTrial), '_', thisEvent.trial_type]);
 
             waitFor(cfg, cfg.timing.ISI);
 

From b857284ee2eeea08237e14fe8d9a9b7022f508a2 Mon Sep 17 00:00:00 2001
From: marcobarilari <marcobarilr@gmail.com>
Date: Fri, 16 Dec 2022 18:16:36 +0100
Subject: [PATCH 5/6] Change output dir path to within the experiment folder

---
 setParameters.m | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/setParameters.m b/setParameters.m
index 04dd784..736ce84 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

From 4ee6438fafc16886d86fe945b87acada9fa060c2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 16 Dec 2022 17:18:20 +0000
Subject: [PATCH 6/6] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 setParameters.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setParameters.m b/setParameters.m
index 736ce84..24b0c79 100644
--- a/setParameters.m
+++ b/setParameters.m
@@ -9,7 +9,7 @@
 
     % 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, 
+    % 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')), ...