Merge pull request #41 from Remi-Gau/remi-paced_by_scanner

use triggers to pace experiment

Author: Remi-Gau

initEnv.m

@@ -59,7 +59,7 @@
     % If external dir is empty throw an exception
     % and ask user to update submodules.
     libDirectory = fullfile(fileparts(mfilename('fullpath')), 'lib');
-    
+
     if numel(dir(libDirectory)) <= 2 % Means that the external is empty
         error(['Git submodules are not cloned!', ...
               'Try this in your terminal:', ...
@@ -89,8 +89,7 @@ function addDependencies()
 
     pth = fileparts(mfilename('fullpath'));
     addpath(genpath(fullfile(pth, 'lib', 'CPP_BIDS', 'src')));
-    addpath(fullfile(pth, 'lib', 'CPP_PTB'));
-%     addpath(genpath(fullfile(pth, 'lib', 'CPP_PTB', 'src')));
+    addpath(genpath(fullfile(pth, 'lib', 'CPP_PTB', 'src')));
     addpath(fullfile(pth, 'subfun'));
 
 end

lib/CPP_PTB

@@ -21,7 +21,7 @@
     %% Engine parameters
 
     cfg.testingDevice = 'mri';
-    cfg.eyeTracker.do = true;
+    cfg.eyeTracker.do = false;
     cfg.audio.do = false;
 
     cfg = setMonitor(cfg);
@@ -32,6 +32,8 @@
     % MRI settings
     cfg = setMRI(cfg);
 
+    cfg.pacedByTriggers.do = true;
+
     %% Experiment Design
 
     %     cfg.design.motionType = 'translation';
@@ -49,6 +51,8 @@
     % IBI
     % block length = (cfg.eventDuration + cfg.ISI) * cfg.design.nbEventsPerBlock
 
+    cfg.timing.eventDuration = 0.850; % second
+
     % Time between blocs in secs
     cfg.timing.IBI = 1.8;
     % Time between events in secs
@@ -58,7 +62,23 @@
     % Number of seconds after the end all the stimuli before ending the run
     cfg.timing.endDelay = 3.6;
 
-    cfg.timing.eventDuration = 0.9; % second
+    % reexpress those in terms of repetition time
+    if cfg.pacedByTriggers.do
+
+        cfg.pacedByTriggers.quietMode = true;
+        cfg.pacedByTriggers.nbTriggers = 1;
+
+        cfg.timing.eventDuration = cfg.mri.repetitionTime / 2 - 0.04; % second
+
+        % Time between blocs in secs
+        cfg.timing.IBI = 1;
+        % Time between events in secs
+        cfg.timing.ISI = 0;
+        % Number of seconds before the motion stimuli are presented
+        cfg.timing.onsetDelay = 0;
+        % Number of seconds after the end all the stimuli before ending the run
+        cfg.timing.endDelay = 2;
+    end
 
     %% Visual Stimulation
 
@@ -106,10 +126,10 @@
 
 function cfg = setKeyboards(cfg)
     cfg.keyboard.escapeKey = 'ESCAPE';
-    cfg.keyboard.responseKey = {...
+    cfg.keyboard.responseKey = { ...
         'r', 'g', 'y', 'b', ...
         'd', 'n', 'z', 'e', ...
-        't'}; %dnze rgyb
+        't'}; % dnze rgyb
     cfg.keyboard.keyboard = [];
     cfg.keyboard.responseBox = [];
 

setParameters.m

@@ -77,7 +77,7 @@
 
     getResponse('start', cfg.keyboard.responseBox);
 
-    WaitSecs(cfg.timing.onsetDelay);
+    waitFor(cfg, cfg.timing.onsetDelay);
 
     %% For Each Block
 
@@ -99,6 +99,15 @@
             thisEvent.speed = cfg.design.speeds(iBlock, iEvent);
             thisEvent.target = cfg.design.fixationTargets(iBlock, iEvent);
 
+            % we wait for a trigger every 2 events
+            if cfg.pacedByTriggers.do && mod(iEvent, 2) == 1
+                waitForTrigger( ...
+                    cfg, ...
+                    cfg.keyboard.responseBox, ...
+                    cfg.pacedByTriggers.quietMode, ...
+                    cfg.pacedByTriggers.nbTriggers);
+            end
+
             % play the dots and collect onset and duraton of the event
             [onset, duration] = doDotMo(cfg, thisEvent);
 
@@ -107,14 +116,14 @@
             thisEvent.keyName = 'n/a';
             thisEvent.duration = duration;
             thisEvent.onset = onset - cfg.experimentStart;
-            
+
             % % this value should be in degrees / second in the log file
             % % highlights that the way speed is passed around could be
             % % simplified.
             % %
             % thisEvent.speed
             % %
-            
+
             % Save the events txt logfile
             % we save event by event so we clear this variable every loop
             thisEvent.fileID = logFile.fileID;
@@ -132,14 +141,13 @@
             triggerString = ['trigger_' cfg.design.blockNames{iBlock}];
             saveResponsesAndTriggers(responseEvents, cfg, logFile, triggerString);
 
-            % wait for the inter-stimulus interval
-            WaitSecs(cfg.timing.ISI);
+            waitFor(cfg, cfg.timing.ISI);
 
         end
 
         eyeTracker('StopRecordings', cfg);
 
-        WaitSecs(cfg.timing.IBI);
+        waitFor(cfg, cfg.timing.IBI);
 
         % trigger monitoring
         triggerEvents = getResponse('check', cfg.keyboard.responseBox, cfg, ...
@@ -151,7 +159,7 @@
     end
 
     % End of the run for the BOLD to go down
-    WaitSecs(cfg.timing.endDelay);
+    waitFor(cfg, cfg.timing.endDelay);
 
     cfg = getExperimentEnd(cfg);