final fixes

Author: Remi-Gau

initEnv.m

@@ -1,88 +1,86 @@
-% 
+%
 % 1 - Check if version requirements
-% are satisfied and the packages are 
+% are satisfied and the packages are
 % are installed/loaded:
-% 	Octave > 4  
-% 		- image 
-%   	- optim 
-%   	- struct 
-%   	- statistics 
+%   Octave > 4
+%       - image
+%       - optim
+%       - struct
+%       - statistics
 %
-% 	MATLAB > R2017a
+%   MATLAB > R2017a
 %
 % 2 - Add project to the O/M path
 
 function initEnv
-    
+
     octaveVersion = '4.0.3';
     matlabVersion = '9.2.0';
 
-if isOctave
+    if isOctave
 
-% Exit if min version is not satisfied
-if ~compare_versions(OCTAVE_VERSION,octaveVersion,'>=')
-	error('Minimum required Octave version: %s', octaveVersion);
-end
+        % Exit if min version is not satisfied
+        if ~compare_versions(OCTAVE_VERSION, octaveVersion, '>=')
+            error('Minimum required Octave version: %s', octaveVersion);
+        end
 
-installlist = {'statistics'};
-for ii=1:length(installlist)
-        try
-        	% Try loading Octave packages
-            disp(['loading ' installlist{ii}])
-            pkg('load',installlist{ii})
-        
-        catch
-            errorcount = 1;
-            while errorcount % Attempt twice in case installation fails
-                try
-                    pkg('install','-forge',installlist{ii})
-                    pkg('load',installlist{ii})
-                    errorcount = 0;
-                catch err
-                    errorcount = errorcount+1;
-                    if errorcount>2
-                        error(err.message)
+        installlist = {'statistics'};
+        for ii = 1:length(installlist)
+            try
+                % Try loading Octave packages
+                disp(['loading ' installlist{ii}]);
+                pkg('load', installlist{ii});
+
+            catch
+                errorcount = 1;
+                while errorcount % Attempt twice in case installation fails
+                    try
+                        pkg('install', '-forge', installlist{ii});
+                        pkg('load', installlist{ii});
+                        errorcount = 0;
+                    catch err
+                        errorcount = errorcount + 1;
+                        if errorcount > 2
+                            error(err.message);
+                        end
                     end
                 end
             end
         end
-end
-	
 
+    else % MATLAB ----------------------------
 
-else % MATLAB ----------------------------
-
-if verLessThan('matlab', matlabVersion)
-	error('Sorry, minimum required version is R2017b. :(');
-end
+        if verLessThan('matlab', matlabVersion)
+            error('Sorry, minimum required version is R2017b. :(');
+        end
 
-end
+    end
 
-% If external dir is empty throw an exception 
-% and ask user to update submodules.
-if numel(dir('lib')) <= 2 % Means that the external is empty
-	error(['Git submodules are not cloned! \n' ...
-		  'try this in your terminal: \n ...'
-		  'git submodule update --recursive ']);	
-else 
-	addDependencies();
-end		
+    % If external dir is empty throw an exception
+    % and ask user to update submodules.
+    if numel(dir('lib')) <= 2 % Means that the external is empty
+        error(['Git submodules are not cloned! \n' ...
+              'try this in your terminal: \n ...'
+              'git submodule update --recursive ']);
+    else
+        addDependencies();
+    end
 
-disp('Correct matlab/octave verions and added to the path!');
+    disp('Correct matlab/octave verions and added to the path!');
 
 end
 
 %%
 %% Return: true if the environment is Octave.
 %%
 function retval = isOctave
-  persistent cacheval;  % speeds up repeated calls
+    persistent cacheval   % speeds up repeated calls
 
-  if isempty (cacheval)
-    cacheval = (exist ("OCTAVE_VERSION", "builtin") > 0);
-  end
+    if isempty (cacheval)
+        cacheval = (exist ("OCTAVE_VERSION", "builtin") > 0);
+    end
 
-  retval = cacheval;
+    retval = cacheval;
 end
 
 function addDependencies()

setParameters.m

@@ -24,6 +24,7 @@
 
     cfg.testingDevice = 'pc';
     cfg.eyeTracker = false;
+    cfg.initAudio = false;
 
     [cfg, expParameters] = setMonitor(cfg, expParameters);
 
@@ -86,7 +87,9 @@
 
 function [cfg, expParameters] = setKeyboards(cfg, expParameters)
     cfg.keyboard.escapeKey = 'ESCAPE';
-    expParameters.responseKey = {'space'};
+    cfg.keyboard.responseKey = {'space'};
+    cfg.keyboard.keyboard = [];
+    cfg.keyboard.responseBox = [];
 
     if strcmpi(cfg.testingDevice, 'mri')
         cfg.keyboard.keyboard = [];
@@ -101,6 +104,9 @@
 
     expParameters.bids.MRI.RepetitionTime = 2;
 
+    expParameters.bids.MRI.Instructions = 'Detect the RED fixation cross';
+    expParameters.bids.MRI.TaskDescription = [];
+
 end
 
 function [cfg, expParameters] = setMonitor(cfg, expParameters)

subfun/doDotMo.m

@@ -117,7 +117,8 @@
         % NaN out-of-circle dots
         % We use Pythagore's theorem to figure out which dots are out of the
         % circle
-        outCircle = sqrt(xy_pix(1, :).^2 + xy_pix(2, :).^2) + dotSizePix / 2 > (diamAperturePix / 2);
+        outCircle = sqrt(xy_pix(1, :).^2 + xy_pix(2, :).^2) + ...
+            dotSizePix / 2 > (diamAperturePix / 2);
         xy_pix(:, outCircle) = NaN;
 
         %% PTB draws the dots stimulation

subfun/expDesign.m

@@ -1,7 +1,8 @@
 function [expParameters] = expDesign(expParameters, displayFigs)
     % Creates the sequence of blocks and the events in them
     %
-    % The conditions are consecutive static and motion blocks (Gives better results than randomised).
+    % The conditions are consecutive static and motion blocks
+    % Gives better results than randomised.
     %
     % It can be run as a stand alone without inputs to display a visual example of possible design.
     %
@@ -63,7 +64,7 @@
     maxNumFixTargPerBlock = expParameters.maxNumFixationTargetPerBlock;
 
     if mod(numEventsPerBlock, length(motionDirections)) ~= 0
-        warning('the number of events per block is not a multiple of the number of motion/static diection');
+        warning('Number of events/block not a multiple of number of motion/static direction');
     end
 
     %% Adapt some variables according to input
@@ -151,7 +152,8 @@
         Ind = zeros(length(expParameters.designBlockNames), length(uniqueNames)) ;
 
         for i = 1:length(uniqueNames)
-            CondInd(:, i) = find(strcmp(expParameters.designBlockNames, uniqueNames{i})) ; %#ok<*AGROW>
+            CondInd(:, i) = find( ...
+                strcmp(expParameters.designBlockNames, uniqueNames{i})) ; %#ok<*AGROW>
             Ind(CondInd(:, i), i) = 1 ;
         end
 

visualLocTanslational.m

@@ -25,6 +25,7 @@
 [cfg, expParameters] = createFilename(cfg, expParameters);
 
 disp(expParameters);
+disp(cfg);
 
 % Prepare for fixation Cross
 cfg.xCoords = [-expParameters.fixCrossDimPix expParameters.fixCrossDimPix 0 0] + ...
@@ -58,15 +59,15 @@
     logFile = saveEventsFile('open', expParameters, logFile);
 
     % Wait for space key to be pressed
-    pressSpaceForme();
+    pressSpaceForMe();
 
     % prepare the KbQueue to collect responses
     getResponse('init', cfg.keyboard.responseBox, cfg);
     getResponse('start', cfg.keyboard.responseBox);
 
     % Show instructions
 
-    DrawFormattedText(cfg.win, expParameters.TaskInstruction, ...
+    DrawFormattedText(cfg.win, expParameters.taskInstruction, ...
         'center', 'center', cfg.textColor);
     Screen('Flip', cfg.win);
 
@@ -115,22 +116,25 @@
             thisEvent.fileID = logFile.fileID;
             thisEvent.extraColumns = logFile.extraColumns;
 
+            disp(1)
             saveEventsFile('save', expParameters, thisEvent);
-
+            disp(2)
+            
             clear thisEvent;
 
             % collect the responses and appends to the event structure for
             % saving in the tsv file
             responseEvents = getResponse('check', cfg.keyboard.responseBox, cfg, getOnlyPress);
 
-            if ~isempty(responseEvents(1).onset)
+            if isfield(responseEvents(1), 'onset') && ~isempty(responseEvents(1).onset)
 
                 responseEvents.fileID = logFile.fileID;
 
                 for iResp = 1:size(responseEvents, 1)
                     responseEvents(iResp).onset = ...
                         responseEvents(iResp).onset - cfg.experimentStart;
-                    responseEvents(iResp).target = expParameters.designFixationTargets(iBlock, iEvent);
+                    responseEvents(iResp).target = ...
+                        expParameters.designFixationTargets(iBlock, iEvent);
                     responseEvents(iResp).event = iEvent;
                     responseEvents(iResp).block = iBlock;
                 end
@@ -165,7 +169,9 @@
     eyeTracker('Shutdown', cfg, expParameters);
 
     % save the whole workspace
-    matFile = fullfile(expParameters.outputDir, strrep(expParameters.fileName.events, 'tsv', 'mat'));
+    matFile = fullfile( ...
+        expParameters.outputDir, ...
+        strrep(expParameters.fileName.events, 'tsv', 'mat'));
     if IsOctave
         save(matFile, '-mat7-binary');
     else