Merge pull request #15 from Remi-Gau/remi-dev_save_output

[WIP] make behavioral and eyetracking output BIDS compliant

Author: Remi-Gau

.gitignore

@@ -6,3 +6,5 @@
 # exclude content of logfiles folders
 */logfiles/*
 */*/*/logfiles/*
+*.tsv
+*.mat

Visual-loc_translational/setParameters.m

@@ -1,159 +1,164 @@
-function [ExpParameters, Cfg] = setParameters
+function [expParameters, cfg] = setParameters
 
-ExpParameters = struct; % Initialize the parameters variables
-Cfg           = struct; % Initialize the general configuration variables
+% Initialize the parameters and general configuration variables
+expParameters = struct;
+cfg           = struct;
 
-ExpParameters.task = 'VisualLoc';
+expParameters.task = 'VisualLoc';
 
+% 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
+expParameters.outputDir = fullfile(...
+    fileparts(mfilename('fullpath')), '..', ...
+    'output');
 
 %% Debug mode settings
-Cfg.debug               = true;  % To test the script out of the scanner, skip PTB sync
-Cfg.testingSmallScreen  = false; % To test on a part of the screen, change to 1
-Cfg.testingTranspScreen = true;  % To test with trasparent full size screen 
-Cfg.stimPosition        = 'PC';  % 'Scanner': means that it removes the lower 1/3 of the screen (the coil hides the lower part of the screen)
+cfg.debug               = true;  % To test the script out of the scanner, skip PTB sync
+cfg.testingSmallScreen  = false; % To test on a part of the screen, change to 1
+cfg.testingTranspScreen = true;  % To test with trasparent full size screen
+cfg.stimPosition        = 'pc';  % 'Scanner': means that it removes the lower 1/3 of the screen (the coil hides the lower part of the screen)
 
 
 %% MRI settings
-Cfg.device        = 'PC';  % 'PC': does not care about trigger - otherwise use 'Scanner'
-Cfg.triggerKey    = 't';   % Set the letter sent by the trigger to sync stimulation and volume acquisition
-Cfg.numTriggers   = 4;     
-Cfg.eyeTracker    = false; % Set to 'true' if you are testing in MRI and want to record ET data
+cfg.device        = 'scanner';  % 'PC': does not care about trigger - otherwise use 'Scanner'
+cfg.triggerKey    = 't';        % Set the letter sent by the trigger to sync stimulation and volume acquisition
+cfg.numTriggers   = 4;
+cfg.eyeTracker    = false;      % Set to 'true' if you are testing in MRI and want to record ET data
 
 
 %% Keyboards
 
-% cfg.responseBox would be the device used by the participant to give his/her response: 
+% cfg.responseBox would be the device used by the participant to give his/her response:
 %   like the button box in the scanner or a separate keyboard for a behavioral experiment
 %
-% cfg.keyboard is the keyboard on which the experimenter will type or press the keys necessary 
+% cfg.keyboard is the keyboard on which the experimenter will type or press the keys necessary
 %   to start or abort the experiment.
 %   The two can be different or the same.
 
-% Using empty vectors should work for linux when to select the "main"
-%   keyboard. You might have to try some other values for MacOS or Windows
-Cfg.keyboard = []; 
-Cfg.responseBox = []; 
+% Using empty vectors should work for linux and MacOS when to select the
+%   "main" keyboard. You might have to try some other values for Windows
+cfg.keyboard = [];
+cfg.responseBox = [];
 
 
 %% Engine parameters
 
 % Monitor parameters
-Cfg.monitorWidth  	  = 42;  % Monitor Width in cm
-Cfg.screenDistance    = 134; % Distance from the screen in cm
-Cfg.diameterAperture  = 8;   % Diameter/length of side of aperture in Visual angles
+cfg.monitorWidth  	  = 42;  % Monitor Width in cm
+cfg.screenDistance    = 134; % Distance from the screen in cm
+cfg.diameterAperture  = 8;   % Diameter/length of side of aperture in Visual angles
 
 % Monitor parameters for PTB
-Cfg.screen           = max(Screen('Screens')); % Main screen
-Cfg.white            = [255 255 255];
-Cfg.black            = [ 0   0   0 ];
-Cfg.red              = [255  0   0 ];
-Cfg.grey             = mean([Cfg.black; Cfg.white]);
-Cfg.backgroundColor  = Cfg.black;
-Cfg.textColor        = Cfg.white;
-Cfg.textFont         = 'Courier New';
-Cfg.textSize         = 18;
-Cfg.textStyle        = 1;
+cfg.white            = [255 255 255];
+cfg.black            = [ 0   0   0 ];
+cfg.red              = [255  0   0 ];
+cfg.grey             = mean([cfg.black; cfg.white]);
+cfg.backgroundColor  = cfg.black;
+cfg.textColor        = cfg.white;
+cfg.textFont         = 'Courier New';
+cfg.textSize         = 18;
+cfg.textStyle        = 1;
 
 % Keyboard
-Cfg.escapeKey        = 'Escape';
+cfg.escapeKey        = 'Escape';
 
 
 
-% The code below will help you decide which keyboard device to use for the partipant and the experimenter 
+% The code below will help you decide which keyboard device to use for the partipant and the experimenter
 
 % Computer keyboard to quit if it is necessary
 % Cfg.keyboard
-% 
+%
 % For key presses for the subject
 % Cfg.responseBox
 
-[Cfg.keyboardNumbers, Cfg.keyboardNames] = GetKeyboardIndices;
-Cfg.keyboardNumbers
-Cfg.keyboardNames
+[cfg.keyboardNumbers, cfg.keyboardNames] = GetKeyboardIndices;
+cfg.keyboardNumbers
+cfg.keyboardNames
 
 
-switch Cfg.device
+switch lower(cfg.device)
 
 
     % this part might need to be adapted because the "default" device
     % number might be different for different OS or set up
-
-    case 'PC'
+    
+    case 'pc'
 
-        Cfg.keyboard = [];
-        Cfg.responseBox = [];
+        cfg.keyboard = [];
+        cfg.responseBox = [];
 
         if ismac
-            Cfg.keyboard = [];
-            Cfg.responseBox = [];
+            cfg.keyboard = [];
+            cfg.responseBox = [];
         end
-
+        
     case 'scanner'
 
     otherwise
 
         % Cfg.keyboard = max(Cfg.keyboardNumbers);
         % Cfg.responseBox = min(Cfg.keyboardNumbers);
 
-        Cfg.keyboard = [];
-        Cfg.responseBox = [];
+        cfg.keyboard = [];
+        cfg.responseBox = [];
 
 end
 
 %% Experiment Design
-ExpParameters.names              = {'static','motion'};
-ExpParameters.possibleDirections = [-1 1]; % 1 motion , -1 static
-ExpParameters.numBlocks          = size(ExpParameters.possibleDirections,2);
-ExpParameters.numRepetitions     = 1;      %AT THE MOMENT IT IS NOT SET IN THE MAIN SCRIPT
-ExpParameters.IBI                = 0; %8;      
-ExpParameters.ISI                = 0.1;    % Time between events in secs
-ExpParameters.onsetDelay         = 5;      % Number of seconds before the motion stimuli are presented
-ExpParameters.endDelay           = 1;      % Number of seconds after the end all the stimuli before ending the run
+expParameters.names              = {'static','motion'};
+expParameters.possibleDirections = [-1 1]; % 1 motion , -1 static
+expParameters.numBlocks          = size(expParameters.possibleDirections,2);
+expParameters.numRepetitions     = 1;      %AT THE MOMENT IT IS NOT SET IN THE MAIN SCRIPT
+expParameters.IBI                = 0; %8;
+expParameters.ISI                = 0.1;    % Time between events in secs
+expParameters.onsetDelay         = 5;      % Number of seconds before the motion stimuli are presented
+expParameters.endDelay           = 1;      % Number of seconds after the end all the stimuli before ending the run
 
 
 %% Visual Stimulation
-ExpParameters.experimentType    = 'Dots';  % Visual modality is in RDKs %NOT USED IN THE MAIN SCIPT
-ExpParameters.speedEvent        = 8;       % speed in visual angles
-ExpParameters.numEventsPerBlock = 12;      % Number of events per block (should not be changed)
-ExpParameters.eventDuration     = .9;
-ExpParameters.coh               = 1;       % Coherence Level (0-1)
-ExpParameters.maxDotsPerFrame   = 300;     % Maximum number dots per frame (Number must be divisible by 3)
-ExpParameters.dotLifeTime       = 0.2;     % Dot life time in seconds
-ExpParameters.dontClear         = 0;
-ExpParameters.dotSize           = 0.1;     % Dot Size (dot width) in visual angles.
-ExpParameters.dotColor          = Cfg.white;
+expParameters.experimentType    = 'Dots';  % Visual modality is in RDKs %NOT USED IN THE MAIN SCIPT
+expParameters.speedEvent        = 8;       % speed in visual angles
+expParameters.numEventsPerBlock = 12;      % Number of events per block (should not be changed)
+expParameters.eventDuration     = 1;
+expParameters.coh               = 1;       % Coherence Level (0-1)
+expParameters.maxDotsPerFrame   = 300;     % Maximum number dots per frame (Number must be divisible by 3)
+expParameters.dotLifeTime       = 1;       % Dot life time in seconds
+expParameters.dontClear         = 0;
+expParameters.dotSize           = 0.1;     % Dot Size (dot width) in visual angles.
+expParameters.dotColor          = cfg.white;
 
 
 %% Task(s)
 
 % Instruction
-ExpParameters.TaskInstruction = '1-Detect the RED fixation cross\n \n\n';
+expParameters.TaskInstruction = '1-Detect the RED fixation cross\n \n\n';
 
-ExpParameters.responseKey = {'space'};
+expParameters.responseKey = {'space'};
 
 
 %% Task 1 - Fixation cross
-ExpParameters.Task1 = true; % true / false
+expParameters.Task1 = true; % true / false
 
-if ExpParameters.Task1
+if expParameters.Task1
     % Used Pixels here since it really small and can be adjusted during the experiment
-    ExpParameters.fixCrossDimPix               = 10;   % Set the length of the lines (in Pixels) of the fixation cross
-    ExpParameters.lineWidthPix                 = 4;    % Set the line width (in Pixels) for our fixation cross
-    ExpParameters.maxNumFixationTargetPerBlock = 2;
-    ExpParameters.fixationChangeDuration       = 0.15; % In secs
-    ExpParameters.xDisplacementFixCross        = 0;    % Manual displacement of the fixation cross
-    ExpParameters.yDisplacementFixCross        = 0;    % Manual displacement of the fixation cross
-    ExpParameters.fixationCrossColor           = Cfg.white;
-    ExpParameters.fixationCrossColorTarget     = Cfg.red;
+    expParameters.fixCrossDimPix               = 10;   % Set the length of the lines (in Pixels) of the fixation cross
+    expParameters.lineWidthPix                 = 4;    % Set the line width (in Pixels) for our fixation cross
+    expParameters.maxNumFixationTargetPerBlock = 2;
+    expParameters.targetDuration               = 0.15; % In secs
+    expParameters.xDisplacementFixCross        = 0;    % Manual displacement of the fixation cross
+    expParameters.yDisplacementFixCross        = 0;    % Manual displacement of the fixation cross
+    expParameters.fixationCrossColor           = cfg.white;
+    expParameters.fixationCrossColorTarget     = cfg.red;
 end
 
 
-%% Setting some defaults: no need to change things here
-if mod(ExpParameters.maxDotsPerFrame,3) ~= 0
-    error('Number of dots should be divisible by 3.')
-end
+% Setting some defaults: no need to change things here
+expParameters = checkCFG(expParameters);
+
 
-if Cfg.debug
+if cfg.debug
     fprintf('\n\n\n\n')
     fprintf('######################################## \n')
     fprintf('##  DEBUG MODE, NOT THE SCANNER CODE  ## \n')

Visual-loc_translational/subfun/CPP_BIDS/checkCFG.m

@@ -0,0 +1,28 @@
+function expParameters = checkCFG(expParameters)
+% check that we have all the fields that we need in the experiment
+% parameters
+
+if ~isfield(expParameters, 'outputDir')
+    expParameters.outputDir = fullfile(...
+        fileparts(mfilename('fullpath')), ...
+        '..', ...
+        'output');
+end
+
+% set empty values for a series of field if they have not been specified
+fields2Check = { ...
+    'ce', ...
+    'dir', ...  % For BIDS file naming: phase encoding direction of acquisition for fMRI
+    'rec', ...  % For BIDS file naming: reconstruction of fMRI images
+    'echo', ... % For BIDS file naming: echo fMRI images
+    'acq'       % For BIDS file naming: acquisition of fMRI images
+    };
+
+for iField = 1:numel(fields2Check)
+    if ~isfield(expParameters, fields2Check{iField})
+        expParameters = setfield(expParameters, fields2Check{iField}, []); %#ok<SFLD>
+    end
+end
+
+
+end