Merge pull request #7 from marcobarilari/marco_cleaning-setParam

move and rename some vars in `setParameters` and update the README

Author: marcobarilari

README.md

@@ -8,35 +8,27 @@ For instructions see the following links:
 
 | Requirements                                             | Used version |
 |----------------------------------------------------------|--------------|
-| [CPP_BIDS](https://github.com/cpp-lln-lab/CPP_BIDS)      | ?            |
-| [CPP_PTB](https://github.com/cpp-lln-lab/CPP_PTB)        | ?            |
 | [PsychToolBox](http://psychtoolbox.org/)                 | >=3.0.14     |
-| [Matlab](https://www.mathworks.com/products/matlab.html) | >=2017      |
+| [Matlab](https://www.mathworks.com/products/matlab.html) | >=2017b      |
 | or [octave](https://www.gnu.org/software/octave/)        | >=4.?        |
 
-## Installing dependencies
+## Installation
 
-All the dependencies needed to run this are listed in the [mpm-requirements.txt file](.mpm-requirements.txt). If those functions are not in the matlab path the scripts in this repository will not work.
+The CPP_BIDS and CPP_PTB dependencies are already set up as submodule to this repository.
+You can install it all with git by doing.
 
-If you are using the [matlab package manager](https://github.com/mobeets/mpm), you can simply download the appropriate version of those dependencies and add them to your path by running the `getDependencies` function.
-
-```matlab
-getDependencies('update')
+```bash
+git clone --recurse-submodules https://github.com/cpp-lln-lab/localizer_auditory_motion.git
 ```
 
-If you already have the appropriate version but just want to add them to the matlab path, then run.
-
-```matlab
-getDependencies()
-```
 ## Structure and function details
 
 
-### visualLocTranslational
+### audioLocTranslational
 
-Running this script will play blocks of motion static sounds. Motion blocks will play sounds moving in one of four directions (up-, down-, left-, and right-ward)
+Running this script will play blocks of motion/static sounds. Motion blocks will play sounds moving in one of four directions (up-, down-, left-, and right-ward)
 
-By default it is run in `Debug mode` meaning that it does not run care about subjID, run n., fMRI triggers, Eye Tracker, etc..
+By default it is run in `Debug mode` meaning that it does not care about subjID, run n., fMRI triggers, Eye Tracker, etc..
 
 Any details of the experiment can be changed in `setParameters.m` (e.g., experiment mode, motion stimuli details, exp. design, etc.)
 
@@ -45,12 +37,13 @@ Any details of the experiment can be changed in `setParameters.m` (e.g., experim
 `setParameters.m` is the core engine of the experiment. It contains the following tweakable sections:
 
 - Debug mode setting
-- MRI settings
 - Engine parameters:
+  - Devices parameters
   - Monitor parameters
-  - Monitor parameters for PsychToolBox
-- Keyboards
+  - Keyboard parameters
+  - MRI parameters
 - Experiment Design
+- Timing
 - Auditory Stimulation
 - Task(s)
   - Instructions

audioLocTranslational.m

@@ -62,7 +62,7 @@
 
     getResponse('start', cfg.keyboard.responseBox);
 
-    WaitSecs(cfg.onsetDelay);
+    WaitSecs(cfg.timing.onsetDelay);
 
     %% For Each Block
 
@@ -110,18 +110,18 @@
             saveResponsesAndTriggers(responseEvents, cfg, logFile, triggerString);
 
             % wait for the inter-stimulus interval
-            WaitSecs(cfg.ISI);
+            WaitSecs(cfg.timing.ISI);
 
         end
 
         eyeTracker('StopRecordings', cfg);
 
-        WaitSecs(cfg.IBI);
+        WaitSecs(cfg.timing.IBI);
 
     end
 
     % End of the run for the BOLD to go down
-    WaitSecs(cfg.endDelay);
+    WaitSecs(cfg.timing.endDelay);
 
     % Close the logfiles
     saveEventsFile('close', cfg, logFile);

setParameters.m

@@ -32,30 +32,38 @@
     % MRI settings
     cfg = setMRI(cfg);
 
-    cfg.audio.channels = 2;
-
     %% Experiment Design
-    cfg.names              = {'static', 'motion'};
-    cfg.possibleDirections = [-1 1]; % 1 motion , -1 static
-    cfg.numBlocks          = size(cfg.possibleDirections, 2);
-    cfg.numRepetitions     = 1;      % AT THE MOMENT IT IS NOT SET IN THE MAIN SCRIPT
+
+    cfg.design.names = {'static', 'motion'};
+    cfg.design.possibleDirections = [-1 1]; % 1 motion , -1 static %NOT IN USE AT THE MOMENT
+    cfg.design.nbBlocks          = size(cfg.design.names, 2); % TO CHECK
+    cfg.design.nbRepetitions = 1;  % AT THE MOMENT IT IS NOT SET IN THE MAIN SCRIPT
+    cfg.design.nbEventsPerBlock = 12;
 
     %% Timing
-    cfg.IBI                = 0; % 8;
-    cfg.ISI                = 0.1;    % Time between events in secs
-    cfg.onsetDelay         = 1;      % Number of seconds before the motion stimuli are presented
-    cfg.endDelay           = 1;      % Number of seconds after the end all the stimuli before ending the run
+
+    % FOR 7T: if you want to create localizers on the fly, the following must be
+    % multiples of the scanneryour sequence TR
+    %
+    % IBI
+    % block length = (cfg.eventDuration + cfg.ISI) * cfg.design.nbEventsPerBlock
+
+    % Time between blocs in secs
+    cfg.timing.IBI = 1.8 * 3; % 8;
+    % Time between events in secs
+    cfg.timing.ISI = 0.1;
+    % Number of seconds before the motion stimuli are presented
+    cfg.timing.onsetDelay = .1;
+    % Number of seconds after the end all the stimuli before ending the run
+    cfg.timing.endDelay = .1;
 
     %% Auditory Stimulation
 
-    % expParameters.experimentType    = 'Gratings';  %Dots/Gratings % Visual modality is in RDKs %NOT USED IN THE MAIN SCIPT
-    cfg.speedEvent        = 8;       % speed in visual angles
-    cfg.numEventsPerBlock = 12;      % Number of events per block (should not be changed)
-    cfg.eventDuration     = 10;
+    cfg.audio.channels = 2;
 
-    %% Task
+    %% Task(s)
 
-    cfg.task.name = 'visual localizer';
+    cfg.task.name = 'auditory localizer';
 
     % Instruction
     cfg.task.instruction = '1-Detect the RED fixation cross\n \n\n';
@@ -76,6 +84,26 @@
 
 end
 
+function cfg = setMonitor(cfg)
+
+    % Monitor parameters for PTB
+    cfg.color.white = [255 255 255];
+    cfg.color.black = [0 0 0];
+    cfg.color.red = [255 0 0];
+    cfg.color.grey = mean([cfg.color.black; cfg.color.white]);
+    cfg.color.background = cfg.color.black;
+    cfg.text.color = cfg.color.white;
+
+    % Monitor parameters
+    cfg.screen.monitorWidth = 50; % in cm
+    cfg.screen.monitorDistance = 40; % distance from the screen in cm
+
+    if strcmpi(cfg.testingDevice, 'mri')
+        cfg.screen.monitorWidth = 50;
+        cfg.screen.monitorDistance = 40;
+    end
+end
+
 function cfg = setKeyboards(cfg)
     cfg.keyboard.escapeKey = 'ESCAPE';
     cfg.keyboard.responseKey = {'space', 't'};
@@ -99,23 +127,3 @@
     cfg.bids.MRI.TaskDescription = [];
 
 end
-
-function cfg = setMonitor(cfg)
-
-    % Monitor parameters for PTB
-    cfg.color.white = [255 255 255];
-    cfg.color.black = [0 0 0];
-    cfg.color.red = [255 0 0];
-    cfg.color.grey = mean([cfg.color.black; cfg.color.white]);
-    cfg.color.background = cfg.color.black;
-    cfg.text.color = cfg.color.white;
-
-    % Monitor parameters
-    cfg.screen.monitorWidth = 50; % in cm
-    cfg.screen.monitorDistance = 40; % distance from the screen in cm
-
-    if strcmpi(cfg.testingDevice, 'mri')
-        cfg.screen.monitorWidth = 50;
-        cfg.screen.monitorDistance = 40;
-    end
-end

subfun/expDesign.m

@@ -1,7 +1,8 @@
 function [cfg] = expDesign(cfg, 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.
     %
@@ -24,14 +25,13 @@
     %   - ExpParameters.designBlockNames      = cell array (nr_blocks, 1) with the
     %    name for each block
     %
-    %   - ExpParameters.designDirections      = array (nr_blocks, numEventsPerBlock)
+    %   - ExpParameters.designDirections      = array (nr_blocks, nbEventsPerBlock)
     %    with the direction to present in a given block
     %       - 0 90 180 270 indicate the angle
     %       - -1 indicates static
     %
-    %   - ExpParameters.designSpeeds          = array (nr_blocks, numEventsPerBlock) * speedEvent
     %
-    %   - ExpParameters.designFixationTargets = array (nr_blocks, numEventsPerBlock)
+    %   - ExpParameters.designFixationTargets = array (nr_blocks, nbEventsPerBlock)
     %   showing for each event if it should be accompanied by a target
     %
 
@@ -48,11 +48,10 @@
 
     % Set variables here for a dummy test of this function
     if nargin < 1 || isempty(cfg)
-        cfg.names             = {'static', 'motion'};
-        cfg.numRepetitions    = 4;
-        cfg.speedEvent        = 4;
-        cfg.numEventsPerBlock = 12;
-        cfg.maxNumFixationTargetPerBlock = 2;
+        cfg.design.names             = {'static', 'motion'};
+        cfg.design.nbRepetitions    = 4;
+        cfg.design.nbEventsPerBlock = 12;
+        cfg.target.maxNbPerBlock = 2;
     end
 
     % Set to 1 for a visualtion of the trials design order
@@ -61,46 +60,44 @@
     end
 
     % Get the parameters
-    names = cfg.names;
-    numRepetitions = cfg.numRepetitions;
-    speedEvent = cfg.speedEvent;
-    numEventsPerBlock = cfg.numEventsPerBlock;
-    maxNumFixTargPerBlock = cfg.target.maxNbPerBlock;
-
-    if mod(numEventsPerBlock, length(motionDirections)) ~= 0
-        warning('the number of events per block is not a multiple of the number of motion/static diection');
+    names = cfg.design.names;
+    nbRepetitions = cfg.design.nbRepetitions;
+    nbEventsPerBlock = cfg.design.nbEventsPerBlock;
+    maxNbFixTargPerBlock = cfg.target.maxNbPerBlock;
+
+    if mod(nbEventsPerBlock, length(motionDirections)) ~= 0
+        warning('the n. of events per block is not a multiple of experimental conditions');
     end
 
     %% Adapt some variables according to input
 
     % Set directions for static and motion condition
-    motionDirections = repmat(motionDirections, 1, numEventsPerBlock / length(motionDirections));
-    staticDirections = repmat(staticDirections, 1, numEventsPerBlock / length(staticDirections));
+    motionDirections = repmat(motionDirections, 1, nbEventsPerBlock / length(motionDirections));
+    staticDirections = repmat(staticDirections, 1, nbEventsPerBlock / length(staticDirections));
 
     % Assign the conditions
-    condition = repmat(names, 1, numRepetitions);
+    condition = repmat(names, 1, nbRepetitions);
     nrBlocks = length(condition);
     % Get the index of each condition
     staticIndex = find(strcmp(condition, 'static'));
     motionIndex = find(strcmp(condition, 'motion'));
 
     % Assign the targets for each condition
-    rangeTargets = [1 maxNumFixTargPerBlock];
+    rangeTargets = [1 maxnbFixTargPerBlock];
     % Get random number of targets for one condition
-    targetPerCondition = randi(rangeTargets, 1, numRepetitions);
+    targetPerCondition = randi(rangeTargets, 1, nbRepetitions);
     % Assign the number of targets for each condition after shuffling
-    numTargets = zeros(1, nrBlocks);
-    numTargets(staticIndex) = Shuffle(targetPerCondition);
-    numTargets(motionIndex) = Shuffle(targetPerCondition);
+    nbTargets = zeros(1, nrBlocks);
+    nbTargets(staticIndex) = Shuffle(targetPerCondition);
+    nbTargets(motionIndex) = Shuffle(targetPerCondition);
 
     %% Give the blocks the names with condition
 
     cfg.designBlockNames      = cell(nrBlocks, 1);
-    cfg.designDirections      = zeros(nrBlocks, numEventsPerBlock);
-    cfg.designSpeeds          = ones(nrBlocks, numEventsPerBlock) * speedEvent;
-    cfg.designFixationTargets = zeros(nrBlocks, numEventsPerBlock);
+    cfg.designDirections      = zeros(nrBlocks, nbEventsPerBlock);
+    cfg.designFixationTargets = zeros(nrBlocks, nbEventsPerBlock);
 
-    for iMotionBlock = 1:numRepetitions
+    for iMotionBlock = 1:nbRepetitions
 
         cfg.designDirections(motionIndex(iMotionBlock), :) = Shuffle(motionDirections);
         cfg.designDirections(staticIndex(iMotionBlock), :) = Shuffle(staticDirections);
@@ -125,20 +122,20 @@
 
         chosenTarget = [];
 
-        tmpTarget = numTargets(iBlock);
+        tmpTarget = nbTargets(iBlock);
 
         switch tmpTarget
 
             case 1
 
-                chosenTarget = randsample(2:numEventsPerBlock - 1, tmpTarget, false);
+                chosenTarget = randsample(2:nbEventsPerBlock - 1, tmpTarget, false);
 
             case 2
 
                 targetDifference = 0;
 
                 while targetDifference <= 2
-                    chosenTarget = randsample(2:numEventsPerBlock - 1, tmpTarget, false);
+                    chosenTarget = randsample(2:nbEventsPerBlock - 1, tmpTarget, false);
                     targetDifference = (max(chosenTarget) - min(chosenTarget));
                 end