Commit 170707

.gitignore

+*.mat
\ No newline at end of file

TaskPipeline_v2.m

+% Pipeline including task practice/threshold estimation, MAT pre, checkerboard and MAT post assessment
+
+%%%%%%%%%%%%%%%%%%%%%%
+%% enter subject ID %%
+%%%%%%%%%%%%%%%%%%%%%%
+
+subj = 'TEST_v1';
+
+%% add required paths
+
+pn.root = '/Volumes/LNDG-1/Julian/Projects/DYNSAT/C_Paradigm/';
+pn.CB = [pn.root, 'checker/'];
+pn.MAT = [pn.root, 'dotsx/'];
+
+addpath(genpath([pn.root, 'functions/']));
+addpath(pn.CB);
+addpath(pn.MAT);
+
+addpath(genpath('/Users/Shared/Psychtoolbox/')); % PTB 3.0.13 (160606)
+
+%% create results directory
+
+subjectsPath = [pn.root, '/data/', subj '_' datestr(now, 'yymmdd_HHMM') '/']; mkdir(subjectsPath);
+
+%% set up PTB
+
+Screen('Preference', 'SkipSyncTests', 1);
+oldLevel = Screen('Preference', 'Verbosity', 4); % output debugging info
+PsychDebugWindowConfiguration(0,0.3)
+
+%% practice MAT task
+
+cd(pn.root);
+
+% staircase parameters
+P.PM.priorAlphaRange = .5:.02:.8;
+P.PM.stimRange = .5:.01:.8;         % only allow values in range from 50 to 80%
+P.PM.numtrials = 32;                % (numtrials/2) needs to be round
+P.PM.gamma = 0.5;                   % assumed chance level
+P.PM.priorLambdaRange = .2;
+
+dotInfo = createDotInfo_JQK_170704;
+dotInfo.dataDir = subjectsPath;
+
+cursubj = [subj, '_practice'];
+DEBUG = 1; opacity = 1;
+thresholds = MAT_practice_170704(dotInfo, cursubj, DEBUG, opacity, P);
+
+disp(thresholds); disp('Please check whether they are reasonable.')
+
+%% run MAT Task (Pre-CB) 
+
+dotInfo = createDotInfo_JQK_170704(thresholds);
+dotInfo.dataDir = [pn.root, 'data/'];
+
+cursubj = [subj, '_PreMAT'];
+DEBUG = 1; opacity = 1;
+MAT_experiment_170704(dotInfo, cursubj, DEBUG, opacity)
+
+%% practice checkerboard task
+
+subjectsPath = [pn.root, '/data/', subj '_' datestr(now, 'yymmdd_HHMM') '/']; mkdir(subjectsPath);
+
+setup.subj          = subj;
+setup.design        = 1;
+setup.ET            = 0;
+setup.in_scanner    = 0;
+setup.dummyScans    = 0;
+setup.add_display   = 0; % if not in scanner: additional display connected?
+setup.test_trigger  = 0; % test scanner trigger (1) or not (0)
+setup.DEBUG         = 1; % debug mode?
+setup.transparency  = .99; % only relevant if DEBUG == 1
+setup.verbosity     = 4; % magnitude of PTB output
+setup.EPI           = 0;
+setup.BGmode        = 'black'; % black/grey mode
+setup.mode          = 'task';
+
+[checkerInfo_practice, setup] = PureCheckerParameters_Practice_170403(setup);
+setup.catchPractice = 0;
+checkerBoard_Practice_Threshold_170705(checkerInfo_practice, subjectsPath, setup);
+
+%% set up and run checkerboard
+
+subjectsPath = [pn.root, '/data/', subj '_' datestr(now, 'yymmdd_HHMM') '/']; mkdir(subjectsPath);
+
+setup.subj          = subj;
+setup.design        = 1;
+setup.ET            = 0;
+setup.in_scanner    = 0;
+setup.dummyScans    = 0;
+setup.add_display   = 0; % if not in scanner: additional display connected?
+setup.test_trigger  = 0; % test scanner trigger (1) or not (0)
+setup.DEBUG         = 1; % debug mode?
+setup.transparency  = .99; % only relevant if DEBUG == 1
+setup.verbosity     = 4; % magnitude of PTB output
+setup.EPI           = 0;
+setup.BGmode        = 'black'; % black/grey mode
+setup.mode          = 'task';
+
+[checkerInfo, setup] = PureCheckerParameters_170403(setup);
+checkerContrastComp_170705(checkerInfo, [subjectsPath, 'CB_Task_'], setup)
+
+%% run MAT Task (post-CB)
+
+dotInfo = createDotInfo_JQK_170704(thresholds);
+dotInfo.dataDir = [pn.root, 'data/'];
+
+cursubj = [subj, '_PostMAT'];
+DEBUG = 1; opacity = 1;
+MAT_experiment_170704(dotInfo, cursubj, DEBUG, opacity)

TaskPipeline_v3.m

+% Pipeline including task practice/threshold estimation, MAT pre, checkerboard and MAT post assessment
+
+%%%%%%%%%%%%%%%%%%%%%%
+%% enter subject ID %%
+%%%%%%%%%%%%%%%%%%%%%%
+
+subj = 'TEST_v1';
+
+%% add required paths
+
+pn.root = '/Volumes/LNDG-1/Julian/Projects/DYNSAT/C_Paradigm/';
+pn.CB = [pn.root, 'checker/'];
+pn.MAT = [pn.root, 'dotsx/'];
+
+addpath(genpath([pn.root, 'functions/']));
+addpath(pn.CB);
+addpath(pn.MAT);
+
+addpath(genpath('/Users/Shared/Psychtoolbox/')); % PTB 3.0.13 (160606)
+
+%% create results directory
+
+subjectsPath = [pn.root, '/data/', subj '_' datestr(now, 'yymmdd_HHMM') '/']; mkdir(subjectsPath);
+
+%% set up PTB
+
+Screen('Preference', 'SkipSyncTests', 1);
+oldLevel = Screen('Preference', 'Verbosity', 4); % output debugging info
+PsychDebugWindowConfiguration(0,0.3)
+
+%% practice MAT task
+
+cd(pn.root);
+
+% staircase parameters
+P.PM.priorAlphaRange = .5:.02:.8;
+P.PM.stimRange = .5:.01:.8;         % only allow values in range from 50 to 80%
+P.PM.numtrials = 32;                % (numtrials/2) needs to be round
+P.PM.gamma = 0.5;                   % assumed chance level
+P.PM.priorLambdaRange = .2;
+
+dotInfo = [];
+dotInfo = createDotInfo_JQK_170704;
+dotInfo.dataDir = subjectsPath;
+
+DEBUG = 1; opacity = 1;
+cursubj = [subj, '_MAT_Practice'];
+thresholds = MAT_practice_170704(dotInfo, cursubj, DEBUG, opacity, P);
+
+disp(thresholds); disp('Please check whether they are reasonable.')
+
+%% run MAT Task (Pre-CB) 
+
+dotInfo = createDotInfo_JQK_170704(thresholds);
+dotInfo.dataDir = [pn.root, 'data/'];
+
+cursubj = [subj, '_MAT_Pre'];
+DEBUG = 1; opacity = 1;
+MAT_experiment_170704(dotInfo, cursubj, DEBUG, opacity)
+
+%% practice checkerboard task
+
+setup.subj          = subj;
+setup.design        = 1;
+setup.ET            = 0;
+setup.in_scanner    = 0;
+setup.dummyScans    = 0;
+setup.add_display   = 0; % if not in scanner: additional display connected?
+setup.test_trigger  = 0; % test scanner trigger (1) or not (0)
+setup.DEBUG         = 1; % debug mode?
+setup.transparency  = .99; % only relevant if DEBUG == 1
+setup.verbosity     = 4; % magnitude of PTB output
+setup.EPI           = 0;
+setup.BGmode        = 'black'; % black/grey mode
+setup.mode          = 'task';
+
+[checkerInfo_practice, setup] = PureCheckerParameters_Practice_170403(setup);
+setup.catchPractice = 0;
+setup.subjectsPath = subjectsPath;
+checkerBoard_Practice_Threshold_170705(checkerInfo_practice, setup);
+
+%% set up and run checkerboard
+
+setup               = [];
+setup.subj          = subj;
+setup.design        = 1;
+setup.ET            = 0;
+setup.in_scanner    = 0;
+setup.dummyScans    = 0;
+setup.add_display   = 0; % if not in scanner: additional display connected?
+setup.test_trigger  = 0; % test scanner trigger (1) or not (0)
+setup.DEBUG         = 1; % debug mode?
+setup.transparency  = .99; % only relevant if DEBUG == 1
+setup.verbosity     = 4; % magnitude of PTB output
+setup.EPI           = 0;
+setup.BGmode        = 'black'; % black/grey mode
+setup.mode          = 'task';
+
+[checkerInfo, setup] = PureCheckerParameters_170403(setup);
+setup.outputName = 'Task';
+setup.subjectsPath = subjectsPath;
+checkerContrastComp_170706(checkerInfo, setup)
+
+%% run MAT Task (post-CB)
+
+dotInfo         = [];
+dotInfo         = createDotInfo_JQK_170704(thresholds);
+dotInfo.dataDir = subjectsPath;
+
+cursubj = [subj, '_MAT_Post'];
+DEBUG = 1; opacity = 1;
+MAT_experiment_170704(dotInfo, cursubj, DEBUG, opacity)

Z_old/MAT_Setup_170327.m

+%% add paths
+
+% add PTB
+
+addpath(genpath('/Users/Shared/Psychtoolbox'));
+
+% add dotsx functions
+
+pn.workingFolder = '/Volumes/fb-lip/LNDG/Julian/Projects/DYNSAT/C_Paradigm/MAT_V2/';
+
+addpath(genpath([pn.workingFolder, 'functions/']));
+addpath(genpath([pn.workingFolder, 'dotsx/']));
+
+addpath(genpath('/Volumes/fb-lip/LNDG/Julian/Projects/DYNSAT/C_Paradigm/Z_tools/'));
+
+%% set up and run RDM experiment
+Screen('Preference', 'SkipSyncTests', 1);
+%OSXCompositorIdiocyTest()
+%oldLevel = Screen('Preference', 'Verbosity', 4); % output debugging info
+%PsychDebugWindowConfiguration(0,0.3)
+
+dotInfo = createDotInfo_JQK_170327;
+dotInfo.dataDir = [pn.workingFolder, 'data/']; %mkdir(dotInfo.dataDir);
+
+subj = 'JQK_Test_170626_01';
+DEBUG = 1;
+opacity = 1;
+dotsExperiment_JQK_170327(dotInfo, subj, 0, DEBUG, opacity)
\ No newline at end of file

Z_old/MAT_TrainingEstimation_170626_WIP.m

+%MAT_TrainingEstimation_170626_WIP
+
+subj = 'JQK_Test_170704_v1';
+
+%% add PTB
+
+addpath(genpath('/Users/Shared/Psychtoolbox/'));
+
+%% practice MAT task
+
+pn.workingFolder = '/Volumes/fb-lip/LNDG/Julian/Projects/DYNSAT/C_Paradigm/MAT_V2/';
+
+addpath(genpath([pn.workingFolder, 'functions/']));
+addpath(genpath([pn.workingFolder, 'dotsx/']));
+
+addpath(genpath('/Volumes/fb-lip/LNDG/Julian/Projects/DYNSAT/C_Paradigm/Z_tools/'));
+
+% staircase parameters
+
+P.PM.priorAlphaRange = .5:.02:.8;
+P.PM.stimRange = .5:.01:.8; % only allow values in range from 50 to 80%
+P.PM.numtrials = 30;
+P.PM.gamma = 0.5; % assumed chance level
+P.PM.priorLambdaRange = .2;
+
+Screen('Preference', 'SkipSyncTests', 1);
+
+dotInfo = createDotInfo_JQK_170327;
+dotInfo.dataDir = [pn.workingFolder, 'data/'];
+
+cursubj = [subj, '_practice'];
+DEBUG = 1; opacity = 1;
+%MAT_practice_170626_WIP(dotInfo, cursubj, 0, DEBUG, opacity, P)
+
+MAT_practice_CompleteOnly_170704_WIP(dotInfo, cursubj, 0, DEBUG, opacity, P)
\ No newline at end of file

Z_old/TaskPipeline_v1.m

+% Pipeline including practice, MAT pre, checkerboard and MAT post assessment
+
+%% enter subject info
+
+subj = 'Sub01_v1';
+
+%% add PTB
+
+addpath(genpath('/Users/Shared/Psychtoolbox/'));
+
+%% practice checkerboard task
+
+experimentFolder = '/Volumes/MyPassport3TB/RDM_Distract/CheckerContrastComp_V11/';
+addpath(genpath(experimentFolder));
+
+cd(experimentFolder);
+
+% set up experiment
+Screen('Preference', 'SkipSyncTests', 1);
+oldLevel = Screen('Preference', 'Verbosity', 4); % output debugging info
+PsychDebugWindowConfiguration(0,0.3)
+
+subjectsPath = [subj '_' datestr(now, 'dd-mm-yyyy_HH-MM-SS') '/']; mkdir(subjectsPath);
+
+checkerInfo = [];
+[checkerInfo] = checkerParameters_170213;
+
+DEBUG = 1; opacity = 1;
+checkerBoard_Practice_170328(subjectsPath, checkerInfo, DEBUG, opacity)
+
+%% practice MAT task
+
+pn.workingFolder = '/Volumes/MyPassport3TB/RDM_Distract/MAT_V2/';
+
+addpath(genpath([pn.workingFolder, 'functions/']));
+addpath(genpath([pn.workingFolder, 'dotsx/']));
+
+Screen('Preference', 'SkipSyncTests', 1);
+
+dotInfo = createDotInfo_JQK_170327;
+dotInfo.dataDir = [pn.workingFolder, 'data/'];
+
+cursubj = [subj, '_practice'];
+DEBUG = 1; opacity = 1;
+MAT_practice_170328(dotInfo, cursubj, 0, DEBUG, opacity)
+
+%% run MAT Task (Pre-CB) 
+
+% add dotsx functions
+
+pn.workingFolder = '/Volumes/MyPassport3TB/RDM_Distract/MAT_V2/';
+
+addpath(genpath([pn.workingFolder, 'functions/']));
+addpath(genpath([pn.workingFolder, 'dotsx/']));
+
+Screen('Preference', 'SkipSyncTests', 1);
+
+dotInfo = createDotInfo_JQK_170327;
+dotInfo.dataDir = [pn.workingFolder, 'data/']; mkdir(dotInfo.dataDir);
+
+cursubj = [subj, '_PreMAT'];
+DEBUG = 1; opacity = 1;
+dotsExperiment_JQK_170327(dotInfo, cursubj, 0, DEBUG, opacity)
+
+%% set up and run checkerboard
+
+experimentFolder = '/Volumes/MyPassport3TB/RDM_Distract/CheckerContrastComp_V11/';
+addpath(genpath(experimentFolder));
+
+cd(experimentFolder);
+
+% set up experiment
+Screen('Preference', 'SkipSyncTests', 1);
+oldLevel = Screen('Preference', 'Verbosity', 4); % output debugging info
+PsychDebugWindowConfiguration(0,0.3)
+
+subjectsPath = [subj '_' datestr(now, 'dd-mm-yyyy_HH-MM-SS') '/']; mkdir(subjectsPath);
+
+checkerInfo = [];
+[checkerInfo] = checkerParameters_170213;
+
+DEBUG = 1; verbosity = 1;
+checkerContrastComp_JQK_170213(checkerInfo, subjectsPath, DEBUG, verbosity)
+
+%% run MAT Task (post-CB)
+
+pn.workingFolder = '/Volumes/MyPassport3TB/RDM_Distract/MAT_V2/';
+addpath(genpath([pn.workingFolder, 'functions/']));
+addpath(genpath([pn.workingFolder, 'dotsx/']));
+cd(pn.workingFolder);
+
+Screen('Preference', 'SkipSyncTests', 1);
+
+dotInfo = createDotInfo_JQK_170327;
+dotInfo.dataDir = [pn.workingFolder, 'data/'];
+
+cursubj = [subj, '_PostMAT'];
+DEBUG = 1; opacity = 1;
+dotsExperiment_JQK_170327(dotInfo, cursubj, 0, DEBUG, opacity)
\ No newline at end of file

Z_old/addContinuousInfo_170113.m

+
+
+
+% timing is fixed according to this vector 
+
+% let's also fix coherence for now (e.g. Kelly & O'Connell, 2014)
+% 6 of each direction-coherence level
+
+dotInfo.cohLevels = [0.25, 0.35, 0.5, 0.7];
+dotInfo.directions = [0 180]; % 1 - left, 2 - right
+
+% TO DO: set random seed
+
+distrib = repmat([1:8],1,6);
+tmp_rand = randperm(numel(distrib));
+distrib_rand = distrib(tmp_rand);
+
+dotInfo.coh = NaN(1,numel(distrib_rand));
+dotInfo.dir = NaN(1,numel(distrib_rand));
+for indDis = 1:8
+    if indDis <= 4
+        indDir = 1;
+        indCoh = indDis;
+    else
+        indDir = 2;
+        indCoh = indDis-4;
+    end;
+    curDis = find(distrib_rand==indDis);
+    dotInfo.coh(curDis) = dotInfo.cohLevels(indCoh);
+    dotInfo.dir(curDis) = dotInfo.directions(indDir);
+end;
+
+dotInfo.timeTarget = 1.9; % target time in s
+dotInfo.timeNontarget = [3.6, 6.6, 8.4]; % target time in s
+
+tmp = []; tmp2 = [];
+for indCoh = 1:numel(dotInfo.coh)
+    tmp = [tmp, 0, dotInfo.coh(indCoh)];
+    tmp2 = [tmp2, NaN, dotInfo.dir(indCoh)];
+end;
+% tmp = [tmp, 0];
+% tmp2 = [tmp2, NaN];
+
+dotInfo.coh = tmp;
+dotInfo.dir = tmp2;
+
+nonTargets = find(dotInfo.coh == 0);
+Targets = find(dotInfo.coh ~= 0);
+
+nontargetDur = repmat([1:3], 1, 16); % create vector for non-target duration
+tmp_rand = randperm(numel(nontargetDur));
+targetDur_rand = nontargetDur(tmp_rand);
+
+dotInfo.presTime = NaN(1,numel(dotInfo.coh));
+dotInfo.presTime(nonTargets) = dotInfo.timeNontarget(targetDur_rand);
+dotInfo.presTime(Targets) = dotInfo.timeTarget;