OSCR

Disentangling Respiratory Phase-Dependent and Phase-Independent Components of Anticipatory Cardiac Deceleration.

Code ↔ Paper

16 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 16 matches · 1 of them tie a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
  1. [1] § Methods › Behavioral Task Paradigm › Eye‐Tracking Calibration and Controlling for the Fixation Breaks ↔ VTD/VTD_experiment/trials_VTDnew_egeVersion.m, lines 440–488 · score 0.91 · blink allowance, 0.5–0.7 s, intertrial interval, visual angle, April Tags, radius
  2. [2] § Methods › Behavioral Task Paradigm › Training and Threshold Assessment ↔ VTD/VTD_experiment/trials_VTDnew_egeVersion.m, lines 275–344 · score 0.83 · tGuess, QUEST algorithm, hit rate, stimulus absent, calibration, grating
  3. [3] § Methods › Statistical Methods and Analyses › RSA Estimations ↔ VTD/VTD_analysis/VTD_baseline_breathingPhaseLocking.m, lines 193–234 · score 0.80 · 0.12–0.4 Hz, bandpass filtered, Porges Bohrer, overlap, 0.12 Hz, segmented
  4. [4] § Results › Differential Contributions of Respiratory Phase‐Dependent and Phase‐Independent Heart Rate Modulations to Visual Stimulus Detection ↔ VTD/VTD_analysis/VTD_van_acd_timeCourseCorrelations.m, lines 105–148 · score 0.70 · 188–318 ms, correlation coefficient, 188 ms, VAN, linear, window
  5. [5] § Methods › Statistical Methods and Analyses › Linear Correlations ↔ VTD/VTD_analysis/VTD_ACD_inhalationVsExhalation.m, lines 1210–1257 · score 0.68 · robust linear regression, correlation coefficients, Huber, fitlm, intercept, fitting
  6. [6] § Methods › Data Preprocessing › EEG Data Pre‐Processing ↔ VTD/VTD_preProcessing/VTD_EEG_PreProcessMAIN.m, lines 573–652 · score 0.68 · surrogate VEP, corrected VEP, subtracted, epoched, pre, EEG
  7. [7] § Results › Differential Contributions of Respiratory Phase‐Dependent and Phase‐Independent Heart Rate Modulations to Visual Stimulus Detection ↔ VTD/VTD_analysis/VTD_van_acd_timeCourseCorrelations.m, lines 105–148 · score 0.67 · 188–318 ms, correlation coefficient, 188 ms, Spearman, VAN, linear
  8. [8] § Methods › Behavioral Task Paradigm › Stimulus Properties ↔ VTD/VTD_experiment/params_VTD_egeVersion.m, lines 191–196 · score 0.64 · outer radius, visual angle, inner, annulus, grating
  9. [9] § Methods › Statistical Methods and Analyses › RSA Estimations ↔ VTD/VTD_rsaSinusoidalModel/RSA_sinusoidalFit.m, the whole file · a weak match · score 0.61 · initial guesses, loss function, fminsearch, IBI, RSA, phase
  10. [10] § Results › The Role of RSA and Respiratory Phase Alignment in Anticipatory Cardiac Deceleration (ACD) ↔ VTD/VTD_analysis/VTD_ACD_inhalationVsExhalation.m, lines 1259–1302 · score 0.61 · Porges Bohrer, linear regression, correlation coefficient, RSA amplitude, horizontal, Sinusoidal
  11. [11] § Methods › Data Preprocessing › EEG Data Pre‐Processing ↔ VTD/VTD_preProcessing/VTD_EEG_PreProcessMAIN.m, lines 654–741 · score 0.60 · target stimulus onset, pre processed, EEGLAB, downsampled, epoched
  12. [12] § Methods › Data Preprocessing › EEG Data Pre‐Processing ↔ VTD/VTD_preProcessing/VTD_EEG_PreProcessMAIN.m, lines 430–442 · score 0.58 · ICA components, EEGLAB, SD, epochs, Pre
  13. [13] § Methods › Behavioral Task Paradigm › Eye‐Tracking Calibration and Controlling for the Fixation Breaks ↔ VTD/VTD_experiment/trials_VTDnew_egeVersion.m, lines 567–679 · score 0.56 · gaze position, Pupil Labs, Breaks, fixation
  14. [14] § Methods › Experimental Recordings › Pupillometry ↔ VTD/VTD_experiment/trials_VTDnew_egeVersion.m, lines 41–69 · score 0.54 · eye positions, Eye tracking, Pupil
  15. [15] § Methods › Behavioral Task Paradigm ↔ VTD/VTD_experiment/trials_VTDnew_egeVersion.m, lines 1349–1441 · score 0.54 · gaze locations, April Tags, axis, surface, block, EEG
  16. [16] § Methods › Data Preprocessing › ECG Data Pre‐Processing ↔ VTD/VTD_preProcessing/VTD_baselineECG_BR_preProcess.m, lines 36–47 · score 0.52 · QRS complex, bandpass, ECG, 45 Hz, Pre, 0.5 Hz

Paper

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The authors' code

MATLAB · 1,596 lines · 75 KB · no license · 5 matches

  1. function [output, keyboard_events, params, ET, gazes] = trials_VTDnew_egeVersion(params)
  2. % Trials function for MAIN_VTD.m
  4. % Sukanya C, Ege Kingir (MSc Thesis, IMPRS)
  5. % 12 Nov 2023
  6. % Trials function for the visual detection task after threshold calibration
  8. %%% This function contains the trial loop. The loop is a state-based one:
  9. %%% If the subject fixates to the center successfully (state=1), we move on
  10. %%% to the warning cue state (state=2). Afterwards, the stimulus is
  11. %%% presented. Then some delay and "detection (yes/no)" and "confidence"
  12. %%% reports by the subject.
  14. %%% If the subject breaks fixation to the center during the pre-stimulus
  15. %%% window, the trial restarts.
  17. %%% 60 trials per block: 87% stimulus-present, 13% catch.
  18. %%% 6-8 blocks in a session.
  20. %% CHANGE LOG
  21. % Following changes made by XX on XX.XX.XXX
  22. % 30.11.2023 -- EK updates:
  23. % 1) Added the continuous confidence scale bar.
  25. % 2) Under state==1, flag2 should be defined as zero before you enter the...
  26. % %...loop. Otherwise the variable is not recognized (I added the...
  27. % %...definition).
  29. % 13.12.2023 updates:
  30. % Removed the online plots for gaze and accuracy as they are slowing the
  31. % code down
  34. %% FUNCTIONS CALLED IN THIS SCRIPT / RELEVANT FILES
  35. % params_VTD.m
  36. % startupEyetracking.m
  37. % SendSignal.m
  38. % display_cycle_clock.m
  41. %% Set up eye tracking
  42. if params.eyetracking == 1
  43. if params.whicheyetracker == 1
  44. params.samplingrate = 1000;
  46. params.maxeyesamples = params.numtrials*params.totaltrialdur*params.samplingrate;
  48. params.eyedatafile = sprintf('M%s_%d.edf', params.subject, params.runnumber); % has to be less than 8 characters
  50. % Initialize Eyelink
  51. el = startupEyetracking(params.window, params.eyedatafile);
  53. % start recording eye position
  54. Eyelink('StartRecording');
  55. % record a few samples before we actually start displaying
  56. WaitSecs(0.1);
  57. % mark zero-plot time in data file
  58. Eyelink('Message', 'SYNCTIME');
  60. % Initialize eye data structure
  61. eyetrack.trial(1:params.maxeyesamples,1) = NaN;
  62. eyetrack.state(1:params.maxeyesamples,1) = NaN;
  63. eyetrack.eyetime(1:params.maxeyesamples,1) = NaN;
  64. eyetrack.ptbtime(1:params.maxeyesamples,1) = NaN;
  65. eyetrack.xpos(1:params.maxeyesamples,2) = NaN;
  66. eyetrack.ypos(1:params.maxeyesamples,2) = NaN;
  67. eyetrack.pupil(1:params.maxeyesamples,2) = NaN;
  69. elseif params.whicheyetracker == 2
  71. %%% Initialize Pupil Labs Remote Control
  72. % Pupil Remote address -- you can check this from PupilCapture
  73. endpoint = 'tcp://169.254.53.40:50020';
  75. % Setup zmq context and remote helper
  76. ctx = zmq.core.ctx_new();
  77. socket = zmq.core.socket(ctx, 'ZMQ_REQ');
  78. % set timeout to 1000ms in order to not get stuck in a blocking
  79. % mex-call if server is not reachable, see
  80. % http://api.zeromq.org/4-0:zmq-setsockopt#toc19
  81. zmq.core.setsockopt(socket, 'ZMQ_RCVTIMEO', 1000);
  83. fprintf('Connecting to %s\n', endpoint);
  84. zmq.core.connect(socket, endpoint);
  86. % Request sub port
  87. zmq.core.send(socket, uint8('SUB_PORT'));
  88. sub_port = char(zmq.core.recv(socket));
  89. fprintf('Received sub port: %s\n', sub_port);
  91. if isequal(sub_port, false)
  92. warning('No valid sub port received');
  93. return; % exit script
  94. end
  96. % Create and connect sub socket
  97. ip_address = '169.254.53.40';
  98. sub_endpoint = sprintf('tcp://%s:%s', ip_address, sub_port);
  99. sub_socket = zmq.core.socket(ctx, 'ZMQ_SUB');
  100. %Connect to sub port
  101. zmq.core.connect(sub_socket, sub_endpoint);
  102. zmq.core.setsockopt(sub_socket, 'ZMQ_RCVTIMEO', 1000);
  103. fprintf('Connecting to SUB: %s\n', sub_endpoint);
  105. tic; % Measure round trip delay
  106. zmq.core.send(socket, uint8('t'));
  107. result = zmq.core.recv(socket);
  108. fprintf('%s\n', char(result));
  109. fprintf('Round trip command delay: %s\n', toc);
  111. % set current Pupil time to 0.0
  112. zmq.core.send(socket, uint8('T 0.0'));
  113. result = zmq.core.recv(socket);
  114. fprintf('%s\n', char(result));
  116. % start recording
  117. pause(1.0);
  118. zmq.core.send(socket, uint8('R')); %%%%
  119. result = zmq.core.recv(socket); %%%%
  120. fprintf('Recording should start: %s\n', char(result));
  122. % zmq.core.send(socket, uint8('t'));
  123. % currentTime = zmq.core.recv(socket);
  124. end;
  126. end;
  128. %% Pupil Labs calibration
  129. if params.eyetracking == 1
  131. if params.whicheyetracker == 2
  133. %open a grey window
  134. [params.window, params.windowRect] = PsychImaging('OpenWindow', params.screenNumber, params.grey);
  136. % Size of the on screen window in pixels
  137. % [params.screenXpixelscalib, params.screenYpixelscalib] = Screen('WindowSize', params.window);
  138. Screen('BlendFunction', params.window, 'GL_SRC_ALPHA', 'GL_ONE_MINUS_SRC_ALPHA');
  140. %get the center coordinates (in pixels, bottom-left of the screen
  141. %is [0 0].
  142. [params.screenXcentre_pix, params.screenYcentre_pix] = RectCenter(params.windowRect);
  143. params.centercoords = [params.screenXcentre_pix params.screenYcentre_pix];
  144. %% get the pupil labs calibration marker
  145. % % marker = imread('calibMarker.jpg');
  146. % % markerTexture = Screen('MakeTexture', params.window, marker);
  147. % %
  148. % % Screen('DrawTexture', params.window, markerTexture, [], [], 0);
  149. baseRect1 = [0 0 165 165];
  150. baseRect2 = [0 0 160 160];
  151. baseRect3 = [0 0 100 100];
  152. baseRect4 = [0 0 60 60];
  153. baseRect5 = [0 0 30 30];
  154. x=[0 -params.screenX_pix/2+baseRect1(3) params.screenX_pix/2-baseRect1(3) -params.screenX_pix/2+baseRect1(3) params.screenX_pix/2-baseRect1(3)];
  155. y=[0 -params.screenY_pix/2+baseRect1(3) -params.screenY_pix/2+baseRect1(3) params.screenY_pix/2-baseRect1(3) params.screenY_pix/2-baseRect1(3)];
  156. valid = 1;
  157. for valid=1:4
  158. for stim=1:5
  160. centeredRect1 = CenterRectOnPointd(baseRect1, params.screenXcentre_pix+x(stim), params.screenYcentre_pix+y(stim));
  161. centeredRect2 = CenterRectOnPointd(baseRect2, params.screenXcentre_pix+x(stim), params.screenYcentre_pix+y(stim));
  162. centeredRect3 = CenterRectOnPointd(baseRect3, params.screenXcentre_pix+x(stim), params.screenYcentre_pix+y(stim));
  163. centeredRect4 = CenterRectOnPointd(baseRect4, params.screenXcentre_pix+x(stim), params.screenYcentre_pix+y(stim));
  164. centeredRect5 = CenterRectOnPointd(baseRect5, params.screenXcentre_pix+x(stim), params.screenYcentre_pix+y(stim));
  166. xCoords = [-2 2 0 0];
  167. yCoords = [0 0 -2 2];
  168. allCoords = [xCoords; yCoords];
  169. lineWidthPix = 2;
  171. %nested doughnut shaped ovals to make calibration spots...
  172. %recognizable by PupilCapture.
  173. Screen('FillOval', params.window, [0.5 0.5 0.5],centeredRect1, max(baseRect1)*1.01);
  174. Screen('FillOval', params.window, [1 1 1],centeredRect2, max(baseRect2)*1.01);
  175. Screen('FillOval', params.window, [0 0 0],centeredRect3, max(baseRect3)*1.01);
  176. Screen('FillOval', params.window, [1 1 1],centeredRect4, max(baseRect4)*1.01);
  177. Screen('FillOval', params.window, [0 0 0],centeredRect5, max(baseRect5)*1.01);
  179. %fixation cross
  180. Screen('DrawLines', params.window, allCoords, lineWidthPix, [1 1 1], [params.screenXcentre_pix+x(stim) params.screenYcentre_pix+y(stim)],2);
  181. % Screen('DrawLines', params.window,
  182. Screen('Flip', params.window);
  183. KbStrokeWait;
  185. end
  186. Screen('Flip', params.window);
  187. % calibstart = input('Do you want to restart the calibration (in case accuracy is low) (1 = Yes, 0 = No) ');
  188. % if calibstart == 1
  189. % valid = 1;
  190. % elseif calibstart == 0
  191. % valid = 0;
  192. % %
  193. % end
  195. end
  196. WaitSecs(5);
  197. Screen('Flip',params.window);
  198. end
  199. end
  201. %% Initialisation of parameters for checking fixation
  202. ET.TrialAborted = false;
  203. ET.FixationEstablished = false;
  204. ET.FixationPending = false;
  205. ET.FixationPendingStartTime = NaN;
  206. ET.AbortPending = false;
  207. ET.AbortPendingStartTime = NaN;
  208. ET.AbortStartTime = NaN;
  209. ET.IsFixation = false;
  211. %% Cycling warm up if necessary
  212. if strcmp(params.runtype, 'TC') || strcmp(params.runtype, 'L') || strcmp(params.runtype, 'H')
  213. display_cycle_clock_VTD(params);
  214. end
  217. %% Output struct
  218. output = struct('condition', [], 'trialonset', []);
  221. %% Initialising
  223. triggertime = NaN;
  224. triggerout = 0;
  225. cursample = 0;
  228. %% Keyboard set up
  229. % Enable unified mode of KbName, so KbName accepts identical key names on
  230. % all operating systems:
  231. KbName('UnifyKeyNames');
  233. % Prevent spilling of keystrokes into console:
  234. ListenChar(-1); % suppress keyboard input
  236. % Define key list
  237. keylist = zeros(1,256); % create mask for keys
  238. % set keylist / mask to 1 for all the keys you want to monitor
  239. % keylist(KbName('1!')) = 1;
  240. keylist(KbName('3#')) = 1;
  241. keylist(KbName('2@')) = 1;
  242. keylist(KbName('1!')) = 1;
  243. % keylist(KbName('5%')) = 1;
  245. % create and start a restricted KbQueue
  246. KbQueueCreate(-1, keylist); %'-1' uses default keyboard, this is a restricted KbQueue, used for detecting button presses
  247. KbQueueStart;
  249. % Initialize keyboard_events as an empty structure array
  250. keyboard_events = struct([]);
  252. trial = 0;
  253. flag = 0;
  255. % Define your response keys
  256. responseKeys = {'3#', '2@', '1!'};
  259. %% Set up fixed and variable delays
  261. fixation_Duration = 2.7; %% In Park et al., fixation duration is specified as 0.5 to 0.7 seconds,
  262. % and if stable gaze fixation
  263. % is achieved for the said duration, a trial is initiated. However, since
  264. % it is yet not well sorted how to feed in Pupil Capture data into MATLAB,
  265. % we choose to define a range of 0.7s (max gaze fixation defined in Park et
  266. % al., 2014) + 0.5 seconds i.e., 1.2 seconds.
  268. warning_before_stimRange = [1.5, 1.7]; % this is the variable delay for which the fixation remains red before the stimulus appears
  269. % stimulusDuration = 0.05; % this is the fixed stimulus presentation duration in seconds, converted to frames
  270. stimulusFrames = round(0.05/params.flipinterval);
  271. stimulusDuration = 0.05;
  272. var_delay_after_stimRange = [0.3, 0.7]; % this is the variable delay range after stimulus presentation
  273. time_for_response = 3; % this is the time accounted to the participant to make a key press
  275. %% Initialise parameters for the QUEST algorithm
  277. tGuess = 0.04; % Estimated signal strength (contrast value) which is the threshold for detection
  278. tGuessSd = 2; % Standard Deviation allowed to the QUEST algorithm for the distribution centred on tGuess
  279. pThreshold = 0.65; % Probability of correct response - We want the hit rate to be at 65%
  280. beta = 3.5; % Slope of the Weibull function
  281. delta = 0.01;
  282. gamma = 0; % Guess rate or probabilty of an incorrect guess at values high above threshold
  283. grain = 0.0025; % Step shift in contrast - WE DO NOT CHANGE THE GRAIN
  284. range = 0.075; %Range of contrast values under practical testing conditions
  285. keyHit = '2@'; % Key for hit
  286. keyMiss = '3#'; % Key for miss
  288. % Initialize QUEST parameters
  289. q=QuestCreate(tGuess,tGuessSd,pThreshold,beta,delta,gamma, grain, range);
  290. p = QuestPdf(q,tGuess);
  291. % q.x = linspace(0,1,501);
  292. % q.x2 = linspace(0,2,1001);
  294. % Define the center of the screen as empty!
  295. center = [];
  297. % Define the iterations fo getting gaze on surface inputs
  298. iter=1;
  300. for block = 1:params.numblocks
  302. random_trl_order = params.trialorder;
  303. Screen('TextSize',params.window, 30)
  304. Screen('DrawText',params.window, 'FIXATION CALIBRATION!',(params.screenX_pix/2)-100, params.screenY_pix*0.5, params.black);
  305. Screen('Flip', params.window);
  306. WaitSecs(1);
  308. % Plotting parameters initialisation
  309. hitCount = 0;
  310. missCount = 0;
  311. faCount = 0;
  312. hitRates = zeros(1, length(random_trl_order)); % Initialize hit rates vector
  313. falseAlarmRates = zeros(1, length(random_trl_order)); % Initialize false alarm rates vector
  314. stimPresentCount = 0;
  315. stimAbsentCount = 0;
  316. contrasts = zeros(1, length(random_trl_order)); % Initialize contrasts vector
  318. x1 = [];
  319. y1 = [];
  320. x2 = [];
  321. y2 = [];
  322. x3 = [];
  323. y3 = [];
  325. % figure(1);
  326. % subplot(2, 1, 1);
  327. % % % % plot1 = plot(x1, y1, 'r-'); % Initialize plot 1 (red line)
  328. % xlabel('Trial');
  329. % ylabel('Hit and False Alarm Rates');
  330. % title('QUEST modulated accuracy');
  333. % subplot(2, 1, 2);
  334. % % % % plot3 = plot(x3, y3, 'k-'); % Initialize plot 1 (red line)
  335. % xlabel('Trial');
  336. % ylabel('Grating Contrast');
  337. % title('QUEST modulated contrast');
  340. %figure(10);
  341. % % % plot1 = plot(x1, y1, 'r-'); % Initialize plot 1 (red line)
  342. % xlabel('x gaze');
  343. % ylabel('y gaze');
  344. % title('Real Time gaze');
  347. %% Main Trials Loop
  348. %% Display April tags on PTB screen to detect surface via PupilLabs
  349. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  350. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  351. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  352. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  353. % fixation circle
  354. Screen('FillOval', params.window, params.black, params.centeredcircleRectOUT, params.maxDiameterOUT);
  355. Screen('FillOval', params.window, params.grey, params.centeredcircleRectIN, params.maxDiameterIN);
  356. Screen('DrawDots', params.window, [params.xcenter_pix, params.ycenter_pix], params.fixationSize_pix, params.white, [], 1);
  357. Screen('Flip', params.window);
  358. if params.eyetracking == 1
  359. if params.whicheyetracker == 2
  360. zmq.core.setsockopt(sub_socket, 'ZMQ_SUBSCRIBE', 'surface'); %now you can subscribe to surface because we drew it!
  361. end
  362. end
  363. WaitSecs(2);
  365. initialSurfaceDef = 3; %number of secs allowed to define the surface and at the same time get baseline gaze data
  366. startSurfDef = GetSecs();
  367. gazes = [];
  368. while 1
  369. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  370. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  371. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  372. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  373. % fixation circle
  374. Screen('FillOval', params.window, params.black, params.centeredcircleRectOUT, params.maxDiameterOUT);
  375. Screen('FillOval', params.window, params.grey, params.centeredcircleRectIN, params.maxDiameterIN);
  376. Screen('DrawDots', params.window, [params.xcenter_pix, params.ycenter_pix], params.fixationSize_pix, [0.8 0.8 0.8], [], 1);
  377. Screen('Flip', params.window);
  378. if params.eyetracking == 1
  379. if params.whicheyetracker == 2
  380. cursample = cursample + 1;
  381. % Get gaze positions from pupil labs
  382. % (filtermessages)
  383. [topic, note] = recv_message(sub_socket, 2500);
  384. if ~isequal(note, false) % test for valid message
  385. gaze_positions{1,iter}= [topic, note('gaze_on_surfaces')]; % print pupil norm_pos
  386. for j=2:size(gaze_positions{1,iter},2)
  387. gazecoordinates = gaze_positions{1,iter}{1,j}('norm_pos');
  388. x(j) = gazecoordinates{1,1};
  389. y(j) = gazecoordinates{1,2};
  391. end
  393. %This alternative is decreasing the temporal...
  394. %...resolution in case matlab fails.
  395. ET.CurrentGaze(1,1) = x(j);
  396. ET.CurrentGaze(1,2) = y(j);
  397. % plot(x(j),y(j),'p')
  398. % drawnow
  399. % hold on
  400. end
  401. gazes(end+1,1) = ET.CurrentGaze(1,1);
  402. gazes(end,2) = ET.CurrentGaze(1,2);
  403. ET.currentTime = GetSecs();
  404. ET.eyetime(cursample,1) = ET.currentTime;
  405. % ET = CheckFixation_VTD_egeVersion(ET, trial, params, output);
  406. iter=iter+1;
  407. end
  408. elseif params.eyetracking == 0
  409. cursample = cursample + 1;
  410. [ET.CurrentGaze(1,1) ET.CurrentGaze(1,2)] = GetMouse(params.window);
  411. ET.currentTime = GetSecs();
  412. ET.eyetime(cursample,1) = ET.currentTime;
  413. gazes(end+1,1) = ET.CurrentGaze(1,1);
  414. gazes(end,2) = ET.CurrentGaze(1,2);
  416. end
  418. if GetSecs()> startSurfDef + initialSurfaceDef
  419. break
  420. end
  421. end
  422. meanGazeOne = [mean(gazes(:,1)) mean(gazes(:,2))];
  423. meanGazeOne
  424. %% start the trial loop here
  425. while 1
  427. trial=trial+1;
  428. if random_trl_order(trial) == 1 % For stimulus present trials
  429. stimPresentCount = stimPresentCount + 1; % Increment stimulus present trial count
  430. % WaitSecs(fixation_Duration);
  431. elseif random_trl_order(trial) == 2 % For stimulus absent trials
  432. stimAbsentCount = stimAbsentCount + 1; % Increment stimulus absent count
  433. % WaitSecs(fixation_Duration);
  434. end
  435. % We only have a single trial type for now, as we are not considering
  436. % the inter-trial interval separately, but rather adding it in with the
  437. % fixation check to initiate trial
  438. if flag == 1
  439. Screen('DrawText', params.window, 'FIXATE PLEASE!', (params.screenX_pix/2)-100, (params.screenY_pix/2), params.black);
  440. %% Display April tags on PTB screen to detect surface via PupilLabs
  441. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  442. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  443. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  444. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  445. Screen('Flip', params.window);
  446. WaitSecs(2);
  447. end
  449. ET.TrialAborted = false;
  450. ET.FixationEstablished = false;
  451. ET.FixationPending = false;
  452. ET.FixationPendingStartTime = NaN;
  453. ET.AbortPending = false;
  454. ET.AbortPendingStartTime = NaN;
  455. ET.AbortStartTime = NaN;
  456. ET.IsFixation = false;
  457. flag = 0;
  458. earlyResponseFlag=0;
  459. flagResponse=1;
  462. output(trial).condition = random_trl_order(trial);
  463. delayBeforeStimulus = warning_before_stimRange(1) + rand() * (warning_before_stimRange(2) - warning_before_stimRange(1));
  464. delayAfterStimulus = var_delay_after_stimRange(1) + rand() * (var_delay_after_stimRange(2) - var_delay_after_stimRange(1));
  465. totaldur = fixation_Duration + delayBeforeStimulus + delayAfterStimulus + 6.05;
  466. totaldurtoresponse = fixation_Duration + delayBeforeStimulus + delayAfterStimulus + 0.05;
  467. params.fixRadiusdeg = 2; % Window in degrees of visual angles for checking for fixation
  468. params.fixRadius = params.fixRadiusdeg*params.pixperdeg; % Window in pixels for checking for fixation
  469. intertrial_Interval_Range = [1.5, 2]; % this is the variable delay range for intertrial interval in seconds - default in Park et al. ,
  470. % is 1.5 to 2, but since we allow another additional 1 sec to the subjects to start the fixation,
  471. % we have reduced this range accordingly
  472. intertrialInterval = intertrial_Interval_Range(1) + rand() * (intertrial_Interval_Range(2) - intertrial_Interval_Range(1));
  473. params.TimeToBeginFixation = intertrialInterval; % Time allowed after the ITI to start fixating
  474. establish_fixation_range = [0.5, 0.7];
  475. establishFixation = establish_fixation_range(1) + rand() * (establish_fixation_range(2) - establish_fixation_range(1));
  476. params.TimeToEstablishFixation = establishFixation; % Time allowed to establish fixation after the time to begin fixation
  477. params.BlinkAllowance = 0.2; % Time given to allow for blinks, usually around 200-300 ms.
  479. %reliance on previous fixation centers vs. the most recent fixation
  480. weightOld = 0.90;
  481. weightNew = 0.10;
  483. % target stimulus contrast in the current trial
  484. currentEstimate = QuestMean(q);
  485. output(trial).AllContrastEstimatesMean = currentEstimate;
  486. currentContrast = QuestQuantile(q);
  487. output(trial).AllContrastEstimatesQuantile = currentContrast;
  488. contrasts(trial) = currentContrast;
  490. %% STATE 1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  491. fprintf('\nTrial %d of %d, Run %d, Trial Type - SP (1) or SA (2): %d \n\n\n\n\n\n', trial, params.numtrials, params.runnumber, random_trl_order(trial));
  493. % Hereon starts the first state - fixation on the central black circle
  494. state = 1;
  495. flag2 = 0;
  497. Screen('FillOval', params.window, params.black, params.centeredcircleRectOUT, params.maxDiameterOUT);
  498. Screen('FillOval', params.window, params.grey, params.centeredcircleRectIN, params.maxDiameterIN);
  499. Screen('DrawDots', params.window, [params.xcenter_pix, params.ycenter_pix], params.fixationSize_pix, params.black, [], 1);
  500. %% Display April tags on PTB screen to detect surface via PupilLabs
  501. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  502. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  503. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  504. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  505. vbl = Screen('Flip', params.window);
  506. output(trial).trialonset = vbl;
  508. % Send EEG trigger code for trial start
  509. if params.EEG == 1
  510. SendSignal(params.ioObj, params.address, random_trl_order(trial)); %1 for stimulus present, 2 for stimulus absent
  511. triggerout = 1;
  512. triggertime = GetSecs;
  513. else
  514. end
  516. if params.eyetracking == 1 % Send Annotation from Matlab to Pupil Labs
  517. if params.whicheyetracker == 2
  518. zmq.core.send(socket, uint8('t'));
  519. currentTime_bytes = zmq.core.recv(socket,20);
  520. % fprintf('first measure: %s\n', char(currentTime_bytes));
  521. currentTimeChar = char(currentTime_bytes);
  522. currentTimeNum = str2num(currentTimeChar);
  523. keys_start = {'topic', 'label', 'timestamp', 'duration'};
  524. values_start = {'annotation.TrialStart', strcat('Trial #', num2str(trial),' started'), currentTimeNum, 1.0};
  525. start_annotation = containers.Map(keys_start, values_start);
  526. send_annotation(socket, start_annotation);
  527. result = zmq.core.recv(socket);
  528. end
  529. end
  531. gazes = []; %to note down all of the recorded gaze locations within the surface, during a trial! It is redefined as empty when the trial restarts due to fixation.
  532. if params.checkfix == 1
  533. if trial == 1
  534. center(trial,:) = meanGazeOne
  535. % center
  536. elseif trial == 2
  537. oldGaze = meanGazeOne * weightOld;
  538. newGaze = output(1).meanGazes * weightNew;
  539. % vector = [meanGazeOne;output(1).meanGazes];
  540. center(trial,:) = oldGaze + newGaze
  541. % center
  542. else
  543. oldGaze = center(trial-1,:) * weightOld;
  544. newGaze = output(trial-1).meanGazes * weightNew;
  545. % vector = [center(trial-1,:);output(trial-1).meanGazes];
  546. center(trial,:) = oldGaze + newGaze
  547. % center
  548. end
  549. end
  551. while state == 1
  553. [pressed, firstPress] = KbQueueCheck;
  555. if pressed
  556. % Extract information about the key presses
  557. [key,ind] = max(firstPress);
  558. % Check if any of the response keys are pressed
  560. if ismember(ind, KbName(responseKeys(1:2)))
  561. % Identify the pressed key
  562. % idx = find(ismember(KbName(responseKeys), pressedKeys));
  563. % response = responseKeys{idx}; % Assign the pressed key as response
  564. Screen('TextSize',params.window, 30);
  565. Screen('DrawText',params.window, 'WAIT QUESTION MARK TO RESPOND!',(params.screenX_pix/2)-100, params.screenY_pix*0.5, params.black);
  566. % Screen('DrawText',params.window, 'Please wait till the question mark sign appears on screen to make your report.',(params.screenX_pix/2)-100, params.screenY_pix*0.55, params.black);
  567. %% Display April tags on PTB screen to detect surface via PupilLabs
  568. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  569. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  570. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  571. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  572. Screen('Flip', params.window);
  573. WaitSecs(2);
  574. flag2 = 1;
  576. end
  578. end
  580. if flag2 == 1
  581. fprintf('early response');
  582. earlyResponseFlag=1; %apart from trial abortion by fixation break; this is another way to abort the trial: because the subject pressed a response button earlier than they were supposed to!
  583. break
  585. end
  587. % If eyetracking
  588. %
  589. if params.eyetracking == 1
  590. if params.whicheyetracker == 2
  591. if params.checkfix == 1
  592. cursample = cursample + 1;
  593. % Get gaze positions from pupil labs
  594. % (filtermessages)
  595. [topic, note] = recv_message(sub_socket, 2500);
  596. if ~isequal(note, false) % test for valid message
  597. gaze_positions{1,iter}= [topic, note('gaze_on_surfaces')]; % print pupil norm_pos
  598. for j=2:size(gaze_positions{1,iter},2)
  599. gazecoordinates = gaze_positions{1,iter}{1,j}('norm_pos');
  600. x(j) = gazecoordinates{1,1};
  601. y(j) = gazecoordinates{1,2};
  603. end
  605. end
  607. ET.CurrentGaze(1,1) = x(j);
  608. ET.CurrentGaze(1,2) = y(j);
  610. if GetSecs() > output(trial).trialonset + params.TimeToBeginFixation % we do not consider the gazes during the ITI for calculating the center for the next trial
  611. gazes(end+1,1) = ET.CurrentGaze(1,1);
  612. gazes(end,2) = ET.CurrentGaze(1,2);
  613. end
  615. ET.currentTime = GetSecs();
  616. ET.eyetime(cursample,1) = ET.currentTime;
  617. if trial == 1
  618. %
  619. dx = abs(x(j) - center(trial,1));
  620. dy = abs(y(j) - center(trial,2));
  621. % center
  622. elseif trial ==2
  623. %
  624. dx = abs(x(j) - center(trial,1));
  625. dy = abs(y(j) - center(trial,2));
  626. % center
  627. else
  628. %
  629. dx = abs(x(j) - center(trial,1));
  630. dy = abs(y(j) - center(trial,2));
  631. % center
  632. end
  633. ET.offset_x = dx * params.pix_x;
  634. ET.offset_y = dy * params.pix_y;
  635. ET = CheckFixation_VTD_egeVersion(ET, trial, params, output);
  637. end
  638. end
  640. elseif params.eyetracking == 0
  641. cursample = cursample + 1;
  642. [ET.CurrentGaze(1,1) ET.CurrentGaze(1,2)] = GetMouse(params.window);
  643. ET.currentTime = GetSecs();
  644. ET.eyetime(cursample,1) = ET.currentTime;
  645. gazes(end+1,1) = ET.CurrentGaze(1,1);
  646. gazes(end,2) = ET.CurrentGaze(1,2);
  647. x = ET.CurrentGaze(1,1);
  648. y = ET.CurrentGaze(1,2);
  649. % figure(10);
  650. plot(x,y,'p')
  651. drawnow
  652. hold on
  653. if trial == 1
  654. center(trial,:) = meanGazeOne;
  655. center
  656. elseif trial == 2
  657. oldGaze = meanGazeOne * weightOld;
  658. newGaze = output(1).meanGazes * weightNew;
  659. % vector = [meanGazeOne;output(1).meanGazes];
  660. center(trial,:) = oldGaze + newGaze
  661. % center
  662. else
  663. oldGaze = center(trial-1,:) * weightOld;
  664. newGaze = output(trial-1).meanGazes * weightNew;
  665. % vector = [center(trial-1,:);output(trial-1).meanGazes];
  666. center(trial,:) = oldGaze + newGaze
  667. % center
  668. end
  669. ET = CheckFixation_VTD_egeVersion(ET, trial, params, output, center);
  670. end
  672. if ET.TrialAborted == true
  673. flag = 1;
  674. if params.EEG == 1
  675. SendSignal(params.ioObj, params.address,55); %trial aborted trigger
  676. triggerout = 1;
  677. triggertime = GetSecs;
  678. else
  679. end
  680. %% Display April tags on PTB screen to detect surface via PupilLabs
  681. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  682. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  683. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  684. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  685. Screen('DrawText', params.window, 'FIXATE PLEASE!', (params.screenX_pix/2)-100, (params.screenY_pix/2), params.black);
  686. Screen('Flip',params.window);
  687. break
  688. end
  690. if params.checkfix==1
  691. if ET.FixationEstablished && GetSecs>output(trial).trialonset+params.TimeToBeginFixation
  692. state = 2;
  693. end
  694. else
  695. if GetSecs>output(trial).trialonset+params.TimeToBeginFixation
  696. state = 2;
  697. end
  698. end
  699. end
  701. if flag == 1 || earlyResponseFlag ==1 %if trial is aborted, 'continue' comment takes you back to line with 'while 1'
  702. if random_trl_order(trial) == 1
  703. stimPresentCount=stimPresentCount-1;
  704. elseif random_trl_order(trial) == 2
  705. stimAbsentCount=stimAbsentCount-1;
  706. end
  707. trial = trial - 1;
  708. continue
  709. end
  711. %% STATE 2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  713. if random_trl_order(trial) == 1 % For stimulus present trials
  715. % Change fixation circle to red and wait for
  716. % variable delay before stimulus presentation
  717. Screen('FillOval', params.window, [0.5 0 0], params.centeredcircleRectOUT, params.maxDiameterOUT);
  718. Screen('FillOval', params.window, params.grey, params.centeredcircleRectIN, params.maxDiameterIN);
  719. Screen('DrawDots', params.window, [params.xcenter_pix, params.ycenter_pix], params.fixationSize_pix, [0.5 0 0], [], 1);
  720. %% Display April tags on PTB screen to detect surface via PupilLabs
  721. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  722. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  723. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  724. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  725. Screen('Flip', params.window);
  726. % Get warning onset time
  727. output(trial).warningOnset = GetSecs;
  729. elseif random_trl_order(trial) == 2 % For stimulus absent trials
  731. % Change fixation circle to red and wait for
  732. % variable delay before stimulus presentation
  733. Screen('FillOval', params.window, [0.5 0 0], params.centeredcircleRectOUT, params.maxDiameterOUT);
  734. Screen('FillOval', params.window, params.grey, params.centeredcircleRectIN, params.maxDiameterIN);
  735. Screen('DrawDots', params.window, [params.xcenter_pix, params.ycenter_pix], params.fixationSize_pix, [0.5 0 0], [], 1);
  736. %% Display April tags on PTB screen to detect surface via PupilLabs
  737. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  738. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  739. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  740. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  741. Screen('Flip', params.window);
  742. % Get warning onset time
  743. output(trial).warningOnset = GetSecs;
  744. end
  746. flag3=0;
  747. earlyResponseFlag=0;
  748. while state == 2
  749. [pressed, firstPress] = KbQueueCheck;
  751. if pressed
  752. % Extract information about the key presses
  753. [~,pressedKeys] = find(firstPress);
  755. % Check if any of the response keys are pressed
  756. if any(ismember(pressedKeys, KbName(responseKeys(1:2))))
  757. % Identify the pressed key
  758. % idx = find(ismember(KbName(responseKeys), pressedKeys));
  759. % response = responseKeys{idx}; % Assign the pressed key as response
  760. Screen('TextSize',params.window, 30)
  761. Screen('DrawText',params.window, 'WAIT QUESTION MARK TO RESPOND!',(params.screenX_pix/2)-100, params.screenY_pix*0.5, params.black);
  762. % Screen('DrawText',params.window, 'Please wait till the question mark sign appears on screen to make your report.',(params.screenX_pix/2)-100, params.screenY_pix*0.55, params.black);
  763. %% Display April tags on PTB screen to detect surface via PupilLabs
  764. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  765. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  766. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  767. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  768. Screen('Flip', params.window);
  769. WaitSecs(2);
  770. flag3 = 1;
  772. end
  773. end
  774. if flag3 == 1
  775. fprintf('early response');
  776. earlyResponseFlag = 1;
  777. break
  778. end
  779. % If eyetracking
  780. if params.eyetracking == 1
  781. if params.whicheyetracker == 2
  782. if params.checkfix == 1
  783. cursample = cursample + 1;
  784. % Get gaze positions from pupil labs
  785. % (filtermessages)
  786. [topic, note] = recv_message(sub_socket, 2500);
  787. if ~isequal(note, false) % test for valid message
  788. gaze_positions{1,iter}= [topic, note('gaze_on_surfaces')]; % print pupil norm_pos
  789. for j=2:size(gaze_positions{1,iter},2)
  790. gazecoordinates = gaze_positions{1,iter}{1,j}('norm_pos');
  791. x(j) = gazecoordinates{1,1};
  792. y(j) = gazecoordinates{1,2};
  794. end
  795. %This alternative is decreasing the temporal...
  796. %...resolution in case matlab fails.
  797. end
  799. ET.CurrentGaze(1,1) = x(j);
  800. ET.CurrentGaze(1,2) = y(j);
  801. gazes(end+1,1) = ET.CurrentGaze(1,1);
  802. gazes(end,2) = ET.CurrentGaze(1,2);
  803. ET.currentTime = GetSecs();
  804. ET.eyetime(cursample,1) = ET.currentTime;
  805. if trial == 1
  806. % center(trial,:) = meanGazeOne;
  807. dx = abs(x(j) - center(trial,1));
  808. dy = abs(y(j) - center(trial,2));
  809. % center
  810. elseif trial ==2
  811. % vector = [meanGazeOne;output(1).meanGazes];
  812. % center(trial,:) = mean(vector,1);
  813. dx = abs(x(j) - center(trial,1));
  814. dy = abs(y(j) - center(trial,2));
  815. % center
  816. else
  817. % vector = [center(trial-1,:);output(trial-1).meanGazes];
  818. % center(trial,:) = mean(vector,1);
  819. dx = abs(x(j) - center(trial,1));
  820. dy = abs(y(j) - center(trial,2));
  821. % center
  822. end
  823. ET.offset_x = dx * params.pix_x;
  824. ET.offset_y = dy * params.pix_y;
  825. % offset = sqrt(offset_x^2 + offset_y^2);
  826. ET = CheckFixation_VTD_egeVersion(ET, trial, params, output, center);
  827. end
  828. end
  830. elseif params.eyetracking == 0
  831. cursample = cursample + 1;
  832. [ET.CurrentGaze(1,1) ET.CurrentGaze(1,2)] = GetMouse(params.window);
  833. ET.currentTime = GetSecs();
  834. ET.eyetime(cursample,1) = ET.currentTime;
  835. gazes(end+1,1) = ET.CurrentGaze(1,1);
  836. gazes(end,2) = ET.CurrentGaze(1,2);
  837. x = ET.CurrentGaze(1,1);
  838. y = ET.CurrentGaze(1,2);
  839. % figure(10);
  840. % plot(x,y,'p')
  841. % drawnow
  842. % hold on
  843. if trial == 1
  844. center(trial,:) = meanGazeOne;
  845. center
  846. elseif trial ==2
  847. vector = [meanGazeOne;output(1).meanGazes];
  848. center(trial,:) = mean(vector,1);
  849. center
  850. else
  851. vector = [center(trial-1,:);output(trial-1).meanGazes];
  852. center(trial,:) = mean(vector,1);
  853. center
  854. end
  855. ET = CheckFixation_VTD_egeVersion(ET, trial, params, output, center);
  856. end
  859. if ET.TrialAborted == true
  860. flag = 1;
  861. if params.EEG == 1
  862. SendSignal(params.ioObj, params.address,55); %trial aborted trigger
  863. triggerout = 1;
  864. triggertime = GetSecs;
  865. else
  866. end
  867. %% Display April tags on PTB screen to detect surface via PupilLabs
  868. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  869. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  870. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  871. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  872. Screen('DrawText', params.window, 'FIXATE PLEASE!', (params.screenX_pix/2)-100, (params.screenY_pix/2), params.black);
  873. Screen('Flip',params.window);
  874. break
  875. end
  878. % Timeout after state2
  879. if GetSecs>=output(trial).warningOnset+delayBeforeStimulus
  880. state = 3;
  881. break;
  882. else
  883. end
  885. end
  887. if flag == 1 || earlyResponseFlag==1
  888. fprintf('This trial is aborted at state # %d',state);
  889. if random_trl_order(trial) == 1
  890. stimPresentCount=stimPresentCount-1;
  891. elseif random_trl_order(trial) == 2
  892. stimAbsentCount=stimAbsentCount-1;
  893. end
  894. trial = trial - 1;
  895. continue
  896. end
  899. %% STATE 3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  900. % Send EEG trigger code for trial start
  903. if random_trl_order(trial) == 1 % For stimulus present trials
  904. % Apply the circular aperture to the
  905. % grating with the contrast recommended
  906. % by the QUEST algorithm
  907. params.gratingannulus = params.grey + params.grey * currentContrast * params.gratingtex;
  908. params.gratingannulus(params.annulusaperture == 0) = params.grey; % Set areas outside the annulus to gray
  910. % Creating the final texture from the grating with gray outside the annulus with PTB
  911. params.gratingannulustex = Screen('MakeTexture', params.window, params.gratingannulus);
  912. Screen('DrawTexture', params.window, params.gratingannulustex);
  913. Screen('FillOval', params.window, [0.5 0 0], params.centeredcircleRectOUT, params.maxDiameterOUT);
  914. Screen('FillOval', params.window, params.grey, params.centeredcircleRectIN, params.maxDiameterIN);
  915. Screen('DrawDots', params.window, [params.xcenter_pix, params.ycenter_pix], params.fixationSize_pix, [0.5 0 0], [], 1);
  916. %Draw the peripheral white square for the photodiode
  917. Screen('DrawDots', params.window, [params.dotXpos1, params.dotYpos1], 10, [0.7 0.7 0.7], [], 4);
  918. %% Display April tags on PTB screen to detect surface via PupilLabs
  919. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  920. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  921. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  922. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  923. % Get timestamp
  924. vbl = Screen('Flip', params.window);
  925. output(trial).stimulusOnset = vbl;
  926. if params.EEG == 1 %we only need this in stimulus present trials
  927. SendSignal(params.ioObj, params.address, 3); %3 = stimulus onset
  928. triggerout = 1;
  929. triggertime = GetSecs;
  930. else
  931. end
  933. if params.eyetracking == 1 % Send Annotation from Matlab to Pupil Labs
  934. if params.whicheyetracker == 2
  935. zmq.core.send(socket, uint8('t'));
  936. currentTime_bytes = zmq.core.recv(socket,20);
  937. % fprintf('first measure: %s\n', char(currentTime_bytes));
  938. currentTimeChar = char(currentTime_bytes);
  939. currentTimeNum = str2num(currentTimeChar);
  940. keys_start = {'topic', 'label', 'timestamp', 'duration'};
  941. values_start = {'annotation.StimulusOnset', strcat('Trial #', num2str(trial),' Stimulus Onset'), currentTimeNum, 1.0};
  942. start_annotation = containers.Map(keys_start, values_start);
  943. send_annotation(socket, start_annotation);
  944. result = zmq.core.recv(socket);
  945. end
  946. end
  947. elseif random_trl_order(trial) == 2 % For stimulus present trials
  949. % Draw stimulus and wait for stimulus presentation
  950. % duration but no stimulus is actually
  951. % presented
  952. % Screen('DrawTexture', params.window, params.gratingannulustex);
  953. % Get stimulus onset time
  954. output(trial).stimulusOnset = GetSecs;
  956. end
  958. flag4=0;
  959. earlyResponseFlag = 0;
  960. while state == 3
  961. [pressed, firstPress] = KbQueueCheck;
  963. if pressed
  964. % Extract information about the key presses
  965. [~,pressedKeys] = find(firstPress);
  967. % Check if any of the response keys are pressed
  968. if any(ismember(pressedKeys, KbName(responseKeys)))
  969. % Identify the pressed key
  970. % idx = find(ismember(KbName(responseKeys), pressedKeys));
  971. % response = responseKeys{idx}; % Assign the pressed key as response
  972. Screen('TextSize',params.window, 30)
  973. Screen('DrawText',params.window, 'WAIT QUESTION MARK TO RESPOND!',(params.screenX_pix/2)-100, params.screenY_pix*0.5, params.black);
  974. % Screen('DrawText',params.window, 'Please wait till the question mark sign appears on screen to make your report.',(params.screenX_pix/2)-100, params.screenY_pix*0.55, params.black);
  975. %% Display April tags on PTB screen to detect surface via PupilLabs
  976. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  977. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  978. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  979. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  980. Screen('Flip',params.window);
  981. WaitSecs(2);
  982. flag4 = 1;
  984. end
  985. end
  986. if flag4 == 1
  987. earlyResponseFlag=1;
  988. fprintf('early response');
  989. break
  990. end
  992. % Timeout after [params.LCandHC] seconds
  993. if GetSecs>=output(trial).stimulusOnset+ stimulusDuration
  994. state = 4;
  995. break;
  996. else
  997. end
  998. %
  999. end
  1000. %
  1003. %% STATE 4 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  1004. state = 4;
  1005. if random_trl_order(trial) == 1
  1006. % Remove stimulus and wait for variable
  1007. % delay duration after stimulus, during
  1008. % this period the red fixation mark still
  1009. % remains
  1010. Screen('FillOval', params.window, [0.5 0 0], params.centeredcircleRectOUT, params.maxDiameterOUT);
  1011. Screen('FillOval', params.window, params.grey, params.centeredcircleRectIN, params.maxDiameterIN);
  1012. Screen('DrawDots', params.window, [params.xcenter_pix, params.ycenter_pix], params.fixationSize_pix, [0.5 0 0], [], 1);
  1013. %% Display April tags on PTB screen to detect surface via PupilLabs
  1014. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  1015. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  1016. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  1017. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  1018. Screen('Flip', params.window, output(trial).stimulusOnset + (stimulusFrames - 0.5) * params.flipinterval);
  1019. output(trial).delayOnset = GetSecs;
  1020. % Get delay onset time
  1022. elseif random_trl_order(trial) == 2 % For stimulus present trials
  1023. % Remove stimulus and wait for variable
  1024. % delay duration after stimulus, during
  1025. % this period the red fixation mark still
  1026. % remains
  1027. Screen('FillOval', params.window, [0.5 0 0], params.centeredcircleRectOUT, params.maxDiameterOUT);
  1028. Screen('FillOval', params.window, params.grey, params.centeredcircleRectIN, params.maxDiameterIN);
  1029. Screen('DrawDots', params.window, [params.xcenter_pix, params.ycenter_pix], params.fixationSize_pix, [0.5 0 0], [], 1);
  1030. %% Display April tags on PTB screen to detect surface via PupilLabs
  1031. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  1032. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  1033. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  1034. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  1035. Screen('Flip', params.window, output(trial).stimulusOnset + (stimulusFrames - 0.5) * params.flipinterval);
  1036. % Get delay onset time
  1037. output(trial).delayOnset = GetSecs;
  1038. end
  1040. flag5=0;
  1041. earlyResponseFlag = 0;
  1042. while state == 4
  1043. [pressed, firstPress] = KbQueueCheck;
  1045. if pressed
  1046. % Extract information about the key presses
  1047. [~,pressedKeys] = find(firstPress);
  1049. % Check if any of the response keys are pressed
  1050. if any(ismember(pressedKeys, KbName(responseKeys)))
  1051. % Identify the pressed key
  1052. % idx = find(ismember(KbName(responseKeys), pressedKeys));
  1053. % response = responseKeys{idx}; % Assign the pressed key as response
  1054. Screen('TextSize',params.window, 30)
  1055. Screen('DrawText',params.window, 'WAIT QUESTION MARK TO RESPOND!',(params.screenX_pix/2)-100, params.screenY_pix*0.5, params.black);
  1056. % Screen('DrawText',params.window, 'Please wait till the question mark sign appears on screen to make your report.',(params.screenX_pix/2)-100, params.screenY_pix*0.55, params.black);
  1057. %% Display April tags on PTB screen to detect surface via PupilLabs
  1058. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  1059. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  1060. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  1061. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  1062. Screen('Flip',params.window);
  1063. WaitSecs(2);
  1064. flag5 = 1;
  1066. end
  1067. end
  1068. if flag5 == 1
  1069. earlyResponseFlag=1;
  1070. fprintf('early response');
  1071. break
  1072. end
  1073. % If eyetracking
  1074. if params.eyetracking == 1
  1075. if params.whicheyetracker == 2
  1076. if params.checkfix == 1
  1077. cursample = cursample + 1;
  1078. % Get gaze positions from pupil labs
  1079. % (filtermessages)
  1080. [topic, note] = recv_message(sub_socket, 2500);
  1081. if ~isequal(note, false) % test for valid message
  1082. gaze_positions{1,iter}= [topic, note('gaze_on_surfaces')]; % print pupil norm_pos
  1083. for j=2:size(gaze_positions{1,iter},2)
  1084. gazecoordinates = gaze_positions{1,iter}{1,j}('norm_pos');
  1085. x(j) = gazecoordinates{1,1};
  1086. y(j) = gazecoordinates{1,2};
  1088. end
  1089. %This alternative is decreasing the temporal...
  1090. %...resolution in case matlab fails.
  1091. end
  1093. ET.CurrentGaze(1,1) = x(j);
  1094. ET.CurrentGaze(1,2) = y(j);
  1095. gazes(end+1,1) = ET.CurrentGaze(1,1);
  1096. gazes(end,2) = ET.CurrentGaze(1,2);
  1097. ET.currentTime = GetSecs();
  1098. ET.eyetime(cursample,1) = ET.currentTime;
  1099. if trial == 1
  1100. % center(trial,:) = meanGazeOne;
  1101. dx = abs(x(j) - center(trial,1));
  1102. dy = abs(y(j) - center(trial,2));
  1103. % center
  1104. elseif trial ==2
  1105. % vector = [meanGazeOne;output(1).meanGazes];
  1106. % center(trial,:) = mean(vector,1);
  1107. dx = abs(x(j) - center(trial,1));
  1108. dy = abs(y(j) - center(trial,2));
  1109. % center
  1110. else
  1111. % vector = [center(trial-1,:);output(trial-1).meanGazes];
  1112. % center(trial,:) = mean(vector,1);
  1113. dx = abs(x(j) - center(trial,1));
  1114. dy = abs(y(j) - center(trial,2));
  1115. % center
  1116. end
  1117. ET.offset_x = dx * params.pix_x;
  1118. ET.offset_y = dy * params.pix_y;
  1119. % offset = sqrt(offset_x^2 + offset_y^2);
  1120. ET = CheckFixation_VTD_egeVersion(ET, trial, params, output, center);
  1121. end
  1122. end
  1124. elseif params.eyetracking == 0
  1125. cursample = cursample + 1;
  1126. [ET.CurrentGaze(1,1) ET.CurrentGaze(1,2)] = GetMouse(params.window);
  1127. ET.currentTime = GetSecs();
  1128. ET.eyetime(cursample,1) = ET.currentTime;
  1129. gazes(end+1,1) = ET.CurrentGaze(1,1);
  1130. gazes(end,2) = ET.CurrentGaze(1,2);
  1131. x = ET.CurrentGaze(1,1);
  1132. y = ET.CurrentGaze(1,2);
  1133. % figure(10);
  1134. % plot(x,y,'p')
  1135. % drawnow
  1136. % hold on
  1137. if trial == 1
  1138. center(trial,:) = meanGazeOne;
  1139. center
  1140. elseif trial ==2
  1141. vector = [meanGazeOne;output(1).meanGazes];
  1142. center(trial,:) = mean(vector,1);
  1143. center
  1144. else
  1145. vector = [center(trial-1,:);output(trial-1).meanGazes];
  1146. center(trial,:) = mean(vector,1);
  1147. center
  1148. end
  1149. ET = CheckFixation_VTD_egeVersion(ET, trial, params, output, center);
  1150. end
  1152. if ET.TrialAborted == true
  1153. flag = 1;
  1154. if params.EEG == 1
  1155. SendSignal(params.ioObj, params.address,55); %trial aborted trigger
  1156. triggerout = 1;
  1157. triggertime = GetSecs;
  1158. else
  1159. end
  1160. %% Display April tags on PTB screen to detect surface via PupilLabs
  1161. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  1162. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  1163. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  1164. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  1165. Screen('DrawText', params.window, 'FIXATE PLEASE!', (params.screenX_pix/2)-100, (params.screenY_pix/2), params.black);
  1166. Screen('Flip',params.window);
  1167. break
  1168. end
  1170. % EEG trigger off
  1171. % if triggerout == 1 && GetSecs >= triggertime + params.triggerofftime
  1172. % SendSignal(0);
  1173. % triggerout = 0;
  1174. % triggertime = NaN;
  1175. % else
  1176. % end
  1178. % Timeout after [params.LCandHC] seconds
  1179. if GetSecs>=output(trial).delayOnset+delayAfterStimulus
  1180. state = 5;
  1181. break;
  1182. else
  1183. end
  1185. end
  1187. if earlyResponseFlag==1
  1188. if params.EEG == 1
  1189. SendSignal(params.ioObj, params.address,55); %trial aborted trigger
  1190. triggerout = 1;
  1191. triggertime = GetSecs;
  1192. else
  1193. end
  1194. end
  1196. if earlyResponseFlag==1 || flag==1
  1197. fprintf('this trial is aborted at state # %d',state);
  1198. if random_trl_order(trial) == 1
  1199. stimPresentCount=stimPresentCount-1;
  1200. elseif random_trl_order(trial) == 2
  1201. stimAbsentCount=stimAbsentCount-1;
  1202. end
  1203. trial = trial - 1;
  1204. continue
  1205. end
  1206. %% STATE 5 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  1209. % Set the background to gray and display message
  1210. % for participant to give their report and
  1211. % confidence
  1212. % Screen('FillRect', params.window, params.grey);
  1213. % Screen('Flip', params.window);
  1214. Report = '?';
  1215. Screen('FillOval', params.window, params.black, params.centeredcircleRectOUT, params.maxDiameterOUT);
  1216. Screen('FillOval', params.window, params.grey, params.centeredcircleRectIN, params.maxDiameterIN);
  1217. Screen('TextSize', params.window, 30);
  1218. Screen('DrawText', params.window, Report, (params.screenX_pix/2)-10, (params.screenY_pix/2)-10, params.black);
  1219. %% Display April tags on PTB screen to detect surface via PupilLabs
  1220. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  1221. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  1222. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  1223. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  1224. Screen('Flip', params.window);
  1225. % WaitSecs(time_for_response);
  1227. response = [];
  1228. flag6 = 0;
  1229. flagResponse=1;
  1230. responseStartTime = GetSecs(); % Record response start time
  1231. while GetSecs() - responseStartTime <= time_for_response
  1232. [pressed, firstPress] = KbQueueCheck;
  1234. if pressed
  1235. % Extract information about the key presses
  1236. [~,pressedKeys] = find(firstPress);
  1238. % Check if any of the response keys are pressed
  1239. if any(ismember(pressedKeys, KbName(responseKeys)))
  1240. % Identify the pressed key
  1241. idx = find(ismember(KbName(responseKeys), pressedKeys));
  1242. response = responseKeys{idx}; % Assign the pressed key as response
  1243. break; % Exit the loop upon response detection
  1244. end
  1246. end
  1247. end
  1249. if ~isempty(response)
  1250. if random_trl_order(trial) == 1
  1251. if strcmp(response, keyHit)
  1252. % Update QUEST for 'hit'
  1253. outputSP(stimPresentCount).response = 1;
  1254. output(trial).response = 1;
  1255. hitCount = hitCount + 1;
  1257. if params.EEG == 1 %we only need this in stimulus present trials
  1258. SendSignal(params.ioObj, params.address, 4); %4 = response 'hit'
  1259. triggerout = 1;
  1260. triggertime = GetSecs;
  1261. else
  1262. end
  1264. if stimPresentCount <= 10 | strcmp (params.runtype, 'TR') %if we are in the test run, we want contrast update after every trial
  1265. q = QuestUpdate(q, currentContrast, 1);
  1266. else
  1267. last10 = [outputSP(stimPresentCount-10:stimPresentCount).response];
  1268. sumlast10=sum(last10);
  1269. if sumlast10/10<0.5
  1270. q = QuestUpdate(q, currentContrast, 1);
  1271. elseif sumlast10/10>0.8
  1272. q = QuestUpdate(q, currentContrast, 1);
  1273. else
  1274. end
  1275. end
  1277. elseif strcmp(response, keyMiss)
  1278. % Update QUEST for 'miss'
  1279. outputSP(stimPresentCount).response = 0;
  1280. output(trial).response = 0;
  1281. missCount = missCount + 1;
  1283. if params.EEG == 1 %we only need this in stimulus present trials
  1284. SendSignal(params.ioObj, params.address, 5); %5 = response 'miss'
  1285. triggerout = 1;
  1286. triggertime = GetSecs;
  1287. else
  1288. end
  1290. if stimPresentCount <= 10
  1291. q = QuestUpdate(q, currentContrast, 0);
  1292. else
  1293. last10 = [outputSP(stimPresentCount-10:stimPresentCount).response]
  1294. sumlast10=sum(last10)
  1295. if sumlast10/10<0.5
  1296. q = QuestUpdate(q, currentContrast, 0);
  1297. elseif sumlast10/10>0.8
  1298. q = QuestUpdate(q, currentContrast, 0);
  1299. else
  1300. end
  1301. end
  1303. end
  1304. elseif random_trl_order(trial) == 2
  1305. if strcmp(response, keyHit)
  1306. faCount = faCount + 1;
  1307. output(trial).response = 1;
  1308. elseif strcmp(response, keyMiss)
  1309. output(trial).response = 0;
  1310. end
  1311. end
  1312. elseif isempty(response)
  1313. flag6 = 1;
  1314. Screen('TextSize',params.window, 30)
  1315. Screen('DrawText',params.window, 'RESPOND ON TIME!',(params.screenX_pix/2)-100, params.screenY_pix*0.5, params.black);
  1316. %% Display April tags on PTB screen to detect surface via PupilLabs
  1317. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  1318. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  1319. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  1320. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  1321. Screen('Flip',params.window);
  1322. WaitSecs(2);
  1323. end
  1326. if flag6 == 1
  1327. flagResponse = 0;
  1328. end
  1330. if flagResponse == 0
  1331. if params.EEG == 1
  1332. SendSignal(params.ioObj, params.address,55); %trial aborted trigger
  1333. triggerout = 1;
  1334. triggertime = GetSecs;
  1335. else
  1336. end
  1337. fprintf('this trial is aborted at state # %d',state);
  1338. if random_trl_order(trial) == 1
  1339. stimPresentCount=stimPresentCount-1;
  1340. elseif random_trl_order(trial) == 2
  1341. stimAbsentCount=stimAbsentCount-1;
  1342. end
  1343. trial = trial - 1;
  1344. continue
  1345. end
  1347. WaitSecs(0.5);
  1348. [pos_conf] = slideScale(params.window, 'Rate your confidence', params.resolution, {'LOW', 'AVERAGE', 'HIGH'},params, 'device','keyboard');
  1349. %% Display April tags on PTB screen to detect surface via PupilLabs
  1350. Screen('DrawTextures', params.window, params.txt1, [], params.dstRects(:,1));
  1351. Screen('DrawTextures', params.window, params.txt2, [], params.dstRects(:,2));
  1352. Screen('DrawTextures', params.window, params.txt3, [], params.dstRects(:,3));
  1353. Screen('DrawTextures', params.window, params.txt4, [], params.dstRects(:,4));
  1354. Screen('Flip',params.window);
  1355. WaitSecs(0.5);
  1356. output(trial).confidenceAnswer = pos_conf; %deviation from the center
  1358. hitRates(trial) = (hitCount / stimPresentCount)*100; % Calculate hit rate
  1359. falseAlarmRates(trial) = (faCount / stimAbsentCount)*100; % Calculate false alarm rate
  1360. output(trial).accuracy = hitRates(trial);
  1361. output(trial).falsealarm = falseAlarmRates(trial);
  1362. fprintf('Current hit rate: %d',hitRates(trial));
  1363. fprintf('\nCurrent false alarm rate: %d',falseAlarmRates(trial));
  1365. % % % Update data arrays
  1366. % x1 = [x1, trial]; % X-axis as index
  1367. % y1 = [y1, hitRates(trial)];
  1368. % x2 = [x2, trial]; % X-axis as index
  1369. % y2 = [y2, falseAlarmRates(trial)];
  1370. % x3 = [x3, trial];
  1371. % y3 = [y3, currentContrast];
  1372. %
  1373. % % Plot online for the first figure
  1374. % figure(1); % Activate the first figure
  1375. % subplot(2, 1, 1);
  1376. % plot(x1, y1, 'r-', 'LineWidth', 2); % Plot updated data for plot 1
  1377. % hold on; % Hold the current plot to add more data
  1378. % plot(x1, y2, 'b--', 'LineWidth', 2); % Plot y2 in red dashed line
  1379. % hold off
  1380. % % Release the current plot
  1381. % xlabel('Trial');
  1382. % ylabel('Hits and False Alarms');
  1383. % ylim([0,1]);
  1384. % title('QUEST modulated accuracy');
  1385. % drawnow; % Refresh the plot
  1386. %
  1387. %
  1388. % % Plot online for the second figure
  1389. % % figure(2); % Activate the second figure
  1390. % subplot(2, 1, 2);
  1391. % plot(x3, y3, 'k-', 'LineWidth', 2); % Plot updated data for plot 2
  1392. % xlabel('Trial');
  1393. % ylabel('Grating Contrast');
  1394. % ylim([0,0.3]);
  1395. % title('QUEST modulated contrast');
  1396. % drawnow; % Refresh the plot
  1401. % EEG trigger off
  1402. % if triggerout == 1 && GetSecs >= triggertime + params.triggerofftime
  1403. % SendSignal(0);
  1404. % triggerout = 0;
  1405. % triggertime = NaN;
  1406. % else
  1407. % end;
  1410. fprintf('\nThis trial is successfully completed, trial number: %d',trial);
  1412. if params.checkfix == 1
  1413. newMean = [mean(gazes(:,1)) mean(gazes(:,2))]; %after a successful completion of a trial, you get the mean gaze locations to re-define it as the center!
  1414. output(trial).meanGazes = newMean;
  1415. end
  1417. if trial == params.numtrials
  1418. break
  1419. end
  1421. end; % end of trial loop
  1423. WaitSecs(2);
  1424. KbQueueStop; % Stop delivering events to the queue
  1426. [pressed, firstPress] = KbQueueCheck;
  1428. % [pressed, firstPress, firstRelease, lastPress, lastRelease] = KbQueueCheck;
  1430. % Create key presses struct
  1431. for i = 1:KbEventAvail
  1432. [evt, n] = KbEventGet;
  1433. if i == 1
  1434. keyboard_events = evt;
  1435. else
  1436. keyboard_events(end+1) = evt;
  1437. end;
  1438. end;
  1441. end % end of blocks loop
  1442. %% Close properly
  1444. % Show end message for the subject
  1445. Screen('DrawText', params.window, 'Done - Thank you!', (params.screenX_pix/2)-100, (params.screenY_pix/2), params.black);
  1446. Screen('Flip', params.window);
  1447. WaitSecs(2);
  1449. % Show mouse cursor again
  1450. ShowCursor;
  1452. % % Calculate hit rate and false alarm rate as percentages
  1453. overallhitRate = (hitCount / stimPresentCount) * 100;
  1454. overallfalseAlarmRate = (faCount / stimAbsentCount) * 100;
  1457. % Save data to .mat file
  1458. cd(params.savepath);
  1460. save(params.filename,'params','output','keyboard_events','ET','gazes','-v7.3');
  1462. disp('Data saved');
  1464. KbQueueRelease;
  1465. ListenChar(0);
  1467. if strcmp (params.runtype, 'TR')| strcmp (params.runtype, 'TC')
  1468. % Display the estimated threshold
  1469. disp(['Estimated Threshold from the Calibration Run: ' num2str(QuestMean(q))]);
  1470. elseif strcmp (params.runtype, 'R')| strcmp (params.runtype, 'H')
  1471. disp(['Estimated Threshold from the Last Run: ' num2str(QuestMean(q))]);
  1472. end
  1474. % Close Eyelink eyetracker
  1475. if params.eyetracking == 1
  1476. if params.whicheyetracker == 1
  1477. Eyelink('StopRecording');
  1478. Eyelink('CloseFile');
  1479. % download data file
  1480. try
  1481. fprintf('Receiving data file ''%s''\n', params.eyedatafile);
  1482. status=Eyelink('ReceiveFile');
  1483. if status > 0
  1484. fprintf('ReceiveFile status %d\n', status);
  1485. end
  1486. if 2==exist(params.eyedatafile, 'file')
  1487. fprintf('Data file ''%s'' can be found in ''%s''\n', params.eyedatafile, pwd );
  1488. end
  1489. catch rdf
  1490. fprintf('Problem receiving data file ''%s''\n', params.eyedatafile);
  1491. rdf;
  1492. end
  1494. Eyelink('Command', 'set_idle_mode');
  1495. WaitSecs(0.05);
  1496. Eyelink('shutdown')
  1497. elseif params.whicheyetracker == 2
  1498. %stop the recording of Pupil Labs
  1499. zmq.core.send(socket, uint8('r'));
  1500. result = zmq.core.recv(socket);
  1501. fprintf('Recording stopped: %s\n', char(result));
  1503. % disconnect sub socket
  1504. zmq.core.disconnect(sub_socket, sub_endpoint);
  1505. zmq.core.close(sub_socket);
  1506. fprintf('Disconnected from SUB: %s\n', sub_endpoint);
  1508. zmq.core.disconnect(socket, endpoint);
  1509. zmq.core.close(socket);
  1511. % zmq.core.ctx_shutdown(ctx);
  1512. % zmq.core.ctx_term(ctx);
  1513. end
  1514. end
  1518. % Find indices of stimulus-absent trials
  1519. stimulusAbsentIdx = find(random_trl_order == 2);
  1520. % Generate plots
  1521. % Plot for Accuracy (hit rate and false alarm rate vs Trial Number)
  1522. trialNumbers = 1:length(random_trl_order);
  1523. figure;
  1524. subplot(2, 1, 1);
  1525. plot(trialNumbers, hitRates, 'Color', [0.6, 0, 0], 'LineWidth', 2); % Plot hit rate
  1526. hold on;
  1527. plot(trialNumbers, falseAlarmRates, 'Color', [0, 0.6, 0], 'LineWidth', 2); % Plot false alarm rate
  1528. xlabel('Trial Number');
  1529. ylabel('Accuracy (%)');
  1530. % legend('Hit Rate', 'False Alarm Rate', 'Location','eastoutside');
  1531. title('Accuracy');
  1532. xlim([1, length(trialNumbers)]);
  1534. % Plot the stimulus-absent trials individually with a grey background
  1535. for i = 1:length(stimulusAbsentIdx)
  1536. idx = stimulusAbsentIdx(i);
  1538. % Check if this is not the last stimulus-absent trial
  1539. if i < length(stimulusAbsentIdx)
  1540. % Define x-coordinates for the grey background area
  1541. x = [idx, trialNumbers(idx+1), trialNumbers(idx+1), idx];
  1542. else
  1543. % For the last stimulus-absent trial
  1544. if idx == trialNumbers(end)
  1545. x = [idx, trialNumbers(end), trialNumbers(end), idx];
  1546. else
  1547. x = [idx, trialNumbers(idx+1), trialNumbers(idx+1), idx];
  1548. end
  1549. end
  1551. % Define y-coordinates for the grey background area (0 to 0.25 for contrast)
  1552. y = [0, 0, 100, 100];
  1554. % Plot the grey background area for this stimulus-absent trial
  1555. patch(x, y, 'k', 'EdgeColor', 'none', 'FaceColor', [0.8, 0.8, 0.8], 'FaceAlpha', 0.3);
  1556. end
  1559. % Plot for currentContrast vs Trial Number
  1560. subplot(2, 1, 2);
  1561. plot(trialNumbers, contrasts, 'Color', [0.6, 0, 0], 'LineWidth', 2);
  1562. xlabel('Trial Number');
  1563. ylabel('Stimulus Contrast');
  1564. title('QUEST recommended contrast');
  1565. ylim([0, 0.25]); % Set y-axis limits for contrast plot
  1566. xlim([1, length(trialNumbers)]);
  1568. % Plot the stimulus-absent trials individually with a grey background
  1569. for i = 1:length(stimulusAbsentIdx)
  1570. idx = stimulusAbsentIdx(i);
  1572. % Check if this is not the last stimulus-absent trial
  1573. if i < length(stimulusAbsentIdx)
  1574. % Define x-coordinates for the grey background area
  1575. x = [idx, trialNumbers(idx+1), trialNumbers(idx+1), idx];
  1576. else
  1577. % For the last stimulus-absent trial
  1578. if idx == trialNumbers(end)
  1579. x = [idx, trialNumbers(end), trialNumbers(end), idx];
  1580. else
  1581. x = [idx, trialNumbers(idx+1), trialNumbers(idx+1), idx];
  1582. end
  1583. end
  1585. % Define y-coordinates for the grey background area (0 to 0.25 for contrast)
  1586. y = [0, 0, 0.25, 0.25];
  1588. % Plot the grey background area for this stimulus-absent trial
  1589. patch(x, y, 'k', 'EdgeColor', 'none', 'FaceColor', [0.8, 0.8, 0.8], 'FaceAlpha', 0.3);
  1590. end
  1591. hold off;
  1593. % Save the plots
  1594. saveas(gcf, fullfile(params.savepathplot, params.filenameplot));
  1596. end

trials_VTDnew_egeVersion.m at commit bd6707d, no license · at the source

Overview

Authors: Ege Kingir1, Sukanya Chakraborty1, Caspar M Schwiedrzik2,3,4, Melanie Wilke1,5
ORCID iDs: Ege Kingir, Melanie Wilke
  1. Department of Cognitive Neurology, Heart and Brain Center Goettingen, University Medical Center, Goettingen, Germany
  2. Neural Circuits and Cognition Lab, European Neuroscience Institute Goettingen—A Joint Initiative of the University Medical Center Goettingen and the Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
  3. Perception and Plasticity Group, German Primate Center—Leibniz Institute for Primate Research, Göttingen, Germany
  4. Cognitive Neurobiology, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Biology and Biotechnology, Ruhr‐University Bochum, Bochum, Germany
  5. Cognitive Neurology Group, German Primate Center, Cognitive Neuroscience Laboratory, Leibniz Institute for Primate Research, Goettingen, Germany
Institutions: Universitätsmedizin Göttingen (Germany); University of Göttingen (Germany); German Primate Center (Germany); European Neuroscience Institute Göttingen (Germany); Max Planck Institute for Multidisciplinary Sciences (Germany); Ruhr University Bochum (Germany)
Journal: Psychophysiology, volume 63, issue 3, article e70271
Dates: received 15 August 2025; accepted 18 February 2026; published online 9 March 2026; in print March 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1111/psyp.70271 · PMID 41800588 · PMCID PMC12969548 · OpenAlex W7134230605
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: EEG (modality), other (modality), human (organism), cognitive (subfield)
Methods: Spectral & time-frequency, Connectivity, Statistics, Smoothing, state filtering, decompositions, Preprocessing, Evoked potentials, Physiology & signal measures, Machine learning
Keywords: anticipatory cardiac deceleration, heart rate variability, respiration, respiratory sinus arrhythmia, visual perception
MeSH: Anticipation, Psychological*, Evoked Potentials*, Heart Rate*, Respiratory Sinus Arrhythmia*, Visual Perception*, Adult, Electrocardiography, Electroencephalography, Female, Humans, Male, Young Adult (* major topic)
Topic: Heart Rate Variability and Autonomic Control (Cardiology and Cardiovascular Medicine, Medicine), according to OpenAlex
Funding: International Max Planck Research School for Neurosciences (IMPRS); International Max Planck Research School for Advanced Methods in Process and Systems Engineering; Else Kröner-Fresenius-Stiftung; Deutsche Forschungsgemeinschaft (SCHW1683/2‐1, GRK 2824); German Research Foundation (GRK 2824, SCHW1683/2-1)
Citations: not cited yet (Europe PMC); 65 references in the paper

Abstract

The heart does not beat like a metronome: varying parasympathetic input to the heart leads to constant heart rate variability. Vagal cardiomotor neuron activity is coupled to the respiratory cycle, leading to respiratory sinus arrhythmia (RSA), a permanent oscillation of heart rate synchronized to respiration. Heart rate also temporarily decelerates in specific conditions such as in freezing due to perceived threat or in anticipation of a salient stimulus. Anticipatory cardiac deceleration (ACD) is observed consistently in anticipation of a stimulus in perceptual tasks, but its relationship with perceptual performance is debated. Previous quantifications of ACD neglect ongoing heart rate oscillations due to RSA, which may have led to inconsistencies in the ACD‐related analyses across studies. Here, we suggest a novel approach to estimate trial‐averaged RSA amplitude and respiratory phase‐independent cardiac deceleration simultaneously and apply it to an EEG‐ECG dataset from a visual detection task. While the total ACD was not associated with perception, dissociating RSA‐dependent and non‐respiratory cardiac modulations revealed that they showed negative and positive correlations with perceptual performance, respectively. Additionally, we found that participants with higher ACD amplitudes also displayed larger Visual Awareness Negativity potentials, further supporting a contribution of ACD to visual perception.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 16 matches between paragraphs and lines of code.

ege-kingir/VisualThresholdDetection

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: bd6707dfffe9276a67c0b1cae2260bc1041f9070, 26 February 2026
Languages: MATLAB (21)
Size: 26 files, 21 scripts
Software Heritage: not archived
Found in: “Data Availability Statement”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Psychtoolbox (7 files), EEGLAB (5 files), Statistics and Machine Learning Toolbox (3 files), CircStat (2 files), FieldTrip (1 file), Image Processing Toolbox (1 file), Signal Processing Toolbox (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
22 files
At the source: github.com/ege-kingir/VisualThresholdDetection

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 21 scripts, each with its path and the digest of its content;
  • 16 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data Availability Statement

The datasets generated and analyzed for the current study, and the corresponding code, are available from the corresponding author on request. Code for running the visual perception task, physiological data preprocessing, and analysis can be found in this public GitHub repository: https://github.com/ege‐kingir/VisualThresholdDetection (https://github.com/ege-kingir/VisualThresholdDetection).

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 4 authors, 5 keywords, 12 MeSH terms, 5 funders, 63 references.

Cite

This paper

Kingir, E., Chakraborty, S., Schwiedrzik, C. M., & Wilke, M. (2026). Disentangling Respiratory Phase-Dependent and Phase-Independent Components of Anticipatory Cardiac Deceleration. Psychophysiology, 63(3), e70271. https://doi.org/10.1111/psyp.70271

BibTeX

@article{kingir2026disentangling,
author = {Kingir, Ege and Chakraborty, Sukanya and Schwiedrzik, Caspar M and Wilke, Melanie},
title = {{Disentangling Respiratory Phase-Dependent and Phase-Independent Components of Anticipatory Cardiac Deceleration}},
journal = {Psychophysiology},
year = {2026},
month = mar,
volume = {63},
number = {3},
pages = {e70271},
publisher = {Wiley},
issn = {0048-5772},
doi = {10.1111/psyp.70271},
url = {https://doi.org/10.1111/psyp.70271},
pmid = {41800588},
pmcid = {PMC12969548}
}

RIS

TY - JOUR
AU - Kingir, Ege
AU - Chakraborty, Sukanya
AU - Schwiedrzik, Caspar M
AU - Wilke, Melanie
TI - Disentangling Respiratory Phase-Dependent and Phase-Independent Components of Anticipatory Cardiac Deceleration
T2 - Psychophysiology
J2 - Psychophysiology
PY - 2026
DA - 2026/03/01
VL - 63
IS - 3
SP - e70271
SN - 0048-5772
PB - Wiley
DO - 10.1111/psyp.70271
UR - https://doi.org/10.1111/psyp.70271
LA - en
ER -

CSL-JSON

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"id": "10.1111/psyp.70271",
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"author": [
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"given": "Ege"
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"container-title-short": "Psychophysiology",
"volume": "63",
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"page": "e70271",
"DOI": "10.1111/psyp.70271",
"PMID": "41800588",
"PMCID": "PMC12969548",
"ISSN": "0048-5772",
"publisher": "Wiley",
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"date-parts": [
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2026,
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1
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}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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