OSCR

Differential Effects of Balanced and Imbalanced Binocular Stimulation on Visual Cortex Responses in Amblyopic Children.

Code ↔ Paper

9 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 9 matches
  1. [1] § Materials and Methods › MRI Sequence ↔ mripy/dicom.py, lines 80–155 · score 0.96 · phase encoding direction, gradient recalled, echo planar, GE EPI, distortion correction, FOV
  2. [2] § Materials and Methods › MRI Sequence ↔ mripy/dicom_report.py, lines 23–80 · score 0.79 · distortion correction, MPRAGE, TE, FA, FOV, Siemens
  3. [3] § Materials and Methods › fMRI Data Analysis › Preprocessing ↔ mripy/preprocess.py, lines 1888–2011 · score 0.70 · rigid body, AFNI, lpc, preprocessed, EPI, transformations
  4. [4] § Materials and Methods › Visual Stimuli for Cortical Activation ↔ stimuli/gratingStimulus.m, lines 1–121 · score 0.63 · square wave, temporal frequency, sinusoidally, modulated, deg, SF
  5. [5] § Materials and Methods › Visual Stimuli for Cortical Activation ↔ stimuli/colourGratingStimulus.m, lines 1–133 · score 0.61 · square wave, temporal frequency, sinusoidally, deg, SF, angle
  6. [6] § Materials and Methods › Apparatus ↔ calibration/calibrateLuminance.m, lines 1–81 · score 0.56 · SpectroCal, instructed, monitored, Linux, luminance, asked
  7. [7] § Materials and Methods › Apparatus ↔ calibration/calibrateLuminanceNew.m, lines 1–81 · score 0.56 · SpectroCal, instructed, monitored, Linux, luminance, asked
  8. [8] § Materials and Methods › Retinotopic Mapping ↔ stimuli/colourGratingStimulus.m, lines 1–133 · score 0.56 · square wave, phase reversed, ratio, background, setup
  9. [9] § Materials and Methods › Retinotopic Mapping ↔ stimuli/polarGratingStimulus.m, lines 1–144 · score 0.56 · square wave, phase reversed, ratio, background, setup

Paper

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The authors' code

MATLAB · 605 lines · 21 KB · LGPL-3.0 · 2 matches

  1. % ========================================================================
  2. %> @brief colour grating stimulus, inherits from baseStimulus
  3. %> COLOURGRATINGSTIMULUS colour grating stimulus, inherits from baseStimulus
  4. %> The basic properties are:
  5. %> type = 'sinusoid' or 'square', if square you should set sigma which
  6. %> smoothes the interface and stops pixel motion artifacts that normally
  7. %> inflict square wave gratings, set sigma to 0 to remove smoothing.
  8. %> colour = first grating colour
  9. %> colour2 = second grating colour
  10. %> baseColour = the midpoint between the two from where contrast works,
  11. %> defult just inherits the background colour from screenManager
  12. %> correctBaseColour = automatically generate baseColour as the average
  13. %> of colour and colour2
  14. %> contrast = contrast from 0 - 1
  15. %> sf = spatial frequency in degrees
  16. %> tf = temporal frequency in degs/s
  17. %> angle = angle in degrees
  18. %> rotateTexture = do we rotate the grating texture (true) or the patch itself (false)
  19. %> phase = phase of grating
  20. %> mask = use circular mask (true) or not (false)
  21. %>
  22. %> See docs for more property details.
  23. %>
  24. %> @todo phase appears different to gratingStimulus, work out why
  25. %>
  26. %> Copyright ©2014-2022 Ian Max Andolina — released: LGPL3, see LICENCE.md
  27. % ========================================================================
  28. classdef colourGratingStimulus < baseStimulus
  30. properties %--------------------PUBLIC PROPERTIES----------%
  31. %> family type, can be 'sinusoid' or 'square'
  32. type char = 'sinusoid'
  33. %> spatial frequency of the grating
  34. sf(1,1) double = 1
  35. %> temporal frequency of the grating
  36. tf(1,1) double = 1
  37. %> second colour of a colour grating stimulus
  38. colour2(1,:) double = [0 1 0 1]
  39. %> base colour from which colour and colour2 are blended via contrast value
  40. %> if empty [default], uses the background colour from screenManager
  41. baseColour(1,:) double = []
  42. %> rotate the grating patch (false) or the grating texture within the patch (default = true)?
  43. rotateTexture logical = true
  44. %> phase of grating
  45. phase(1,1) double = 0
  46. %> contrast of grating (technically the contrast from the baseColour)
  47. contrast(1,1) double = 0.5
  48. %> use a circular mask for the grating (default = true).
  49. mask logical = true
  50. %> direction of the drift; default = false means drift left>right when angle is 0deg.
  51. %This switch can be accomplished simply setting angle, but this control enables
  52. %simple reverse direction protocols.
  53. reverseDirection logical = false
  54. %> the direction of the grating object if moving.
  55. direction double = 0
  56. %> Do we need to correct the phase to be relative to center not edge? This enables
  57. %> centre surround stimuli are phase matched, and if we enlarge a grating object its
  58. %> phase stays identical at the centre of the object (where we would imagine our RF)
  59. correctPhase logical = false
  60. %> In certain cases the base colour should be calculated
  61. %> dynamically from colour and colour2, and this enables this to
  62. %> occur blend
  63. correctBaseColour logical = false
  64. %> Reverse phase of grating X times per second? Useful with a static grating for linearity testing
  65. phaseReverseTime(1,1) double = 0
  66. %> What phase to use for reverse?
  67. phaseOfReverse(1,1) double = 180
  68. %> sigma of square wave smoothing, use -1 for sinusoidal gratings
  69. sigma(1,1) double = -1
  70. %> aspect ratio of the grating
  71. aspectRatio(1,1) double = 1;
  72. %> turn stimulus on/off at X hz, [] diables this
  73. visibleRate = []
  74. end
  76. properties (SetAccess = protected, GetAccess = public)
  77. %stimulus family
  78. family char = 'grating'
  79. %> scale is used when changing size as an independent variable to keep sf accurate
  80. scale double = 1
  81. %> the phase amount we need to add for each frame of animation
  82. phaseIncrement double = 0
  83. end
  85. properties (Constant)
  86. typeList cell = {'sinusoid';'square'}
  87. end
  89. properties (SetAccess = protected, GetAccess = {?baseStimulus})
  90. %> properties to not show in the UI panel
  91. ignorePropertiesUI = 'alpha';
  92. end
  94. properties (SetAccess = protected, GetAccess = protected)
  95. %> as get methods are slow, we cache sf, then recalculate sf whenever
  96. %> changeScale event is called
  97. sfCache = []
  98. %>to stop a loop between set method and an event
  99. sfRecurse = false
  100. %> allowed properties passed to object upon construction
  101. allowedProperties = {'type','colour2', 'sf', 'tf', 'angle', 'direction', 'phase', 'rotateTexture', ...
  102. 'contrast', 'mask', 'reverseDirection', 'speed', 'startPosition', 'aspectRatio', ...
  103. 'sigma', 'correctPhase', 'phaseReverseTime', 'phaseOfReverse','visibleRate',...
  104. 'correctBaseColour'}
  105. %> properties to not create transient copies of during setup phase
  106. ignoreProperties = {'type', 'scale', 'phaseIncrement', 'correctPhase', 'contrastMult', 'mask', 'typeList'}
  107. %> how many frames between phase reverses
  108. phaseCounter = 0
  109. %> mask value (radius for the procedural shader)
  110. maskValue
  111. %> the raw shader, we can try to change colours.
  112. shader
  113. %> these store the current colour so we can check if update needs
  114. %to regenerate the shader
  115. colourCache
  116. colour2Cache
  117. visibleTick = 0
  118. visibleFlip = Inf
  119. end
  121. %=======================================================================
  122. methods %------------------PUBLIC METHODS
  123. %=======================================================================
  125. % ===================================================================
  126. %> @brief Class constructor
  127. %>
  128. %> More detailed description of what the constructor does.
  129. %>
  130. %> @param args are passed as a structure of properties which is
  131. %> parsed.
  132. %> @return instance of class.
  133. % ===================================================================
  134. function me = colourGratingStimulus(varargin)
  135. args = optickaCore.addDefaults(varargin,...
  136. struct('name','colour-grating','colour',[1 0 0 1],'colour2',[0 1 0 1]));
  137. me=me@baseStimulus(args); %we call the superclass constructor first
  138. me.parseArgs(args, me.allowedProperties);
  140. me.isRect = true; %uses a rect for drawing
  142. me.ignoreProperties = [me.ignorePropertiesBase me.ignoreProperties];
  143. me.salutation('constructor method','Stimulus initialisation complete');
  144. end
  146. % ===================================================================
  147. %> @brief Setup this object in preparation for use
  148. %> When displaying a stimulus object, the main properties that are to be
  149. %> modified are copied into cache copies of the property, both to convert from
  150. %> visual description (c/d, Hz, degrees) to
  151. %> computer metrics, and to be animated and modified as independant
  152. %> variables. So xPosition is copied to xPositionOut and converted from
  153. %> degrees to pixels. The animation and drawing functions use these modified
  154. %> properties, and when they are updated, for example to change to a new
  155. %> xPosition, internal methods ensure reconversion and update any dependent
  156. %> properties. This method initialises the object with all the cache properties
  157. %> for display.
  158. %>
  159. %> @param sM screenManager object to use
  160. % ===================================================================
  161. function setup(me,sM)
  163. reset(me); %reset object back to its initial state
  164. me.inSetup = true; me.isSetup = false;
  165. if isempty(me.isVisible); show(me); end
  167. me.sM = sM;
  168. if ~sM.isOpen; error('Screen needs to be Open!'); end
  169. me.ppd=sM.ppd;
  170. me.screenVals = sM.screenVals;
  171. me.texture = []; %we need to reset this
  173. fn = sort(properties(me));
  174. for j=1:length(fn)
  175. if ~matches(fn{j}, me.ignoreProperties)
  176. p=me.addprop([fn{j} 'Out']);
  177. if strcmp(fn{j}, 'sf'); p.SetMethod = @set_sfOut; end
  178. if strcmp(fn{j}, 'tf')
  179. p.SetMethod = @set_tfOut; p.SetObservable = true;
  180. addlistener(me, [fn{j} 'Out'], 'PostSet', @me.calculatePhaseIncrement);
  181. end
  182. if strcmp(fn{j}, 'reverseDirection')
  183. p.SetMethod = @set_reverseDirectionOut; p.SetObservable = true;
  184. addlistener(me, [fn{j} 'Out'], 'PostSet', @me.calculatePhaseIncrement);
  185. end
  186. if strcmp(fn{j}, 'size')
  187. p.SetMethod = @set_sizeOut; p.SetObservable = true;
  188. addlistener(me, [fn{j} 'Out'], 'PostSet', @me.calculateScale);
  189. end
  190. if strcmp(fn{j}, 'xPosition'); p.SetMethod = @set_xPositionOut; end
  191. if strcmp(fn{j}, 'yPosition'); p.SetMethod = @set_yPositionOut; end
  192. if strcmp(fn{j}, 'colour')
  193. p.SetMethod = @set_cOut; p.SetObservable = true;
  194. addlistener(me, [fn{j} 'Out'], 'PostSet', @me.fixBaseColour);
  195. end
  196. if strcmp(fn{j}, 'colour2')
  197. p.SetMethod = @set_c2Out; p.SetObservable = true;
  198. addlistener(me, [fn{j} 'Out'], 'PostSet', @me.fixBaseColour);
  199. end
  200. me.([fn{j} 'Out']) = me.(fn{j}); %copy our property value to our temporary copy
  201. end
  202. end
  204. addRuntimeProperties(me);
  206. if ~isprop(me,'rotateMode'); addprop(me,'rotateMode'); end
  207. if me.rotateTexture
  208. me.rotateMode = kPsychUseTextureMatrixForRotation;
  209. else
  210. me.rotateMode = [];
  211. end
  213. if ~isprop(me,'gratingSize'); addprop(me,'gratingSize'); end
  214. me.gratingSize = round(me.ppd*me.size); %virtual support larger than initial size
  216. if ~isprop(me,'driftPhase'); addprop(me,'driftPhase'); end
  217. if me.correctPhase
  218. ps = me.calculatePhase;
  219. me.driftPhase = me.phaseOut-ps;
  220. else
  221. me.driftPhase = me.phaseOut;
  222. end
  224. if ~isprop(me,'res'); addprop(me,'res'); end
  226. switch length(me.aspectRatio)
  227. case 1
  228. me.res = round([me.gratingSize*me.aspectRatio me.gratingSize]);
  229. case 2
  230. me.res = round([me.gratingSize*me.aspectRatio(1) me.gratingSize*me.aspectRatio(2)]);
  231. end
  232. if max(me.res) > me.sM.screenVals.width %scale to be no larger than screen width
  233. me.res = floor( me.res / (max(me.res) / me.sM.screenVals.width));
  234. end
  236. if me.mask == true
  237. me.maskValue = floor((me.ppd*me.size))/2;
  238. else
  239. me.maskValue = [];
  240. end
  242. if me.phaseReverseTime > 0
  243. me.phaseCounter = round(me.phaseReverseTime / me.sM.screenVals.ifi);
  244. end
  246. if isempty(me.baseColour)
  247. if me.correctBaseColour
  248. me.baseColourOut = (me.colourOut(1:3) + me.colour2Out(1:3)) / 2;
  249. me.baseColourOut(4) = me.alpha;
  250. else
  251. me.baseColourOut = me.sM.backgroundColour;
  252. me.baseColourOut(4) = me.alpha;
  253. end
  254. end
  256. if strcmpi(me.type,'square')
  257. if me.sigma < 0; me.sigma = 0.05; me.sigmaOut = me.sigma; end
  258. else
  259. me.salutation('SETUP', 'Reset sigma to -1 as type=squarewave', true)
  260. me.sigmaOut = -1; %just make sure type overrides sigma if conflict
  261. end
  263. % this is a two color grating, passing in colorA and colorB.
  264. [me.texture, ~, me.shader] = CreateProceduralColorGrating(me.sM.win, me.res(1),...
  265. me.res(2), me.colourOut, me.colour2Out, me.maskValue);
  266. me.colourCache = me.colourOut; me.colour2Cache = me.colour2Out;
  268. if ~isempty(me.visibleRateOut) && isnumeric(me.visibleRateOut)
  269. me.visibleTick = 0;
  270. me.visibleFlip = round((me.screenVals.fps/2) / me.visibleRateOut);
  271. else
  272. me.visibleFlip = Inf; me.visibleTick = 0;
  273. end
  275. me.inSetup = false; me.isSetup = true;
  276. computePosition(me);
  277. setRect(me);
  279. function set_cOut(me, value)
  280. len=length(value);
  281. switch len
  282. case {4,3}
  283. c = [value(1:3) me.alpha]; %force our alpha to override
  284. case 1
  285. c = [value value value me.alpha]; %construct RGBA
  286. otherwise
  287. c = [1 1 1 me.alpha]; %return white for everything else
  288. end
  289. c(c<0)=0; c(c>1)=1;
  290. me.colourOut = c;
  291. end
  292. function set_c2Out(me, value) %#ok<*MCSGP>
  293. len=length(value);
  294. switch len
  295. case {4,3}
  296. c = [value(1:3) me.alpha]; %force our alpha to override
  297. case 1
  298. c = [value value value me.alpha]; %construct RGBA
  299. otherwise
  300. c = [1 1 1 me.alpha]; %return white for everything else
  301. end
  302. c(c<0)=0; c(c>1)=1;
  303. me.colour2Out = c;
  304. end
  305. function set_sfOut(me,value)
  306. if me.sfRecurse == false
  307. me.sfCache = (value / me.ppd);
  308. me.sfOut = me.sfCache * me.scale;
  309. else
  310. me.sfOut = value;
  311. me.sfRecurse = false;
  312. end
  313. %fprintf('\nSET SFOut: %d | cache: %d | in: %d\n', me.sfOut, me.sfCache, value);
  314. end
  315. function set_tfOut(me,value)
  316. me.tfOut = value;
  317. end
  318. function set_reverseDirectionOut(me,value)
  319. me.reverseDirectionOut = value;
  320. end
  321. function set_sizeOut(me,value)
  322. me.sizeOut = value*me.ppd;
  323. me.szPx = me.sizeOut;
  324. end
  325. function set_xPositionOut(me, value)
  326. me.xPositionOut = value * me.ppd;
  327. end
  328. function set_yPositionOut(me,value)
  329. me.yPositionOut = value*me.ppd;
  330. end
  331. end
  333. % ===================================================================
  334. %> @brief Update this stimulus object for display
  335. %>
  336. % ===================================================================
  337. function update(me)
  338. resetTicks(me);
  339. if me.correctPhase
  340. ps=me.calculatePhase;
  341. me.driftPhase=me.phaseOut-ps;
  342. else
  343. me.driftPhase=me.phaseOut;
  344. end
  345. if ~all(me.colourCache(1:3) == me.colourOut(1:3)) || ...
  346. ~all(me.colour2Cache(1:3) == me.colour2Out(1:3))
  347. glUseProgram(me.shader);
  348. glUniform4f(glGetUniformLocation(me.shader, 'color1'),...
  349. me.colourOut(1),me.colourOut(2),me.colourOut(3),me.alphaOut);
  350. glUniform4f(glGetUniformLocation(me.shader, 'color2'),...
  351. me.colour2Out(1),me.colour2Out(2),me.colour2Out(3),me.alphaOut);
  352. if me.mask == true
  353. me.maskValue = me.sizeOut/2;
  354. else
  355. me.maskValue = 0;
  356. end
  357. glUniform1f(glGetUniformLocation(me.shader, 'radius'), me.maskValue);
  358. glUseProgram(0);
  359. me.colourCache = me.colourOut; me.colour2Cache = me.colour2Out;
  360. end
  361. if ~isempty(me.visibleRateOut) && isnumeric(me.visibleRateOut)
  362. me.isVisible = true;
  363. me.visibleTick = 0;
  364. me.visibleFlip = round((me.screenVals.fps/2) / me.visibleRateOut);
  365. else
  366. me.visibleFlip = Inf; me.visibleTick = 0;
  367. end
  368. computePosition(me);
  369. setRect(me);
  370. end
  372. % ===================================================================
  373. %> @brief Draw this stimulus object for display
  374. %>
  375. %>
  376. % ===================================================================
  377. function draw(me)
  378. if me.isVisible && me.tick >= me.delayTicks && me.tick < me.offTicks
  379. Screen('DrawTexture', me.sM.win, me.texture, [], me.mvRect,...
  380. me.angleOut, [], [], me.baseColourOut, [], me.rotateMode,...
  381. [me.driftPhase, me.sfOut, me.contrastOut, me.sigmaOut]);
  382. me.drawTick = me.drawTick + 1;
  383. end
  384. if me.isVisible; me.tick = me.tick + 1; end
  385. end
  387. % ===================================================================
  388. %> @brief Animate this object for runExperiment
  389. %>
  390. % ===================================================================
  391. function animate(me)
  392. if (me.isVisible || ~isempty(me.visibleRate)) && me.tick >= me.delayTicks
  393. if me.mouseOverride
  394. getMousePosition(me);
  395. if me.mouseValid
  396. me.mvRect = CenterRectOnPointd(me.mvRect, me.mouseX, me.mouseY);
  397. end
  398. end
  399. if me.doMotion
  400. me.mvRect=OffsetRect(me.mvRect,me.dX_,me.dY_);
  401. end
  402. if me.doDrift
  403. me.driftPhase = me.driftPhase + me.phaseIncrement;
  404. end
  405. if mod(me.tick,me.phaseCounter) == 0
  406. me.driftPhase = me.driftPhase + me.phaseOfReverse;
  407. end
  408. me.visibleTick = me.visibleTick + 1;
  409. if me.visibleTick == me.visibleFlip
  410. me.isVisible = ~me.isVisible;
  411. me.visibleTick = 0;
  412. end
  413. end
  414. end
  416. % ===================================================================
  417. %> @brief Reset an structure for runExperiment
  418. %>
  419. %> @param rE runExperiment object for reference
  420. %> @return stimulus structure.
  421. % ===================================================================
  422. function reset(me)
  423. resetTicks(me);
  424. me.inSetup = false; me.isSetup = false;
  425. if ~isempty(me.texture) && Screen(me.texture,'WindowKind') == -1
  426. try Screen('Close',me.texture); end %#ok<*TRYNC>
  427. end
  428. me.visibleFlip = Inf; me.visibleTick = 0;
  429. me.texture=[];
  430. me.shader=[];
  431. if me.mask > 0
  432. me.mask = true;
  433. end
  434. me.maskValue = [];
  435. me.removeTmpProperties;
  436. list = {'res','gratingSize','driftPhase','rotateMode'};
  437. for l = list; if isprop(me,l{1});delete(me.findprop(l{1}));end;end
  438. end
  440. % ===================================================================
  441. %> @brief calculate phase offset
  442. %>
  443. % ===================================================================
  444. function phase = calculatePhase(me)
  445. phase = 0;
  446. if me.correctPhase > 0
  447. ppd = me.ppd;
  448. size = (me.sizeOut / 2); %divide by 2 to get the 0 point
  449. sfTmp = (me.sfOut / me.scale) * ppd;
  450. md = size / (ppd / sfTmp);
  451. md = md - floor(md);
  452. % note for some reason colourgratings are 180° different to
  453. % gratings, so we compensate here so they should align if
  454. % correctPhase is true
  455. phase = (360 * md) + 180;
  456. end
  457. end
  459. % ===================================================================
  460. %> @brief sf Set method
  461. %>
  462. % ===================================================================
  463. function set.sf(me,value)
  464. if value <= 0
  465. value = 0.05;
  466. end
  467. me.sf = value;
  468. me.salutation(['set sf: ' num2str(value)],'Custom set method')
  469. end
  471. % ===================================================================
  472. %> @brief SET Colour2 method
  473. %> Allow 1 (R=G=B) 3 (RGB) or 4 (RGBA) value colour
  474. % ===================================================================
  475. function set.colour2(me,value)
  476. len=length(value);
  477. switch len
  478. case 4
  479. c = value;
  480. case 3
  481. c = [value(1:3) me.alpha]; %force our alpha to override
  482. case 1
  483. c = [value value value me.alpha]; %construct RGBA
  484. otherwise
  485. c = [1 1 1 me.alpha]; %return white for everything else
  486. end
  487. c(c<0)=0; c(c>1)=1;
  488. me.colour2 = c;
  489. if isprop(me, 'baseColour') && me.correctBaseColour %#ok<*MCSUP>
  490. me.baseColour = (me.colour(1:3) + me.colour2(1:3))/2;
  491. end
  492. end
  494. % ===================================================================
  495. %> @brief SET baseColour method
  496. %> Allow 1 (R=G=B) 3 (RGB) or 4 (RGBA) value colour
  497. % ===================================================================
  498. function set.baseColour(me,value)
  499. len=length(value);
  500. switch len
  501. case 4
  502. c = value;
  503. case 3
  504. c = [value(1:3) me.alpha]; %force our alpha to override
  505. case 1
  506. c = [value value value me.alpha]; %construct RGBA
  507. otherwise
  508. c = [1 1 1 me.alpha]; %return white for everything else
  509. end
  510. c(c<0)=0; c(c>1)=1;
  511. me.baseColour = c;
  512. end
  515. % ===================================================================
  516. %> @brief sfOut Pseudo Get method
  517. %>
  518. % ===================================================================
  519. function sf = getsfOut(me)
  520. sf = 0;
  521. if ~isempty(me.sfCache)
  522. sf = me.sfCache * me.ppd;
  523. end
  524. end
  526. end %---END PUBLIC METHODS---%
  528. %=======================================================================
  529. methods ( Access = protected ) %-------PROTECTED METHODS-----%
  530. %=======================================================================
  532. % ===================================================================
  533. %> @brief setRect
  534. %> setRect makes the PsychRect based on the texture and screen values
  535. %> this is modified over parent method as gratings have slightly different
  536. %> requirements.
  537. % ===================================================================
  538. function setRect(me)
  539. %me.dstRect=Screen('Rect',me.texture);
  540. me.dstRect=ScaleRect([0 0 me.res(1) me.res(2)],me.scale,me.scale);
  541. if me.mouseOverride && me.mouseValid
  542. me.dstRect = CenterRectOnPointd(me.dstRect, me.mouseX, me.mouseY);
  543. else
  544. if isprop(me, 'directionOut')
  545. [sx, sy]=pol2cart(me.d2r(me.directionOut),me.startPosition);
  546. else
  547. [sx, sy]=pol2cart(me.d2r(me.direction),me.startPosition);
  548. end
  549. me.dstRect=CenterRectOnPointd(me.dstRect,me.sM.xCenter,me.sM.yCenter);
  550. if isprop(me, 'xPositionOut')
  551. me.dstRect=OffsetRect(me.dstRect,me.xPositionOut+(sx*me.ppd),me.yPositionOut+(sy*me.ppd));
  552. else
  553. me.dstRect=OffsetRect(me.dstRect,(me.xPosition)*me.ppd,(me.yPosition)*me.ppd);
  554. end
  555. end
  556. me.mvRect=me.dstRect;
  557. me.szPx = RectWidth(me.dstRect);
  558. setAnimationDelta(me);
  559. end
  561. % ===================================================================
  562. %> @brief calculateScale
  563. %> Use an event to recalculate scale as get method is slower (called
  564. %> many more times), than an event which is only called on update
  565. % ===================================================================
  566. function calculateScale(me,~,~)
  567. me.scale = me.sizeOut/(me.size*me.ppd);
  568. me.maskValue = me.sizeOut / 2;
  569. me.sfRecurse = true;
  570. me.sfOut = me.sfCache * me.scale;
  571. %fprintf('\nCalculate SFOut: %d | in: %d | scale: %d\n', me.sfOut, me.sfCache, me.scale);
  572. end
  574. % ===================================================================
  575. %> @brief calculatePhaseIncrement
  576. %> Use an event to recalculate as get method is slower (called
  577. %> many more times), than an event which is only called on update
  578. % ===================================================================
  579. function calculatePhaseIncrement(me,~,~)
  580. if isprop(me,'tfOut')
  581. me.phaseIncrement = (me.tfOut * 360) * me.sM.screenVals.ifi;
  582. if isprop(me,'reverseDirectionOut')
  583. if me.reverseDirectionOut == false
  584. me.phaseIncrement = -me.phaseIncrement;
  585. end
  586. end
  587. end
  588. end
  590. % ===================================================================
  591. %> @brief fixBaseColour POST SET
  592. %>
  593. % ===================================================================
  594. function fixBaseColour(me,varargin)
  595. if me.correctBaseColour %#ok<*MCSUP>
  596. if isprop(me, 'baseColourOut')
  597. me.baseColourOut = (me.getP('colour',[1:3]) + me.getP('colour2',[1:3])) / 2;
  598. else
  599. me.baseColour = (me.getP('colour',[1:3]) + me.getP('colour2',[1:3])) / 2;
  600. end
  601. end
  602. end
  604. end
  605. end

colourGratingStimulus.m at commit dd582c8, under LGPL-3.0 · at the source

Overview

Authors: Yuanyang Huang1, Shu Wang1, Yazhu Qian2, Linghan Kong3, Peijun Zhao3, Yan Liu4, Shahab Aldin Zarei5, Peng Zhang2, Ian Max Andolina5, Hong Liu1,6
ORCID iDs: Yuanyang Huang, Yazhu Qian, Shahab Aldin Zarei, Ian Max Andolina
  1. Department of Ophthalmology, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
  2. State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
  3. School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, People’s Republic of China
  4. Department of Ophthalmology and Visual Science, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
  5. Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Brain Cognition and Brain-inspired Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, People’s Republic of China
  6. College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, People’s Republic of China
Institutions: Shanghai Jiao Tong University (China); Shanghai Children's Medical Center (China); Chinese Academy of Sciences (China); Institute of Biophysics (China); State Key Laboratory of Brain and Cognitive Science; Shanghai Medical College of Fudan University (China); Fudan University (China); Eye & ENT Hospital of Fudan University (China); Center for Excellence in Brain Science and Intelligence Technology (China); Fujian Medical University (China)
Journal: Clinical ophthalmology (Auckland, N.Z.), volume 20, article 590186
Dates: received 19 December 2025; accepted 5 April 2026; published online 23 April 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.2147/opth.s590186 · PMID 42052216 · PMCID PMC13117856 · OpenAlex W7155367740
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: fMRI (modality), human (organism), other condition (population)
Methods: Statistics, Connectivity, fMRI & imaging
Keywords: anisometropic amblyopia, fMRI, dichoptic, pediatric
Topic: Visual perception and processing mechanisms (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: Natural Science Foundation of Shanghai (23ZR1459200); National Natural Science Foundation of China (32070 992, 81770957)
Citations: not cited yet (Europe PMC); 86 references in the paper

Abstract

Purpose: To investigate the changes in neural activity in V1, V2, and V3 visual cortical areas of control participants and amblyopic patients during visual stimulation under four differing visual inputs.

Patients and Methods: A total of 14 children with monocular amblyopia and 11 age-matched healthy controls were recruited for the study. A fast meridional retinotopic mapping paradigm was employed to efficiently localize regions of interest (ROIs) within the visual cortex. Four types of visual stimulation were achieved using a spatiotemporally modulating checkerboard paired with anaglyph red-blue glasses: amblyopic or non-dominant eye only (AE), fellow or dominant eye only (FE), balanced dichoptic (BE), and imbalanced-dichoptic stimulation (DE).

Results: Amblyopic patients exhibit significantly reduced neural activity across V1, V2, and V3 compared to control participants. DE resulted in the most significant reductions in cortical responses for amblyopes. In the control group, significant differences were observed between AE and BE, FE and BE, and BE and DE, while no significant differences were found between AE and DE. In the amblyopic group, significant differences were identified between AE and DE, FE and DE, AE and BE, FE and BE, as well as between BE and DE.

Conclusion: Imbalanced dichoptic stimulation produced the largest and most significant reductions in cortical responses, observed exclusively in the patient group, indicating a suppressive influence from the fellow eye. These exploratory data support the view that imbalanced dichoptic stimulation may offer greater potential for neural response recovery compared to monocular approaches. The experimental protocols and findings reported here provide a comparative framework to inform the development of more effective rehabilitation strategies for children with amblyopia.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 9 matches between paragraphs and lines of code.

CogPlatform/binocularMRI

License: MIT
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 3e1faabdf18ee50cf6eaeac658aa77dba468e387, 8 May 2026
Languages: MATLAB (1)
Size: 5 files, 1 script
Software Heritage: not archived
Found in: the text, “Visual Stimuli for Cortical Activation”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Psychtoolbox (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
3 files
At the source: github.com/CogPlatform/binocularMRI

herrlich10/mripy

License: MIT
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: db1324a1a712c1948cc10ea3c629e74e7d2ea430, 17 April 2025
Languages: Python (48), MATLAB (19), Shell (1)
Size: 112 files, 68 scripts
Software Heritage: archived
Found in: the text, “Preprocessing”
Holds: README, license file, environment (requirements.txt, setup.py, docs/requirements.txt), tests, documentation
Not found: CITATION.cff, continuous integration
Tools: NumPy (29 files), SciPy (12 files), Matplotlib (9 files), pandas (8 files), AFNI (4 files), Statistics and Machine Learning Toolbox (3 files), scikit-learn (3 files), seaborn (3 files), SPM (2 files), CoSMoMVPA (1 file), CuPy (1 file), FreeSurfer (1 file), NiBabel (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
70 files
At the source: github.com/herrlich10/mripy

Zenodo 592253

License: CC-BY-4.0
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: the references
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Psychtoolbox (82 files), FieldTrip (4 files), Statistics and Machine Learning Toolbox (4 files), Chronux (2 files), Image Processing Toolbox (2 files), Signal Processing Toolbox (2 files), Curve Fitting Toolbox (1 file), Parallel Computing Toolbox (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers (HTTP 200)
  • 29 September 2026: the link answers (HTTP 200)
231 files
At the source:

iandol/opticka

License: LGPL-3.0
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: dd582c8c3fd22468856fd54a836051a42478c62a, 24 August 2026
Languages: MATLAB (287), Shell (1), Perl (1)
Size: 562 files, 289 scripts
Software Heritage: archived
Found in: the Zenodo archive record
Holds: README, license file, CITATION.cff, tests, continuous integration
Not found: environment file, documentation
Tools: Psychtoolbox (88 files), FieldTrip (4 files), Statistics and Machine Learning Toolbox (4 files), Chronux (2 files), Curve Fitting Toolbox (2 files), Image Processing Toolbox (2 files), Signal Processing Toolbox (2 files), Parallel Computing Toolbox (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
291 files
At the source: github.com/iandol/opticka/tree/V2.17.0

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:

  • 4 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 587 scripts, each with its path and the digest of its content;
  • 9 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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Versions

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Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 10 authors, 4 keywords, 2 funders, 81 references.

Cite

This paper

Huang, Y., Wang, S., Qian, Y., Kong, L., Zhao, P., Liu, Y., Zarei, S. A., Zhang, P., Andolina, I. M., & Liu, H. (2026). Differential Effects of Balanced and Imbalanced Binocular Stimulation on Visual Cortex Responses in Amblyopic Children. Clinical ophthalmology (Auckland, N.Z.), 20, 590186. https://doi.org/10.2147/opth.s590186

BibTeX

@article{huang2026differential,
author = {Huang, Yuanyang and Wang, Shu and Qian, Yazhu and Kong, Linghan and Zhao, Peijun and Liu, Yan and Zarei, Shahab Aldin and Zhang, Peng and Andolina, Ian Max and Liu, Hong},
title = {{Differential Effects of Balanced and Imbalanced Binocular Stimulation on Visual Cortex Responses in Amblyopic Children}},
journal = {Clinical ophthalmology (Auckland, N.Z.)},
year = {2026},
month = apr,
volume = {20},
pages = {590186},
publisher = {Dove Press},
issn = {1177-5467},
doi = {10.2147/opth.s590186},
url = {https://doi.org/10.2147/opth.s590186},
pmid = {42052216},
pmcid = {PMC13117856}
}

RIS

TY - JOUR
AU - Huang, Yuanyang
AU - Wang, Shu
AU - Qian, Yazhu
AU - Kong, Linghan
AU - Zhao, Peijun
AU - Liu, Yan
AU - Zarei, Shahab Aldin
AU - Zhang, Peng
AU - Andolina, Ian Max
AU - Liu, Hong
TI - Differential Effects of Balanced and Imbalanced Binocular Stimulation on Visual Cortex Responses in Amblyopic Children
T2 - Clinical ophthalmology (Auckland, N.Z.)
J2 - Clin Ophthalmol
PY - 2026
DA - 2026/04/23
VL - 20
SP - 590186
SN - 1177-5467
PB - Dove Press
DO - 10.2147/opth.s590186
UR - https://doi.org/10.2147/opth.s590186
LA - en
ER -

CSL-JSON

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"issued": {
"date-parts": [
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23
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