[ENH] update after testing 20210303

.all-contributorsrc

@@ -16,6 +16,23 @@
         "ideas"
       ]
     },
+    {
+      "login": "Remi-Gau",
+      "name": "Remi Gau",
+      "avatar_url": "https://avatars3.githubusercontent.com/u/6961185?v=4",
+      "profile": "https://remi-gau.github.io/",
+      "contributions": [
+        "code",
+        "design",
+        "ideas",
+        "bug",
+        "userTesting",
+        "review",
+        "question",
+        "infra",
+        "maintenance"
+      ]
+    },
     {
       "login": "marcobarilari",
       "name": "marcobarilari",

README.md

@@ -1,6 +1,6 @@
 [![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/localizer_auditory_motion/actions)
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-2-orange.svg?style=flat-square)](#contributors-)
+[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 ![](https://github.com/cpp-lln-lab/localizer_auditory_motion/workflows/CI/badge.svg)
 
@@ -143,6 +143,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 <table>
   <tr>
     <td align="center"><a href="https://github.com/mohmdrezk"><img src="https://avatars2.githubusercontent.com/u/9597815?v=4" width="100px;" alt=""/><br /><sub><b>Mohamed Rezk</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_auditory_motion/commits?author=mohmdrezk" title="Code">💻</a> <a href="#design-mohmdrezk" title="Design">🎨</a> <a href="#ideas-mohmdrezk" title="Ideas, Planning, & Feedback">🤔</a></td>
+    <td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars3.githubusercontent.com/u/6961185?v=4" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_auditory_motion/commits?author=Remi-Gau" title="Code">💻</a> <a href="#design-Remi-Gau" title="Design">🎨</a> <a href="#ideas-Remi-Gau" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/localizer_auditory_motion/issues?q=author%3ARemi-Gau" title="Bug reports">🐛</a> <a href="#userTesting-Remi-Gau" title="User Testing">📓</a> <a href="https://github.com/cpp-lln-lab/localizer_auditory_motion/pulls?q=is%3Apr+reviewed-by%3ARemi-Gau" title="Reviewed Pull Requests">👀</a> <a href="#question-Remi-Gau" title="Answering Questions">💬</a> <a href="#infra-Remi-Gau" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-Remi-Gau" title="Maintenance">🚧</a></td>
     <td align="center"><a href="https://github.com/marcobarilari"><img src="https://avatars3.githubusercontent.com/u/38101692?v=4" width="100px;" alt=""/><br /><sub><b>marcobarilari</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/localizer_auditory_motion/commits?author=marcobarilari" title="Code">💻</a> <a href="#design-marcobarilari" title="Design">🎨</a> <a href="#ideas-marcobarilari" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/localizer_auditory_motion/issues?q=author%3Amarcobarilari" title="Bug reports">🐛</a> <a href="#userTesting-marcobarilari" title="User Testing">📓</a> <a href="https://github.com/cpp-lln-lab/localizer_auditory_motion/pulls?q=is%3Apr+reviewed-by%3Amarcobarilari" title="Reviewed Pull Requests">👀</a> <a href="#question-marcobarilari" title="Answering Questions">💬</a> <a href="#infra-marcobarilari" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-marcobarilari" title="Maintenance">🚧</a></td>
   </tr>
 </table>

audioLocTranslational.m

@@ -45,6 +45,7 @@
 
     % Prepare for the output logfiles with all
     logFile.extraColumns = cfg.extraColumns;
+    logFile = saveEventsFile('init', cfg, logFile);
     logFile = saveEventsFile('open', cfg, logFile);
 
     %     disp(cfg);
@@ -85,13 +86,15 @@
             thisEvent.fixationTarget = cfg.design.fixationTargets(iBlock, iEvent);
             thisEvent.soundTarget = cfg.design.soundTargets(iBlock, iEvent);
 
+            thisEvent.isStim = logFile.isStim;
+
             % we wait for a trigger every 2 events
             if cfg.pacedByTriggers.do && mod(iEvent, 2) == 1
                 waitForTrigger( ...
-                    cfg, ...
-                    cfg.keyboard.responseBox, ...
-                    cfg.pacedByTriggers.quietMode, ...
-                    cfg.pacedByTriggers.nbTriggers);
+                               cfg, ...
+                               cfg.keyboard.responseBox, ...
+                               cfg.pacedByTriggers.quietMode, ...
+                               cfg.pacedByTriggers.nbTriggers);
             end
 
             % % % REFACTOR THIS FUNCTION % % %
@@ -116,7 +119,7 @@
             % collect the responses and appends to the event structure for
             % saving in the tsv file
             responseEvents = getResponse('check', cfg.keyboard.responseBox, cfg, ...
-                getOnlyPress);
+                                         getOnlyPress);
 
             triggerString = ['trigger_' cfg.design.blockNames{iBlock}];
             saveResponsesAndTriggers(responseEvents, cfg, logFile, triggerString);
@@ -132,7 +135,7 @@
 
         % trigger monitoring
         triggerEvents = getResponse('check', cfg.keyboard.responseBox, cfg, ...
-            getOnlyPress);
+                                    getOnlyPress);
 
         triggerString = 'trigger_baseline';
         saveResponsesAndTriggers(triggerEvents, cfg, logFile, triggerString);

initEnv.m

@@ -56,8 +56,8 @@
 
     if numel(dir(libDirectory)) <= 2 % Means that the external is empty
         error(['Git submodules are not cloned!', ...
-              'Try this in your terminal:', ...
-              ' git submodule update --recursive ']);
+               'Try this in your terminal:', ...
+               ' git submodule update --recursive ']);
     else
         addDependencies();
     end

input/equateRmsWav.m

@@ -55,7 +55,7 @@ function runFunction (referenceWavFn, targetWavFn)
 
     % correct for the rms differences in each channel
     finalWav = [targetWav(:, 1) * (referenceRMS(1) / targetRms(1)) ...
-                   targetWav(:, 2) * (referenceRMS(2) / targetRms(2))];
+                targetWav(:, 2) * (referenceRMS(2) / targetRms(2))];
 
     % check that the rms of the final is similar to the original
     finalRms = rms(finalWav);

setParameters.m

@@ -9,16 +9,18 @@
     % setParamters.m file is
     % change that if you want the data to be saved somewhere else
     cfg.dir.output = fullfile( ...
-        fileparts(mfilename('fullpath')), '..', ...
-        'output');
+                              fileparts(mfilename('fullpath')), 'output');
 
     %% Debug mode settings
 
     cfg.debug.do = false; % To test the script out of the scanner, skip PTB sync
     cfg.debug.smallWin = false; % To test on a part of the screen, change to 1
     cfg.debug.transpWin = false; % To test with trasparent full size screen
 
-    cfg.verbose = false;
+    cfg.verbose = 1;
+    cfg.skipSyncTests = 0;
+
+    cfg.audio.devIdx = 3; % 5 %11
 
     %% Engine parameters
 
@@ -32,9 +34,11 @@
     cfg = setKeyboards(cfg);
 
     % MRI settings
+
     cfg = setMRI(cfg);
+    cfg.suffix.acquisition = '0p75mmEv';
 
-    cfg.pacedByTriggers.do = true;
+    cfg.pacedByTriggers.do = false;
 
     %% Experiment Design
 
@@ -43,19 +47,20 @@
     cfg.design.motionType = 'translation';
     cfg.design.names = {'static'; 'motion'};
     % 0: L--R--L; 180: R--L--R;
-    cfg.design.motionDirections = [0 0 180 180];
-    cfg.design.nbRepetitions = 14;
-    cfg.design.nbEventsPerBlock = 12;
+    cfg.design.motionDirections = [0 180];
+    cfg.design.nbRepetitions = 21;
+    cfg.design.nbEventsPerBlock = 6;
 
     %% Timing
 
     % FOR 7T: if you want to create localizers on the fly, the following must be
-    % multiples of the scanneryour sequence TR
+    % multiples of the scanner sequence TR
     %
     % IBI
     % block length = (cfg.eventDuration + cfg.ISI) * cfg.design.nbEventsPerBlock
 
-    cfg.timing.eventDuration = 0.850; % second
+    % for info: not actually used since "defined" by the sound duration
+    %     cfg.timing.eventDuration = 0.850; % second
 
     % Time between blocs in secs
     cfg.timing.IBI = 0;
@@ -94,7 +99,7 @@
 
     % Instruction
     cfg.task.instruction = ['1 - Detect the RED fixation cross\n' ...
-      '2 - Detected the shorter repeated sounds'];
+                            '2 - Detected the shorter repeated sounds'];
 
     % Fixation cross (in pixels)
     cfg.fixation.type = 'cross';
@@ -105,7 +110,7 @@
     cfg.fixation.xDisplacement = 0;
     cfg.fixation.yDisplacement = 0;
 
-    cfg.target.maxNbPerBlock = 2;
+    cfg.target.maxNbPerBlock = 1;
     cfg.target.duration = 0.5; % In secs
 
     cfg.extraColumns = {'direction', 'soundTarget', 'fixationTarget', 'event', 'block', 'keyName'};
@@ -135,9 +140,9 @@
 function cfg = setKeyboards(cfg)
     cfg.keyboard.escapeKey = 'ESCAPE';
     cfg.keyboard.responseKey = { ...
-        'r', 'g', 'y', 'b', ...
-        'd', 'n', 'z', 'e', ...
-        't'}; % dnze rgyb
+                                'r', 'g', 'y', 'b', ...
+                                'd', 'n', 'z', 'e', ...
+                                't'}; % dnze rgyb
     cfg.keyboard.keyboard = [];
     cfg.keyboard.responseBox = [];
 
@@ -155,7 +160,7 @@
     cfg.mri.repetitionTime = 1.8;
 
     cfg.bids.MRI.Instructions = ['1 - Detect the RED fixation cross\n' ...
-      '2 - Detected the shorter repeated sounds'];
+                                 '2 - Detected the shorter repeated sounds'];
     cfg.bids.MRI.TaskDescription = [];
 
 end

subfun/doAuditoryMotion.m

@@ -76,6 +76,6 @@
     % Get the end time
     waitForEndOfPlayback = 1; % hard coding that will need to be moved out
     [onset, ~, ~, estStopTime] = PsychPortAudio('Stop', cfg.audio.pahandle, ...
-        waitForEndOfPlayback);
+                                                waitForEndOfPlayback);
 
     duration = estStopTime - onset;

subfun/expDesign.m

@@ -86,23 +86,23 @@
             % 2 events apart
             % - targets cannot be on the first or last event of a block
 
-            % Fixation targets
             nbTarget = numTargetsForEachBlock(iBlock);
 
+            % Fixation targets
+            forbiddenPositions = [];
             chosenPosition = setTargetPositionInSequence( ...
-                NB_EVENTS_PER_BLOCK, ...
-                nbTarget, ...
-                [1 NB_EVENTS_PER_BLOCK]);
+                                                         NB_EVENTS_PER_BLOCK, ...
+                                                         nbTarget, ...
+                                                         forbiddenPositions);
 
             fixationTargets(iBlock, chosenPosition) = 1;
 
             % Sound targets
-            nbTarget = numTargetsForEachBlock(iBlock);
-
+            forbiddenPositions = [chosenPosition];
             chosenPosition = setTargetPositionInSequence( ...
-                NB_EVENTS_PER_BLOCK, ...
-                nbTarget, ...
-                [1 NB_EVENTS_PER_BLOCK]);
+                                                         NB_EVENTS_PER_BLOCK, ...
+                                                         nbTarget, ...
+                                                         forbiddenPositions);
 
             soundTargets(iBlock, chosenPosition) = 1;
 
@@ -150,8 +150,8 @@
     NB_REPEATS_BASE_VECTOR = NB_EVENTS_PER_BLOCK / length(STATIC_DIRECTIONS);
 
     static_directions = repmat( ...
-        STATIC_DIRECTIONS, ...
-        1, NB_REPEATS_BASE_VECTOR);
+                               STATIC_DIRECTIONS, ...
+                               1, NB_REPEATS_BASE_VECTOR);
 
     for iMotionBlock = 1:NB_REPETITIONS
 

subfun/saveResponsesAndTriggers.m

@@ -15,6 +15,7 @@ function saveResponsesAndTriggers(responseEvents, cfg, logFile, triggerString)
             end
         end
 
+        responseEvents(1).isStim = logFile.isStim;
         responseEvents(1).fileID = logFile.fileID;
         responseEvents(1).extraColumns = logFile.extraColumns;
         saveEventsFile('save', cfg, responseEvents);

tests/test_expDesign.m

@@ -28,8 +28,9 @@ function test_exDesignBasic()
 
     % make sure that we have the right number of blocks of the right length
     assertTrue(all(size(cfg.design.directions) == [ ...
-        cfg.design.nbRepetitions * numel(cfg.design.names), ...
-        cfg.design.nbEventsPerBlock]));
+                                                   cfg.design.nbRepetitions * ...
+                                                   numel(cfg.design.names), ...
+                                                   cfg.design.nbEventsPerBlock]));
 
     %  check that we do not have more than the required number of targets per
     %  block
@@ -62,8 +63,9 @@ function test_exDesignBasicOtherSetUp()
 
     % make sure that we have the right number of blocks of the right length
     assertTrue(all(size(cfg.design.directions) == [ ...
-        cfg.design.nbRepetitions * numel(cfg.design.names), ...
-        cfg.design.nbEventsPerBlock]));
+                                                   cfg.design.nbRepetitions * ...
+                                                   numel(cfg.design.names), ...
+                                                   cfg.design.nbEventsPerBlock]));
 
     %  check that we do not have more than the required number of targets per
     %  block