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Merge pull request #98 from cpp-lln-lab/release_candidate_v0.4.0
candidate for v0.4.0
2 parents b208a68 + 86be184 commit dcb8a6a

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‎.github/workflows/moxunit.yml

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push:
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branches:
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- master
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- dev
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pull_request:
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branches: ['*']
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: true
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fetch-depth: 1
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- name: MOxUnit Action
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uses: joergbrech/moxunit-action@v1.1
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uses: joergbrech/moxunit-action@v1.2.0
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with:
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tests: tests
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src: subfun
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# add CPP_PTB to the path but don't include it the coverage
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ext: lib/CPP_PTB/src
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# Octave packages needed
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pkg: statistics
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with_coverage: true
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cover_xml_file: coverage.xml
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- name: Code coverage
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uses: codecov/codecov-action@v1
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with:

‎README.md

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[![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/localizer_visual_motion/actions)
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![](https://github.com/cpp-lln-lab/localizer_visual_motion/workflows/CI/badge.svg)
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[![codecov](https://codecov.io/gh/cpp-lln-lab/localizer_visual_motion/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/localizer_visual_motion)
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<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
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[![All Contributors](https://img.shields.io/badge/all_contributors-5-orange.svg?style=flat-square)](#contributors-)
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<!-- ALL-CONTRIBUTORS-BADGE:END -->
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![](https://github.com/cpp-lln-lab/localizer_visual_motion/workflows/CI/badge.svg)
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[![codecov](https://codecov.io/gh/cpp-lln-lab/localizer_visual_motion/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/localizer_visual_motion)
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[![Build Status](https://travis-ci.com/cpp-lln-lab/localizer_visual_motion.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/localizer_visual_motion)
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<!-- TOC -->
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- [fMRI localizers for visual motion](#fmri-localizers-for-visual-motion)
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- [Translational Motion](#translational-motion)
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- [Requirements](#requirements)
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- [Installation](#installation)
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- [Structure and function details](#structure-and-function-details)
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- [visualLocTranslational](#visualloctranslational)
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- [visualMotionLocalizer](#visualmotionlocalizer)
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- [setParameters](#setparameters)
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- [Let the scanner pace the experiment](#let-the-scanner-pace-the-experiment)
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- [subfun/doDotMo](#subfundodotmo)
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- [Input](#input)
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- [Output](#output)
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- [subfun/expDesign](#subfunexpdesign)
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- [EVENTS](#events)
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- [TARGETS](#targets)
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- [Input](#input-1)
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- [Output](#output-1)
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- [subfun/design/expDesign](#subfundesignexpdesign)
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- [Events](#events)
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- [Pseudorandomization rules:](#pseudorandomization-rules)
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- [Input:](#input-1)
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- [Output:](#output-1)
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- [Contributors ✨](#contributors-)
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<!-- TOC -->
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# fMRI localizers for visual motion
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| Requirements | Used version |
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| --------------------------------------------------------------- | ------------ |
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| [CPP_BIDS](https://github.com/cpp-lln-lab/CPP_BIDS) (submodule) | 2.1.0 |
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| [CPP_PTB](https://github.com/cpp-lln-lab/CPP_PTB) (submodule) | 1.2.0 |
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| [CPP_BIDS](https://github.com/cpp-lln-lab/CPP_BIDS) (submodule) | 2.1.1 |
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| [CPP_PTB](https://github.com/cpp-lln-lab/CPP_PTB) (submodule) | 1.2.1 |
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| [PsychToolBox](http://psychtoolbox.org/) | >=3.0.14 |
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| [Matlab](https://www.mathworks.com/products/matlab.html) | >=2017 |
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| or [octave](https://www.gnu.org/software/octave/) | >=4.? |
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> NB: The dots are drawn on a square that contains the round aperture, then any dots outside of the aperture is turned into a NaN so effectively the actual number of dots on the screen at any given time is not the one that you input but a smaller number (nDots / Area of aperture) on average.
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### subfun/expDesign(MtMst)
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### subfun/design/expDesign
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These functions, one per MT+ and one per MT/MST localizer, create the sequence of blocks and the events in them. The conditions are consecutive static and motion blocks (Gives better results than randomised).
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This function and its companions creates the sequence of blocks (static/motion) and the events (the single directions) for MT+ and MT/MST localizers. The conditions are consecutive static and motion blocks (fixed in this order gives better results than randomised).
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It can be run as a stand alone without inputs and display a visual example of the possible design. See `getMockConfig` to set up the mock configuration.
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It can be run as a stand alone without inputs and displays a visual example of the possible design. See `getMockConfig` to set up the mock configuration.
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It computes the directions to display and the task(s), at the moment
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It computes the directions to display and the task(s), at the moment:
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1. detection of change in the color of the fixation target
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2. detection of different speed of the moving dots [ W I P - if selected as a task it will give the same null output as if not selected ie no difference in speed]
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‎setParameters.m

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% - MST: radial motion centered in a circle aperture that is on the opposite
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% side of the screen relative to the fixation
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% - alternates fixaton left and fixation right
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cfg.design.localizer = 'MT';
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% cfg.design.localizer = 'MT_MST';
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% cfg.design.localizer = 'MT';
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cfg.design.localizer = 'MT_MST';
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cfg.design.motionType = 'translation';
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cfg.design.motionDirections = [0 0 180 180];
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cfg.design.names = {'static'; 'motion'};
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% if you have static and motion and `nbRepetions` = 4, this will return 8 blocks (n blocks per
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% hemifield in case of MT/MST localizer)
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% if you have static and motion and `nbRepetions` = 4, this will return 8 blocks (for MT/MST
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% localizer && 2 hemifield it is 8 blocks per hemifield), i.e. how many times each condition
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% will be repeated
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cfg.design.nbRepetitions = 12;
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cfg.design.nbEventsPerBlock = 12;
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cfg.design.motionType = 'radial';
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cfg.design.motionDirections = [666 -666];
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% cfg.design.names = {'motion'};
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cfg.design.names = {'static'; 'motion'};
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cfg.design.fixationPosition = {'fixation_left'; 'fixation_right'};
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% cfg.design.fixationPosition = {'fixation_right'; 'fixation_left'};
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cfg.design.names = {'motion'};
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% cfg.design.names = {'static'; 'motion'};
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cfg.design.fixationPosition = {'fixation_left'};
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% cfg.design.fixationPosition = {'fixation_right'; 'fixation_left'};
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cfg.design.xDisplacementFixation = 7;
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cfg.design.xDisplacementAperture = 3;
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% here we double the repetions (2 hemifields)
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cfg.design.nbRepetitions = cfg.design.nbRepetitions * length(cfg.design.fixationPosition);
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% inward&outward are presented as separated event
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% inward and outward are presented as separated event
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cfg.design.nbEventsPerBlock = cfg.design.nbEventsPerBlock * 2;
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cfg.timing.IBI = 4;

‎subfun/design/diplayDesign.m

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function diplayDesign(cfg, displayFigs)
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%
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% diplayDesign(cfg, displayFigs)
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%
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%
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% (C) Copyright 2020 CPP visual motion localizer developpers
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myColorMap = lines(5);
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colormap(myColorMap);
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title('Block (static and motion) & Events (motion direction)');
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if strcmp(cfg.design.localizer, 'MT') || ...
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strcmp(cfg.design.localizer, 'MT_MST') && ...
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length(cfg.design.names) == 2
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title(['Blocks (rows, static-odd and motion-even) & ' ...
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'Events (columns, colors: motion direction)']);
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else
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title(['Block (rows, only motion blocks) & ' ...
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'Events (columns, colors: motion direction)']);
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end
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% Shows the fixation targets design in each event (1 or 0)
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fixationTargets = cfg.design.fixationTargets;
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subplot(3, 1, 3);
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hist(itargetPosition);
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labelAxesFreq();
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labelAxesFreqTarget();
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title('Fixation Targets position distribution');
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% Show the direction presented distribution per event position
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% in the blocks across the experiment
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figure(2);
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[~, motionDirections] = getDirectionBaseVectors(cfg);
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subplot(2, 2, iMotion);
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hist(position);
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scaleAxes();
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labelAxesFreq();
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labelAxesFreqDirection();
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title(num2str(motionDirections(iMotion)));
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end
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suptitle('Distribution of events for each direction');
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end
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end
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xlabel('Events', 'Fontsize', 8);
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function labelAxesFreq()
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function labelAxesFreqTarget()
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% an old viking saying because they really cared about their axes
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ylabel('Number of targets', 'Fontsize', 8);
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xlabel('Events', 'Fontsize', 8);
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end
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function labelAxesFreqDirection()
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% an old viking saying because they really cared about their axes
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ylabel('Number of directions', 'Fontsize', 8);
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xlabel('Events', 'Fontsize', 8);
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end
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function scaleAxes()
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xlim([1 12]);
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ylim([0 5]);

‎subfun/design/expDesign.m

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function [cfg] = expDesign(cfg, displayFigs)
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function [cfg] = expDesign(cfg)
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%
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% Creates the sequence of blocks and the events in them
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%
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% The conditions are consecutive static and motion blocks. It gives better results than
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% randomised.
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% The conditions are consecutive static and motion blocks.
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% It gives better results than randomised.
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%
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% It can be run as a stand alone without inputs and display a visual example of the
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% possible design. See `getMockConfig` to set up the mock configuration.
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%
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% It computes the directions to display and the task(s), at the moment:
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% (1) detection of change in the color of the fixation target
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% (2) detection of different speed of the moving dots [ W I P - if selected as a task it will
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% give the same null output as if not selected ie no difference in speed ]
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% (2) detection of different speed of the moving dots
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% [ W I P - if selected as a task it will give the same null output
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% as if not selected ie no difference in speed ]
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%
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% EVENTS
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% The ``nbEventsPerBlock`` should be a multiple of the number of motion directions requested in
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% ``motionDirections`` (which should be more than 1) e.g.:
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%
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% MT localizer: ``cfg.design.motionDirections = [ 0 90 180 270 ]; % right down left up``
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% MT_MST localizer: ``cfg.design.motionDirections = [666 -666]; % outward inward``
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%
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% Output:
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% - cfg.design.blockNames: cell array (nbBlocks, 1) with the condition name for each block
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% - cfg.design.nbBlocks: integer for th etotal number of blocks in the run
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% - cfg.design.directions: array (nbBlocks, nbEventsPerBlock) with the direction to present in a
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% given event of a block.
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% - cfg.design.directions: array (nbBlocks, nbEventsPerBlock) with the direction
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% to present in a given event of a block.
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% - cfg.design.blockFixationPosition: [MT_MST] array (nbBlocks, 1)
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% with the position in the hemifiled
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% where to show the fixation cross
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% - 0 90 180 270 indicate the angle for translational motion direction
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% - 666 -666 indicate in/out-ward direction in radial motion
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% - -1 indicates static
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% - cfg.design.speeds: array (nbBlocks, nbEventsPerBlock) indicate the dots speed
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% in each event, the target is represented by a higher/lower value
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% - cfg.design.fixationTargets: array (nbBlocks, numEventsPerBlock) showing for each event if it
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% should be accompanied by a target
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% - cfg.design.fixationTargets: array (nbBlocks, numEventsPerBlock) showing
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% for each event if it should be accompanied by a target
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%
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%
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% (C) Copyright 2020 CPP visual motion localizer developpers
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if nargin < 1 || isempty(cfg)
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% make sure we got access to all the required functions and inputs
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run('../../initEnv.m');
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% ``true`` for MT+ translational localizer
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% ``false`` for MT/MST localizer
64-
isMT = true;
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isMT = false;
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% Get mock inputs to run this function as a stand alone and get a flavour of how the design
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% looks like given certain inputs. Open this function to set different inputs.
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% Compute a matrix [nbBlocks x nbEventsPerBlock]
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cfg.design.directions = setDirections(cfg);
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% Compute the fixation position (left/right hemifield) for MT/MST
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cfg.design.blockFixationPosition = setFixationPosition(cfg);
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%% Task(s) design
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% Compute a matrix [nbBlocks x nbEventsPerBlock] with

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