update README

Author: Remi-Gau

README.md

@@ -5,33 +5,30 @@
 
 [![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)
 
-<!-- vscode-markdown-toc -->
-
-- 1. [Requirements](#Requirements)
-- 2. [Installation](#Installation)
-- 3. [Structure and function details](#Structureandfunctiondetails)
-     _ 3.1. [visualLocTranslational](#visualLocTranslational)
-     _ 3.2. [setParameters](#setParameters)
-     _ 3.3. [subfun/doDotMo](#subfundoDotMo)
-     _ 3.3.1. [Input:](#Input:)
-     _ 3.3.2. [Output:](#Output:)
-     _ 3.4. [subfun/expDesign](#subfunexpDesign)
-     _ 3.4.1. [EVENTS](#EVENTS)
-     _ 3.4.2. [TARGETS:](#TARGETS:)
-     _ 3.4.3. [Input:](#Input:-1)
-     _ 3.4.4. [Output:](#Output:-1)
-
-<!-- vscode-markdown-toc-config
-	numbering=true
-	autoSave=true
-	/vscode-markdown-toc-config -->
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+<!-- TOC -->
+- [fMRI localizers for visual motion](#fmri-localizers-for-visual-motion)
+  - [Translational Motion](#translational-motion)
+  - [Requirements](#requirements)
+  - [Installation](#installation)
+  - [Structure and function details](#structure-and-function-details)
+    - [visualLocTranslational](#visualloctranslational)
+    - [setParameters](#setparameters)
+      - [Let the scanner pace the experiment](#let-the-scanner-pace-the-experiment)
+    - [subfun/doDotMo](#subfundodotmo)
+      - [Input](#input)
+      - [Output](#output)
+    - [subfun/expDesign](#subfunexpdesign)
+      - [EVENTS](#events)
+      - [TARGETS](#targets)
+      - [Input](#input-1)
+      - [Output](#output-1)
+<!-- TOC -->
 
 # fMRI localizers for visual motion
 
-# Translational Motion
+## Translational Motion
 
-## 1. <a name='Requirements'></a>Requirements
+## Requirements
 
 Make sure that the following toolboxes are installed and added to the matlab / octave path.
 
@@ -45,7 +42,7 @@ For instructions see the following links:
 | [Matlab](https://www.mathworks.com/products/matlab.html) | >=2017       |
 | or [octave](https://www.gnu.org/software/octave/)        | >=4.?        |
 
-## 2. <a name='Installation'></a>Installation
+## Installation
 
 The CPP_BIDS and CPP_PTB dependencies are already set up as submodule to this repository.
 You can install it all with git by doing.
@@ -54,17 +51,17 @@ You can install it all with git by doing.
 git clone --recurse-submodules https://github.com/cpp-lln-lab/localizer_visual_motion.git
 ```
 
-## 3. <a name='Structureandfunctiondetails'></a>Structure and function details
+## Structure and function details
 
-### 3.1. <a name='visualLocTranslational'></a>visualLocTranslational
+### visualLocTranslational
 
 Running this script will show blocks of motion dots (soon also moving gratings) and static dots. Motion blocks will show dots(/gratings) moving in one of four directions (up-, down-, left-, and right-ward)
 
 By default it is run in `Debug mode` meaning that it does not run care about subjID, run n., fMRI triggers, Eye Tracker, etc..
 
 Any details of the experiment can be changed in `setParameters.m` (e.g., experiment mode, motion stimuli details, exp. design, etc.)
 
-### 3.2. <a name='setParameters'></a>setParameters
+### setParameters
 
 `setParameters.m` is the core engine of the experiment. It contains the following tweakable sections:
 
@@ -105,40 +102,40 @@ if cfg.pacedByTriggers.do
 end
 ```
 
-### 3.3. <a name='subfundoDotMo'></a>subfun/doDotMo
+### subfun/doDotMo
 
-#### 3.3.1. <a name='Input:'></a>Input:
+#### Input
 
 - `cfg`: PTB/machine configurations returned by `setParameters` and `initPTB`
 - `expParameters`: parameters returned by `setParameters`
 - `logFile`: structure that stores the experiment logfile to be saved
 
-#### 3.3.2. <a name='Output:'></a>Output:
+#### Output
 
 - Event `onset`
 - Event `duration`
 
 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.
 
-### 3.4. <a name='subfunexpDesign'></a>subfun/expDesign
+### subfun/expDesign
 
 Creates the sequence of blocks and the events in them. The conditions are consecutive static and motion blocks (Gives better results than randomised). It can be run as a stand alone without inputs to display a visual example of possible design.
 
-#### 3.4.1. <a name='EVENTS'></a>EVENTS
+#### EVENTS
 
 The `numEventsPerBlock` should be a multiple of the number of "base" listed in the `motionDirections` and `staticDirections` (4 at the moment).
 
-#### 3.4.2. <a name='TARGETS:'></a>TARGETS:
+#### TARGETS
 
 - If there are 2 targets per block we make sure that they are at least 2 events apart.
 - Targets cannot be on the first or last event of a block
 
-#### 3.4.3. <a name='Input:-1'></a>Input:
+#### Input
 
 - `expParameters`: parameters returned by `setParameters`
 - `displayFigs`: a boolean to decide whether to show the basic design matrix of the design
 
-#### 3.4.4. <a name='Output:-1'></a>Output:
+#### Output
 
 - `expParameters.designBlockNames` is a cell array `(nr_blocks, 1)` with the name for each block
 - `expParameters.designDirections` is an array `(nr_blocks, numEventsPerBlock)` with the direction to present in a given block