move config related doc into docs folder

Author: Remi-Gau

README.md

@@ -13,19 +13,27 @@
 # Auditory Translational Motion
 
 - [Auditory Translational Motion](#auditory-translational-motion)
+  - [`audioLocTranslational`](#audioloctranslational)
+    - [`setParameters`](#setparameters)
   - [Requirements](#requirements)
   - [Installation](#installation)
-  - [Structure and function details](#structure-and-function-details)
-    - [audioLocTranslational](#audioloctranslational)
-    - [setParameters](#setparameters)
-      - [Let the scanner pace the experiment](#let-the-scanner-pace-the-experiment)
-    - [subfun/expDesign](#subfunexpdesign)
-      - [EVENTS](#events)
-      - [TARGETS](#targets)
-      - [Input](#input)
-      - [Output](#output)
   - [Contributors ✨](#contributors-)
 
+## `audioLocTranslational`
+
+Running this script will play blocks of motion/static sounds. Motion blocks will
+play sounds 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 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.)
+
+### `setParameters`
+
+`setParameters.m` is the core engine of the experiment. See [docs/configuration](.docs/../docs/configuration.md) for more information.
+
 ## Requirements
 
 Make sure that the following toolboxes are installed and added to the matlab /
@@ -48,100 +56,7 @@ repository. You can install it all with git by doing.
 git clone --recurse-submodules https://github.com/cpp-lln-lab/localizer_auditory_motion.git
 ```
 
-## Structure and function details
-
-### audioLocTranslational
-
-Running this script will play blocks of motion/static sounds. Motion blocks will
-play sounds 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 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.)
-
-### setParameters
-
-`setParameters.m` is the core engine of the experiment. It contains the
-following tweakable sections:
-
-- Debug mode setting
-- Engine parameters:
-  - Devices parameters
-  - Monitor parameters
-  - Keyboard parameters
-  - MRI parameters
-- Experiment Design
-- Timing
-- Auditory Stimulation
-- Task(s)
-  - Instructions
-  - Task #1 parameters
-
-#### Let the scanner pace the experiment
-
-Set `cfg.pacedByTriggers.do` to `true` and you can then set all the details in
-this `if` block
-
-```matlab
-% Time is here in in terms of number repetition time (i.e MRI volumes)
-if cfg.pacedByTriggers.do
-
-  cfg.pacedByTriggers.quietMode = true;
-  cfg.pacedByTriggers.nbTriggers = 1;
-
-  cfg.timing.eventDuration = cfg.mri.repetitionTime / 2 - 0.04; % second
-
-  % Time between blocs in secs
-  cfg.timing.IBI = 0;
-  % Time between events in secs
-  cfg.timing.ISI = 0;
-  % Number of seconds before the motion stimuli are presented
-  cfg.timing.onsetDelay = 0;
-  % Number of seconds after the end all the stimuli before ending the run
-  cfg.timing.endDelay = 2;
-
-end
-```
-
-### 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 a
-possible design.
-
-#### EVENTS
-
-The `numEventsPerBlock` should be a multiple of the number of "base" listed in
-the `motionDirections` and `staticDirections` (4 at the moment).
-
-#### 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
-
-#### Input
-
-- `expParameters`: parameters returned by `setParameters`
-- `displayFigs`: a boolean to decide whether to show the basic design matrix of
-  the design
-
-#### 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
-  - `0 90 180 270` indicate the angle
-  - `-1` indicates static
-- `expParameters.designSpeeds` is an array
-  `(nr_blocks, numEventsPerBlock) * speedEvent`
-- `expParameters.designFixationTargets` is an array
-  `(nr_blocks, numEventsPerBlock)` showing for each event if it should be
-  accompanied by a target
 
 ## Contributors ✨
 

audioLocTranslational.m

@@ -90,8 +90,7 @@
 
             % we wait for a trigger every 2 events
             if cfg.pacedByTriggers.do && mod(iEvent, 2) == 1
-                waitForTrigger( ...
-                               cfg, ...
+                waitForTrigger(cfg, ...
                                cfg.keyboard.responseBox, ...
                                cfg.pacedByTriggers.quietMode, ...
                                cfg.pacedByTriggers.nbTriggers);

docs/configuration.md

@@ -0,0 +1,82 @@
+## Structure and function details
+
+`setParameters.m` is the core engine of the experiment. It contains the
+following tweakable sections. See
+[docs/configuration](.docs/../docs/configuration.md) for more information.
+
+- Debug mode setting
+- Engine parameters:
+  - Devices parameters
+  - Monitor parameters
+  - Keyboard parameters
+  - MRI parameters
+- Experiment Design
+- Timing
+- Auditory Stimulation
+- Task(s)
+  - Instructions
+  - Task #1 parameters
+
+#### Let the scanner pace the experiment
+
+Set `cfg.pacedByTriggers.do` to `true` and you can then set all the details in
+this `if` block
+
+```matlab
+% Time is here in in terms of number repetition time (i.e MRI volumes)
+if cfg.pacedByTriggers.do
+
+  cfg.pacedByTriggers.quietMode = true;
+  cfg.pacedByTriggers.nbTriggers = 1;
+
+  cfg.timing.eventDuration = cfg.mri.repetitionTime / 2 - 0.04; % second
+
+  % Time between blocs in secs
+  cfg.timing.IBI = 0;
+  % Time between events in secs
+  cfg.timing.ISI = 0;
+  % Number of seconds before the motion stimuli are presented
+  cfg.timing.onsetDelay = 0;
+  % Number of seconds after the end all the stimuli before ending the run
+  cfg.timing.endDelay = 2;
+
+end
+```
+
+### 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 a
+possible design.
+
+#### EVENTS
+
+The `numEventsPerBlock` should be a multiple of the number of "base" listed in
+the `motionDirections` and `staticDirections` (4 at the moment).
+
+#### 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
+
+#### Input
+
+- `expParameters`: parameters returned by `setParameters`
+- `displayFigs`: a boolean to decide whether to show the basic design matrix of
+  the design
+
+#### 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
+  - `0 90 180 270` indicate the angle
+  - `-1` indicates static
+- `expParameters.designSpeeds` is an array
+  `(nr_blocks, numEventsPerBlock) * speedEvent`
+- `expParameters.designFixationTargets` is an array
+  `(nr_blocks, numEventsPerBlock)` showing for each event if it should be
+  accompanied by a target

setParameters.m

@@ -8,8 +8,7 @@
     % by default the data will be stored in an output folder created where the
     % setParamters.m file is
     % change that if you want the data to be saved somewhere else
-    cfg.dir.output = fullfile( ...
-                              fileparts(mfilename('fullpath')), 'output');
+    cfg.dir.output = fullfile(fileparts(mfilename('fullpath')), 'output');
 
     %% Debug mode settings