Merge pull request #15 from Remi-Gau/remi-update_to_other_CPP_repos

update to other cpp repos

Author: Remi-Gau

.gitattributes

@@ -0,0 +1,2 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto

.gitmodules

@@ -1,6 +1,6 @@
-[submodule "Visual-loc_translational/subfun/CPP_PTB"]
-	path = Visual-loc_translational/subfun/CPP_PTB
+[submodule "lib/CPP_PTB"]
+	path = lib/CPP_PTB
 	url = https://github.com/cpp-lln-lab/CPP_PTB.git
-[submodule "Visual-loc_translational/subfun/CPP_BIDS"]
-	path = Visual-loc_translational/subfun/CPP_BIDS
+[submodule "lib/CPP_BIDS"]
+	path = lib/CPP_BIDS
 	url = https://github.com/cpp-lln-lab/CPP_BIDS.git

README.md

@@ -1,6 +1,99 @@
-# Motion Visual-Localizer
+# fMRI localizers for visual motion
 
-This repo collects the most common localizers in use to define hMT/V5
+# Translational Motion
 
-1. Radial Motion
-2. [Translational motion](/Visual-loc_translational) (4 directions: up-, dowm-, left-, right-ward)
+## Requirements
+
+Make sure that the following toolboxes are installed and added to the matlab / octave path.
+
+For instructions see the following links:
+
+| Requirements                                             | Used version |
+|----------------------------------------------------------|--------------|
+| [CPP_BIDS](https://github.com/cpp-lln-lab/CPP_BIDS)      | ?            |
+| [CPP_PTB](https://github.com/cpp-lln-lab/CPP_PTB)        | ?            |
+| [PsychToolBox](http://psychtoolbox.org/)                 | >=3.0.14     |
+| [Matlab](https://www.mathworks.com/products/matlab.html) | >=2017      |
+| or [octave](https://www.gnu.org/software/octave/)        | >=4.?        |
+
+## Installing dependencies
+
+All the dependencies needed to run this are listed in the [mpm-requirements.txt file](.mpm-requirements.txt). If those functions are not in the matlab path the scripts in this repository will not work.
+
+If you are using the [matlab package manager](https://github.com/mobeets/mpm), you can simply download the appropriate version of those dependencies and add them to your path by running the `getDependencies` function.
+
+```matlab
+getDependencies('update')
+```
+
+If you already have the appropriate version but just want to add them to the matlab path, then run.
+
+```matlab
+getDependencies()
+```
+## Structure and function details
+
+### 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.)
+
+### setParameters
+
+`setParameters.m` is the core engine of the experiment. It contains the following tweakable sections:
+
+- Debug mode setting
+- MRI settings
+- Engine parameters:
+  - Monitor parameters
+  - Monitor parameters for PsychToolBox
+- Keyboards
+- Experiment Design
+- Visual Stimulation
+- Task(s)
+  - Instructions
+  - Task #1 parameters
+
+### subfun/doDotMo
+
+#### 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
+
+#### 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.
+
+### 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.
+
+#### 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
+
+### subfun/eyeTracker
+Eyetracker script, still to be debugged. Will probably moved in the CPP_PTB package. It deals with the calibration (dufault or custom), eye movements recording and saving the files.
+
+### subfun/wait4Trigger
+Simple functions that counts the triggers sent by the MRI computer to the stimulation computer to sync brain volume recordings and stimulation.