• fMRI localizers for visual motion
  • Requirements
  • Installation
  • Structure and function details
    • visualMotionLocalizer
    • setParameters
      • Let the scanner pace the experiment
    • subfun/doDotMo
      • Input
      • Output
    • subfun/design/expDesign
      • Events
      • Pseudorandomization rules:
      • Input:
      • Output:
  • Contributors ✨

fMRI localizers for visual motion

Requirements

Make sure that the following toolboxes are installed and added to the matlab / octave path. See the next section on how to install the submodule toolboxes.

For instructions see the following links:

Requirements	Used version
CPP_BIDS (submodule)	2.1.1
CPP_PTB (submodule)	1.2.1
PsychToolBox	>=3.0.14
Matlab	>=2017
or octave	>=4.?

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.

git clone --recurse-submodules https://github.com/cpp-lln-lab/localizer_visual_motion.git

Structure and function details

visualMotionLocalizer

Running this script will show blocks of motion dots and static dots. Motion blocks will show dots moving in one of four directions (up-, down-, left-, and right-ward) (MT+ localizer) or dots moving inward and outward in the peripheral of the screen (MT/MST localizer).

Run in Debug mode (see setParameters.m) it does not care about subjID, run n., Eye Tracker (soon, at the moment it needs to be set off manually), 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

Let the scanner pace the experiment

Set cfg.pacedByTriggers.do to true and you can then set all the details in this if block

% Time is here in terms of `repetition time (TR)` (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/doDotMo

Wrapper function that present the dot stimulation (static or motion) per event.

Input

• cfg: PTB/machine and experiment configurations returned by setParameters and initPTB
• logFile: structure that stores the experiment logfile to be saved
• thisEvent: structure that stores information about the event to present regarding the dots (static or motion, direction, etc.)
• thisFixation: structure that stores information about the fixation cross task to present
• dots: [...]
• iEvent: index of the event of the block at the moment of the presentation

Output

• Event onset
• Event duration
• dots: [...]

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.

subfun/design/expDesign

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).

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.

It computes the directions to display and the task(s), at the moment:

1. detection of change in the color of the fixation target
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]

Events

The nbEventsPerBlock should be a multiple of the number of motion directions requested in motionDirections (which should be more than 1) e.g.:

• MT localizer: cfg.design.motionDirections = [ 0 90 180 270 ]; % right down left up
• MT_MST localizer: cfg.design.motionDirections = [666 -666]; % outward inward

Pseudorandomization rules:

• Directions:

1. Directions are all presented in random orders in numEventsPerBlock/nDirections consecutive chunks. This evenly distribute the directions across the block.
2. No same consecutive direction

• Color change detection of the fixation cross:

1. If there are 2 targets per block we make sure that they are at least 2 events apart.
2. Targets cannot be on the first or last event of a block.
3. No less than 1 target per event position in the whole run

Input:

• cfg: parameters returned by setParameters
• displayFigs: a boolean to decide whether to show the basic design matrix of the design

Output:

• cfg.design.blockNames: cell array (nbBlocks, 1) with the condition name for each block
• cfg.design.nbBlocks: integer for th etotal number of blocks in the run
• cfg.design.directions: array (nbBlocks, nbEventsPerBlock) with the direction to present in a given event of a block.
  • 0 90 180 270 indicate the angle for translational motion direction
  • 666 -666 indicate in/out-ward direction in radial motion
  • -1 indicates static
• cfg.design.speeds: array (nbBlocks, nbEventsPerBlock) indicate the dots speed in each event, the target is represented by a higher/lower value
• cfg.design.fixationTargets: array (nbBlocks, numEventsPerBlock) showing for each event if it should be accompanied by a target

Contributors ✨

Thanks goes to these wonderful people (emoji key):

Mohamed Rezk 💻 🎨 🤔

marcobarilari 💻 🎨 🤔 🐛 📓 👀 💬 🚇 🚧

Remi Gau 💻 🎨 🤔 🐛 📓 👀 💬 🚇 🚧

CerenB 🐛 📓

iqrashahzad14 💻 🤔

This project follows the all-contributors specification. Contributions of any kind welcome!