This repository contains MATLAB scripts for running an experimental task related to psychiatry in an fMRI environment. The experiment includes stimuli presentation, response recording, and synchronization with fMRI triggers. The repository is organized to facilitate running the task, managing stimuli, and configuring the experiment for different setups (e.g., different computers or fMRI centers).
MATLAB (version R2023b or later) PsychToolbox (version 3.0.19 or later) fMRI-compatible computer Joystick or button-box for response collection
Below is an explanation of the key files and folders:
C:.
│ .gitignore % Standard git ignore file
│ init_experiment.m % Script to initialize experiment parameters
│ README.md % This readme file
│ run_main_task.m % Main script for running the fMRI task
│ settings_main.m % Configuration settings for the main task
│
├───celeritas
│ celeritas.joystick.amgp % Joystick setup/configuration file
│
├───events
│ sub-test_task-sentences_events.xlsx % Event timing and stimuli-related information (BIDS-style)
│
├───legacy % Archive of outdated scripts (not in use anymore)
├───mainTrSynch % Main experiment task whose entire synchronization is dependent on fMRI triggers to run
├───restingState
│ eyes_closed.m % Script for running the resting-state session (eyes closed)
│
├───setup
│ lenovo_pc_setup.m % Setup script for Lenovo PC environment
│ tower_computer_setup.m % Setup script for Tower computer environment
│
├───stimuli % Contains all stimuli used in the experiment
│ ├───active_stimuli % Images for active task-related stimuli
│ ├───crosses % Fixation cross images
│ ├───neutral_stimuli % Images for neutral stimuli
│ └───stars % Star images for task feedback
│
├───testing % Scripts for simulation/testing of the experiment
│ eyes_closed_sim.m % Simulated version of resting-state session (for testing)
│ run_main_task_sim.m % Simulated version of the main task (for testing)
│ settings_main_sim.m % Configuration for simulated testing of the main task
│
├───training % Scripts for training participants outside the scanner
│ settings_training.m % Configuration for training task
│ training.m % Training script (similar to main task but for practice)
│
└───utils % Utility scripts used throughout the project
addResponseOptions.m % Adds response collection options
drawCross.m % Function to draw fixation cross
drawText.m % Function to display text
- Connect the usb-c and hdmi cables to the pc.
- Open device manager and check the ports.
- Connect the port in the code.
- Initial Setup PsychToolbox: Ensure that PsychToolbox is installed and properly configured. The preferred version is 3.0.19. You can check the version with PsychtoolboxVersion.
Joystick: If using a joystick, confirm that it is properly set up using the script celeritas.joystick.amgp.
-
Configure the Experiment Edit settings_main.m to set up experiment-specific parameters like fMRI trigger timing. Participant information is added on the main script.
-
Training If you want to familiarize participants with the task before the scan, use the training script training.m. This script is configured with different parameters for outside-scanner practice.
-
Resting-State Task For the resting-state scan, run eyes_closed.m. The subject should be instructed to close their eyes during this task. You may customize this script based on the duration of the scan.
-
Run the Main Task To start the main fMRI task, use the script run_main_task.m. This script handles the presentation of stimuli and the collection of responses during the scanning session.
Joystick issues: Ensure the joystick is connected and configured using the celeritas.joystick.amgp script.
PsychToolbox issues: If PsychToolbox fails to initialize, verify that all display settings are correct and that MATLAB has the required permissions.
Timing issues: Adjust the TR setting in settings_main.m or settings_training.m if your scanner's TR differs from the default.
Check the init_experiment.m script for more troubleshooting tips.
- Lenovo PC
Hardware:
Host Name: LAPTOP-N37ECEH3
OS Name: Microsoft Windows 11 Home
OS Version: 10.0.22631 N/A Build 22631
OS Manufacturer: Microsoft Corporation
OS Configuration: Standalone Workstation
OS Build Type: Multiprocessor Free
Registered Owner: SpikeUrban
Registered Organization: N/A
Product ID: 00342-21901-78821-AAOEM
Original Install Date: 8/25/2023, 5:42:36 AM
System Boot Time: 9/17/2024, 11:21:21 AM
System Manufacturer: LENOVO
System Model: 82XW
System Type: x64-based PC
Processor(s): 1 Processor(s) Installed.
[01]: Intel64 Family 6 Model 186 Stepping 2 GenuineIntel ~2400 Mhz
BIOS Version: LENOVO LZCN30WW, 6/15/2023
Windows Directory: C:\Windows
System Directory: C:\Windows\system32
Boot Device: \Device\HarddiskVolume1
System Locale: en-us;English (United States)
Input Locale: pt;Portuguese (Portugal)
Time Zone: (UTC+00:00) Dublin, Edinburgh, Lisbon, London
Total Physical Memory: 16,108 MB
Available Physical Memory: 1,192 MB
Virtual Memory: Max Size: 29,932 MB
Virtual Memory: Available: 10,780 MB
Virtual Memory: In Use: 19,152 MB
Page File Location(s): C:\pagefile.sys
Domain: WORKGROUP
Logon Server: \\LAPTOP-N37ECEH3
Hotfix(s): 5 Hotfix(s) Installed.
[01]: KB5042099
[02]: KB5012170
[03]: KB5027397
[04]: KB5043076
[05]: KB5043937
Network Card(s): 3 NIC(s) Installed.
[01]: Realtek PCIe GbE Family Controller
Connection Name: Ethernet
Status: Media disconnected
[02]: Bluetooth Device (Personal Area Network)
Connection Name: Bluetooth Network Connection
Status: Media disconnected
[03]: Realtek RTL8852BE WiFi 6 802.11ax PCIe Adapter
Connection Name: Wi-Fi
DHCP Enabled: Yes
DHCP Server: 10.20.0.1
IP address(es)
[01]: 10.20.8.180
[02]: fe80::221e:8e6a:c989:f2db
Hyper-V Requirements: A hypervisor has been detected. Features required for Hyper-V will not be displayed.
Software:
-----------------------------------------------------------------------------------------------------
MATLAB Version: 23.2.0.2515942 (R2023b) Update 7
MATLAB License Number: 41137037
Operating System: Microsoft Windows 11 Home Version 10.0 (Build 22631)
Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
-----------------------------------------------------------------------------------------------------
MATLAB Version 23.2 (R2023b)
Simulink Version 23.2 (R2023b)
5G Toolbox Version 23.2 (R2023b)
AUTOSAR Blockset Version 23.2 (R2023b)
Aerospace Blockset Version 23.2 (R2023b)
Aerospace Toolbox Version 23.2 (R2023b)
Antenna Toolbox Version 23.2 (R2023b)
Audio Toolbox Version 23.2 (R2023b)
Automated Driving Toolbox Version 23.2 (R2023b)
Bioinformatics Toolbox Version 23.2 (R2023b)
Bluetooth Toolbox Version 23.2 (R2023b)
C2000 Microcontroller Blockset Version 23.2 (R2023b)
Communications Toolbox Version 23.2 (R2023b)
Computer Vision Toolbox Version 23.2 (R2023b)
Control System Toolbox Version 23.2 (R2023b)
Curve Fitting Toolbox Version 23.2 (R2023b)
DDS Blockset Version 23.2 (R2023b)
DSP HDL Toolbox Version 23.2 (R2023b)
DSP System Toolbox Version 23.2 (R2023b)
Data Acquisition Toolbox Version 23.2 (R2023b)
Database Toolbox Version 23.2 (R2023b)
Datafeed Toolbox Version 23.2 (R2023b)
DatapixxToolbox Version 0.9, Aug
Deep Learning HDL Toolbox Version 23.2 (R2023b)
Deep Learning Toolbox Version 23.2 (R2023b)
EEGLAB Toolbox to process EEG data Version - see
EEGLAB Toolbox to process EEG data Version - see
Econometrics Toolbox Version 23.2 (R2023b)
Embedded Coder Version 23.2 (R2023b)
Filter Design HDL Coder Version 23.2 (R2023b)
Financial Instruments Toolbox Version 23.2 (R2023b)
Financial Toolbox Version 23.2 (R2023b)
Fixed-Point Designer Version 23.2 (R2023b)
Fuzzy Logic Toolbox Version 23.2 (R2023b)
GPU Coder Version 23.2 (R2023b)
Global Optimization Toolbox Version 23.2 (R2023b)
HDL Coder Version 23.2 (R2023b)
HDL Verifier Version 23.2 (R2023b)
Image Acquisition Toolbox Version 23.2 (R2023b)
Image Processing Toolbox Version 23.2 (R2023b)
Industrial Communication Toolbox Version 23.2 (R2023b)
Instrument Control Toolbox Version 23.2 (R2023b)
LTE Toolbox Version 23.2 (R2023b)
Lidar Toolbox Version 23.2 (R2023b)
MATLAB Coder Version 23.2 (R2023b)
MATLAB Compiler Version 23.2 (R2023b)
MATLAB Compiler SDK Version 23.2 (R2023b)
MATLAB Report Generator Version 23.2 (R2023b)
MATLAB Test Version 23.2 (R2023b)
Mapping Toolbox Version 23.2 (R2023b)
Medical Imaging Toolbox Version 23.2 (R2023b)
Mixed-Signal Blockset Version 23.2 (R2023b)
Model Predictive Control Toolbox Version 23.2 (R2023b)
Model-Based Calibration Toolbox Version 23.2 (R2023b)
Motor Control Blockset Version 23.2 (R2023b)
Navigation Toolbox Version 23.2 (R2023b)
Optimization Toolbox Version 23.2 (R2023b)
Parallel Computing Toolbox Version 23.2 (R2023b)
Partial Differential Equation Toolbox Version 23.2 (R2023b)
Phased Array System Toolbox Version 23.2 (R2023b)
Powertrain Blockset Version 23.2 (R2023b)
Predictive Maintenance Toolbox Version 23.2 (R2023b)
Psychtoolbox Version 3.0.19 17 February
Psychtoolbox Version 3.0.19 17 February
RF Blockset Version 23.2 (R2023b)
RF PCB Toolbox Version 23.2 (R2023b)
RF Toolbox Version 23.2 (R2023b)
ROS Toolbox Version 23.2 (R2023b)
Radar Toolbox Version 23.2 (R2023b)
Reinforcement Learning Toolbox Version 23.2 (R2023b)
Requirements Toolbox Version 23.2 (R2023b)
Risk Management Toolbox Version 23.2 (R2023b)
Robotics System Toolbox Version 23.2 (R2023b)
Robust Control Toolbox Version 23.2 (R2023b)
Satellite Communications Toolbox Version 23.2 (R2023b)
Sensor Fusion and Tracking Toolbox Version 23.2 (R2023b)
SerDes Toolbox Version 23.2 (R2023b)
Signal Integrity Toolbox Version 23.2 (R2023b)
Signal Processing Toolbox Version 23.2 (R2023b)
SimBiology Version 23.2 (R2023b)
SimEvents Version 23.2 (R2023b)
Simscape Version 23.2 (R2023b)
Simscape Battery Version 23.2 (R2023b)
Simscape Driveline Version 23.2 (R2023b)
Simscape Electrical Version 23.2 (R2023b)
Simscape Fluids Version 23.2 (R2023b)
Simscape Multibody Version 23.2 (R2023b)
Simulink 3D Animation Version 23.2 (R2023b)
Simulink Check Version 23.2 (R2023b)
Simulink Code Inspector Version 23.2 (R2023b)
Simulink Coder Version 23.2 (R2023b)
Simulink Compiler Version 23.2 (R2023b)
Simulink Control Design Version 23.2 (R2023b)
Simulink Coverage Version 23.2 (R2023b)
Simulink Design Optimization Version 23.2 (R2023b)
Simulink Design Verifier Version 23.2 (R2023b)
Simulink Desktop Real-Time Version 23.2 (R2023b)
Simulink Fault Analyzer Version 23.2 (R2023b)
Simulink PLC Coder Version 23.2 (R2023b)
Simulink Real-Time Version 23.2 (R2023b)
Simulink Report Generator Version 23.2 (R2023b)
Simulink Test Version 23.2 (R2023b)
SoC Blockset Version 23.2 (R2023b)
Spreadsheet Link Version 23.2 (R2023b)
Stateflow Version 23.2 (R2023b)
Statistical Parametric Mapping Version 7771 (SPM12)
Statistics and Machine Learning Toolbox Version 23.2 (R2023b)
Symbolic Math Toolbox Version 23.2 (R2023b)
System Composer Version 23.2 (R2023b)
System Identification Toolbox Version 23.2 (R2023b)
Text Analytics Toolbox Version 23.2 (R2023b)
UAV Toolbox Version 23.2 (R2023b)
Vehicle Dynamics Blockset Version 23.2 (R2023b)
Vehicle Network Toolbox Version 23.2 (R2023b)
Vision HDL Toolbox Version 23.2 (R2023b)
WLAN Toolbox Version 23.2 (R2023b)
Wavelet Toolbox Version 23.2 (R2023b)
Wireless HDL Toolbox Version 23.2 (R2023b)
Wireless Testbench Version 23.2 (R2023b)
PsychtoolboxVersion: '3.0.19 - Flavor: Manual Install, 13-Feb-2024 12:07:36'
- Tower Computer
Host Name: DESKTOP-UJUVJ70
OS Name: Microsoft Windows 10 Education
OS Version: 10.0.19045 N/A Build 19045
OS Manufacturer: Microsoft Corporation
OS Configuration: Standalone Workstation
OS Build Type: Multiprocessor Free
Registered Owner: Windows User
Registered Organization:
Product ID: 00328-00205-96228-AA809
Original Install Date: 25/10/2021, 17:08:40
System Boot Time: 06/09/2024, 03:55:31
System Manufacturer: Micro-Star International Co., Ltd.
System Model: MS-7B48
System Type: x64-based PC
Processor(s): 1 Processor(s) Installed.
[01]: Intel64 Family 6 Model 158 Stepping 10 GenuineIntel ~3696 Mhz
BIOS Version: American Megatrends Inc. 2.20, 27/10/2017
Windows Directory: C:\Windows
System Directory: C:\Windows\system32
Boot Device: \Device\HarddiskVolume2
System Locale: en-us;English (United States)
Input Locale: pt;Portuguese (Portugal)
Time Zone: (UTC+00:00) Dublin, Edinburgh, Lisbon, London
Total Physical Memory: 32 728 MB
Available Physical Memory: 15 827 MB
Virtual Memory: Max Size: 37 592 MB
Virtual Memory: Available: 16 436 MB
Virtual Memory: In Use: 21 156 MB
Page File Location(s): C:\pagefile.sys
Domain: WORKGROUP
Logon Server: \\DESKTOP-UJUVJ70
Hotfix(s): 32 Hotfix(s) Installed.
[01]: KB5042097
[02]: KB5030841
[03]: KB4562830
[04]: KB5003791
[05]: KB5011048
[06]: KB5012170
[07]: KB5015684
[08]: KB5043064
[09]: KB5006753
[10]: KB5007273
[11]: KB5011352
[12]: KB5011651
[13]: KB5014032
[14]: KB5014035
[15]: KB5014671
[16]: KB5015895
[17]: KB5016705
[18]: KB5018506
[19]: KB5020372
[20]: KB5022924
[21]: KB5023794
[22]: KB5025315
[23]: KB5028318
[24]: KB5029709
[25]: KB5031539
[26]: KB5036447
[27]: KB5037018
[28]: KB5037995
[29]: KB5039336
[30]: KB5041579
[31]: KB5043935
[32]: KB5005699
Network Card(s): 3 NIC(s) Installed.
[01]: Realtek PCIe GbE Family Controller
Connection Name: Ethernet
DHCP Enabled: Yes
DHCP Server: 10.105.4.4
IP address(es)
[01]: 10.105.150.66
[02]: fe80::c1f7:ca5b:ed4c:7ad1
[02]: Bluetooth Device (Personal Area Network)
Connection Name: Bluetooth Network Connection 3
Status: Media disconnected
[03]: TP-Link Wireless N PCI Express Adapter
Connection Name: Wi-Fi 3
Status: Media disconnected
Hyper-V Requirements: VM Monitor Mode Extensions: Yes
Virtualization Enabled In Firmware: Yes
Second Level Address Translation: Yes
Data Execution Prevention Available: Yes
MATLAB Version: 24.1.0.2628055 (R2024a) Update 4
MATLAB License Number: 41137037
Operating System: Microsoft Windows 10 Education Version 10.0 (Build 19045)
Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
-----------------------------------------------------------------------------------------------------
MATLAB Version 24.1 (R2024a)
Simulink Version 24.1 (R2024a)
5G Toolbox Version 24.1 (R2024a)
AUTOSAR Blockset Version 24.1 (R2024a)
Aerospace Blockset Version 24.1 (R2024a)
Aerospace Toolbox Version 24.1 (R2024a)
Antenna Toolbox Version 24.1 (R2024a)
Audio Toolbox Version 24.1 (R2024a)
Automated Driving Toolbox Version 24.1 (R2024a)
Bioinformatics Toolbox Version 24.1 (R2024a)
Bluetooth Toolbox Version 24.1 (R2024a)
C2000 Microcontroller Blockset Version 24.1 (R2024a)
Communications Toolbox Version 24.1 (R2024a)
Computer Vision Toolbox Version 24.1 (R2024a)
Control System Toolbox Version 24.1 (R2024a)
Curve Fitting Toolbox Version 24.1 (R2024a)
DDS Blockset Version 24.1 (R2024a)
DSP HDL Toolbox Version 24.1 (R2024a)
DSP System Toolbox Version 24.1 (R2024a)
Data Acquisition Toolbox Version 24.1 (R2024a)
Database Toolbox Version 24.1 (R2024a)
Datafeed Toolbox Version 24.1 (R2024a)
DatapixxToolbox Version 0.9, Aug
Deep Learning HDL Toolbox Version 24.1 (R2024a)
Deep Learning Toolbox Version 24.1 (R2024a)
EEGLAB Toolbox to process EEG data Version - see
EEGLAB Toolbox to process EEG data Version - see
Econometrics Toolbox Version 24.1 (R2024a)
Embedded Coder Version 24.1 (R2024a)
FieldTrip Version unknown www.fieldtriptoolbox.org
Filter Design HDL Coder Version 24.1 (R2024a)
Financial Instruments Toolbox Version 24.1 (R2024a)
Financial Toolbox Version 24.1 (R2024a)
Fixed-Point Designer Version 24.1 (R2024a)
Fuzzy Logic Toolbox Version 24.1 (R2024a)
GPU Coder Version 24.1 (R2024a)
Global Optimization Toolbox Version 24.1 (R2024a)
HDL Coder Version 24.1 (R2024a)
HDL Verifier Version 24.1 (R2024a)
Image Acquisition Toolbox Version 24.1 (R2024a)
Image Processing Toolbox Version 24.1 (R2024a)
Industrial Communication Toolbox Version 24.1 (R2024a)
Instrument Control Toolbox Version 24.1 (R2024a)
LTE Toolbox Version 24.1 (R2024a)
Lidar Toolbox Version 24.1 (R2024a)
MATLAB Coder Version 24.1 (R2024a)
MATLAB Compiler Version 24.1 (R2024a)
MATLAB Compiler SDK Version 24.1 (R2024a)
MATLAB Report Generator Version 24.1 (R2024a)
MATLAB Test Version 24.1 (R2024a)
Mapping Toolbox Version 24.1 (R2024a)
Medical Imaging Toolbox Version 24.1 (R2024a)
Mixed-Signal Blockset Version 24.1 (R2024a)
Model Predictive Control Toolbox Version 24.1 (R2024a)
Model-Based Calibration Toolbox Version 24.1 (R2024a)
Motor Control Blockset Version 24.1 (R2024a)
Navigation Toolbox Version 24.1 (R2024a)
Optimization Toolbox Version 24.1 (R2024a)
Parallel Computing Toolbox Version 24.1 (R2024a)
Partial Differential Equation Toolbox Version 24.1 (R2024a)
Phased Array System Toolbox Version 24.1 (R2024a)
Powertrain Blockset Version 24.1 (R2024a)
Predictive Maintenance Toolbox Version 24.1 (R2024a)
Psychtoolbox Version 3.0.18 13 October
RF Blockset Version 24.1 (R2024a)
RF PCB Toolbox Version 24.1 (R2024a)
RF Toolbox Version 24.1 (R2024a)
ROS Toolbox Version 24.1 (R2024a)
Radar Toolbox Version 24.1 (R2024a)
Reinforcement Learning Toolbox Version 24.1 (R2024a)
Requirements Toolbox Version 24.1 (R2024a)
Risk Management Toolbox Version 24.1 (R2024a)
Robotics System Toolbox Version 24.1 (R2024a)
Robust Control Toolbox Version 24.1 (R2024a)
Satellite Communications Toolbox Version 24.1 (R2024a)
Sensor Fusion and Tracking Toolbox Version 24.1 (R2024a)
SerDes Toolbox Version 24.1 (R2024a)
Signal Integrity Toolbox Version 24.1 (R2024a)
Signal Processing Toolbox Version 24.1 (R2024a)
SimBiology Version 24.1 (R2024a)
SimEvents Version 24.1 (R2024a)
Simscape Version 24.1 (R2024a)
Simscape Battery Version 24.1 (R2024a)
Simscape Driveline Version 24.1 (R2024a)
Simscape Electrical Version 24.1 (R2024a)
Simscape Fluids Version 24.1 (R2024a)
Simscape Multibody Version 24.1 (R2024a)
Simulink 3D Animation Version 24.1 (R2024a)
Simulink Check Version 24.1 (R2024a)
Simulink Code Inspector Version 24.1 (R2024a)
Simulink Coder Version 24.1 (R2024a)
Simulink Compiler Version 24.1 (R2024a)
Simulink Control Design Version 24.1 (R2024a)
Simulink Coverage Version 24.1 (R2024a)
Simulink Design Optimization Version 24.1 (R2024a)
Simulink Design Verifier Version 24.1 (R2024a)
Simulink Desktop Real-Time Version 24.1 (R2024a)
Simulink Fault Analyzer Version 24.1 (R2024a)
Simulink PLC Coder Version 24.1 (R2024a)
Simulink Real-Time Version 24.1 (R2024a)
Simulink Report Generator Version 24.1 (R2024a)
Simulink Test Version 24.1 (R2024a)
SoC Blockset Version 24.1 (R2024a)
Spreadsheet Link Version 24.1 (R2024a)
Stateflow Version 24.1 (R2024a)
Statistics and Machine Learning Toolbox Version 24.1 (R2024a)
Symbolic Math Toolbox Version 24.1 (R2024a)
System Composer Version 24.1 (R2024a)
System Identification Toolbox Version 24.1 (R2024a)
Text Analytics Toolbox Version 24.1 (R2024a)
UAV Toolbox Version 24.1 (R2024a)
Vehicle Dynamics Blockset Version 24.1 (R2024a)
Vehicle Network Toolbox Version 24.1 (R2024a)
Vision HDL Toolbox Version 24.1 (R2024a)
WLAN Toolbox Version 24.1 (R2024a)
Wavelet Toolbox Version 24.1 (R2024a)
Wireless HDL Toolbox Version 24.1 (R2024a)
Wireless Testbench Version 24.1 (R2024a)
ans =
'3.0.18 - Flavor: beta - Corresponds to SVN Revision 12862
For more info visit:
https://github.com/Psychtoolbox-3/Psychtoolbox-3'