Stimulation PC🔗

The stimulation PC is connected to the stimulation devices. It can boot on Windows 10 or on Ubuntu 22.04 LTS (generic or lowlatency kernel). In both case, users should use the non-admin account meguser and projects should be stored in ~/projects.

Specifications🔗

The stimulation PC runs on an intel Xeon W-2245 (8 cores, 16 threads) with 32 GB of RAM and an Nvidia Quadro P2200. This hardware is recent but not high-end. Stimulation paradigms rarely require high-end hardware with high throughput. Instead, latency and regularity are more valuable and are similar between high-end and middle-end hardware.

E-Prime🔗

E-Prime is designed to work with a Chronos device to manage both auditory outputs and I/O lines, among which triggers. If the Chronos is not used, the settings should be set to:

parallel port to LPT4
audio driver to ASIO

Warning

With audio stimulation, the DirectSound driver yields unreliable timings.

Finally, the monitor index should be set to 1 or 2, but E-Prime does not identify the monitor index reliably and might swap the monitor index between 2 reboots.

Python🔗

For Python, virtual environments are used to separate the dependencies of different projects and paradigms. The virtual environment can be created either through VSCode or through a terminal. The python version defined in the SPEC 0 by the scientific python community are available on the stimulation PC, as of writing, python 3.9 to python 3.12.

Important

The stimulation PC prevents pip installation of packages within the base environment.

VSCode

In VSCode, open the folder from your project, e.g. ~/projects/my_project. Using the command palette (Ctrl+Shift+P), search for Python: Select Interpreter. You can then create an environment using venv and the python interpreter (version) of your choice.

The created virtual environment will be placed in the current directory in the folder .venv, i.e. ~/projects/my_project/.venv. Subsequent terminals opened in VSCode while this folder is opened will automatically activate the virtual environment.

You can now install packages in this virtual environment with pip:

$ pip install numpy

This method works both for Windows and Linux.

Windows

In a command prompt or terminal (recommended: Cmder), navigate to the project location and to the folder in which you wish to create the virtual environment. You can create the virtual environment with venv:

$ py -m venv .venv

Note

You can replace .venv with the name of the environment. This name will be used to create the folder in which the environment will be stored.

Note

If you wish to select a different python version than the version bind to py, specify the version after py. For instance the command below launches a 3.11 python interpreter (if installed on the system).

$ py -3.11

Once created, you can activate the environment with:

$ .venv\Scripts\activate.bat

Note

You will always have to manually activate the environment in new terminals.

You can now install packages in this virtual environment with pip:

$ pip install numpy

Linux

In a terminal, navigate to the project location and to the folder in which you wish to create the virtual environment. You can create the virtual environment with venv:

$ python3.10 -m venv .venv --copies

Note

You can replace .venv with the name of the environment. This name will be used to create the folder in which the environment will be stored.

Note

If you wish to select a different python version, replace python3.10 with, the appropriate version. For instance, the command below launches a 3.12 python interpreter.

$ python3.12

You can now install packages in this virtual environment with pip:

$ pip install numpy

PsychoPy🔗

A default PsychoPy 2023.2.3 installation is available on the Windows partition. However, it is recommended to use a virtual environment to install the latest version of PsychoPy when able.

MATLAB🔗

MATLAB R2024a is installed on both the Windows and Linux partition of the stimulation PC.

Windows

On Windows, a shortcut on the desktops are available. Psychtoolbox version 3.0.19.13 is installed.

Linux

On Linux, the executable is located here: /usr/local/bin/matlab.

Triggers🔗

The stimulation PC can send triggers to the first 8 bits of the trigger interface on the main desk, STI102, via a parallel port (DB-25) or via the Chronos if E-Prime is in-use. The triggers should last a couple of millisecond, 10 ms is recommended. The parallel port should be initialized to 0 at the beginning of the paradigm and it should be reset to 0 after each trigger.

Python (Windows)

The platform provides byte-triggers to send triggers in paradigm. It supports MockTrigger (for testing purposes), LSLTrigger (for software triggers) and ParallelPortTrigger (for hardware triggers).

from byte_triggers import ParallelPortTrigger

trigger = ParallelPortTrigger(0x2FB8)  # hexadecimal address
trigger.signal(101)

Note

ParallelPortTrigger automatically resets the parallel port to 0 after each trigger, in a separate thread. This avoids blocking the main thread. The default reset delay is set to 10 ms.

Note

Note that the stimulation PC is pre-configured. On other computers, microsoft redistributables and the inpoutx64.dll file in C:\Windows\system32 may be required.

Python (Linux)

from byte_triggers import ParallelPortTrigger

trigger = ParallelPortTrigger("/dev/parport0")
trigger.signal(101)

Note

ParallelPortTrigger automatically resets the parallel port to 0 after each trigger, in a separate thread. This avoids blocking the main thread. The default reset delay is set to 10 ms.

MATLAB (Windows)

Download io64.mexw64 in your MATLAB path
In MATLAB, use the following code to send triggers between 1 and 255:

%% Initialize the parallel port object
address = hex2dec("2FB8");
ioObj = io64;
status = io64(ioObj);
io64(ioObj, address, 0);  % set the parallel port to 0 (default state)

%% Deliver the trigger 101
io64(ioObj, address, 101);  % set the parallel port to 101
pause(0.01);  % wait for 10 ms
io64(ioObj, address, 0);  % set the parallel port back to 0

Note

Note that the stimulation PC is pre-configured. On other computers, microsoft redistributables and the inpoutx64.dll file in C:\Windows\system32 may be required.

Note

If you need precise control on the monitor refresh rate, make sure that the wait delay is smaller than the interval between 2 frames. On the stimulation PC, the ProPixx projector has a 120 refresh rate, i.e. 2 frames are separated y 8.33 ms.

Measuring trigger to event delay🔗

Delays between an MEG trigger and an event can be measured by connecting a measuring device to a miscellaneous channel of the MEG system. The sampling rate can be increased to 5 kHz to measure higher frequency content.

For visual task, a photodiode is available. The photodiode optical fiber should be connected to the powered digitizer. The analogical output of the digitizer is sufficient in most cases, and should be preferred above the thresholded digital output.

For auditory task, one of the monitoring output from the Crimson 3, Phones 1 can be connected via a jack to BNC cable to a miscellaneous channel, MISC 006. See additional information about this measure in the trigger to sound onset delay section and in the tutorial MISC 006: a proxy measure of the audio stimuli.

Ethernet TCP/UDP🔗

The stimulation PC has an extra GigE network card, TP-Link TG-3468, which can be used in paradigms for network based communications.