FrameTracker: Monitor flicker
Even expensive monitors can have bad habits with respect to flickering. This is not a case of operating system video drivers causing tearing in the display, but the monitor itself adding high-frequency flicker. Whether your monitor exhibits this kind of flickering is a function not only of its type, but also of its user settings.
Brightness control via PWM
Pulse width modulation, or PWM, is a way of controlling perceived strength of a signal by flickering it at a rate that is significantly faster than the human brain can detect, resulting in a smoothed or averaged perception of the stimulus. For example, PWM can control the perceived brightness of an LED: if the duty cycle of an LED flickering at 120 Hz is increased or decreased, you will perceive a corresponding increase or decrease in brightness, but you will not perceive a flicker.
That's exactly what many monitors do, and while that isn't a problem for your enjoyment of the screen, it is a confound for visual neuroscience. Does your monitor behave this way? Use your FrameTracker to find out! Since the FrameTracker can respond at a time scale much faster than the PWM cycle, it will detect these flickers, and report their exact timing on the BNC outputs.
Real-world example
Below, in red, is an example of what you might see if your monitor is lowering the brightness via PWM. Here, the monitor is flashing the image on the screen four times per frame for approximately 1 ms every 8 milliseconds or so. This way, the monitor has lowered the brightness to an eighth of its maximum brightness.
We learned monitors do this the hard way: these data are from an actual experiment. In green is what the output might look like if the screen were operating at 100% brightness. Use the FrameTracker to ensure you know what is happening in your experimental rigs, and correct it before you waste time on bad data.

The solution
The solution in our case was simple: crank the brightness all the way up and disable all “dynamic” settings. That way, the monitor did not flicker.
Back to your setup
You can check for monitor flicker by looking at the output of your FrameTracker with a physical oscilloscope or your favorite software oscilloscope (may we suggest EScope)? Simply put a light part of a program window against the light sensor, and see whether the FrameTracker reports a continuous “high” signal (good) or reports a rapidly oscillating output (not good). In the latter case, it is likely that changing the settings on your monitor can solve the problem. Your experimental results will be the more reliable for it!