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Before the subject enters the scanner, you should:

  1. Turn the eye-tracker computer on, and select 'Eyelink' as the startup operating system.
  2. Turn the LCD circuit on
  3. If using the 32 channel coil, make sure the subject's eyes are roughly in the center of the eye-holes of the coil.
  4. Affix the illuminator to the scanner bed.

Viewing the subject's eye

After the subject has entered the scanner, go to the 'Camera Setup' screen of the Eyelink software interface. This is the default screen after you turn the Eyelink computer on. Check if you have a view of the illuminated eye (typically the left eye). If you cannot see this eye, you may need to adjust the camera position. To do this:

  1. Connect your stimulus presentation computer to one of the CNI's scanner display screens.
  2. Run a calibration script on your stimulus presentation computer. An example calibration script for Matlab Psychtoolbox, by Karen LaRocque, adapted from scripts by the Grill-Spector Lab is here.
  3. Select 'Display Image' on the Eyelink computer. Now the image of the subject's eye will be displayed on the screen in the scanner. Using the left and right arrow keys on the Eyelink computer, you can toggle a large or small angle shot. When initially searching for the eye, it's helpful to use the large angle shot.
  4. Now you can adjust the angle of the eye tracker camera, checking the screen behind you, until you see the subject's eye.

Note that the subject's eye may also be occluded by the mirrors or coil. Often, when the dorsal part of a subject's head is flush with the 32 channel coil, the camera will not have view of her eyes. To rectify this, ask the subject to scoot out of the scanner, 1 cm at a time, until you can see her eyes.

Adjusting the Pupil and Corneal Thresholds

  1. Adjust the pupil threshold, using the arrows in the top left corner of the Camera Setup screen. The threshold should be set such that the subject's pupils are optimally labeled in dark blue, with minimal labeling in the areas immediately outside the eye. When a pupil is detected, you will see a message indicating "PUPIL OK" in green.
  2. Adjust the CR (corneal reflection) threshold, using the arrows in the top left corner of the Camera Setup screen. When corneal reflection is detected, you will see a message indicating "CR OK" The threshold should be set such that "CR OK" is displayed when subjects look at each region of the display screen.


Now you can run a calibration, to give Eyelink parameters to help it guess where the subject is looking, in screen coordinates.

  1. Run the calibration script on your presentation computer, and display it on the scanner presentation screen. Again, a sample calibration script is here.
  2. Press "Calibrate" on the Eyelink computer. A dot will appear in the center of the screen. When the subject is fixating on it, select "accept fixation."
  3. Now Eyelink will complete the calibration process. Dots will appear at various points of the screen, and the subject is required to fixate on each presented dot.
  4. After calibration is complete press "accept." Then, validate the calibration by pressing "Validate." Another run of dot presentation will be conducted, and measurements will be computed indicating the error between estimated points of fixation for the calibration and validation runs. Based on the computed error, Eyelink will label the validation as "good" "fair" or "poor." If you are satisfied with the precision of your measurement, click "accept." Otherwise, you can repeat the full calibration and validation process.

Running your study

Now you are ready to run your study. You can update your presentation scripts to include code that communicates with Eyelink, in order to label trials and download data from the Eyelink computer. For more info about the Eyelink system, you can view the Eyelink manual.

Technical Details

We found that the standard IR light source from SR Research did not adequately focus the light onto the subject's eye, so we built a small MR-safe IR source using a single high-power IR LED epoxied to a non-metallic heat sink. The illuminator is mounted on the head coil using a loc-line stalk and can be positioned to nicely illuminate the target eye. It's powered from the same 5v source that powered the original SR illustrator (and that powers the camera) via a simple circuit based around a 1.8v linear regulator (it turns out that 1.8v drives this LED with just the right amount of current). The circuit was just the standard "typical application" circuit for a fixed voltage regulator, with a 100uF capacitor on the input and one on the output. We did have an issue with the RF pulses from the scanner causing some flicker in the illuminator, so we added a pair of 1000uF capacitors in parallel with the 100uF caps, and that minimized the flicker to a level that didn't interfere with eye tracking.

Parts list:

Here are some pictures of the very crude, "dead-bug" style circuit. Note that we neatly tucked it into the original eyelink IR illuminator case and we used an old cat-5 cable to connect the regulator with with IR source. The IR source was mounted to the plastic heat sink using thermal epoxy.

We've recently added a small enclosure. You can get the stl file or the scad code from our github 3d models repo.


If you normally set-up the eye tracker in the back of the room using the large screen and this does not work, it may be because the setup is in a different mode (where the eye tracker screen is projected on the little screen at the front of the scanner above the bore). Have a look at the figures at the right to correct the issue.

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