Prerequisite
You need the Eyelink recording files in the original .edf format.
You also need access to the Eyelink software, Matlab, and dataHandler.
Goal of this tutorial
This tutorial teaches you how to read the Eyelink files and create markers corresponding to the different eye-related events (blinks, saccades) using dataHandler. These markers can be used as events for MEG data analysis.
Step-by-step guide
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1. The Eyelink data files
a. During acquisition
The name you choose for this file has to be short, otherwise it can create problems when saving the data. When saving the data with your stimulation script, you need to leave some time for the system to save the file (with a command waitsecs after the command to save the Eyelink data, for example), otherwise the file will be corrupted or not saved.
b. Data conversion after acquisition
Eyelink data is saved in .edf format by the software. After your recordings, you have to convert the .edf file to .asc. You can use the Eyelink software installed in the stimulation computer at the MEG.
c. Inside the data file
The .asc data file can be viewed as a text file, using the command
gedit run1.asc
Code Block | ||||||
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** CONVERTED FROM C:\manips\XXX.edf using edfapi 3.1 Win32 Nov 24 2009 on Thu Oct 01 17:29:36 2015
** DATE: Fri Sep 25 10:43:59 2015
[[ A lot of header text was removed here for clarity. ]]
START 90220983 RIGHT SAMPLES EVENTS
PRESCALER 1
VPRESCALER 1
PUPIL DIAMETER
EVENTS GAZE RIGHT RATE 1000.00 TRACKING CR FILTER 2
SAMPLES GAZE RIGHT RATE 1000.00 TRACKING CR FILTER 2
MSG 90220983 !MODE RECORD CR 1000 2 1 R
90220983 685.8 446.1 5794.0 ...
INPUT 90220983 0
90220984 685.9 446.0 5796.0 ...
90220985 685.5 445.9 5799.0 ...
90220986 684.8 445.8 5799.0 ...
90220987 684.4 445.8 5800.0 ...
90220988 684.7 445.8 5801.0 ...
90220989 685.2 445.8 5801.0 ...
SFIX R 90220990
90220990 685.9 445.9 5801.0 ...
90220991 686.0 446.0 5801.0 ...
90220992 685.5 446.0 5802.0 ...
90220993 684.8 446.1 5803.0 ...
90220994 684.2 446.2 5802.0 ...
90220995 684.6 446.2 5801.0 ...
[[ The file goes on...]]
90221820 663.8 468.3 5514.0 ...
90221821 663.7 467.8 5514.0 ...
90221822 663.5 467.9 5515.0 ...
90221823 663.4 467.6 5516.0 ...
90221824 662.9 467.2 5515.0 ...
EFIX R 90221475 90221824 350 655.1 475.1 5879
SSACC R 90221825
90221825 662.5 466.5 5513.0 ...
90221826 662.3 466.2 5509.0 ...
90221827 663.0 466.3 5507.0 ...
90221828 663.8 466.8 5499.0 ...
90221829 664.8 467.3 5493.0 ...
90221830 666.2 467.7 5489.0 ...
90221831 668.4 468.2 5491.0 ...
90221832 671.4 468.7 5492.0 ...
90221833 674.4 468.9 5490.0 ...
90221834 677.2 468.9 5483.0 ...
90221835 680.1 469.0 5476.0 ...
90221836 682.4 470.1 5471.0 ...
90221837 686.0 471.5 5471.0 ...
90221838 689.2 472.9 5473.0 ...
90221839 693.8 473.4 5476.0 ...
90221840 698.0 473.7 5479.0 ...
90221841 704.0 474.0 5475.0 ...
90221842 710.0 474.3 5468.0 ...
90221843 716.4 474.5 5458.0 ...
90221844 720.7 474.3 5452.0 ...
90221845 723.7 474.0 5444.0 ...
90221846 725.1 473.4 5437.0 ...
90221847 726.0 472.5 5432.0 ...
90221848 726.8 471.1 5430.0 ...
90221849 727.5 469.8 5429.0 ...
90221850 727.5 468.6 5427.0 ...
90221851 726.6 468.0 5424.0 ...
ESACC R 90221825 90221851 27 662.5 466.5 726.6 468.0 2.53 183
SFIX R 90221852
90221852 725.6 467.4 5423.0 ...
90221853 725.1 467.3 5424.0 ...
[[ And the file goes on...]] |
This file contains a header with information related to the acquisition (date, Eyelink version, format conversions performed…). You will also see information about the calibration(s) data were done, and then 4 columns of numeric values: the 1st column is the sample number, the 2nd column is the x coordinate of the eye position on the screen, the 3rd column is the y coordinate, and the 4th column is the pupil diameter.
Some eye-related events are automatically identified by Eyelink:
- Fixation: SFIX and EFIX for start and end fixation
- Saccades: SSACC and and ESACC for start and end fixation
Next to EFIX and ESACC, the numbers indicate the sample corresponding to the end of fixation/saccade, the sample corresponding to the start of the fixation/saccade, the duration of the fixation/saccade, the x, y coordinates and the pupil diameter.
2. Creating markers with Eyelink information
a. Insert markers
To insert Eyelink markers from a run1.asc file on a run1_trans_tsss.fif file, you can use the following dataHandler command on a terminal:
dataHandler -r -edf run1.asc run1_trans_tsss.fif
You can also run this command from matlab, by doing the following:
str_Eyelink = 'dataHandler -r -edf run1.asc run1_trans_tsss.fif';
command(str_Eyelink)
For help on this dataHandler function, type from a terminal:
dataHandler -help -edf
b. What are these Eyelink markers
Eyelink markers are saved in run1_trans_tsss.mrk. You will find different sorts of markers:
- EL_SBLINK_R, EL_EBLINK_R: these indicate the beginning (SBLINK) and the end (EBLINK) of blinks. '_R' indicates the eye chosen during the recording ('_R' for right or '_L' for left).
- EL_SSACC_R_0, EL_ESACC_R_0, EL_SSACC_R_1, EL_ESACC_R_1...: beginning (SSACC) and end (ESACC) of a saccade. 'R_' indicates the eye chosen during the recording ('_R' for right, '_L' for left). The number indicates the amplitude in degrees of visual angle: 0 for angles < 1 degree, 1 for angles < 2 degrees…, 5 for angles > 5 degrees.
No information about the pupil diameter is entered automatically. You will have to read it yourself, either by reading the .asc file, or by using the acquisition data channel where Eyelink pupil diameter data was sent to at recording.
c. How to read these markers with fieldtrip
You can read the .mrk file using the function my_ft_read_event. For more information, see 'Computing ERPs'.
3. Some adjustments and checks to make
a. Visualize the markers
To visualize the markers, you can open your .fif data file with Muse, it will automatically read the corresponding .mrk file containing the Eyelink markers.
You will be able to browse through the data, especially EOG if you had it recorded, to check that the markers are where they should be.
You can also visualize the 3 channels on your data file containing the Eyelink data (x coordinate, y coordinate and pupil diameter), usually set up at acquisition.
Example of saccades: The first two channels correspond to the position of the eye on the screen, the last channel corresponds to pupil diameter. The markers here indicate the beginning and end of saccades. You can see that the second saccade (EL_SSACC_R_2 / EL_ESACC_R_2) was larger than the others (EL_SSACC_R_0 / EL_ESACC_R_0). The first saccade was defined only along the x-axis (horizontal eye movement).
Example of blink: You can see here the occurrence of a blink, delimited by the red markers. Note how this blink was preceded and followed by a saccade, corresponding to the eye movement associated with the blink. Note also how blinks affect all measures (position on the screen and pupil diameter).
b. Incorrect pupil diameter data
It can happen that Eyelink is not able to measure the pupil diameter, so you will see saturated signal. This may not be detected by any automatic Eyelink marker, so you have to check for that.
c. Blink time window
If the precise time window defining a blink is of some importance for your analysis, you should check the Eyelink blink markers. The blink window defined is typically rather restricted, so you may want to add some extra timing before and after, to extend the blink time window. For example, in the figure above illustrating a blink, you can see how the red markers delimiting the blink could have been extended in order to catch all the blink event.
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