The extension for Tobii allows you to integrate the recording of eye movs with the experimental design – as you say, specify when to start recording, which areas of interest in your stimulus to include in the output, etc. It also means that the gaze data file can be programmed to contain E-Prime specific information such as RT, response accuracy, etc.
It seems to me you should be able to align independent output files (Tobii gaze, and E-Prime) if you work without the extension, and then work with the gaze coordinates to figure out what was happening at certain points in the experiment in the areas of interest. It will probably be a lot of work, though...
Inés
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