Hello,
Processing epochs of different durations is quite complicated: you cannot average them or display them simultaneously.
But in most cases, you don’t need to have epochs of different durations. What is your question?
For instance, if you are interested in what the brain does after the second dot disappears (S16/S32), then you just need to epoch around this time, and use the same epoch length for all the conditions.
If you are interested both in the presentation of the dots and the subject response, you can import epochs for both with different epoch durations if you want. It doesn’t matter because these are epochs you won’t compare or average directly (it doesn’t make much sense to compare a visual presentation with a motor response).
What you need to do before epoching is classifying your markers before epoching so that you can import and average separately the trials where the dot position is correct vs. incorrect, or when the response of the subject is correct/incorrect. You can find many processes to help you sorting your events in the category “Events”, especially “Combine stim/response”.
For the computation of the noise covariance: use as much data as possible, but not data in the middle of the sequence of stimulation, you can use rest recordings, or the concatenation of the pre-stimulus baselines (before the presentation of the first dot).
For the data covariance: I don’t know, I don’t have much experience with this. I will try to ask if someone else can help you with this.
Cheers,
Francois