[Eeglablist] Pre-processing pipeline questions

[Mina Marmpena]

Dear EEGLAB list,

I have some EEG data from a cognitive experiment which I will analyze for
my master thesis. I am not experienced with preprocessing and after I read
Makoto's guidelines and other information in the internet I would like to
ask for your help in some dilemmas I face.

1) Removing bad channels *before* epoching: During examination of the
continuous signal, if the parts that consist the epochs of interest are
quite ok and only need to reject less than 5-10% of the epochs for bad
channels, would it be ok to avoid interpolation, reject bad epochs, and
*then* re-reference the good epochs that are left?

2) Re-referencing to the common average: The data acquisition system was
referencing to the common average online for some (unfortunate I guess)
reason. Supposing I can extract enough epochs without bad electrode
contamination, should I re-reference and if yes to what formula?

3) Regarding the baseline subtraction: I am oriented towards single trial
brain connectivity analysis. Should I do baseline subtraction? The
experiment has around 2 sec fixation cross and then the stimulus appears
for 1 minute during which the subjects produce responses in self-paced
manner. Whenever they come up with a response the press the button and say
it. The epochs I will analyse are -1250 to -250 ms relative to the button
press. If I should do baseline correction should I use the fixation cross
interval or some resting eyes open intervals collected at the beginning of
the experiment.

4) ICA: I did some tests and ended up with AMICA for EOG artifact removal,
and then subsequently I used AAR to remove EMG artifact. Do you think this
a proper way to deal with the artifacts?

Please take into consideration it's my first effort in the field and
forgive my ignorance.

Thank you very much,
Mina
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