[FieldTrip] preprocessing procedures for ECoG/iEEG data

Vitória Piai v.piai.research at gmail.com
Thu Feb 2 10:45:18 CET 2017

Hi Tim,

The answers to your questions will depend a lot on what you're planning 
on doing later.

For 1), again it depends. If you're mainly interested in high gamma, it 
doesn't really matter that much since you'll do spectral decomposition 
later on. You could demean the data and not use any filters (or maybe a 
low-pass if you want to get some help with artifact rejection).

For 2) here some more recent references that may help. The bottom line 
is, as David said, all methods have prons and cons. Choose wisely 
depending on what you want to be able to claim about your data!
Mercier, M. R., Bickel, S., Megevand, P., Groppe, D. M., Schroeder, C. 
E., Mehta, A. D., & Lado, F. A. (2017). Evaluation of cortical local 
field potential diffusion in stereotactic electro-encephalography 
recordings: a glimpse on white matter signal. NeuroImage, 147, 219–232.
Arnulfo, G., Hirvonen, J., Nobili, L., Palva, S., & Palva, J. M. (2015). 
Phase and amplitude correlations in resting-state activity in human 
stereotactical EEG recordings. NeuroImage, 112, 114–127.
Shirhatti, V., Borthakur, A., & Ray, S. (2016). Effect of reference 
scheme on power and phase of the local field potential. Neural 
Computation, 28, 882–913.
Trongnetrpunya, A., Nandi, B., Kang, D., Kocsis, B., Schroeder, C. E., & 
Ding, M. (2016). Assessing granger causality in electrophysiological 
data: removing the adverse effects of Common Signals via Bipolar 
Derivations. Frontiers in Systems Neuroscience, 9: 189.

Since you're mentioning high gamma, I'm assuming you have stimuli being 
presented and you want to look at changes in high gamma as a function of 
those. In that case, I guess you have a good idea what your time windows 
will be like. So for 3) your suggestion would be a good way to go. What 
I usually do is to segment longer chunks of data than my narrow time 
windows of interest, mark the artifacts but do not reject any trials 
yet. I then save the artifacts and once I finally settle on what my time 
windows will be, I exclude trials with artifacts within that time window.
- ft_databrowser will allow you to mark and save artifacts, 
ft_rejectartifact will allow you to remove trials containing the artifacts.

Good luck,

On 1/30/2017 11:10 PM, Tim Meehan wrote:
> Hello all,
> I am a new user of fieldtrip and new to analyzing electrophysiological 
> data. I have familiarized myself with some basics of preprocessing of 
> EEG data, but I would like to know if there are special considerations 
> for dealing with ECoG/iEEG data -- our dataset has recordings from 
> both subdural surface electrodes and depth electrodes, sampled at 
> 2kHz. We are initially most interested in extracting the high-gamma 
> band (70-150 Hz) envelope as a measure of local activity.
> First a general question: is there anyone who could point me to or 
> provide me with a preprocessing procedure in fieldtrip that is 
> tailored for ECoG/iEEG? I've perused the ECoG section in the wiki but 
> there is no information on preprocessing there.
> If this is too vague, some specific questions I have are:
> 1) What cutoffs do people tend to use for low and high-pass filters?
> 2) What is your choice for re-referencing, if any? Our initial 
> reference/ground are the left and right mastoids. I have seen papers 
> that re-reference to the nearest neighbor. I think I need to use 
> ft_apply_montage to do this, but beyond that I could use some guidance.
> 3) At what point do you epoch into trials? My guess is after 
> high/low-pass filtering and re-referencing but before artifact 
> detection and removal?
> Any feedback on these would be very much appreciated. If you need more 
> details please let me know.
> Thanks!
> Tim
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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