[Eeglablist] Auditory steady-state response and ERP analysis pre-processing steps

[Makoto Miyakoshi]

Dear Michael,

> In particular, I am uncertain about the ordering of steps such as
interpolating bad channels before or after re-referencing or ICA

Read Nima's paper.
http://journal.frontiersin.org/article/10.3389/fninf.2015.00016/abstract

> if particular steps work for some analysis strategies but not others
(e.g. if a preprocessing step would work fine for time-frequency analysis
but not be appropriate for source localization). Any feedback is much
appreciated!

Standard filtering policy does not go well with variations of
(multivariate) Granger Causality analysis. Many says 1-Hz high-pass filter
we do is no good for analyzing averaged ERP. High-pass filter should be
done before CleanLine.

> 0. Start with 128-channel EEG from EGI HydroCel Geodesic Sensor Net, with
flags indicating events and epochs around events predefined (-0.1s to 0.9s
around the events).

Use -1 to 2 sec to epoch. This is because you want to use 3-Hz 3-cycle
wavelet later. It does not matter even if this causes overlap of the
trials; it always happen as long as you use sliding windows.

Also, you may want to use continuous data as long as it is cleaned.

> 1. Keep all valid (even if lots of line noise) channels in dataset, only
remove channels which clearly have no physiological information.

I agree, unless you discard all the channels.

> 2. Epoch the data, reject bad epochs by eye (significant movement or
rare, not-stereotyped artifacts)

No, make every effort not to reject epochs due to eye activity (saccade,
blink, etc) This is because ICA is best capable of identifying them. Save
your trials.

> 3. Run ICA on epoched data.

Make sure that you clean your data before running ICA.

> 4. Reject components related to blinks, stereotypical muscle activity,
and 60 Hz noise, and EKG artifacts.

No, do not reject anything. You'll create STUDY later, in doing which ICs
with 15% residual variance and those with outside-brain dipoles are kicked
out. Usually this will reject around 70% of your ICs (depending on your
data).

> 5. Reconstruct sensor-level signals from remaining ICA weights

It's a forward projection. Fine.

> 6. Re-reference all cleaned EEG channels to the average reference

Nima emphasized that when you use average reference you should choose only
clean channels to include. See his paper for details. Jason also said
average reference should be done before ICA, but it will cause rank
reduction (and does not change the results except for zero-centering the
scalp maps) so I would recommend you do it after ICA.

> 7. Interpolate (using spherical splines from neighboring electrodes) any
channels that were rejected in step 1.

No it's not necessary if you stick to ICA-centric analysis to the end.

> 8. Calculate ERPs, time-frequency analysis, source localization

Use STUDY for the group-level analysis.

Additional info can be found here.
http://sccn.ucsd.edu/wiki/Makoto's_preprocessing_pipeline

Makoto

On Tue, Aug 18, 2015 at 11:54 AM, Michael Boyle <mrboyle at live.unc.edu>
wrote:

> Dear EEGLABers,
>
> I would like to know whether or not the particular pre-processing steps
> listed are recommended for ERP analysis, time-frequency analysis (wavelet
> amplitude spectrograms or DFT spectrograms, ITPC), and source localization
> analysis.
>
> In particular, I am uncertain about the ordering of steps such as
> interpolating bad channels before or after re-referencing or ICA, or if
> particular steps work for some analysis strategies but not others (e.g. if
> a preprocessing step would work fine for time-frequency analysis but not be
> appropriate for source localization). Any feedback is much appreciated!
>
> 0. Start with 128-channel EEG from EGI HydroCel Geodesic Sensor Net, with
> flags indicating events and epochs around events predefined (-0.1s to 0.9s
> around the events).
> 1. Keep all valid (even if lots of line noise) channels in dataset, only
> remove channels which clearly have no physiological information.
> 2. Epoch the data, reject bad epochs by eye (significant movement or rare,
> not-stereotyped artifacts)
> 3. Run ICA on epoched data.
> 4. Reject components related to blinks, stereotypical muscle activity, and
> 60 Hz noise, and EKG artifacts.
> 5. Reconstruct sensor-level signals from remaining ICA weights
> 6. Re-reference all cleaned EEG channels to the average reference
> 7. Interpolate (using spherical splines from neighboring electrodes) any
> channels that were rejected in step 1.
> 8. Calculate ERPs, time-frequency analysis, source localization
>
> Best and many thanks,
> Michael
>
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-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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