[Eeglablist] When to perform re-reference?

[Stephen Politzer-Ahles]

Hi Jerry,

If you're using average reference, bad channels should definitely be taken
care of first, otherwise they'll affect the reference. I've also heard it
recommended that referencing should be done before ICA (see e.g.
http://sccn.ucsd.edu/pipermail/eeglablist/2013/006511.html). I've heard
mixed things about channel interpolation and ICA (see e.g. the message
linked above).

As for removing bad epochs, it depends what you mean by bad epochs. ICA
shouldn't include some kinds of noise, so for example you should remove
periods of data where the participant was resting between blocks or things
like that. But typical artifacts, like blinks, can probably be left in
since they will probably result in a separate ICA component (especially if
you mean to remove that component later).  So my recommended order would
probably be: interpolate channels, re-reference, run ICA, remove bad epochs.

Best,
Steve



Stephen Politzer-Ahles
New York University, Abu Dhabi
Neuroscience of Language Lab
http://www.nyu.edu/projects/politzer-ahles/


On Thu, Jun 19, 2014 at 2:45 AM, Jerry Zhu <jerryzhu at siu.edu> wrote:

> Hi Makoto,
> Thank you again for your reply.
>
> Did you mean "averaging AFTER removing bad epoches" in your sentence "you
> should apply average referencing AFTER removing bad channels."?
>
> So here are my processing:
> 1) re-reference  (from Cz to average in my case)
> 2) remove bad epoches
> 3) interpolate bad channels
> 4) ICA
>
> Sounds like you would recommend the order: 2143?
>
> Looking forward to your and others inputs!
> Thanks all!
> Jerry
>
> --
> Jian Zhu, M.A.
> Brain and Cognitive Sciences
> Department of Psychology
> Southern Illinois University Carbondale
> Web: http://zhupsy.com
>
> We have two halves in the brain: left and right. Nothing is right in the
> left. Nothing is left in the right.
>
>
> On Wed, Jun 18, 2014 at 1:38 PM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> wrote:
>
>> Dear Jason,
>>
>> I remember you said that average reference should be applied before ICA,
>> but I did not understand exactly why. Could you comment on this?
>>
>> Jerry, you should apply average referencing AFTER removing bad channels.
>>
>> I don't think it makes big differences between average referencing before
>> or after interpolation. However we don't necessarily recommend
>> interpolation before ICA.
>>
>> Makoto
>>
>>
>> On Tue, Jun 17, 2014 at 12:20 PM, Jerry Zhu <jerryzhu at siu.edu> wrote:
>>
>>> Hi all,
>>> At which stage do you re-reference your data? It was suggested do re-ref
>>> before ICA (http://sccn.ucsd.edu/pipermail/eeglablist/2011/003795.html).
>>> How about re-ref before/after bad epochs rejection and bad channel
>>> interpolation? The note here  (
>>> ftp://ftp.egi.com/pub/documentation/technotes/SplineInterpolation.pdf)
>>> suggests after interpolation. ("Since the interpolated potentials can be
>>> used to better approximate the average reference (Junghofer et al., 1999),
>>> it may be somewhat advantageous to compute the interpolated potentials
>>> directly from the measured data, in which case the voltages below are best
>>> thought of as referring to these measured potentials")
>>>
>>> What is your experience? Thanks for your sharing and suggestions!
>>>
>>> Jerry
>>> --
>>> Jian Zhu, M.A.
>>> Brain and Cognitive Sciences
>>> Department of Psychology
>>> Southern Illinois University Carbondale
>>> Web: http://zhupsy.com
>>>
>>> We have two halves in the brain: left and right. Nothing is right in the
>>> left. Nothing is left in the right.
>>>
>>> _______________________________________________
>>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
>>> To unsubscribe, send an empty email to
>>> eeglablist-unsubscribe at sccn.ucsd.edu
>>> For digest mode, send an email with the subject "set digest mime" to
>>> eeglablist-request at sccn.ucsd.edu
>>>
>>
>>
>>
>> --
>> Makoto Miyakoshi
>> Swartz Center for Computational Neuroscience
>> Institute for Neural Computation, University of California San Diego
>>
>
>
> _______________________________________________
> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
> To unsubscribe, send an empty email to
> eeglablist-unsubscribe at sccn.ucsd.edu
> For digest mode, send an email with the subject "set digest mime" to
> eeglablist-request at sccn.ucsd.edu
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://sccn.ucsd.edu/pipermail/eeglablist/attachments/20140619/1599fbd2/attachment.html>