[Eeglablist] Importing BIOSEMI Data and Re-referencing to the Robust Average using PREP

[Makoto Miyakoshi]

Dear Matthew,

> EEGLAB provides a warning that failing to indicate a reference on
importation will add noise to the data.  Am I correct in understanding
that, regardless of this warning, if BIOSEMI is imported without indicating
a reference and then put through the PREP pipeline, that subtracting out
the robust average reference will negate this issue of noise?  That is what
I think is correct but I would like wiser heads to confirm it.

Basically yes.
Biosemi amps does not perform 'common mode noise rejection' itself, but it
lets users to perform it by re-referencing. For example, when I analyzed
Biosemi data which I forgot to re-reference, I encountered highly
non-stationary 60Hz noise that can't be treated with CleanLine at all.
However, this weird noise got disappeared when I applied re-referencing.

However, I said 'basically' because when you start thinking exact
cancellation of the common mode noise, channel rejections and interpolation
may affect the exactness (of course, still better than including noisy
channels). I believe that this deviation from the 'exact' cancellation is
negligible (without empirically testing it ...)

> Second, I have already imported all of my data using the mastoid
electrodes as the reference.  If I understand correctly, if I apply the
PREP pipeline to this imported and mastoid-referenced data, even after
re-referencing to the robust average, I would still be vulnerable to
contamination from a noisy mastoid electrode, as that noise would have been
added to all of the data.

Yes, I agree with you.

> Or would re-referencing to the average successfully negate that problem?

Yes, re-referencing to average will cancel the effect of the initial
reference.

Whew, thinking about these problems is a good learning experience for
myself too.

Makoto



On Tue, May 31, 2016 at 2:09 PM, Matthew Stief <ms2272 at cornell.edu> wrote:

> Hello,
>
> I have a question regarding the robust referencing approach of PREP and
> how it relates to the importation of BIOSEMI data that asks for an
> reference electrode when it is being imported.  For my data we used mastoid
> electrodes anticipating that these would be used as the reference on
> importation.
>
> EEGLAB provides a warning that failing to indicate a reference on
> importation will add noise to the data.  Am I correct in understanding
> that, regardless of this warning, if BIOSEMI is imported without indicating
> a reference and then put through the PREP pipeline, that subtracting out
> the robust average reference will negate this issue of noise?  That is what
> I think is correct but I would like wiser heads to confirm it.
>
> Second, I have already imported all of my data using the mastoid
> electrodes as the reference.  If I understand correctly, if I apply the
> PREP pipeline to this imported and mastoid-referenced data, even after
> re-referencing to the robust average, I would still be vulnerable to
> contamination from a noisy mastoid electrode, as that noise would have been
> added to all of the data.  Or would re-referencing to the average
> successfully negate that problem?  It would be convenient if I didn't have
> to start from scratch with the unimported data as the channel locations for
> each subject (109 of them) have been set up and they vary slightly by cap
> size so it would be some labor to make sure that that was all set up again
> correctly in the new pipeline of the raw unimported data.
>
> _________________________________________________________________
> Matthew Stief
> Human Development | Sex & Gender Lab | Cornell University
> http://www.human.cornell.edu/hd/sexgender
>
> One ought to know that on the one hand pleasure, joy, laughter, and games,
> and on the other, grief, sorrow, discontent, and dissatisfaction arise only
> from the brain. It is especially by it that we think, comprehend, see, and
> hear, that we distinguish the ugly from the beautiful, the bad from the
> good, the agreeable from the disagreeable.
> -Hippocrates
>
> Is the blood the element with which we think, or the air, or the fire? or
> perhaps nothing of the kind--but the brain may be the originating power of
> the perceptions of hearing and sight and smell, and memory and opinion may
> come from them, and science may be based on memory and opinion when they
> have attained fixity.
> -Plato
>
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-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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