[Eeglablist] When to perform re-reference?

[Jerry Zhu]

Well, this wiki page says average referencing before ICA could reduce the
rank by 1, which seems to be a bad thing.
So I guess, average reference should go after ICA.

http://sccn.ucsd.edu/wiki/Chapter_09:_Decomposing_Data_Using_ICA
close to the end of page
"When computing average reference on n-channel data, the rank of the data
is reduced to n-1. Why? Because the sum of the potential is 0 at all time
points, the last channel activity is equal to minus the sum of the others.
ICA does not behave well in this (*rank-deficient*) condition."

--
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 Mon, Jun 23, 2014 at 11:56 AM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
wrote:

> Dear Brian,
>
> The average referencing is not affected by epoch rejection (assuming that
> bad EEG is restricted to the epochs that are rejected) or component
> rejection. In your case, average referencing can be done either before or
> after two ICAs.
>
> I'm still waiting to hear from Jason though whether it's better to do
> average referencing before ICA and if so, why.
>
> Makoto
>
>
>
> On Thu, Jun 19, 2014 at 8:37 AM, Brian Scally <scallybrian at gmail.com>
> wrote:
>
>> Hi there,
>>
>> I have been following the discussion. So it is recommended to
>> re-reference to average after removing channels/epochs and right before
>> running ICA. Suppose I plan on running ICA twice: the first time to
>> identify epochs that are affected by improbable components, after which the
>> epochs will be removed. The second time would be to remove actual
>> components. Do I need to re-reference before the first, or will before the
>> second suffice?
>>
>> Cheers,
>> Brian
>>
>>
>> On 19 June 2014 00:56, Makoto Miyakoshi <mmiyakoshi at ucsd.edu> wrote:
>>
>>> yes.
>>>
>>>
>>> On Wed, Jun 18, 2014 at 3:45 PM, 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.
>>>>>>
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>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Makoto Miyakoshi
>>>>> Swartz Center for Computational Neuroscience
>>>>> Institute for Neural Computation, University of California San Diego
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Makoto Miyakoshi
>>> Swartz Center for Computational Neuroscience
>>> Institute for Neural Computation, University of California San Diego
>>>
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>>
>>
>>
>> --
>> Brian Scally
>>
>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>
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