[Eeglablist] When to perform re-reference?

[Makoto Miyakoshi]

Dear Jerry,

> Well, this wiki page says average referencing before ICA could reduce the
rank by 1, which seems to be a bad thing.

Yeah, I thought so too. But I hear Jason Palmer, who wrote AMICA, say data
should be average referenced before ICA... I add Jason here again,
expecting to hear from him on this issue.

Makoto

On Thu, Jun 26, 2014 at 1:55 PM, Jerry Zhu <jerryzhu at siu.edu> wrote:

> 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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>>>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
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>>>
>>>
>>>
>>> --
>>> Brian Scally
>>>
>>
>>
>>
>> --
>> 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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