[Eeglablist] How to save the normalized data that we see in scroll data display?

[Makoto Miyakoshi]

Dear Iman,

> When one would want to do grand averaging over subjects this issue may cause
> a problem in averaging ( a subject with thinner  scalp thickness has more
> share on the grand average data)

This is an interesting point. You are right. Scalp EEG is a measure
including all of these factors.

Tim, do you know what we should do if we care about this issue? ICA
does not explain signal decay in volume conduncance, does it?

Makoto

2012/11/7 Iman M.Rezazadeh <irezazadeh at ucdavis.edu>:
> Thanks Tim!
>
> So, you are saying we should plot topomap before normalization using zscore
> for each channel...
>
> The reason behind my question is different subjects have different scalp and
> skull thickness which effects on the magnitude of EEG at electrode level.
> When one would want to do grand averaging over subjects this issue may cause
> a problem in averaging ( a subject with thinner  scalp thickness has more
> share on the grand average data)
>
> Any thought?
>
> Best,
>
> Iman
>
>
>
> From: Tim Mullen [mailto:mullen.tim at gmail.com]
> Sent: Wednesday, November 07, 2012 11:10 PM
> To: Iman M.Rezazadeh
> Cc: Edward Justin Modestino; EEGLAB List
>
>
> Subject: Re: [Eeglablist] How to save the normalized data that we see in
> scroll data display?
>
>
>
> Yes, temporal z-normalization will generally change the voltage topography,
> since each electrode's mean voltage (DC offset) is removed and each
> electrode's voltage has been independently rescaled by a different quantity.
>
>
>
> Note that we are not describing *spatial* z-normalization, which, for a
> given time point, is equivalent to performing a common average reference
> (subtracting spatial mean from each electrode) followed by rescaling all
> electrodes by the same quantity (spatial stdev). This will preserve relative
> voltage between pairs of electrodes within a constant factor (pairwise
> voltage difference is also rescaled by the spatial stdev) -- and, if data is
> already CAR, does not affect pairwise voltage ratios.
>
>
>
> In any case, I can't see why one would want to temporally normalize before
> plotting voltage maps.
>
>
>
> Tim
>
>
>
> On Wed, Nov 7, 2012 at 3:01 PM, Iman M.Rezazadeh <irezazadeh at ucdavis.edu>
> wrote:
>
> Hi,
>
>
>
> So, I have one question here:
>
> If you normalize the data using zscore , then at each time point the
> topography of original data and normalized one will be different since for
> topo map the voltage of adjacent electrodes are also important?
>
> Could you please clarify more ...
>
>
>
> Best,
>
> Iman
>
>
>
> Iman M.Rezazadeh, PhD
>
> Postdoctoral Research Fellow
>
> Center for Mind and Brain
>
> University of California, Davis
>
> irezazadeh at ucdavis.edu
>
> Cell:310-490-1808
>
> Skype: Imanmr
>
>
>
>
>
> From: eeglablist-bounces at sccn.ucsd.edu
> [mailto:eeglablist-bounces at sccn.ucsd.edu] On Behalf Of Edward Justin
> Modestino
> Sent: Tuesday, November 06, 2012 6:50 AM
> To: Tim Mullen
> Cc: EEGLAB List
> Subject: Re: [Eeglablist] How to save the normalized data that we see in
> scroll data display?
>
>
>
> Yes, this code works:
> normdata = zscore(EEG.data,0,2);
> EEG.data = normdata;
>
> On Mon, Nov 5, 2012 at 9:07 PM, Tim Mullen <mullen.tim at gmail.com> wrote:
>
> As I posted earlier, it's simple to compute:
>
>
>
> normdata = zscore(EEG.data,0,2);
>
>
>
> No need to reshape, etc. This will normalize each channel and each epoch
> independently.
>
>
>
> Tim
>
>
>
> On Fri, Nov 2, 2012 at 11:23 AM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> wrote:
>
> Dear Edward,
>
>> Error: Expression or statement is incorrect--possibly unbalanced (, {, or
>> [.
>
> Oops. The line must be
>
>
> tmp = reshape(EEG.data, [size(EEG.data, 1) size(EEG.data, 2) *
>
> size(EEG.data, 3) ]);
>
> The last parenthesis was missing.
> By the way I learned a shortcut for it yesterday, and
>
> tmp = EEG.data(:,:);
>
> should also work.
>
> Makoto
>
>
> 2012/11/2 Edward Justin Modestino <edward.modestino at gmail.com>:
>> Makoto,
>> I need to be able to get this working as well. I tried it and got the
>> following error.
>
>>
>>
>>>> tmp = reshape(EEG.data, [size(EEG.data, 1) size(EEG.data, 2) *
>> size(EEG.data, 3) ];
>> tmp = zscore(tmp, 0, 2);
>> tmp = reshape(tmp, size(EEG.data));
>> EEG.data = tmp;
>
>> ??? tmp = reshape(EEG.data, [size(EEG.data, 1) size(EEG.data, 2) *
>>                                                                   |
>> Error: Expression or statement is incorrect--possibly unbalanced (, {, or
>> [.
>
>>
>>
>> On Thu, Nov 1, 2012 at 1:21 PM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>> wrote:
>>>
>>> Dear nabaraj,
>>>
>>> Check out the function zscore.
>>> If your data are epoched, then the code should be something like
>>>
>>> tmp = reshape(EEG.data, [size(EEG.data, 1) size(EEG.data, 2) *
>>> size(EEG.data, 3) ];
>>> tmp = zscore(tmp, 0, 2);
>>> tmp = reshape(tmp, size(EEG.data));
>>> EEG.data = tmp;
>>>
>>> This should normalizes each channel.
>>>
>>> Makoto
>>>
>>> 2012/10/29 nabaraj dahal <nabarajdahal at gmail.com>:
>>> > Dear list member,
>>> > I wish to save the normalized data of all channels for further
>>> > processing.
>>> > Is there any way I can save the normalized data of all channels that we
>>> > see
>>> > in scroll data display?
>>> > I would be grateful for you help.
>>> >
>>> > Best Regards,
>>> > Nab
>>> >
>>> > _______________________________________________
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>>>
>>>
>>>
>>> --
>>> Makoto Miyakoshi
>>> JSPS Postdoctral Fellow for Research Abroad
>>> Swartz Center for Computational Neuroscience
>>> Institute for Neural Computation, University of California San Diego
>>> _______________________________________________
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>>
>>
>>
>
>
> --
> Makoto Miyakoshi
> JSPS Postdoctral Fellow for Research Abroad
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
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>
>
>
>
>
>
>
> --
>
> ---------  αντίληψη -----------
>
>
>
>
> --
> Edward Justin Modestino, Ph.D.
> Neuroscientist/Faculty
> Atlantic University
>
>
>
>
>
> --
> ---------  αντίληψη -----------
>
>
> _______________________________________________
> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
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-- 
Makoto Miyakoshi
JSPS Postdoctral Fellow for Research Abroad
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego