[Eeglablist] Re-referrence to average and add Cz back

[Isaiah Innis]

Thank you all for your suggestions; I have used them to create a 'template'
dataset for channel locations. By editing the channel locations either
manually or using the code provided earlier I can properly put a 'Cz'
channel in the dataset.

 However, I am still running into the issue where Cz has a different
waveform depending on whether pop_interp was used or the  "add ref channel
back to data" option in pop_reref. This issue shows up even with datasets
that have been preprocessed/cleaned with ICA, so I don't think it's a
matter of bad channels.

Therefore, I am still uncertain as to which option is valid. My current
working assumption is that pop_reref includes 'Cz' in the average
computation, thereby producing different results. The wrinkle in this
hypothesis is that activity at all sites except 'Cz' is identical - only at
'Cz' is there a discrepancy. This can be seen in these images:

https://onedrive.live.com/redir?resid=A1398B0A4C8F85DE!3143&authkey=!ADQdX1b8aLVm9Vo&v=3&ithint=photo%2cpng
https://onedrive.live.com/redir?resid=A1398B0A4C8F85DE!3144&authkey=!AFhRR52ewq1woDc&v=3&ithint=photo%2cpng



Here is a link containing a sample dataset and the code I use for each of
the two options. I would greatly appreciate it if someone could confirm
what I'm witnessing and advise on what is wrong here (perhaps I'm missing
something obvious).


https://onedrive.live.com/redir?resid=A1398B0A4C8F85DE!3146&authkey=!ALCzmvm0xZVfAJk&ithint=folder%2cpng

Thank you,

2016-04-20 23:04 GMT-04:00 Makoto Miyakoshi <mmiyakoshi at ucsd.edu>:

> Dear Isaiah,
>
> > 1) There seem to be two options - interpolation using pop_interp and the
> checkbox to "add ref channel back to data" using pop_reref. They produce
> different results when used:
>
> https://onedrive.live.com/redir?resid=A1398B0A4C8F85DE!2206&authkey=!AMJUTORsc9y3ao4&v=3&ithint=photo%2cpng
> It seems from the discussion here that interpolation after rereferencing
> is the correct option - I assume because these functions differ in how they
> calculate Cz?
>
> I thought whichever works is fine...until I clicked the link. Wow. Why are
> they so different? Are you sure that you rejected all bad channels before
> the process?
>
> > 2) After interpolation I receive the following message: "Warning: some
> channels have the same label." Checking the chanlocs struct there are now
> two Cz entries, one marked as a data channel and one not. Is this a problem?
>
> I believe you can't have two channels with the same name.
>
> > Should I delete the non - data Cz?
>
> Yes, why not.
>
> > 3) When interpolating Cz, do I need to have a dataset with Cz from the
> same subject or can it be any dataset with Cz?
>
> I thought that's easier if you are using EEGLAB. Have one 'template
> subject' who has all the channels, and always refer to the one to
> interpolate whatever is 'missing' compared with it.
>
> > Do I have to manually edit pop_chanedit to get Cz in a dataset?
>
> Whichever more convenient for you (and works) is fine.
>
> Makoto
>
>
>
> On Mon, Apr 18, 2016 at 1:32 PM, Isaiah Innis <isainnis at umail.iu.edu>
> wrote:
>
>> ---------- Mensaje reenviado ----------
>> From: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>> To: Fang-Yu Chang <hardheard101 at gmail.com>, EEGLAB List <
>> eeglablist at sccn.ucsd.edu>
>> Cc:
>> Date: Wed, 13 Apr 2016 12:25:54 -0700
>> Subject: Re: [Eeglablist] Re-referrence to average and add Cz back
>> Dear Fang-Yu,
>>
>> > If I would like to add Cz back with computing average, should I operate
>> " 're-reference'-> 'Compute average reference' with 'add current reference
>> channel back to the data' ?"
>>
>> Compute average reference first and then interpolate Cz next.
>>
>> > I would like to ask more question. You mentioned one(any) channel need
>> to be discarded after computing average. How do I discard one channel? I
>> operated " 'Edit' -> 'Channel locations' -> 'delete channel' " by EEGLAB,
>> but it didn't work. I'm not sure it is right to operate like this.
>>
>> Yes this is confusing. Sorry for that. What you need to do is to 'Select
>> data' and not channel editing. Select a channel to discard from the list,
>> check the box to perform rejection for the selected (otherwise it'll leave
>> the selected).
>>
>> Makoto
>>
>> On Tue, Apr 12, 2016 at 11:44 PM, Fang-Yu Chang <hardheard101 at gmail.com>
>>  wrote:
>>
>>> Dear Makoto,
>>>
>>> Thanks for your reply. I think I just confused with adding Cz back and
>>> interpolating Cz, and Cz dose exist in my dataset.
>>> If I would like to add Cz back with computing average, should I operate
>>> " 're-reference'-> 'Compute average reference' with 'add current reference
>>> channel back to the data' ?"
>>>
>>> I would like to ask more question. You mentioned one(any) channel need
>>> to be discarded after computing average. How do I discard one channel? I
>>> operated " 'Edit' -> 'Channel locations' -> 'delete channel' " by EEGLAB,
>>> but it didn't work. I'm not sure it is right to operate like this.
>>> Thanks for your help in  advanced.
>>>
>>> Sincerely,
>>> Fang-Yu Chang
>>>
>>
>>
>> Hello EEGLab list:
>>
>> I still have some confusion regarding Re-referrencing to average and
>> adding Cz back for an EGI system.
>>
>> 1) There seem to be two options - interpolation using pop_interp and the
>> checkbox to "add ref channel back to data" using pop_reref. They produce
>> different results when used:
>>
>>
>> https://onedrive.live.com/redir?resid=A1398B0A4C8F85DE!2206&authkey=!AMJUTORsc9y3ao4&v=3&ithint=photo%2cpng
>>
>> It seems from the discussion here that interpolation after rereferencing
>> is the correct option - I assume because these functions differ in how they
>> calculate Cz?
>>
>> 2) After interpolation I receive the following message: "Warning: some
>> channels have the same label." Checking the chanlocs struct there are now
>> two Cz entries, one marked as a data channel and one not. Is this a
>> problem? Should I delete the non - data Cz? When importing channel
>> locations for our 64 channel system, there are 68 values in chanlocs; after
>> interpolation there are 69.
>>
>>
>> 3) When interpolating Cz, do I need to have a dataset with Cz from the
>> same subject or can it be any dataset with Cz? Do I have to manually edit
>> pop_chanedit to get Cz in a dataset?  I have been using datasets from the
>> same subject, but this issue has made me question that.
>>
>>
>>
>> Thank you in advance,
>> --
>> Isaiah Innis
>> Indiana University '13
>> EEG Technician, IUB IRF
>>
>>
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>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>



-- 
Isaiah Innis
Indiana University '13
EEG Technician, IUB IRF
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