[Eeglablist] Rank before ICA

[Makoto Miyakoshi]

Dear Eric,

The difference between with- and without-including the initial reference
(i.e. zero-filled channel) is investigated here.
I appreciate you paying close attention to confirm the basics!

https://sccn.ucsd.edu/wiki/Makoto's_preprocessing_pipeline#Why_should_we_add_zero-filled_channel_before_average_referencing.3F_.2808.2F09.2F2020_Updated.3B_prayer_for_Nagasaki.29

> This approach should not be affected by whether it is ERP or resting
state data, right?

Reference issue is independent of whether the data is epoched or continuous.

Makoto

On Tue, Aug 24, 2021 at 11:39 AM Eric HG <erichg2013 at gmail.com> wrote:

> Thanks for the prompt reply!
>
> Would adding a zero-filled channel (only zeros) give some problems with
> the average reference?
>
> Specifically, would the average of all channels when including the
> zero-filled channel give a lower average, which may lead to increased noise
> in the data?
>
> This approach should not be affected by whether it is ERP or resting state
> data, right?
>
> Best regards,
>
> Eric
>
> On Tuesday, August 24, 2021, Iversen, John <jiversen at ucsd.edu> wrote:
>
>> Eric,
>>
>> FYI, Makoto Miyakoshi has written about this, and wrote a plugin as well.
>> See
>> https://sccn.ucsd.edu/wiki/Makoto's_preprocessing_pipeline#Re-reference_the_data_to_average_.2808.2F02.2F2020_Updated.29
>>
>>
>> and
>>
>> https://sccn.ucsd.edu/eeglab/plugin_uploader/plugin_list_all.php
>>
>> His preprocessing page has a wealth of information.
>>
>> Your implementation matches Makoto's fullRankAveRef.m :
>>
>> % Apply average reference after adding initial reference
>> EEG.nbchan = EEG.nbchan+1;
>> EEG.data(end+1,:) = zeros(1, EEG.pnts);
>> EEG.chanlocs(1,EEG.nbchan).labels = 'initialReference';
>> EEG = pop_reref(EEG, []);
>> EEG = pop_select( EEG,'nochannel',{'initialReference'});
>>
>>
>> The only difference is you are using epoched data, while his was designed
>> for continuous data. I see no functional difference between referencing
>> before or after epoching, since it's done on a point-by-point basis.
>>
>> FYI, comments on whether to epoch before of after ICA are here:
>> https://sccn.ucsd.edu/wiki/Makoto's_preprocessing_pipeline#Epoch_data_to_-1_to_2_sec_.2809.2F11.2F2019_updated.29
>>
>> Best,
>>
>> John
>>
>> On Aug 24, 2021, at 4:21 AM, Eric HG via eeglablist <
>> eeglablist at sccn.ucsd.edu> wrote:
>>
>> Dear Eeglablist,
>>
>> I have had some troubles with the rank of the data after re-referencing to
>> average.
>>
>> I have therefore used the following code before ICA:
>>
>> rank_one = rank(EEG.data(:,:));
>>    EEG.nbchan = EEG.nbchan+1;
>>    EEG.data(EEG.nbchan,:,:) = zeros(1, EEG.pnts, EEG.trials);
>>    EEG.chanlocs(EEG.nbchan).labels = 'Ref';
>>    EEG = pop_reref(EEG, []);
>>    EEG = pop_select( EEG,'nochannel',{'Ref'});
>>    rank_two = rank(EEG.data(:,:));
>>
>> Is this a feasible way to overcome this?
>>
>> It gives good results with ICA decomposition.
>>
>> Best regards,
>>
>> Eric
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>>