[Eeglablist] Premature infants preprocessing pipeline with EEGLab tools

[Velu Prabhakar Kumaravel]

Hi Efthymios,

Yes, it is possible to deactivate flat line detection in the GUI of the
plugin. Alternatively, you can use the following command:

[ALLEEG,EEG,CURRENTSET,com] = pop_NEAR(ALLEEG,EEG,CURRENTSET,
'isFlat',0,'isOutlier',1,'cutoff_lof',2.5,'dist_metric','seuclidean','isAdapt',10,'isMuscle',0);

Setting '*isFlat*' to 0 disables the flat-line detection. Ensure you
calibrate '*cutoff_lof'*, which is set to 2.5 by default.

As a side note, LOF is also now available in MNE-Python (version 1.7
onwards) to detect noisy sensors in EEG (and potentially in MEG, as well).

Best wishes on your project!

-Velu

On Wed, 7 Aug 2024 at 11:22, Marco Buiatti <marco.buiatti at unitn.it> wrote:

> Hi Efthymios,
>
> I think it would be feasible to avoid the removal of flat lines in NEAR. I
> put you in contact with Velu Kumaravel (cc), the developer of NEAR, maybe
> he can help you.
>
> Best,
>
> Marco
>
> On Mon, 5 Aug 2024 at 11:09, Efthymios Papatzikis <efp331 at mail.harvard.edu>
> wrote:
>
>> Dear Marco,
>>
>> Thank you for this email. My inquiry still stands indeed, although I have
>> managed since then to create an analysis and statistical preprocessing
>> configuration of steps for my specific needs.
>>
>> Thank you for sharing your pipeline, though. Very informative and
>> particularly the ASR configuration (TuneASR) part. I will definitely study
>> this as it will provide me valuable input. However, I see your pipeline
>> does exactly what I am trying to avoid; that is, reject flat lines instead
>> of accounting for them in the preprocessing pipeline. This is a main
>> characteristic (i.e., continuity/discontinuity ratio) of premature
>> infants that I am working with in my project, and all along, from the very
>> beginning, I was trying to find a pipeline pre-configured for that. I
>> couldn’t, so I tried to create mine. Still needs some fine-tuning of
>> course, but now it seems to do what is meant for.
>>
>> Happy to discuss more if you are interested.
>>
>> Best,
>> Efthymios
>>
>> On 5 Aug 2024, at 10:47, Marco Buiatti <marco.buiatti at unitn.it> wrote:
>>
>> Dear Efthymios,
>>
>> If your request is still ongoing, I suggest you to also consider NEAR,
>> our pipeline for artifact removal in newborn and infant EEG data, available
>> as an EEGLAB plugin:
>> https://urldefense.com/v3/__https://github.com/vpKumaravel/NEAR__;!!Mih3wA!AZai2vola0pJbrQZfeO5oM3y7AIJISYbwB1qvPt3hsYNaeoBIj0Udl8u-ZpVISiK98rNQq-tU2-om63UuJfei2G7n0X-$ 
>>
>> Best,
>>
>> Marco
>>
>> On Tue, 19 Mar 2024 at 22:41, Dr. Efthymios Papatzikis via eeglablist <
>> eeglablist at sccn.ucsd.edu> wrote:
>>
>>> Dear List,
>>>
>>> Is there anyone who has experience with EEGLab on data from premature
>>> infants, and can suggest a preprocessing pipeline or relevant published
>>> articles where EEGLab tools have been used to preprocess the data?
>>>
>>> Any suggestions more than welcome.
>>>
>>> Dr. Efthymios Papatzikis
>>> Infant Brain Development
>>> Oslo Metropolitan University, Norway
>>>
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>>
>>
>> --
>> Marco Buiatti
>>
>> Baby Lab & Neonatal Neuroimaging Unit
>> Center for Mind/Brain Sciences
>> University of Trento,
>> Piazza della Manifattura 1, 38068 Rovereto (TN), Italy
>> E-mail: marco.buiatti at unitn.it
>> Phone: +39 0464-808178
>> https://urldefense.com/v3/__https://sites.google.com/a/unitn.it/marcobuiatti/__;!!Mih3wA!AZai2vola0pJbrQZfeO5oM3y7AIJISYbwB1qvPt3hsYNaeoBIj0Udl8u-ZpVISiK98rNQq-tU2-om63UuJfei6sHy00R$ 
>> https://urldefense.com/v3/__https://r1.unitn.it/babylab/__;!!Mih3wA!AZai2vola0pJbrQZfeO5oM3y7AIJISYbwB1qvPt3hsYNaeoBIj0Udl8u-ZpVISiK98rNQq-tU2-om63UuJfei8KNJceZ$ 
>> ***********************************************
>>
>>
>>
>
> --
> Marco Buiatti
>
> Baby Lab & Neonatal Neuroimaging Unit
> Center for Mind/Brain Sciences
> University of Trento,
> Piazza della Manifattura 1, 38068 Rovereto (TN), Italy
> E-mail: marco.buiatti at unitn.it
> Phone: +39 0464-808178
> https://urldefense.com/v3/__https://sites.google.com/a/unitn.it/marcobuiatti/__;!!Mih3wA!AZai2vola0pJbrQZfeO5oM3y7AIJISYbwB1qvPt3hsYNaeoBIj0Udl8u-ZpVISiK98rNQq-tU2-om63UuJfei6sHy00R$ 
> https://urldefense.com/v3/__https://r1.unitn.it/babylab/__;!!Mih3wA!AZai2vola0pJbrQZfeO5oM3y7AIJISYbwB1qvPt3hsYNaeoBIj0Udl8u-ZpVISiK98rNQq-tU2-om63UuJfei8KNJceZ$ 
> ***********************************************
>