[Eeglablist] PREP pipeline questions

[Makoto Miyakoshi]

Dear Adrien,

> Is there a way to import the data without referencing

This is possible. Just import the data.

> and use the pipeline to remove bad channels and reference with the robust
algorithm?

I thought that's what PREP does--otherwise what's the point?

> Or should I reference to common average at import and then run the PREP
pipeline? Would the latter not still introduce artefacts if there is a
noisy channel?

You don't need to reference when you import them. Re-referencing can be
done anytime after importing. Maybe that EEGLAB warning for biosemi is a
bit misleading.

> The high-pass filter of the prep pipeline is said to be temporary so did
I understand correctly that if the detrend high-pass is set to 1Hz I can
still high-pass filter later at 0.5Hz for example?

When PREP returns the data, they are NOT high-pass filtered at all.

> Lastly, I’d like to use PREP pipeline with the command line (so as to run
it for multiple subjects in a row), does anyone have an example option file
that can be adapted and used to call the prep function?

Did you check if there is sample code for batch process in the downloaded
packet?

Makoto

On Mon, Dec 21, 2015 at 5:20 AM, Adrien Martel <amartel at tcd.ie> wrote:

> Dear all,
>
> I’m trying to use the PREP pipeline to preprocess my data and I have yet
> another question concerning referencing.
> As stated in the paper every form of referencing is problematic and the
> most commonly used (common average) can introduce huge artefacts if only
> one channel is noisy. The solution is to first remove bad channels.
> I’m wondering how to achieve this if during the import of BIOSEMI data a
> reference is required. Is there a way to import the data without
> referencing and use the pipeline to remove bad channels and reference with
> the robust algorithm? Or should I reference to common average at import and
> then run the PREP pipeline? Would the latter not still introduce artefacts
> if there is a noisy channel?
> The converter given by BIOSEMI does not solve the problem as it still
> requires a form of referencing.
>
> The high-pass filter of the prep pipeline is said to be temporary so did I
> understand correctly that if the detrend high-pass is set to 1Hz I can
> still high-pass filter later at 0.5Hz for example?
>
> Lastly, I’d like to use PREP pipeline with the command line (so as to run
> it for multiple subjects in a row), does anyone have an example option file
> that can be adapted and used to call the prep function?
>
> Thanks very much,
> Adrien
>
>
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-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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