[Eeglablist] File editing and epoching

[Elia Valentini]

Dear Tarik,

On 2 October 2012 06:52, Tarik S Bel-Bahar <tarikbelbahar at gmail.com> wrote:

> Hi Ella,
>
> Just a few quick comments, hope these comments help, good luck with the
> process, and let the list know of your success.
>
> 1. if boundaries are added because of rejection of artifactual periods,
> you probably want to keep them in.
> If you are trying to get all the epochs out, and then you will reject some
> of them, then see point #2.
>
> 2. If you use the "cleaned" data with "extra boundaries due to cleaning"
> to generate ICA,
> then you should then apply the IC weights to your pre-ICA continuous data
> (as long it has the same number of channels as the file that went into the
> ICA)
>

 My ICA-cleaned data was processed without extracephalic electrodes (my
impression is that without those electrodes I obtain a better
decomposition). This would imply to either re-run ICA with these electrodes
or exclude them from the pre-ICA continuous data.

2.5. see some recent discussions on the list on topics of ICA and cleaning
> ( in the last month).
>
> OK


> 3. In your step #5 I assume you mean remove baseline of all channels, for
> continuous data.
>
> Yes I do


> 4. keep in mind that you don't have to reject components if you focus on
> analyzing the ICs.
>
> I would prefer to keep my data analysis approach as similar as possible
with the literature for the time being, but I see the opportunity of
focusing on ICs rather than on the original data.


> 5. adding markers/labels can be automated by simple scripts.
>
> OK


> 6. Some of your points are not exactly clear, but, it seems you are going
> in the right direction.
> Most of what you believe can be automated can very certainly easily be
> automated by script.
>
> Let the list know with followup specific questions when you are ready. Be
> sure to provide good details
> so that helpers can best understand what you need and what you are trying
> to do.
>
>
> Thanks for replying. Sorry for not having been clear enough.

Best,

elia

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> On Mon, Oct 1, 2012 at 12:59 PM, Elia Valentini <
> elia.valentini at uniroma1.it> wrote:
>
>> Dear EEGlabers,
>>
>> I'm looking for the expert list help on some difficulties I'm having on
>> adding and deleting markers to my data files, and baseline correcting
>> epoched data.
>>
>> As a premise our design implies:
>> a) two different set of files where a different cognitive manipulation is
>> administered (factor 'mind-set')
>> b) two different type of blocks, pre-post manipulation (factor
>> 'manipulation')
>>
>> within each block we have two different sensory modalities delivered in
>> pairs - S1,S2 - (we are interested in studying ERPs).
>>
>> I did the following:
>> 1) Marge all the single subject datasets (4 neuroscan .cnt files per
>> session).
>> 2) Downsample to 250 Hz (originally 1000 Hz).
>> 2) Re-reference to the average (excluding mastoid and EOG electrodes).
>> 3) Bandpass filter 0.5-30 Hz.
>> 4) Manually reject gross artifacts from the continuous large datafile
>> 5) Remove baseline and run ICA
>> 6) Reject components by maps
>>
>> I'm in the process of
>> 7) Removing "boundary markers" produced by the manual rejection procedure
>> (deleted one by one from the "Event values" interface. I guess this could
>> be automated but I'm doing it manually).
>> 8) Add markers (or rather labels as this are not phasic EEG events) for
>> the levels of the variable 'mind-set' and 'manipulation' (I guess this
>> could be automated but I'm doing it manually).
>> 9) Then I need to generate epoched files from this large file according
>> to the two modalities and locked to the first stimulus of each couple.
>> However, while the first stimulus is baseline corrected to its relative
>> pre-stimulus time, the second stimulus (S2) should be baseline corrected to
>> the S1 prestimulus time (I did not come out yet with a scripting of it -  I
>> guess may not be possible from the GUI).
>>
>> Perhaps I have missed some important past discussion in the list, if this
>> is the case please forgive me.
>> Thanks very much in advance for your time.
>>
>> Elia
>>
>>
>>
>>
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>
>


-- 
Elia Valentini PhD

Social and Cognitive Neuroscience Laboratory - SCNLab
Sapienza University of Rome
Department of  Psychology
Via dei Marsi 78 - 00185 - Roma
Phone: (+39) 06-49917635
Fax: (+39) 06-49917635
e-mail: elia.valentini at uniroma1.it;
Web:  http://w3.uniroma1.it/scnl/index.php/elia-valentini/
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