[Mne_analysis] How is the baseline correction calculated?

[Emanuela Liaci]

Hi Jaakko,

thanks for the enlightenment. Yes of course, now I understand the problem.
But then since I have to apply the correction after the emerging, how can I
do it?

Here my code:

epochs_noRef = mne.EpochsArray(ElectrodeArray, info=info,tmin=-0.06)
    # baseline = (-0.06, 0.04)
epochs_Ref,_= mne.io.set_eeg_reference(epochs_noRef, ['TP9', 'TP10'])
evoked=epochs_Ref.average()

thanks a lot for your help,
Emanuela

On Mon, Sep 5, 2016 at 4:14 PM, Jaakko Leppäkangas <jaeilepp at student.jyu.fi>
wrote:

> Hi Emanuela,
>
> I assume you do the baselining when constructing the epochs
> (mne.Epochs(..., baseline=baseline))? It simply subtracts the mean over the
> baseline period. So the effective lines of code boil down to:
>
> mean = np.mean(data[..., imin:imax], axis=-1)[..., None]
> data -= mean
>
> , where the baseline runs from imin to imax. And yes this should be
> documented better. I'll make the issue to github.
>
> -Jaakko
>
> On 5 September 2016 at 14:48, Emanuela Liaci <emanuela.liaci at gmail.com>
> wrote:
>
>> Hi,
>>
>> I am comparing the evoke data of one subject between my script in Python
>> with mne package and the script in IGOR pro that my lab used so far.
>>
>> I gave the following time interval for baseline correction to both:
>> baseline = (-0.060, 0.040). I noticed that the values of the average
>> change: for each electrode there is always the same difference (between
>> Python and IGOR) across data points.
>>
>> How come? Can I have a more detailed explanation of how the baseline
>> correction is applied?
>>
>> Many thanks,
>> Emanuela Liaci
>>
>>
>>
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160905/3cc36b2a/attachment-0001.html