[Mne_analysis] Baseline correcting pre-stimulus segments for covariance estimation

[Denis-Alexander Engemann]

It would be nice to actually see the baseline.
The question is whether it is roughly zero mean or not. For the covariance
noise model to be appropriate the data should be zero mean, as is typically
roughly the case after baseline correction or filtering with a high pass.
What is plausible here also depends to on your data. Using the noise
covariance here will relate your data to the amplitude structure of what
you declare noise. Plot this for example using an empty room noise cov.
Overall, from the distance your plots look plausible to me.

On Wed, 10 May 2017 at 06:03, Graham Flick <grahamflick00 at gmail.com> wrote:

> Hi All,
>
> I have a set of MEG data collected in a sentence processing paradigm,
> where the critical words occur 6-7 words into the sentence. I'd like to
> look at source-level evoked responses to these words via minimum-norm
> estimates, without applying baseline correction.
>
> In this scenario, should I still apply baseline correction to the
> pre-stimulus intervals that I use to estimate the noise covariance? Note
> that in this design, pre-stimulus is actually pre-sentence, meaning that
> there is about 4 seconds of data between these windows and the onset of the
> epochs that will be inverted to source space.
>
> In attempt to address this question, I've plotted whitened evoked
> responses from the start of the sentence to the target words using
> different methods of covariance estimation, with and without baseline
> correction applied to the 100 ms windows from which I estimated the
> covariance. I've attached an example from one subject, and the pattern
> shown there is consistent across quite a few subjects in the sample.
>
> In general, it looks like if I apply baseline correction to the window
> from which I estimate covariance, the global field power of the whitened
> response never reaches 1, even in the window in which the covariance was
> estimated. In contrast, the GFP in the whitened response without baseline
> correction looks more like what I'd expect to see. This pattern seems
> unusual to me, but does it imply that I should not be be applying baseline
> correction here? Or are there other factors that should be considered?
>
> Thanks!
>
> Graham
>
>
> Here is a sample of the code used to generate the whitened responses for
> the empirical estimator with/without baseline correction:
>
> raw = mne.io.read_raw_fif(fname_raw, preload=True)
> events = mne.read_events(fname_event)
> picks = mne.pick_types(raw.info, meg=True, eeg=False,
> eog=False,exclude=bads)
> epochstargetFull = mne.Epochs(raw, events, event_id = event_id,
> tmin=-4.4,tmax=1.2,
> decim=5,reject=dict(mag=2e-12),baseline=None,picks=picks,on_missing='ignore')
> evokedtargetFull = epochstargetFull.average()
>
> method = 'empirical'
>
> # covariance with baseline correction applied
> epochscov = mne.Epochs(raw, events, event_id=event_id, tmin=-4.4,
> tmax=-4.3, decim=5, reject=dict(mag=2e-12), baseline=(-4.4,-4.3),
> picks=picks, on_missing='ignore')
> cov = mne.compute_covariance(epochscov, tmin=-4.4, tmax=-4.3,
> method=method')
> tmp = evokedtargetFull.plot_white(cov, show=False)
> tmp.savefig('topright_empirical_Baselined.png')
> del(epochscov)
> del(cov)
> del(tmp)
>
> # covariance without baseline correction applied
> epochscov = mne.Epochs(raw, events, event_id=event_AF, tmin=-4.4,
> tmax=-4.3, decim=5, reject=dict(mag=2e-12), baseline=None, picks=picks,
> on_missing='ignore')
> cov = mne.compute_covariance(epochscov, tmin=-4.4, tmax=-4.3,
> method=method)
> tmp = evokedtargetFull.plot_white(cov, show=False)
> tmp.savefig('topleft_empirical_NoBaseline.png')
>
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