[Mne_analysis] using correlation as method for find_bads_ecg

[Lau Møller Andersen]

Hi Alex and Denis

@Alex:
picks = mne.pick_types(ekgEpochs.info, ecg=True)
ch_names = np.array(ekgEpochs.info['ch_names'])
In [22]: ch_names[picks][:10]
Out[22]:
array(['ECG003', 'MEG0111', 'MEG0112', 'MEG0113', 'MEG0121', 'MEG0122',
       'MEG0123', 'MEG0131', 'MEG0132', 'MEG0133'],
      dtype='|S7')

In [23]: ekgEpochs.info['bads']
Out[23]: []


It seems to be in there and not marked as bad.

On a related note: The documentation for find_bads_eog refers to ecg
instead of eog throughout.

@Denis: Actually, for no other reason that that is what I did in an earlier
experiment, and I wanted to follow that analysis for the current experiment
as closely as possible. But I will take your word for the ctps being more
reliable.

Best

Lau

2014-10-16 2:30 GMT-05:00 Denis A. Engemann <denis.engemann at gmail.com>:

>
> Out of curiosity, why would you prefer the correlation method over the
> default phase-locking method? The latter is more reliable and is based on a
> significance test.
>
> -Denis
>
>
> > On 16 Oct 2014, at 09:23, Alexandre Gramfort <
> alexandre.gramfort at telecom-paristech.fr> wrote:
> >
> > hi Lau,
> >
> > would 'ECG003' be marked as bad? is it defined as an ECG channel
> > (check with pick_types)?
> >
> > Alex
> >
> > On Thu, Oct 16, 2014 at 12:15 AM, Lau Møller Andersen
> > <lau.andersen at cnru.dk> wrote:
> >> Dear list
> >>
> >> I can't get the correlation method to work for find_bads_ecg method
> >> It always returns the error: ValueError: ECG003 not in channel list
> >>
> >> method = 'correlation'
> >>
> >> ekgEpochs = mne.preprocessing.create_ecg_epochs(raw)
> >>
> >> ekgIndices, ekgScores = ica.find_bads_ecg(ekgEpochs, method=method)
> >>
> >>
> >> It is in the ekgEpochs as seen below
> >>
> >> ekgEpochs.info['ch_names'][:4]
> >> Out[8]: ['EOG001', 'EOG002', 'ECG003', 'MEG0111']
> >>
> >> it makes no difference whether I include ch_name = 'ECG003' in
> >> create_ecg_epochs or in find_bads_ecg
> >>
> >> Any thoughts on why this could be?
> >>
> >> I'm running MNE 0.8.5 on MacOSX 10.9.5
> >>
> >> Best
> >>
> >> Lau
> >>
> >>
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