[Mne_analysis] using correlation as method for find_bads_ecg

[Alexandre Gramfort]

hi Lau,

can you reproduce the problem with the sample dataset?
If not please share one of your files and the script that crashes.

Best,
Alex


On Thu, Oct 16, 2014 at 6:50 PM, Lau Møller Andersen
<lau.andersen at cnru.dk> wrote:
> 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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