[Mne_analysis] using correlation as method for find_bads_ecg

[Lau Møller Andersen]

Hi Alex

I cannot reproduce the problem with the sample data set.By the way, is 
it the case that the sample data set is version 0.7? It keeps telling me 
to update, but I can't seem to get a newer version
The code below works just fine:

import mne

import os


path = mne.datasets.sample.data_path()

os.chdir(path + '/MEG/sample')


raw = mne.io.Raw('sample_audvis_filt-0-40_raw.fif')

events = mne.read_events('sample_audvis_filt-0-40_raw-eve.fif')

eventID = {'aud_l': 1, 'aud_r': 2, 'vis_l': 3, 'vis_r': 4, 'smiley': 5,

'button': 32}

epochs = mne.Epochs(raw, events, eventID, tmin=-0.2, tmax=0.5)

ekg = mne.preprocessing.create_ecg_epochs(raw)

noiseCov = mne.read_cov('sample_audvis-cov.fif')

ica = mne.preprocessing.ICA(n_components=0.95, n_pca_components=64,

max_pca_components=100, noise_cov=noiseCov)

ica.fit(epochs)

ekgIndices, ekgScores = ica.find_bads_ecg(ekg, method='correlation')



What is the easiest way for me to share a file with you? The raw files 
as they are now are pretty big.

Best

Lau


Den 16-10-2014 kl. 14:16 skrev 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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