[Mne_analysis] using correlation as method for find_bads_ecg

[Alexandre Gramfort]

hi Lau,

maybe use dropbox or google drive? don't hesitate to make a tiny file
before sharing.

Alex

On Thu, Oct 16, 2014 at 11:15 PM, Lau Møller Andersen
<lau.andersen at cnru.dk> wrote:
> 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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