# using correlation as method for find\_bads\_ecg
**URL:** https://mne.discourse.group/t/using-correlation-as-method-for-find-bads-ecg/849
**Category:** Mailing List Archive (read-only)
**Tags:** list-archive
**Created:** [October 15, 2014, 10:15pm UTC](https://mne.discourse.group/t/using-correlation-as-method-for-find-bads-ecg/849 "2014-10-15T22:15:39Z")
**Posts on this page:** 8
**Page:** 1
### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [October 15, 2014, 10:15pm UTC](https://mne.discourse.group/t/using-correlation-as-method-for-find-bads-ecg/849/1 "2014-10-15T22:15:39Z")
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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### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [October 16, 2014, 7:23am UTC](https://mne.discourse.group/t/using-correlation-as-method-for-find-bads-ecg/849/2 "2014-10-16T07:23:49Z")
hi Lau,
would 'ECG003' be marked as bad? is it defined as an ECG channel
(check with pick\_types)?
Alex
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### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [October 16, 2014, 7:30am UTC](https://mne.discourse.group/t/using-correlation-as-method-for-find-bads-ecg/849/3 "2014-10-16T07:30:36Z")
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
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### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [October 16, 2014, 4:50pm UTC](https://mne.discourse.group/t/using-correlation-as-method-for-find-bads-ecg/849/4 "2014-10-16T16:50:19Z")
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 \:
> 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
>
> \>
> \> hi Lau,
> \>
> \> would 'ECG003' be marked as bad? is it defined as an ECG channel
> \> (check with pick\_types)?
> \>
> \> Alex
> \>
> \>\> 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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### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [October 16, 2014, 7:16pm UTC](https://mne.discourse.group/t/using-correlation-as-method-for-find-bads-ecg/849/5 "2014-10-16T19:16:55Z")
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
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### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [October 16, 2014, 9:15pm UTC](https://mne.discourse.group/t/using-correlation-as-method-for-find-bads-ecg/849/6 "2014-10-16T21:15:20Z")
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
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### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [October 17, 2014, 7:29am UTC](https://mne.discourse.group/t/using-correlation-as-method-for-find-bads-ecg/849/7 "2014-10-17T07:29:14Z")
hi Lau,
maybe use dropbox or google drive? don't hesitate to make a tiny file
before sharing.
Alex
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### Author:  [@system](https://mne.discourse.group/u/system)
#### Post date: [October 19, 2014, 4:57pm UTC](https://mne.discourse.group/t/using-correlation-as-method-for-find-bads-ecg/849/8 "2014-10-19T16:57:43Z")
hi,
bug is fixed
[https://github.com/mne-tools/mne-python/pull/1612](https://github.com/mne-tools/mne-python/pull/1612)
thanks for the bug report.
Alex