[Mne_analysis] Problem with mne.pick_types
Denis-Alexander Engemann
denis.engemann at gmail.com
Wed Aug 27 12:51:32 EDT 2014
Hi Maria,
it seems you found a 'bug' in the documentation. If you hit
'mne.pick_types? in and IPython terminal you can see that 'exclude'
defaults to bads.
I guess that would explain your problem?
-Denis
2014-08-27 18:46 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:
> Or could it alternatively be possible to plot also the bad channels?
>
> I have:
>
> picks = mne.pick_types(evoked_raw.info,selection=selection)
>
> I think that this shouldn't exclude bads because I have not exclude='bads'.
>
> However, picks doesn't include the channels in selection that are marked
> as bad.
>
> In the reference of mne.picks_type it is said:
>
> exclude : list of string | str
>
> List of channels to exclude. If empty do not exclude any (default). If
> ‘bads’, exclude channels in info[‘bads’]
>
>
> -Maria
>
>
>
> 2014-08-27 19:02 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:
>
> There was one channel two times in selection...
>>
>> However, it seems to cause a problem if some of the channels in selection
>> is bad.
>> I would like to plot a subset of channels from each data file in a loop
>> as follows:
>>
>> picks = mne.pick_types(evoked.info,selection=selection)
>>
>> idx = 0
>> for ax_row in axes:
>> for ax in ax_row:
>> ax.plot(evoked_raw.times,
>> evoked_raw.data[picks[idx]])
>> idx += 1
>>
>> Is it somehow possible to, for example, plot a blank plot if there is a
>> bad channel in selection?
>>
>> -Maria
>>
>>
>> 2014-08-27 15:05 GMT+03:00 Denis-Alexander Engemann <
>> denis.engemann at gmail.com>:
>>
>> Hi,
>>>
>>> 2014-08-27 14:02 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:
>>>
>>> I manged to solve this already.
>>>>
>>>>
>>> now I'm curious, what was the problem?
>>>
>>> -Denis
>>>
>>>
>>>> -Maria
>>>>
>>>>
>>>> 2014-08-27 13:11 GMT+03:00 Maria Hakonen <maria.hakonen at gmail.com>:
>>>>
>>>> I have one bad channel but it is not included in selection. Can it
>>>>> however cause problems?
>>>>>
>>>>> -Maria
>>>>>
>>>>> Here are the outputs:
>>>>> evoked.info['bads']
>>>>> Out[54]: [u'MEG 2511']
>>>>>
>>>>> but
>>>>>
>>>>> In [53]: selection
>>>>> Out[53]:
>>>>> ['MEG 0133',
>>>>> 'MEG 0212',
>>>>> 'MEG 0223',
>>>>> 'MEG 1313',
>>>>> 'MEG 1322',
>>>>> 'MEG 1443',
>>>>> 'MEG 0132',
>>>>> 'MEG 0213',
>>>>> 'MEG 0222',
>>>>> 'MEG 1312',
>>>>> 'MEG 1323',
>>>>> 'MEG 1442',
>>>>> 'MEG 1513',
>>>>> 'MEG 0242',
>>>>> 'MEG 0233',
>>>>> 'MEG 1343',
>>>>> 'MEG 1332',
>>>>> 'MEG 2613',
>>>>> 'MEG 1512',
>>>>> 'MEG 0243',
>>>>> 'MEG 0232',
>>>>> 'MEG 1343',
>>>>> 'MEG 1333',
>>>>> 'MEG 2612',
>>>>> 'MEG 1523',
>>>>> 'MEG 1612',
>>>>> 'MEG 1623',
>>>>> 'MEG 2413',
>>>>> 'MEG 2422',
>>>>> 'MEG 2643',
>>>>> 'MEG 1522',
>>>>> 'MEG 1613',
>>>>> 'MEG 1622',
>>>>> 'MEG 2412',
>>>>> 'MEG 2423',
>>>>> 'MEG 2642']
>>>>>
>>>>>
>>>>>
>>>>> 2014-08-27 12:56 GMT+03:00 Denis-Alexander Engemann <
>>>>> denis.engemann at gmail.com>:
>>>>>
>>>>> Hi Maria,
>>>>>>
>>>>>> Do you have one bad channel? Take a look at evoked.info['bads']
>>>>>> pick types automatically excludes those.
>>>>>>
>>>>>> -Denis
>>>>>>
>>>>>>
>>>>>> 2014-08-27 11:53 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I have used mne.pick_types as follows:
>>>>>>>
>>>>>>> picks = mne.pick_types(evoked.info,selection=selection)
>>>>>>>
>>>>>>> where selection includes 36 channel names.
>>>>>>> However, picks is an array with only 35 elements.
>>>>>>> I wonder what could be wrong there?
>>>>>>>
>>>>>>> Regards,
>>>>>>> Maria
>>>>>>>
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