[Mne_analysis] Problem with mne.pick_types

Maria Hakonen maria.hakonen at gmail.com
Wed Aug 27 13:09:20 EDT 2014
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Is it somehow possible to include the bads if they are in selection?

-Maria


2014-08-27 19:51 GMT+03:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

> 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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