[Mne_analysis] Problem with mne.pick_types
Denis-Alexander Engemann
denis.engemann at gmail.com
Wed Aug 27 13:16:01 EDT 2014
Have you tried to to pass exclude=[] when invoking mne.pick_types?
-Denis
2014-08-27 19:09 GMT+02:00 Maria Hakonen <maria.hakonen at gmail.com>:
> 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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>
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