[Mne_analysis] Problem with mne.pick_types
Maria Hakonen
maria.hakonen at gmail.com
Wed Aug 27 12:46:55 EDT 2014
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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