[Mne_analysis] Setting the Marker channel

Sat Jul 8 09:54:17 EDT 2017

Hi,

Got events detected successfully with following code.

data = raw[:, :][0]
data[14] *= 1000000
raw = mne.io.RawArray(data, raw.info)

events = mne.find_events(raw, stim_channel='MARKER')

# prints event data
print('Found %s events, first five:' % len(events))
print(events[:30])

event_id = {'auditory/left': 1, 'auditory/right': 2}

epochs = mne.Epochs(raw, events, event_id=event_id , tmin=-0.2, tmax=0.5)

epochs.plot(block=True)

Through raw.plot(block=True) shows channel signal, after epoching,
epochs.plot(block=True) show only events and no signal.

[image: Inline image 1]

Is there something wrong with the code?

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On Sat, Jul 8, 2017 at 1:09 PM, Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr> wrote:

> hi,
>
> just replace
>
> data = raw.get_data()
>
> by
>
> data = raw[:, :][0]
>
> the get_data method will appear in the next release.
>
> Alex
>
> On Sat, Jul 8, 2017 at 2:14 AM, Senaka Amarakeerthi <senakahks at gmail.com>
> wrote:
>
>> Dear Jaakko,
>>
>> Thank you for quick reply. I tried your code and it complains telling
>> that 'Raw' object has no attribute 'get_data'.
>>
>>
>> Here is the full report of error
>>
>> Opening raw data file /Users/Senaka/to_share-raw.fif...
>> Isotrak not found
>>     Range : 0 ... 55935 =      0.000 ...   436.992 secs
>> Ready.
>> Adding average EEG reference projection.
>> 1 projection items deactivated
>> Reading 0 ... 55935  =      0.000 ...   436.992 secs...
>> Traceback (most recent call last):
>>   File "/Users/Senaka//test.py", line 3, in <module>
>>     data = raw.get_data()
>> AttributeError: 'Raw' object has no attribute 'get_data'
>>
>>
>> Thanks and regards,
>>
>> Senaka
>>
>>
>>
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>>
>> On Fri, Jul 7, 2017 at 7:49 PM, Jaakko Leppakangas <jaeilepp at gmail.com>
>> wrote:
>>
>>> Hi,
>>> it seems that the stim channel is assigned as EEG for some reason
>>> (probably a mistake in the acquisition). Also the values on the stim
>>> channel are micro scale causing the event finding to fail. Here's a short
>>> script for fixing raw object.
>>>
>>> import mne
>>> raw = mne.io.read_raw_fif('to_share-raw.fif', preload=True)
>>> data = raw.get_data()
>>> data[14] *= 1000000
>>> raw = mne.io.RawArray(data, raw.info)
>>> raw.set_channel_types({'STI 014': 'stim'})
>>>
>>> -Jaakko
>>>
>>>
>>> On Fri, Jul 7, 2017 at 3:50 PM, Senaka Amarakeerthi <senakahks at gmail.com
>>> > wrote:
>>>
>>>> Dear Alex,
>>>>
>>>> Please find the to_share-raw.fif file by accessing following link.
>>>>
>>>> https://www.dropbox.com/s/58ji93q7xj6nett/to_share-raw.fif?dl=0
>>>>
>>>> Best regards,
>>>>
>>>> Senaka
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> <https://mailtrack.io/> Sent with Mailtrack
>>>> <https://mailtrack.io/install?source=signature&lang=en&referral=senakahks@gmail.com&idSignature=22>
>>>>
>>>> On Fri, Jul 7, 2017 at 12:10 PM, Alexandre Gramfort <
>>>> alexandre.gramfort at telecom-paristech.fr> wrote:
>>>>
>>>>> that's indeed unexpected.
>>>>>
>>>>> can you share the file?
>>>>>
>>>>> data.save('to_share-raw.fif')
>>>>>
>>>>> thx
>>>>> Alex
>>>>>
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>>>>
>>>>
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>>
>>
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>
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>
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