[Mne_analysis] Setting the Marker channel

Senaka Amarakeerthi senakahks at gmail.com
Wed Jul 12 06:42:25 EDT 2017
Search archives: 
Hi all,

One more small problem to get fixed. When I apply a low-pass or high-pass
filter, SOME event ids are not detected. Tested with the code I specified
in the thread with linked data.

Any possible reasons?

Thank you,

Senaka





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On Mon, Jul 10, 2017 at 6:05 PM, Senaka Amarakeerthi <senakahks at gmail.com>
wrote:

> Hi Jaakko and Alex,
>
> Thanks a lot. Finally, Jaakko's trick worked.
>
> This is the plot.
>
> https://ibb.co/eKt6Pa
>
> Thank you again for spending your valuable to get the code fixed up.
>
> Senaka
>
>
>
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>
> On Mon, Jul 10, 2017 at 4:04 PM, Jaakko Leppakangas <jaeilepp at gmail.com>
> wrote:
>
>> You can do
>>
>> import mne
>> mne.sys_info()
>>
>> I think you can also work around the issue by doing
>> raw.set_channel_types({'MARKER': 'stim'})
>>
>> after constructing the RawArray. The amplitude of the stimulus channel is
>> messing up the plot.
>>
>> -Jaakko
>>
>> On Mon, Jul 10, 2017 at 11:52 AM, Senaka Amarakeerthi <
>> senakahks at gmail.com> wrote:
>>
>>> Dear Jaakko,
>>>
>>> I issued the following command
>>> pip install mne --upgrade
>>>
>>> Result:
>>> Requirement already up-to-date: mne in ./mne-python
>>>
>>> Is there a direct command to check the version?
>>>
>>> I use python 2.7 and macOS Sierra.
>>>
>>>
>>> Thanks
>>>
>>> Senaka
>>>
>>>
>>>
>>>
>>>
>>>
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>>>
>>> On Mon, Jul 10, 2017 at 11:19 AM, Jaakko Leppakangas <jaeilepp at gmail.com
>>> > wrote:
>>>
>>>> I was able to reproduce the plot with version 0.13. I'm not sure what's
>>>> the cause of it, but in v. 0.14 it looks better. Can you try updating mne
>>>> to the latest version?
>>>>
>>>> -Jaakko
>>>>
>>>> On Sun, Jul 9, 2017 at 2:22 PM, Senaka Amarakeerthi <
>>>> senakahks at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I am migrating from EEGLAB and tried to apply baseline corrections and
>>>>> filters, unfortunately, those attempts ended up with another set of errors.
>>>>> Highly appreciating somebody's support since I am exhausted.
>>>>>
>>>>> Sample file URL:
>>>>> https://www.dropbox.com/s/vwvy4duwkahysfk/ChinthakaDahnushka.edf?dl=0
>>>>>
>>>>> The code so far I used:
>>>>>
>>>>> import mne
>>>>> import numpy as np
>>>>> import matplotlib.pyplot as plt
>>>>>
>>>>>
>>>>> raw = mne.io.read_raw_edf('ChinthakaDahnushka.edf', preload=True)
>>>>> raw = raw.drop_channels(['COUNTER', 'INTERPOLATED','RAW_CQ','GYROX','GYROY', 'SYNC', 'TIME_STAMP_s', 'TIME_STAMP_ms', 'CQ_AF3', 'CQ_F7', 'CQ_F3', 'CQ_FC5', 'CQ_T7', 'CQ_P7', 'CQ_O1', 'CQ_O2', 'CQ_P8', 'CQ_T8', 'CQ_FC6', 'CQ_F4', 'CQ_F8', 'CQ_AF4', 'CQ_CMS', 'STI 014'])
>>>>>
>>>>> data = raw[:, :][0]
>>>>>
>>>>> data[14] *= 1000000
>>>>>
>>>>> raw = mne.io.RawArray(data, raw.info)
>>>>>
>>>>> events = mne.find_events(raw, stim_channel='MARKER')
>>>>>
>>>>>
>>>>> print('Found %s events, first five:' % len(events))
>>>>> print(events[:5])
>>>>>
>>>>>
>>>>> event_id = {'two': 2}
>>>>>
>>>>> epochs = mne.Epochs(raw, events, event_id=event_id, tmin=-0.2, tmax=1.5)
>>>>>
>>>>>
>>>>> epochs_data = epochs['two'].get_data()
>>>>>
>>>>>
>>>>> print(epochs_data.shape)
>>>>>
>>>>>
>>>>> epochs.plot(block=True)
>>>>>
>>>>>
>>>>> This is the plot I ended up with
>>>>>
>>>>> https://ibb.co/ccKXvF
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Senaka
>>>>>
>>>>>
>>>>>
>>>>> <https://mailtrack.io/> Sent with Mailtrack
>>>>> <https://mailtrack.io/install?source=signature&lang=en&referral=senakahks@gmail.com&idSignature=22>
>>>>>
>>>>> On Sun, Jul 9, 2017 at 1:33 PM, Alexandre Gramfort <
>>>>> alexandre.gramfort at telecom-paristech.fr> wrote:
>>>>>
>>>>>> hi,
>>>>>>
>>>>>> did you baseline correct your Epochs or high pass filter the raw data?
>>>>>> if not please do.
>>>>>>
>>>>>> you may have a big offset in the values.
>>>>>>
>>>>>> HTH,
>>>>>> Alex
>>>>>>
>>>>>> On Sat, Jul 8, 2017 at 4:38 PM, Senaka Amarakeerthi <
>>>>>> senakahks at gmail.com> wrote:
>>>>>>
>>>>>>> Hi Alex,
>>>>>>>
>>>>>>> Thank you for your time. You can check screenshots of the graphs
>>>>>>> below, which were not available in the last post.
>>>>>>>
>>>>>>>
>>>>>>> raw.plot(block=True)
>>>>>>> https://ibb.co/n6GeaF
>>>>>>>
>>>>>>> epochs.plot(block=True)
>>>>>>>
>>>>>>> https://ibb.co/ccKXvF
>>>>>>>
>>>>>>>
>>>>>>> So, I guess this is not a problem with an amplitude of the signal.
>>>>>>> Am I correct?
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Senaka
>>>>>>>
>>>>>>>
>>>>>>> <https://mailtrack.io/> Sent with Mailtrack
>>>>>>> <https://mailtrack.io/install?source=signature&lang=en&referral=senakahks@gmail.com&idSignature=22>
>>>>>>>
>>>>>>> On Sat, Jul 8, 2017 at 7:49 PM, Alexandre Gramfort <
>>>>>>> alexandre.gramfort at telecom-paristech.fr> wrote:
>>>>>>>
>>>>>>>> I don't see any problem. Make sure your data are in Volts not
>>>>>>>> micro-Volts.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> Alex
>>>>>>>>
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>>>
>>>
>>> --
>>> Senaka Amarakeerthi, PhD(Japan)
>>> Senior Lecturer in Computer Science
>>> Faculty of Technology
>>> University of Sri Jayewardenepura
>>> Nugegoda
>>> Sri Lanka
>>> email:   senaka at sjp.ac.lk
>>> Mobile: +(94)-71-2043212 <+94%2071%20204%203212>
>>> Office:  +(94)-11-2802969
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
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>>> it is
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>>>
>>
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>> is
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>> e-mail
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>>
>
>
> --
> Senaka Amarakeerthi, PhD(Japan)
> Senior Lecturer in Computer Science
> Faculty of Technology
> University of Sri Jayewardenepura
> Nugegoda
> Sri Lanka
> email:   senaka at sjp.ac.lk
> Mobile: +(94)-71-2043212 <071%20204%203212>
> Office:  +(94)-11-2802969
>



-- 
Senaka Amarakeerthi, PhD(Japan)
Senior Lecturer in Computer Science
Faculty of Technology
University of Sri Jayewardenepura
Nugegoda
Sri Lanka
email:   senaka at sjp.ac.lk
Mobile: +(94)-71-2043212
Office:  +(94)-11-2802969
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