[Mne_analysis] Setting the Marker channel

Senaka Amarakeerthi senakahks at gmail.com
Wed Jul 12 07:03:51 EDT 2017
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Dear Jaakko,

Your suggestion fixed the problem.

Thanks

Senaka



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On Wed, Jul 12, 2017 at 4:22 PM, Jaakko Leppakangas <jaeilepp at gmail.com>
wrote:

> Could it be because the stim channel is getting filtered as well? You
> should first reassign the channel as stim channel (with
> raw.set_channel_types) and then filter.
>
> -Jaakko
>
> On Wed, Jul 12, 2017 at 12:42 PM, Senaka Amarakeerthi <senakahks at gmail.com
> > wrote:
>
>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> <https://mailtrack.io/> Sent with Mailtrack
>>>>> <https://mailtrack.io/install?source=signature&lang=en&referral=senakahks@gmail.com&idSignature=22>
>>>>>
>>>>> 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
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>>>>>>>
>>>>>>> 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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>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
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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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>>>>>
>>>>
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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 <+94%2071%20204%203212>
>> Office:  +(94)-11-2802969
>>
>> _______________________________________________
>> Mne_analysis mailing list
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