[Mne_analysis] Setting the Marker channel
Senaka Amarakeerthi
senakahks at gmail.com
Mon Jul 10 08:35:28 EDT 2017
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
>>>> <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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>>>>>>
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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
>>
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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
Office: +(94)-11-2802969
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