[Mne_analysis] Setting the Marker channel

Mon Jul 10 06:34:20 EDT 2017

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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>
>
> --
> 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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