[Mne_analysis] Setting the Marker channel

Jaakko Leppakangas jaeilepp at gmail.com
Wed Jul 12 06:52:36 EDT 2017
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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
>
>
>
>
>
> <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 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
>>
>>
>>
>> <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 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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>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Mne_analysis mailing list
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>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>
>>>>>>
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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 <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
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
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