[Mne_analysis] Setting the Marker channel

[Senaka Amarakeerthi]

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
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>> contains patient information, please contact the Partners Compliance
>>>>> HelpLine at
>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>> you in error
>>>>> but does not contain patient information, please contact the sender
>>>>> and properly
>>>>> dispose of the e-mail.
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>> contains patient information, please contact the Partners Compliance
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>>> in error
>>>> but does not contain patient information, please contact the sender and
>>>> properly
>>>> dispose of the e-mail.
>>>>
>>>>
>>>
>>> _______________________________________________
>>> 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
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
>>
>>
>>
>> _______________________________________________
>> 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
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
> _______________________________________________
> 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
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20170710/02bd5f6f/attachment-0001.html