[Mne_analysis] Setting the Marker channel

[Senaka Amarakeerthi]

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.
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20170709/61f5e64f/attachment-0001.html