[Mne_analysis] ERP plot issues

[Lidia Miguel Telega]

        External Email - Use Caution        

Hi,

Here is the code (relevant part highlighted. It should work similarly for
the sample data set for MNE but with different loading):


##############

import mne
import numpy
import matplotlib.pyplot as plt

from os import system
from read_sleep_markers import REM_em_times
from mne.preprocessing import ICA
from mne.preprocessing import create_eog_epochs

system('python read_sleep_markers.py')

# READ DATA #
raw=mne.io.read_raw_edf('B0939.edf',preload='data_preload')

# REMOVE BAD CHANNELS #
raw.drop_channels(['EMGchin','ECG','Lage','Licht','Akku','Beweg.','EOGl:M1','EOGl:M2','EOGr:M1','C3:M2','C4:M1','Fz:M1','Oz:M1','EOGr:M2','F4:M1','O2:M1','F3:M2','O1:M2','Fz:M2','Oz:M2','Fp1:M1','Fp2:M1','T3:M1','T4:M1','P3:M1','P4:M1','F3:M1','STI
014'])

# CREATE MONTAGE #
raw.set_montage('standard_1020')

# SET CHANNEL TYPES
raw.set_channel_types({'EOGl':'eog','EOGr':'eog','EOGV':'eog','AUX':'stim'})

*# CROP RAW DATA #*
*raw.crop(tmin=REM_em_times[0], tmax=REM_em_times[0]+125) #
or tmin=REM_em_times[1],tmax=REM_em_times[5]...*

*# STIM INDEX #*
*auxindex=[x['ch_name'] for x in raw.info
<http://raw.info>['chs']].index('AUX') *
*auxdata,auxtime=raw[auxindex,:]*

*# STIM EVENTS #*
*events=numpy.arange(auxdata.shape[1])[numpy.append(numpy.array([False]),numpy.diff((auxdata>400).astype(int))==1.0)]*
*nevents=events.shape[0]*
*events=numpy.reshape(events,(-1,1))*
*events=numpy.append(events,numpy.zeros((nevents,1),dtype=int),axis=1)*
*events=numpy.append(events,numpy.ones((nevents,1),dtype=int),axis=1)*
*events*

*# READ EPOCHS #*
*epochs = mne.Epochs(raw, events, tmin= -0.2, tmax=1.0, baseline=(None, 0))*
*epochs_array=epochs.get_data() *
*erp=epochs.average()*
*erp.plot()*


I have tried to crop the data at different time points and in different
ways (directly writing integers or through imported variables,...)

It resulted to work once, when selecting tmin and tmax delimiting a large
range of data. But it did not work for other ranges. I do not know why...

Might be something with the data points...

If you could have a fast look to it, would be nice and helpful. I am still
struggling since for the ranges I need to analyze does not work.

Thanks!!


El mar., 29 ene. 2019 a las 15:38, Alexandre Gramfort (<
alexandre.gramfort at inria.fr>) escribió:

>         External Email - Use Caution
>
> hi Lidia,
>
> many things could go wrong. I would suggest you provide a few lines of
> code (as little as possible)
> using the MNE sample data to replicate the problem so we can investigate.
>
> Alex
>
>
> On Tue, Jan 29, 2019 at 1:40 PM Lidia Miguel Telega
> <lidia.migueltelega at gmail.com> wrote:
> >
> >         External Email - Use Caution
> >
> > Dear all,
> >
> > I am having problems creating an erp plot of a cropped segment of data.
> > What I am doing is crop the raw at some specific time points, find the
> stim events at that points using my own code, epoching, averaging the
> epochs and then plotting) and I always get the error: Some of the values to
> be plotted are NaN. While when doing the same procedure with whole raw data
> file it works fine.
> >
> > Do you have any idea which might be the cause of that?
> >
> > Could it be a problem with some values when epoching the short segment
> of  data?
> >
> > Thank you in advance,
> >
> > Lidia
> >
> > --
> > Lidia Miguel Telega
> > M. Sc. Neuroscience
> > Albert-Ludwigs-University of Freiburg, Germany
> > _______________________________________________
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> > Mne_analysis at nmr.mgh.harvard.edu
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>
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-- 
*Lidia Miguel Telega*
*M. Sc. Neuroscience*
*Albert-Ludwigs-University of Freiburg, Germany*
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