[Mne_analysis] Fwd: Re: many epochs dropped due to 'NO_DATA'

Nakagawa Tristan T nakagawa-t at ifrec.osaka-u.ac.jp
Thu Apr 7 06:24:41 EDT 2016
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Hi,

Thanks for the hint; It must have something to do with it.

I must be overlooking something here, but I can't get it right:
Somehow it looks as if the epochs method looks for timestamps from
before the cropping of the data from somewhere (?), although I'm not
sure how that is possible

I first crop my data with raw.crop, save that data, and load it again
from file.
I previously crop the file at 232 seconds - it loses the first 44 epochs.
Other files I don't crop don't have this problem. 

I can't figure out what's wrong about the time indices:

the resulting raw structure has the correct raw.time (from 0 to 618, at
sfreq=1000) and time indices:
raw[0][1] goes from 0 to 618;
len(raw[0][1]): 618001

My events array  goes like this:
In [37]: events
Out[37]:
array([[  9279,      0,      1],
       [ 18677,      0,      2],
       [ 28475,      0,      3],
       [ 38491,      0,      3],
       [ 49491,      0,      1],
       [ 58705,      0,      3],
       [ 69505,      0,      1],
       [ 79905,      0,      1],
       [ 89736,      0,      1],
       [ 99134,      0,      2],
       [108933,      0,      1],
       [118948,      0,      1],
       [128146,      0,      2],
       [138361,      0,      3],
       [147759,      0,      2],
       [157558,      0,      3],
       [167774,      0,      1],
       ......
       [595400,      0,      1]])



Notably, I lose the first epochs, not the last epochs:


epochs = mne.Epochs(raw,events, event_id, tmin=tmin, tmax=tmax,
proj=True, picks=picks_plan2,
                    baseline=None, preload=True,
                    reject=None)

In [35]: 60 matching events found
Applying baseline correction (mode: mean)
0 projection items activated
Loading data for 60 events and 1001 original time points ...
44 bad epochs dropped

In [36]: epochs.drop_log
Out[36]:
[['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 ['NO_DATA'],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 []]

Any Ideas?
Many Thanks,

cheers Tristan

On 2016年04月07日 17:02, Alexandre Gramfort wrote:
> hi Tristan,
>
> this is telling you that your dropped epochs exceed the time window of
> your raw data.
>
> check that the time indices (first column of events) are compatible
> with the raw object.
>
> yes the raw.info['events'] are not used.
>
> HTH
> Alex
>
> On Thu, Apr 7, 2016 at 9:33 AM, Nakagawa Tristan T
> <nakagawa-t at ifrec.osaka-u.ac.jp> wrote:
>> Dear all,
>>
>> When trying to epoch my data, I get 44 out of 60 epochs dropped due to
>> 'NO_DATA'.
>>
>> What does this error mean? it's not dropping epochs due to bad data, right?
>>
>> I thought it might be due to my having cropped the raw data, saved the
>> events in an array, and now trying to do epochs with this 'events' array.
>> After preprocessing, I have 360 channels and last time point at 618000
>> The raw.info['events'] dict returned the old information:
>> [{'channels': array([397], dtype=int32),
>>   'list': array([     36,       1,       0, ..., 1289236,       0,
>> 1], dtype=int32)}]
>>
>> However, setting:
>> raw.info['events'] =[]
>> doesn't help.
>>
>> Here the epoching command I use:
>> epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
>> picks=picks,
>>                     baseline=None, preload=True,
>>                     reject=None)
>>
>> and the epochs array:
>> array([[  8819,      0,      2],
>>        [ 17833,      0,      3],
>>        [ 28433,      0,      3],
>>        [ 39049,      0,      1],
>>        [ 49849,      0,      3],
>>        [ 58846,      0,      3],
>>        ....]])
>>
>> thanks for any help,
>> Tristan
>>
>>
>> --
>> Tristan T. Nakagawa, Ph.D.
>> Laboratory for Brain-Immune Interaction,
>> iFReC, Osaka University
>> 3-1 Yamadaoka, Suita, Osaka, Japan
>> Tel: 0668789710
>> Office: CiNet R 2B6-2
>> http://seymourlab.com
>>
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