[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
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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