[Mne_analysis] Epoch() classifies all epochs as "bad" (Alexandre Gramfort)
d p
aglasis at gmail.com
Mon Jun 4 10:45:12 EDT 2018
External Email - Use Caution
Dear Alex & list,
Following Alex G. recommendation (thanks, by the way) I checked the plot
with events (raw.plot(events=events); which perfectly displays all the
events at the correct timing), the sampling frequency (which is correctly
identified from raw.info['sfreq'] as 2048.0) and the first sample (also
correctly identifying the index of the first sample in the raw data file).
So, I am still stuck: the Epochs command still correctly detects the events
by the event_ids (epoch count is correct), but when the epochs are read it
sets them all as 'IGNORED', and occasionally 'NO_DATA' or 'TOO_SHORT'.
I put some sample data and a simplified version of the code that fails to
produce epochs on the following dropbox folder:
https://www.dropbox.com/sh/09b71oumga8xm4y/AABg04xw-cCiCnn9FMSSqODca?dl=0
Thanks in advance for your help!
Best,
Daniel
On 30 May 2018 at 18:00, <mne_analysis-request at nmr.mgh.harvard.edu> wrote:
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> 1. Re: Epoch() classifies all epochs as "bad" (d p)
> 2. Re: Epoch() classifies all epochs as "bad" (Alexandre Gramfort)
>
>
> ----------------------------------------------------------------------
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> Message: 1
> Date: Wed, 30 May 2018 14:36:12 +0200
> From: d p <aglasis at gmail.com>
> Subject: Re: [Mne_analysis] Epoch() classifies all epochs as "bad"
> To: mne_analysis at nmr.mgh.harvard.edu
> Message-ID:
> <CAED_QJc1kJ+FFzkXSPMgHBZDvtFCntNe7-1iK_
> BNHpJDo57rdg at mail.gmail.com>
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> Dear Marijn & List
>
> Thanks for your suggestion about drop_log. I tried that and also
> plot_drop_log, and according to that all epochs are either "IGNORED" or
> "NO_DATA" according to dropped_log. Also, in the plot_drop_log, 100%
> events are either "NO_DATA" or "TOO_SHORT".
>
> I saw in the documentation that " ?NO_DATA? or ?TOO_SHORT? if epoch didn?t
> contain enough data", but I don't understand what does "didn't contain
> enough data" mean? I have a 64-channel eeg recording, epochs are ~3seconds
> long, and epoch markers, timing, amount of epochs, etc. is identified
> perfectly by the find_events calls. Also, all other pre-processing steps
> (filtering, bad channel interpolation, re-referencing, etc.) worked just
> fine.
>
> Thanks in advance for any comments and suggestions,
> Daniel
>
> PS: Sorry about writing from different emails. I'll make sure that in the
> future I only use the registered one.
>
> Date: Tue, 29 May 2018 20:01:33 +0300
> From: Marijn van Vliet <w.m.vanvliet at gmail.com>
> Subject: Re: [Mne_analysis] Epoch() classifies all epochs as "bad"
> To: Discussion and support Software <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID: <3E3699E3-BEAC-40BD-BB15-B9141C4A96F3 at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Daniel,
>
> you can try looking at epochs.drop_log after all epochs are dropped. The
> drop_log contains for each dropped epoch the reason why it was dropped.
>
> best,
> Marijn.
> > On 29 May 2018, at 18:34, Daniel Preciado <daniel.preciadov at gmail.com>
> wrote:
> >
> > External Email - Use Caution
> >
> >
> > Dear list,
> >
> > I am having trouble with epoching eeg data. For some reason, the epoch()
> call classifies all epochs as bad, and I always end up with an empty Epochs
> object.
> >
> > If I try epoching with "preload=False", it reads correctly the epochs,
> and the detected epochs perfectly matching the amount of trials and other
> experiment parameters. But whenever I try to do anything with the Epochs
> object (e.g. plotting), all events are deleted, and thus everything else
> throws zeroDivisionErrors. And if I call back the epochs object after this,
> it is empty (epoch counts are set to 0).
> >
> > I have tried all types of combinations of arguments, but the result is
> always the same: It seems to correctly recognize the epochs if the data is
> not Preloaded, but everything is discarded if the data is preloade, or if I
> try to do anything with the epochs object. I have tried different things
> with the arguments, including reject=None, Baseline=(None, None),
> preload=False, reject=None, flat=None, reject_tmin=None, reject_tmax=None,
> detrend=None, on_missing='error', metadata=None, verbose=None. I have also
> tried creating the epochs with the minimum arguments necessary (Data,
> Event_data, Event_id), but it is always the same result.
> >
> > I have also tried the same code on different datasets, but it always
> discards all epochs, no matter what.
> >
> > I do not understand why Epoch() classifies all data (from different
> people, different sessions) as bad, can anyone help me to figure this out,
> and hopefully fix it?
> >
> > Thanks!
> >
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> Message: 2
> Date: Wed, 30 May 2018 14:47:41 +0200
> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> Subject: Re: [Mne_analysis] Epoch() classifies all epochs as "bad"
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
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> you can check your events with:
>
> raw.plot(events=events)
>
> also check the sfreq and raw.first_samp.
>
> if you're stuck please share a file and a script with dropbox.
>
> Alex
>
>
>
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