[Mne_analysis] Epoch() classifies all epochs as "bad"
d p
aglasis at gmail.com
Thu Jun 7 07:31:19 EDT 2018
External Email - Use Caution
Hello again,
Alex, thank you very much for your help! I am glad that the solution was so
straightforward, even though it is a little embarrassing that the problem
was such a dumb mistake.
Anyway, as expected, epoching works perfectly with the tmin/max defined in
seconds, rather than ms.
Best,
Daniel
On 5 June 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" (Alexandre
> Gramfort) (Alexandre Gramfort)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 5 Jun 2018 09:27:04 +0200
> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> Subject: Re: [Mne_analysis] Epoch() classifies all epochs as "bad"
> (Alexandre Gramfort)
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <CADeotZpHu5SSftPdxVrnOj=ku_jHy61SVRgxOZWTVCH4fkOeTg at mail.gm
> ail.com>
> Content-Type: text/plain; charset="utf-8"
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>
> hi,
>
> you wrote:
>
> tmin=-500, tmax=2000
>
> so 500s before stim and 2000s after.
>
> Use:
>
> tmin=-0.5, tmax=2.
>
> and it should work.
>
> Best,
> Alex
>
>
> On Mon, Jun 4, 2018 at 4:45 PM, d p <aglasis at gmail.com> wrote:
> > 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-cCiCnn9F
> MSSqODca?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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> >>
> >>
> >> Today's Topics:
> >>
> >> 1. Re: Epoch() classifies all epochs as "bad" (d p)
> >> 2. Re: Epoch() classifies all epochs as "bad" (Alexandre Gramfort)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> 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>
> >> Content-Type: text/plain; charset="utf-8"
> >>
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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>
> >> Message-ID:
> >>
> >> <CADeotZrEDFQRQvyc1EY23qd3g899uzrePgu8vyWCPGYq4zoqFQ at mail.gmail.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> External Email - Use Caution
> >>
> >> 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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