<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div>Hello again, <br></div><div><br></div><div>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. <br></div><div>Anyway, as expected, epoching works perfectly with the tmin/max defined in seconds, rather than ms. <br></div><div>Best, <br></div><div>Daniel<br></div><div><div class="gmail_extra"><br><div class="gmail_quote">On 5 June 2018 at 18:00, <span dir="ltr"><<a href="mailto:mne_analysis-request@nmr.mgh.harvard.edu" target="_blank">mne_analysis-request@nmr.mgh.<wbr>harvard.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Mne_analysis mailing list submissions to<br>
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1. Re: Epoch() classifies all epochs as "bad" (Alexandre<br>
Gramfort) (Alexandre Gramfort)<br>
<br>
<br>
------------------------------<wbr>------------------------------<wbr>----------<br>
<br>
Message: 1<br>
Date: Tue, 5 Jun 2018 09:27:04 +0200<br>
From: Alexandre Gramfort <<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a>><br>
Subject: Re: [Mne_analysis] Epoch() classifies all epochs as "bad"<br>
(Alexandre Gramfort)<br>
To: Discussion and support forum for the users of MNE Software<br>
<<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.<wbr>edu</a>><br>
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<CADeotZpHu5SSftPdxVrnOj=<a href="mailto:ku_jHy61SVRgxOZWTVCH4fkOeTg@mail.gmail.com" target="_blank">ku_jH<wbr>y61SVRgxOZWTVCH4fkOeTg@mail.gm<wbr>ail.com</a>><br>
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External Email - Use Caution <br>
<br>
hi,<br>
<br>
you wrote:<br>
<br>
tmin=-500, tmax=2000<br>
<br>
so 500s before stim and 2000s after.<br>
<br>
Use:<br>
<br>
tmin=-0.5, tmax=2.<br>
<br>
and it should work.<br>
<br>
Best,<br>
Alex<br>
<br>
<br>
On Mon, Jun 4, 2018 at 4:45 PM, d p <<a href="mailto:aglasis@gmail.com" target="_blank">aglasis@gmail.com</a>> wrote:<br>
> External Email - Use Caution<br>
><br>
> Dear Alex & list,<br>
><br>
> Following Alex G. recommendation (thanks, by the way) I checked the plot<br>
> with events (raw.plot(events=events); which perfectly displays all the<br>
> events at the correct timing), the sampling frequency (which is correctly<br>
> identified from <a href="http://raw.info" rel="noreferrer" target="_blank">raw.info</a>['sfreq'] as 2048.0) and the first sample (also<br>
> correctly identifying the index of the first sample in the raw data file).<br>
><br>
> So, I am still stuck: the Epochs command still correctly detects the events<br>
> by the event_ids (epoch count is correct), but when the epochs are read it<br>
> sets them all as 'IGNORED', and occasionally 'NO_DATA' or 'TOO_SHORT'.<br>
><br>
> I put some sample data and a simplified version of the code that fails to<br>
> produce epochs on the following dropbox folder:<br>
> <a href="https://www.dropbox.com/sh/09b71oumga8xm4y/AABg04xw-cCiCnn9FMSSqODca?dl=0" rel="noreferrer" target="_blank">https://www.dropbox.com/sh/09b<wbr>71oumga8xm4y/AABg04xw-cCiCnn9F<wbr>MSSqODca?dl=0</a><br>
><br>
> Thanks in advance for your help!<br>
> Best,<br>
> Daniel<br>
><br>
><br>
> On 30 May 2018 at 18:00, <<a href="mailto:mne_analysis-request@nmr.mgh.harvard.edu" target="_blank">mne_analysis-request@nmr.mgh.<wbr>harvard.edu</a>> wrote:<br>
>><br>
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>> Today's Topics:<br>
>><br>
>> 1. Re: Epoch() classifies all epochs as "bad" (d p)<br>
>> 2. Re: Epoch() classifies all epochs as "bad" (Alexandre Gramfort)<br>
>><br>
>><br>
>> ------------------------------<wbr>------------------------------<wbr>----------<br>
>><br>
>> Message: 1<br>
>> Date: Wed, 30 May 2018 14:36:12 +0200<br>
>> From: d p <<a href="mailto:aglasis@gmail.com" target="_blank">aglasis@gmail.com</a>><br>
>> Subject: Re: [Mne_analysis] Epoch() classifies all epochs as "bad"<br>
>> To: <a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.e<wbr>du</a><br>
>> Message-ID:<br>
>><br>
>> <<a href="mailto:CAED_QJc1kJ%2BFFzkXSPMgHBZDvtFCntNe7-1iK_BNHpJDo57rdg@mail.gmail.com" target="_blank">CAED_QJc1kJ+FFzkXSPMgHBZDvtFC<wbr>ntNe7-1iK_BNHpJDo57rdg@mail.<wbr>gmail.com</a>><br>
>> Content-Type: text/plain; charset="utf-8"<br>
>><br>
>> External Email - Use Caution<br>
>><br>
>> Dear Marijn & List<br>
>><br>
>> Thanks for your suggestion about drop_log. I tried that and also<br>
>> plot_drop_log, and according to that all epochs are either "IGNORED" or<br>
>> "NO_DATA" according to dropped_log. Also, in the plot_drop_log, 100%<br>
>> events are either "NO_DATA" or "TOO_SHORT".<br>
>><br>
>> I saw in the documentation that " ?NO_DATA? or ?TOO_SHORT? if epoch didn?t<br>
>> contain enough data", but I don't understand what does "didn't contain<br>
>> enough data" mean? I have a 64-channel eeg recording, epochs are ~3seconds<br>
>> long, and epoch markers, timing, amount of epochs, etc. is identified<br>
>> perfectly by the find_events calls. Also, all other pre-processing steps<br>
>> (filtering, bad channel interpolation, re-referencing, etc.) worked just<br>
>> fine.<br>
>><br>
>> Thanks in advance for any comments and suggestions,<br>
>> Daniel<br>
>><br>
>> PS: Sorry about writing from different emails. I'll make sure that in the<br>
>> future I only use the registered one.<br>
>><br>
>> Date: Tue, 29 May 2018 20:01:33 +0300<br>
>> From: Marijn van Vliet <<a href="mailto:w.m.vanvliet@gmail.com" target="_blank">w.m.vanvliet@gmail.com</a>><br>
>> Subject: Re: [Mne_analysis] Epoch() classifies all epochs as "bad"<br>
>> To: Discussion and support Software <<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.<wbr>edu</a>><br>
>> Message-ID: <<a href="mailto:3E3699E3-BEAC-40BD-BB15-B9141C4A96F3@gmail.com" target="_blank">3E3699E3-BEAC-40BD-BB15-B9141<wbr>C4A96F3@gmail.com</a>><br>
>> Content-Type: text/plain; charset="us-ascii"<br>
>><br>
>> Dear Daniel,<br>
>><br>
>> you can try looking at epochs.drop_log after all epochs are dropped. The<br>
>> drop_log contains for each dropped epoch the reason why it was dropped.<br>
>><br>
>> best,<br>
>> Marijn.<br>
>> > On 29 May 2018, at 18:34, Daniel Preciado <<a href="mailto:daniel.preciadov@gmail.com" target="_blank">daniel.preciadov@gmail.com</a>><br>
>> wrote:<br>
>> ><br>
>> > External Email - Use Caution<br>
>> ><br>
>> ><br>
>> > Dear list,<br>
>> ><br>
>> > I am having trouble with epoching eeg data. For some reason, the epoch()<br>
>> call classifies all epochs as bad, and I always end up with an empty<br>
>> Epochs<br>
>> object.<br>
>> ><br>
>> > If I try epoching with "preload=False", it reads correctly the epochs,<br>
>> and the detected epochs perfectly matching the amount of trials and other<br>
>> experiment parameters. But whenever I try to do anything with the Epochs<br>
>> object (e.g. plotting), all events are deleted, and thus everything else<br>
>> throws zeroDivisionErrors. And if I call back the epochs object after<br>
>> this,<br>
>> it is empty (epoch counts are set to 0).<br>
>> ><br>
>> > I have tried all types of combinations of arguments, but the result is<br>
>> always the same: It seems to correctly recognize the epochs if the data is<br>
>> not Preloaded, but everything is discarded if the data is preloade, or if<br>
>> I<br>
>> try to do anything with the epochs object. I have tried different things<br>
>> with the arguments, including reject=None, Baseline=(None, None),<br>
>> preload=False, reject=None, flat=None, reject_tmin=None, reject_tmax=None,<br>
>> detrend=None, on_missing='error', metadata=None, verbose=None. I have also<br>
>> tried creating the epochs with the minimum arguments necessary (Data,<br>
>> Event_data, Event_id), but it is always the same result.<br>
>> ><br>
>> > I have also tried the same code on different datasets, but it always<br>
>> discards all epochs, no matter what.<br>
>> ><br>
>> > I do not understand why Epoch() classifies all data (from different<br>
>> people, different sessions) as bad, can anyone help me to figure this out,<br>
>> and hopefully fix it?<br>
>> ><br>
>> > Thanks!<br>
>> ><br>
>> > ______________________________<wbr>_________________<br>
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>> ------------------------------<br>
>><br>
>> Message: 2<br>
>> Date: Wed, 30 May 2018 14:47:41 +0200<br>
>> From: Alexandre Gramfort <<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a>><br>
>> Subject: Re: [Mne_analysis] Epoch() classifies all epochs as "bad"<br>
>> To: Discussion and support forum for the users of MNE Software<br>
>> <<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.<wbr>harvard.edu</a>><br>
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>> Content-Type: text/plain; charset="utf-8"<br>
>><br>
>> External Email - Use Caution<br>
>><br>
>> you can check your events with:<br>
>><br>
>> raw.plot(events=events)<br>
>><br>
>> also check the sfreq and raw.first_samp.<br>
>><br>
>> if you're stuck please share a file and a script with dropbox.<br>
>><br>
>> Alex<br>
>><br>
>><br>
>><br>
>> ------------------------------<br>
>><br>
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