[Mne_analysis] epochs with no data?

Mon Jan 7 11:56:32 EST 2019

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Hi Dillan-

How are you reading in the data?  From the EGI formatted file?  Can you provide more of the code?

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From: Dillan Cellier <cellierdillan at gmail.com>
Reply-To: Discussion and support forum for the users of MNE Software <mne_analysis at nmr.mgh.harvard.edu>
Date: Monday, January 7, 2019 at 11:53 AM
To: Discussion and support forum for the users of MNE Software <mne_analysis at nmr.mgh.harvard.edu>
Subject: Re: [Mne_analysis] epochs with no data?

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Hi Denis,

Apologies for the delay in getting back to you. I've tried reproducing this with a MNE sample dataset, and did not get the same effect. It would appear then, that there might be something special about the data. Unfortunately this dataset is not one that I collected. It was acquired from the Child Mind Institute and as such, the extent of my knowledge about it goes only so far as the public information provided on it!

I tried this on a different subject's data from the same CMI dataset. I got the same results where the epoch.plot() is dropping over half of the epochs, however this time this the drop_log is empty (!?!?!) and at this point i am thoroughly confused. Here is the code where I am constructing this Epoch object, so that you may see that there shouldn't be any automatic rejection taking place:

mne.Epochs(eyes_closed, events=epoch_array, tmin=0, tmax=2, event_id={'twoSec':7}, picks=scalpData, reject_by_annotation=False)

Any other guesses? Thank you for your help!

Best wishes,
Dillan

On Fri, Jan 4, 2019 at 3:30 PM Denis A. Engemann <denis-alexander.engemann at inria.fr<mailto:denis-alexander.engemann at inria.fr>> wrote:

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Hum. That sounds puzzling. Can you reproduce this somehow with the MNE sample data? That could help to see if there is something wrong in the code or if something is special about your data.

Best,
Denis

On 4 Jan 2019, at 22:24, Dillan Cellier <cellierdillan at gmail.com<mailto:cellierdillan at gmail.com>> wrote:

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Hi Denis,

The events are 2 seconds apart from each other.

Thanks!

Dillan

On Fri, Jan 4, 2019 at 3:18 PM Denis A. Engemann <denis-alexander.engemann at inria.fr<mailto:denis-alexander.engemann at inria.fr>> wrote:

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Hi Dillan,

What is then the distance in seconds between any two events that you passed to the epochs constructor?

Denis

On 4 Jan 2019, at 22:12, Dillan Cellier <cellierdillan at gmail.com<mailto:cellierdillan at gmail.com>> wrote:

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Hi Denis,

I limited the tmin and tmax of the epoch to 0 and 2, respectively, since I don't any kind of stimulus onset in these epochs and don't want them to overlap. This is partly what puzzles me, as I would think this would prevent any inclusion of not-real data. My resting state data can be cut into 93 two-second time windows, and this the number of events I am feeding into the epoch object. It is labeling 41 of these 93 as 'NO_DATA'.

Thank you very much!

Dillan

On Fri, Jan 4, 2019 at 3:05 PM Denis A. Engemann <denis-alexander.engemann at inria.fr<mailto:denis-alexander.engemann at inria.fr>> wrote:

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Hi Dillan,

This can happen when the epochs selected include (theoretical) samples beyond the (actual) data range. You should not have many of those epochs. Can you roughly tell how many no_data labels you found? I‘d need to refresh my knowledge of the epochs reading code a bit to see if there may be other reasons for this. Let‘s see what the others say in the meantime.

Best,
Denis

On 4 Jan 2019, at 21:56, Dillan Cellier <cellierdillan at gmail.com<mailto:cellierdillan at gmail.com>> wrote:

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Hello again!

Thank you for your responses on my last question, they were very helpful. I am running into another problem now, however. I am epoching resting state data into arbitrary 2 second windows. I am not automatically rejecting epochs by annotation nor by a rejection parameter. I see that the epoch object's drop_log is recording nearly the whole first half of the epochs as "NO_DATA" epochs, however the raw file contains data for those time indices. I am unsure what could be going on to result in this loss of data, however it seems especially problematic due to the amount of epochs dropped. Thank you in advance, again!

Best wishes,
Dillan
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