reject parameter for epochs and get_data()

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1

Dear MNE-Users,

I created epochs without specifiying any "reject" parameters. By reading
the documentation, this parameter is None by default. However, when I want
to get my data, I use epochs.get_data() and some bad epochs are dropped. On
which criterion are they dropped, given that any reject criterion was set?
How can I get the data without rejecting any epochs?

My lines of code:

epochs_s= mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(tmin_bsl,0))

epochs_s.get_data()

Thanks a lot!

Laetitia
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2

what is the content of event_id and events?

Epochs only keeps the events that belong to event_id

Alex
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3

I have:
event_id = 200 and I got only epochs corresponding to this events when I
created the epochs object. However I still have some bad epochs dropped
(their event_id are also 200) when I am usins epochs.get_data()...

2016-04-05 10:25 GMT+02:00 Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr>:

what is the content of event_id and events?

Epochs only keeps the events that belong to event_id

Alex

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4

For instance, I have the following output: 118 epochs corresponding to
events=200 are found, but when I applied get_data, 19 epochs are dropped...

epochs_s= mne.Epochs(raw,new_events, event_id,tmin,tmax, picks=picks,
baseline=(tmin_bsl,0))

    ...:

118 matching events found

Created an SSP operator (subspace dimension = 1)

1 projection items activated

epochs_s.get_data().shape

Applying baseline correction ... (mode: mean)

19 bad epochs dropped

Out[59]: (99, 366, 1701)

2016-04-05 10:29 GMT+02:00 Laetitia Grabot <laetitia.grabot at gmail.com>:

I have:
event_id = 200 and I got only epochs corresponding to this events when I
created the epochs object. However I still have some bad epochs dropped
(their event_id are also 200) when I am usins epochs.get_data()...

2016-04-05 10:25 GMT+02:00 Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr>:

what is the content of event_id and events?

Epochs only keeps the events that belong to event_id

Alex

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5

Hi Laetitia,

what is the output if you type epochs_s.drop_log? That might give some
clues of why they're dropped.

-Jaakko

6

Ahh, I get a list of [IGNORED], 19 [TOO_SHORT] and ! So do you have an
idea of why some epochs are too short ?

2016-04-05 10:38 GMT+02:00 Jaakko Lepp?kangas <jaeilepp at student.jyu.fi>:

Hi Laetitia,

what is the output if you type epochs_s.drop_log? That might give some
clues of why they're dropped.

-Jaakko

For instance, I have the following output: 118 epochs corresponding to
events=200 are found, but when I applied get_data, 19 epochs are dropped...

epochs_s= mne.Epochs(raw,new_events, event_id,tmin,tmax, picks=picks,
baseline=(tmin_bsl,0))

    ...:

118 matching events found

Created an SSP operator (subspace dimension = 1)

1 projection items activated

epochs_s.get_data().shape

Applying baseline correction ... (mode: mean)

19 bad epochs dropped

Out[59]: (99, 366, 1701)

2016-04-05 10:29 GMT+02:00 Laetitia Grabot <laetitia.grabot at gmail.com>:

I have:
event_id = 200 and I got only epochs corresponding to this events when I
created the epochs object. However I still have some bad epochs dropped
(their event_id are also 200) when I am usins epochs.get_data()...

2016-04-05 10:25 GMT+02:00 Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr>:

what is the content of event_id and events?

Epochs only keeps the events that belong to event_id

Alex

_______________________________________________
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Mne_analysis at nmr.mgh.harvard.edu
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it is
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HelpLine at
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in error
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7

Could it be that you have triggers at the end of the data (or you have a
big tmax) so that the ends of the epochs go beyond the recorded data?

8

Mmh, I'll check that. Thanks a lot for pointing me in the good directions!
Laetitia

2016-04-05 11:31 GMT+02:00 Jaakko Lepp?kangas <jaeilepp at student.jyu.fi>:

Could it be that you have triggers at the end of the data (or you have a
big tmax) so that the ends of the epochs go beyond the recorded data?

Ahh, I get a list of [IGNORED], 19 [TOO_SHORT] and ! So do you have an
idea of why some epochs are too short ?

2016-04-05 10:38 GMT+02:00 Jaakko Lepp?kangas <jaeilepp at student.jyu.fi>:

Hi Laetitia,

what is the output if you type epochs_s.drop_log? That might give some
clues of why they're dropped.

-Jaakko

For instance, I have the following output: 118 epochs corresponding to
events=200 are found, but when I applied get_data, 19 epochs are dropped...

epochs_s= mne.Epochs(raw,new_events, event_id,tmin,tmax, picks=picks,
baseline=(tmin_bsl,0))

    ...:

118 matching events found

Created an SSP operator (subspace dimension = 1)

1 projection items activated

epochs_s.get_data().shape

Applying baseline correction ... (mode: mean)

19 bad epochs dropped

Out[59]: (99, 366, 1701)

2016-04-05 10:29 GMT+02:00 Laetitia Grabot <laetitia.grabot at gmail.com>:

I have:
event_id = 200 and I got only epochs corresponding to this events when
I created the epochs object. However I still have some bad epochs dropped
(their event_id are also 200) when I am usins epochs.get_data()...

2016-04-05 10:25 GMT+02:00 Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr>:

what is the content of event_id and events?

Epochs only keeps the events that belong to event_id

Alex

_______________________________________________
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Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

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whom it is
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