# reject parameter for epochs and get\_data() **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [April 5, 2016, 8:16am UTC](https://mne.discourse.group/t/reject-parameter-for-epochs-and-get-data/984 "2016-04-05T08:16:57Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 5, 2016, 8:16am UTC](https://mne.discourse.group/t/reject-parameter-for-epochs-and-get-data/984/1 "2016-04-05T08:16:57Z")
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 -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20160405/4a62d31e/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160405/4a62d31e/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 5, 2016, 8:25am UTC](https://mne.discourse.group/t/reject-parameter-for-epochs-and-get-data/984/2 "2016-04-05T08:25:18Z")
what is the content of event\_id and events? Epochs only keeps the events that belong to event\_id Alex -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20160405/3177fb5d/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160405/3177fb5d/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 5, 2016, 8:29am UTC](https://mne.discourse.group/t/reject-parameter-for-epochs-and-get-data/984/3 "2016-04-05T08:29:01Z")
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 > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > Mne\_analysis mailing list > Mne\_analysis at nmr.mgh.harvard.edu > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20160405/f8074458/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160405/f8074458/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 5, 2016, 8:34am UTC](https://mne.discourse.group/t/reject-parameter-for-epochs-and-get-data/984/4 "2016-04-05T08:34:23Z")
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 \: > 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 > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Mne\_analysis mailing list > > Mne\_analysis at nmr.mgh.harvard.edu > > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > > > The information in this e-mail is intended only for the person to whom it > > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you > > in error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20160405/ac27206c/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160405/ac27206c/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 5, 2016, 8:38am UTC](https://mne.discourse.group/t/reject-parameter-for-epochs-and-get-data/984/5 "2016-04-05T08:38:20Z")
Hi Laetitia, what is the output if you type epochs\_s.drop\_log? That might give some clues of why they're dropped. -Jaakko ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 5, 2016, 8:55am UTC](https://mne.discourse.group/t/reject-parameter-for-epochs-and-get-data/984/6 "2016-04-05T08:55:41Z")
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 \: > 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 \: > > > > > 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 > > > > > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > > > Mne\_analysis mailing list > > > > Mne\_analysis at nmr.mgh.harvard.edu > > > > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > > > > > > > The information in this e-mail is intended only for the person to whom > > > > it is > > > > addressed. If you believe this e-mail was sent to you in error and the > > > > e-mail > > > > contains patient information, please contact the Partners Compliance > > > > HelpLine at > > > > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you > > > > in error > > > > but does not contain patient information, please contact the sender and > > > > properly > > > > dispose of the e-mail. > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Mne\_analysis mailing list > > Mne\_analysis at nmr.mgh.harvard.edu > > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > > > The information in this e-mail is intended only for the person to whom it > > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you > > in error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > Mne\_analysis mailing list > Mne\_analysis at nmr.mgh.harvard.edu > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20160405/3f8b76bb/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160405/3f8b76bb/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 5, 2016, 9:31am UTC](https://mne.discourse.group/t/reject-parameter-for-epochs-and-get-data/984/7 "2016-04-05T09:31:09Z")
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? ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 5, 2016, 9:50am UTC](https://mne.discourse.group/t/reject-parameter-for-epochs-and-get-data/984/8 "2016-04-05T09:50:40Z")
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 \: > 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 \: > > > > > 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 \: > > > > > > > > > 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 > > > > > > > > > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > > > > > Mne\_analysis mailing list > > > > > > Mne\_analysis at nmr.mgh.harvard.edu > > > > > > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > > > > > > > > > > > The information in this e-mail is intended only for the person to > > > > > > whom it is > > > > > > addressed. If you believe this e-mail was sent to you in error and > > > > > > the e-mail > > > > > > contains patient information, please contact the Partners Compliance > > > > > > HelpLine at > > > > > > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to > > > > > > you in error > > > > > > but does not contain patient information, please contact the sender > > > > > > and properly > > > > > > dispose of the e-mail. > > > > > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > > > Mne\_analysis mailing list > > > > Mne\_analysis at nmr.mgh.harvard.edu > > > > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > > > > > > > The information in this e-mail is intended only for the person to whom > > > > it is > > > > addressed. If you believe this e-mail was sent to you in error and the > > > > e-mail > > > > contains patient information, please contact the Partners Compliance > > > > HelpLine at > > > > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you > > > > in error > > > > but does not contain patient information, please contact the sender and > > > > properly > > > > dispose of the e-mail. > > > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > > Mne\_analysis mailing list > > > Mne\_analysis at nmr.mgh.harvard.edu > > > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > > > > > The information in this e-mail is intended only for the person to whom > > > it is > > > addressed. If you believe this e-mail was sent to you in error and the > > > e-mail > > > contains patient information, please contact the Partners Compliance > > > HelpLine at > > > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you > > > in error > > > but does not contain patient information, please contact the sender and > > > properly > > > dispose of the e-mail. > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Mne\_analysis mailing list > > Mne\_analysis at nmr.mgh.harvard.edu > > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > > > The information in this e-mail is intended only for the person to whom it > > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you > > in error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > Mne\_analysis mailing list > Mne\_analysis at nmr.mgh.harvard.edu > [Mne\_analysis Info Page](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > [MyComplianceReport.com: Compliance and Ethics Reporting](http://www.partners.org/complianceline) . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20160405/be2b3898/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160405/be2b3898/attachment.html)