[Mne_analysis] merge/combine events MNE Python

Teon Brooks teon.brooks at gmail.com
Sun Mar 27 15:54:49 EDT 2016
Search archives: 
Just to follow up here, the merge event bug has been resolved
<https://github.com/mne-tools/mne-python/pull/3076> and it is now available
on the dev version. This fix will be included in the v0.12 release in the
nearby future.



teon
--


Teon Brooks, PhD Candidate
NSF Fellow, Chateaubriand Fellow
Department of Psychology, New York University
Researcher | OpenBCI
Co-Chair | BraiNY, Greater NYC Chapter of Society for Neuroscience

On Thu, Mar 17, 2016 at 10:57 AM, Cushing, Cody <CCUSHING1 at mgh.harvard.edu>
wrote:

> Ah, thank you!
> ------------------------------
> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu [
> mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Teon Brooks [
> teon.brooks at gmail.com]
> *Sent:* Thursday, March 17, 2016 10:54 AM
>
> *To:* Discussion and support forum for the users of MNE Software
> *Subject:* Re: [Mne_analysis] merge/combine events MNE Python
>
> Sorry I followed up directly but forgot to relay it back here. I made pull
> request to fix this behavior. If you would like to follow along the
> process, you can do so here:
> https://github.com/mne-tools/mne-python/pull/3015
> On Thu, Mar 17, 2016 at 10:50 Cushing, Cody <CCUSHING1 at mgh.harvard.edu>
> wrote:
>
>> Hi all,
>>
>> Was any resolution ever found on this?  I'm now experiencing the same
>> thing where trying to multiple merge_events before epoching results in an
>> obscene amount of trial counts per condition (e.g. my condition 1 nave goes
>> from 69 > 228), so I believe my problem to identical to Lucy's below.
>> Thanks for any help or input.
>>
>> Cheers,
>> Cody
>> ------------------------------
>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu [
>> mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Teon Brooks [
>> teon.brooks at gmail.com]
>> *Sent:* Wednesday, February 24, 2016 8:00 PM
>>
>> *To:* Discussion and support forum for the users of MNE Software
>> *Subject:* Re: [Mne_analysis] merge/combine events MNE Python
>> Could you send directly me the code you used and a sample file to
>> reproduce this problem? From what I read, I can't reproduce it with the
>> sample data.
>> On Thu, Feb 18, 2016 at 11:51 Lucy MacGregor <
>> Lucy.MacGregor at mrc-cbu.cam.ac.uk> wrote:
>>
>>> Hi Teon,
>>>
>>>
>>>
>>> Thank you. Your suggestion is what I’d originally hoped to do but I
>>> would like **multiple** new combinations (e.g., condE(11,12) **and**
>>> condF(13,14)) and I couldn’t figure out how I could use the function to do
>>> this to create a list of the events.
>>>
>>>
>>>
>>> Initially I did:
>>>
>>> events=mne.event.merge_events(events, [11,12], 1112,
>>> replace_events=False)
>>>
>>> events=mne.event.merge_events(events, [13,14], 1314 replace_events=False)
>>>
>>> In doing mne.event.merge_events the second time, at a given sample point
>>> the original and new event codes are repeated twice (event codes not
>>> included in recombinations are repeated 4 times).
>>>
>>>
>>>
>>> Best,
>>>
>>> Lucy
>>>
>>>
>>>
>>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:
>>> mne_analysis-bounces at nmr.mgh.harvard.edu] *On Behalf Of *Teon Brooks
>>> *Sent:* 18 February 2016 16:11
>>>
>>>
>>> *To:* Discussion and support forum for the users of MNE Software
>>> *Subject:* Re: [Mne_analysis] merge/combine events MNE Python
>>>
>>>
>>>
>>> Hi Lucy,
>>>
>>> This might help, there's a argument with merge_events named
>>> 'replace_events' that allows you to retain the original values when set to
>>> False. In your example, you could combine 11 and 12 and assign to a value
>>> like 99. In your event_id dict, you could then assign CondE to 99.
>>>
>>> HTH,
>>>
>>>
>>>
>>> On Thu, Feb 18, 2016 at 09:52 Lucy MacGregor <
>>> Lucy.MacGregor at mrc-cbu.cam.ac.uk> wrote:
>>>
>>> Dear Natalie,
>>>
>>>
>>>
>>> Thank you for the suggestion. My understanding of
>>> mne.epochs.combine_event_ids is that it replaces the original events with
>>> new ones whereas I would like to retain the original events which is why I
>>> initially tried mne.event.merge_events.
>>>
>>>
>>>
>>> I can now do what I want to do using Mainak’s suggestion to use the
>>> hierarchical feature of epoch selection. I created multiple evoked files
>>> corresponding to my various event combinations then saved the combinations
>>> into one file using mne.write_evokeds.
>>>
>>>
>>>
>>>
>>>
>>> Thank you both!
>>>
>>>
>>>
>>> Best,
>>>
>>>
>>>
>>> Lucy
>>>
>>>
>>>
>>>
>>>
>>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:
>>> mne_analysis-bounces at nmr.mgh.harvard.edu] *On Behalf Of *Natalie Klein
>>> *Sent:* 18 February 2016 13:02
>>>
>>>
>>> *To:* Discussion and support forum for the users of MNE Software
>>> *Subject:* Re: [Mne_analysis] merge/combine events MNE Python
>>>
>>>
>>>
>>> Dear Lucy,
>>>
>>>
>>>
>>> Maybe I misunderstand what you are trying to do, but it seems
>>> like mne.epochs.combine_event_ids might be helpful. I'm not sure what you
>>> mean about saving them all into one file but you could define new event ids
>>> to combine epochs across conditions then create evoked files from those.
>>>
>>>
>>>
>>> On Thu, Feb 18, 2016 at 7:45 AM, Lucy MacGregor <
>>> Lucy.MacGregor at mrc-cbu.cam.ac.uk> wrote:
>>>
>>> Dear Mainak,
>>>
>>>
>>>
>>> Many thanks for the reply and the pointer. This seems helpful to access
>>> different combinations of the events, but is it then possible to create
>>> multiple new epoch objects (condE and condF) which can be then saved
>>> together in a single evoked file along with the originals? Ideally I would
>>> have the event/condition averages for all conditions (new and old) in one
>>> file.
>>>
>>>
>>>
>>> Best,
>>>
>>>
>>>
>>> Lucy
>>>
>>>
>>>
>>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:
>>> mne_analysis-bounces at nmr.mgh.harvard.edu] *On Behalf Of *Mainak Jas
>>> *Sent:* 18 February 2016 10:22
>>> *To:* Discussion and support forum for the users of MNE Software
>>> *Subject:* Re: [Mne_analysis] merge/combine events MNE Python
>>>
>>>
>>>
>>> Dear Lucy,
>>>
>>> It seems what you want to do is to use the hierarchical epochs
>>> selection. If you have an epochs object which contains condA, condB, condC
>>> and condD, you can get epochs of condE by simply using epochs['condA',
>>> 'condB']. Please take a look at the MNE reference API for the epochs
>>> object:
>>> http://martinos.org/mne/stable/generated/mne.Epochs.html#mne.Epochs
>>> (look at the Notes section). Does this solve your problem?
>>>
>>> Best regards,
>>>
>>> Mainak
>>>
>>>
>>>
>>> On Thu, Feb 18, 2016 at 10:27 AM, Lucy MacGregor <
>>> Lucy.MacGregor at mrc-cbu.cam.ac.uk> wrote:
>>>
>>> Dear MNE Python users,
>>>
>>>
>>>
>>>
>>>
>>> I would like to combine event codes to create a number of new events
>>> whilst retaining the originals. E.g.,
>>>
>>>
>>>
>>> CondA = 11
>>>
>>> CondB = 12
>>>
>>> CondC = 13
>>>
>>> CondD = 14
>>>
>>> CondE = 11,12
>>>
>>> CondF = 13,14
>>>
>>>
>>>
>>>
>>>
>>> Is there a straightforward way to do this? I have seen this thread
>>>
>>>
>>>
>>>
>>> https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2013-April/001498.html
>>> <https://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/2013-April/001498.html>
>>>
>>>
>>>
>>>
>>>
>>> Using mne.event.merge_events works fine when I was just creating one new
>>> event (as does the alternative method of combining events at the evoked
>>> stage) but I’m unsure of the most sensible way to proceed given I want to
>>> create multiple new events. I originally did this:
>>>
>>>
>>>
>>> events=mne.event.merge_events(events, [11,12], 1112,
>>> replace_events=False)
>>>
>>> events=mne.event.merge_events(events, [13,14], 1314 replace_events=False)
>>>
>>>
>>>
>>> but then, because I’m not replacing events, I end up with multiple
>>> copies of all events (even those not included in the merge_events function)
>>>  at a given sample point, which isn’t ideal.
>>>
>>>
>>>
>>> As a new MNE Python user (I previously used MNE) I would be grateful for
>>> any advice as the best way to do this.
>>>
>>>
>>>
>>>
>>>
>>> Thank you,
>>>
>>>
>>>
>>> Lucy MacGregor
>>>
>>>
>>>
>>>
>>>
>>> ******************************************************************
>>>
>>> Lucy MacGregor
>>>
>>> MRC Cognition and Brain Sciences Unit
>>>
>>> 15 Chaucer Road
>>>
>>> Cambridge CB2 7EF
>>>
>>> Tel: 01223 355294 Ext 860
>>>
>>> http://www.mrc-cbu.cam.ac.uk/people/lucy.macgregor/
>>>
>>>
>>>
>>>
>>>
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>>> teon
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>> --
>> teon
>> --
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> --
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> --
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