[Mne_analysis] merge/combine events MNE Python

Teon Brooks teon.brooks at gmail.com
Thu Mar 17 10:54:59 EDT 2016
Search archives: 
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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>>
>>
>>
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>> teon
>> --
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