mne.annotations.rename changes value of key-value pair in event_id variable

💬 Support & Discussions
1
  • MNE version: 1.1.1
  • operating system: ManjaroLinux 21.3.6

I want to rename my annotations. Calling mne.events_from_annotations I can see that the event_id variable looks like this

{
  'New Segment/': 99999, 
  'Stimulus/S240': 240, 
  'Stimulus/S241': 241, 
  'Stimulus/S242': 242, 
  'Stimulus/S243': 243, 
  'Stimulus/S244': 244, 
  'Stimulus/S245': 245, 
  'Stimulus/S246': 246, 
  'Stimulus/S247': 247
}

as the keys are not good descriptors I want to rename the annotations by using mne.annotations.rename

EEG.annotations.rename({'Stimulus/S240': 'Rest',
                                           'Stimulus/S241': 'Right/Open', 
                                           'Stimulus/S242': 'Right/Close', 
                                           'Stimulus/S243': 'Right/Two',
                                           'Stimulus/S244': 'Left/Open',
                                           'Stimulus/S245': 'Left/Close',
                                           'Stimulus/S246': 'Left/Two',
                                           'Stimulus/S247': 'Prepare'})

which changes the event_id variable to

{ 
  'Left/Close': 10001, 
  'Left/Open': 10002, 
  'Left/Two': 10003, 
  'New Segment/': 99999, 
  'Prepare': 10004, 
  'Rest': 10005, 
  'Right/Close': 10006, 
  'Right/Open': 10007, 
  'Right/Two': 10008
}

as you will notice, while the keys changed, the values did too. However, I want to preserve the values. Why does mne.annotations.rename behave like this and how to handle this?

EDIT:

I noticed that this also happens when saving a raw file to fif with fmt=‘double’. After loading the file, the values have changed.

2

Hello @Killua and welcome to the forum!

This seems like a bug to me. Do you think you could produce a very small example that demonstrates the issue and is based on the MNE-Python sample dataset? That way, it will be much easier for the developers to reproduce (and fix) the problem.

Thanks!

Richard

3

mne.events_from_annotations produces non-deterministic numbers for IDs as long

as they are different.

If you rename the annotations and redo mne.events_from_annotations it’s expected
the event_id values can be changed but it should not change your ability to select
epochs with the keys

Alex

2 Likes
4

I believe @agramfort is right and my statement above:

was therefore incorrect.

5

Good to know that this is indeed the intended behavior of the method. However, I’m wondering why mne.events_from_annotations was designed like this, as it seems like behavior that you don’t really want and may be confusing. Maybe in following releases generation of non-deterministic numbers for IDs can be optionally turned off? If you don’t plan to change this method in the near future, I think at least a note in the documentation about this would be beneficial to other users.

6

Annotations don’t have any event IDs associated with them. That’s the source of the problem.

events_from_annotations() tries to work with the event naming scheme of BrainVision data to assign event IDs, if your annotation names follow this scheme. This is just a heuristic, and this behavior is documented:

Screen Shot 2022-09-02 at 12.30.36
Screen Shot 2022-09-02 at 12.30.361104×942 121 KB

By renaming your annotations, you’re essentially destroying the BV naming scheme you started out with, and now MNE has no way to figure out which event IDs should/could be desired, so it just assigns new ones.

You can pass an event_id mapping to events_from_annotations() where you explicitly map the new (renamed) annotation names to your desired event IDs.

Best wishes,
Richard

1 Like
7

Just pass the event_id parameter as a dict to control this behavior

Alex

2 Likes