Average epochs

[mmagnuski]

Summary of feature requests from this discussion:

• epoching (fixed in [MRG] Add handling of epochs #45)
• epoch selection (by condition/event)
• epochs concatenation (will be fixed in Append/concatenate epochs #131)
• epochs averaging (evoked)
• ERP plotting - this should work once epochs averaging is implemented

[mmagnuski]

sorry, accidental posting. :)
I wanted to ask about epoching - it seems not to be available in mnelab.
More broadly it would be good to have a list o mnelab features somewhere in the docs as it is not easy to tell what can be done in mnelab just by looking into main repo the documentation.

To use mnelab in class the following features would be necessary (at least from my perspective):

• epoching
• epoch selection (by condition/event)
• epochs averaging (evoked)
• ERP plotting
• creating new data by applying ICA (fixed in ADD Apply ICA function #43)

are these features within future scope of mnelab? If so I would like to help at some point but first I'd have to teach myself some pyqt. :)

[mmagnuski]

and it would be super useful to display code responsible for certain GUI operations (the equivalence of eeghist in eeglab).

[cbrnr]

I don't have a detailed roadmap for MNELAB, but epoching is definitely at the top of the list. This will require some restructuring (or at least thinking), so I can't say when it will be done. Applying ICA should be easier since computing ICA is already possible, and all that's missing is a simple command.

Something like eeghist already exists in the code, I just need to add a way to access the command history.

[cbrnr]

And regarding the documentation: there is no documentation yet, this would probably be the most important thing to start adding...

[vferat]

Some of these features are implemented in the fork we work on with @TyWR.

Some of them such as epoching and averaging are working fine, but the structure of the code may not be optimal for long term dev. For others features, some of them are custom plot that may not suit the MNE community. But there is several functions such as ICA and filtering which are pure MNE code that could be merged to the main repo.

In addition, we can help to developt new functions that are in neither of the repos

[cbrnr]

@vferat PRs welcome - maybe start with applying ICA to raw data? I will also work on some stuff, we should probably coordinate.

[mmagnuski]

@cbrnr
Oh, I now see that the command history is printed in the console, great!

[hoechenberger]

Two additional features that are essential for my workflow:

• concatenate epochs
• add a reference channel (already implemented)

[TyWR]

@cbrnr Would it possible to set up the Projects tab in your repo to get an overview of what is to be done, or currently in progress ?

That would be nice to coordinate the work on different features. I thought about adapting the code from our fork for the handling of epochs & evoked data type.

[cbrnr]

@hoechenberger concatenating epochs will be added as part of adding epochs in general. You can already add a reference channel if you go to Edit -> Set reference..., then click on Channel(s) and add a name that doesn't exist - this channel will be added as a new reference.

I think documenting the existing features is really the first thing to be done.

[cbrnr]

@TyWR I've never used this tab, but if it helps in tracking current progress I can of course set it up. So far I thought that creating issues was sufficient for that, because you can also assign an issue to specific persons.

[cbrnr]

Maybe let's stick with opening separate issues for missing features for now. I can assign to people if someone volunteers to implement/fix an issue.

[hoechenberger]

@hoechenberger concatenating epochs will be added as part of adding epochs in general. You can already add a reference channel if you go to Edit -> Set reference..., then click on Channel(s) and add a name that doesn't exist - this channel will be added as a new reference.

Great, thank you!

[cbrnr]

@mmagnuski could you please clarify what you mean by "epoch selection (by condition/event)"? Do you mean that epoch creation is based on specific events - this is already implemented in MNELAB. Or do you mean selection of epochs in an already existing Epochs object (if so, how is this done with MNE)?

[mmagnuski]

@cbrnr Hi, I think I might have meant selecting events to epoch by. The other thing is done in MNE with metadata attribute (epochs['stimulus == "face" & rotation == 0']) or event_id (epochs['face/0']). But I don't consider this second thing to be an "epoching feature" per se. However, it is sometimes useful in the epoching context as one can do slow_erp = epochs['RT > 0.65'].average().

[rob-luke]

Whats the latest on this topic? Does anyone have a branch attempting epoch plotting that I can look at? No stress if not, just wondering.

[cbrnr]

@rob-luke epoching is already implemented (which includes plotting). I think the only thing missing from this issue is creating an Evoked object from Epochs.

[rob-luke]

Sorry I was not very precise with my language, I was interested in evoked plotting. But I think you have answered my question, it’s not currently hiding in a branch somewhere and needs to be implemented. Thanks for the update.

[cbrnr]

This has now been implemented, currently only as a plotting option for Epochs objects.