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app-make-epochs

Owned by Aurore Bussalb (Unlicensed)
Last updated: Jun 17, 2021
2 min read

app under development Private app on bl

This App epochs the data thanks to mne.Epochs.

 

GitHub repository

https://github.com/AuroreBussalb/app-make-epochs

 

Brainlife datatype used:

 

Inputs of the App

Files

Format

Datatype

Description

Optional

Files

Format

Datatype

Description

Optional

MEG signals

.fif

meg/fif

The data we want to epoch

No

events

.tsv

meg/fif or meg/fif-override

BIDS compliant events.tsv

no

This events file can be obtained thanks to the app-get-events (if so, the file will be linked to the meg/fif-override datatype) or can be directly available with the meg.fif in the meg/fif datatype. If there are two events.tsv (one from meg/fif datatype and the other from meg/fif-override datatype, only the file from the meg/fif-override will be used (see How to use the meg/fif-override datatype).

 

Outputs of the App:

Files

Format

Datatype

Description

Files

Format

Datatype

Description

MEG signals

.fif

meg/fif

Epoch data

Besides, in the output directory, there are the optional files that can be used in a next App (see How to run Apps one after another).

 

Parameters of the App

The parameters of the App correspond to the parameters passed to the Python functions used in the App. Their default values proposed in Brainlife or in config.json.example correspond to the default values of MNE Python 0.23.

With the MNE function used to create epoch, it is possible to directly removed epoch based on their amplitude with the parameters reject and flat. Unfortunately, these parameters can’t be used on BL (it’s set to “READ ONLY”) because they are dictionaries and BL doesn’t handle Python dictionaries as parameter values and no conversion script has been written in the python file of this app (see Parameters conversion to make an App run on BL

 

Next improvements

  • Be able to use the flat and reject parameters: register this parameter as a STRING in BL and convert it into a Python dict in make_epochs.py

  • Make sure that epochs are correctly created with an events.tsv from meg/fif datatype and from events.tsv extracted from the fif file with app-get-events