Cookiecutter template for working with the healthy brain data
This is a template that implements some nice data-import syntax for the Child Mind Institute's Healthy Brain Data.
The main benefit to using this template is the provided data imports.
To see both live in action, take a look at the following notebooks:
For example, to download some data, you can use:
from data.download import download_sample_eeg download_sample_eeg(n=5)
This will download 5 EEG datasets
You can also import data by simply using an import statement:
from data.eeg.preprocessed.resting_state import raws for raw in raws(): # <your code here>
You can also import the phenotypic data:
from data import phenotypes
Implemented so far
At the moment, I've implemented raw and preprocessed EEG data imports for the resting-state, the video and the surround suppression conditions. For each one, you can import
When import raw data (
from data.eeg.raw...), you will literally just get all the data loaded in an MNE data structure. You can import the events and do the epoching yourself:
from data.eeg.raw.resting_state import events.
So the following:
from data.eeg.preprocessed.resting_state import raws, events for raw, event in zip(raws(), events(): epoch = mne.Epochs(raw, event, tmin=0, tmax=20)
would be equivalent to:
from data.eeg.preprocessed.resting_state import epochs for epoch in epochs(tmin=0, tmax=20): pass
The epoching is done semi-intelligently, so for example, when importing for the
video condition, you get Epochs that start with the video start and end with the video end. Do double check each import and how epochs are defined, simply check the corresponding python scripts!
To be implemented
Similar import statements for the rest of the EEG data, and the MRI data.