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Codecov test_suite CircleCI License Code style: black PyPI - Python Version Documentation Status PyPI Download count

MNE-HFO

MNE-HFO is a Python package that computes estimates of high-frequency oscillations in iEEG data stored in the BIDS-compatible datasets with the help of MNE-Python.

NOTE: This is currently in ALPHA stage, and we are looking for contributors. Please get in touch via Issues tab if you would like to contribute.

High frequency oscillations in epilepsy

A few notes that are worthy of reading. The initial papers on HFOs (Staba et al.) actually only observed HFOs on Hippocampus. In addition, the papers cited that are implemented all selected data before developing their algorithm (i.e. selected channels with HFOs).

It is also noted that the Hilbert detector was used to show HFOs exist in normal brain function, possibly unassociated with the epileptogenic zone.

Why?

Currently HFO detection and algorithms are segmented in Matlab files, which are sometimes not open-source, or possibly difficult to use. In addition, validation of HFO algorithms depend on i) sharing the algorithms ii) sharing the results with others in a readable format and iii) comparing algorithms against each other on the same dataset.

MNE-HFO links BIDS, MNE-Python and iEEG HFO event detection with the goal to make HFO detection more transparent, more robust, and facilitate data and code sharing with co-workers and collaborators.

Installation

Installation can be done via a python virtual environment, using pipenv. The package is hosted on pypi, which can be installed via pip, or pipenv. For additional installation instructions, see CONTRIBUTING.md document.

pip install mne-hfo

or

pipenv install mne-hfo

Note: Installation has been tested on MacOSX and Ubuntu, but should probably work on Windows too.

Documentation and Usage

The documentation can be found under the following links:

Note: Functionality has been tested on MacOSX and Ubuntu.

Basic Working Example

A basic working example is listed here, assuming one has loaded in a mne-Python Raw object already.

from mne_hfo import RMSDetector
detector = RMSDetector()

# assume user has loaded in raw iEEG data using mne-python
detector.fit(raw)

# get the HFO events as an *events.tsv style dataframe
hfo_event_df = detector.hfo_event_df

# get the HFO events as an *events.tsv style dataframe
hfo_annot_df = detector.hfo_df

All output to *events.tsv BIDS-compliant files will look like the following:

onset duration sample trial_type
1 3 1000 hfo_A2-A1

which will imply that there is an HFO detected using a bipolar referencing at channel A2-A1 at 1 second with duration of 3 seconds. The onset sample occurs at sample 1000 (thus sfreq is 1000 Hz). If a monopolar referencing is used, then the trial_type might be hfo_A2 to imply that an HFO was detected at channel A2.

Alternatively, one can output the data in the form of a derivatives Annotations DataFrame, which is the RECOMMENDED way. Outputting data according to BIDS Extension Proposal 21, instead would result in an *annotations.tsv file.

onset duration label channels
1 3 hfo A2-A1

with a corresponding *annotations.json file.

{
    'IntendedFor': sub-01/ses-01/eeg/sub-01_ses-01_task-01_eeg.<ext>,
    'Description': 'Automatic annotations of HFO events using mne-hfo.',
}

Optimizing Hyperparameters

In all MNE-HFO HFO detectors, we assume that there are hyper-parameters specified by the proposed algorithm. These hyper-parameters can be tuned automatically using the scikit-learn API for GridSearchCV.

from sklearn.metrics import make_scorer
from sklearn.model_selection import GridSearchCV
from mne_hfo.score import accuracy
from mne_hfo.sklearn import make_Xy_sklearn, DisabledCV

# define hyperparameter grid to search over
parameters = {'threshold': [1, 2, 3], 'win_size': [50, 100, 250]}

# define HFO detector
detector = LineLengthDetector()

# define a scoring function 
scorer = make_scorer(accuracy)

# we don't use cross-validation since the
# HFO algorithm is deterministic
cv = DisabledCV()

# instantiate the GridSearch object
gs = GridSearchCV(detector, param_grid=parameters, scoring=scorer,
                  cv=cv, refit=False, verbose=True)

# load in raw data
# raw = <load_in_raw_data>

# load in HFO annotations
# annot_df = <load_in_annotations>

# make sklearn compatible
raw_df, y = make_Xy_sklearn(raw, annot_df)

# run hyperparameter tuning based on accuracy score
gs.fit(raw_df, y, groups=None)

# show the results
print(gs.cv_results_["mean_test_score"])

In the above example, to load in raw data, one can use mne-bids and to load in the annotations dataframe, one can check out our API for different ways of doing so.

Citing

For testing and demo purposes, we use the dataset in [1]. If you use the demo/testing dataset, please cite that paper. If you use mne-hfo itself in your research, please cite the paper (TBD).

Adam Li. (2021, February 1). MNE-HFO: An open-source Python implementation of HFO detection algorithms (Version 0.0.1). Zenodo. http://doi.org/10.5281/zenodo.4485036

History and state of development

The initial code was adapted and taken from: https://gitlab.com/icrc-bme/epycom to turn into a sklearn-compatible API that works with mne-python. Additional algorithms and functionality were added.

References

[1] Fedele T, Burnos S, Boran E, Krayenbühl N, Hilfiker P, Grunwald T, Sarnthein J. Resection of high frequency oscillations predicts seizure outcome in the individual patient. Scientific Reports. 2017;7(1):13836. https://www.nature.com/articles/s41598-017-13064-1 doi:10.1038/s41598-017-13064-1