A package to analyse MNE-formatted EEG data for steady-state visually evoked potentials (SSVEPs).
pip install git+https://github.com/janfreyberg/ssvepy.git
As always with pip packages, you can install a "development" version of this package by (forking and) cloning the git repository and installing it via pip install -e /path/to/package
. Please do open a pull request if you make improvements.
The docs for this package are at http://www.janfreyberg.com/ssvepy. There, you'll find the API and an example notebook.
You should load, preprocess and epoch your data using MNE.
Take a look at a notebook that sets up an SSVEP analysis structure with the example data in this package: https://github.com/janfreyberg/ssvepy/blob/master/example.ipynb
Once you have a data structure of the class Epoch
, you can use ssvepy.Ssvep(epoch_data, stimulation_frequency)
, where stimulation_frequency
is the frequency (or list of frequencies) at which you stimulated your participants.
Other input parameters and their defaults are:
- The following parameters, which are equivalent to the parameters in
mne.time_frequency.psd_multitaper
:fmin=0.1
, the low end of the frequency rangefmax=50
, the high end of the frequency rangetmin=None
, the start time of the segment you want to analysetmax=None
, the end time of the segment you want to analyse
noisebandwidth=1.0
, what bandwidth around a frequency should be used to calculate its signal-to-noise-ratio- Whether you want to compute the following nonlinearity frequencies:
compute_harmonics=True
compute_subharmonics=False
compute_intermodulation=True
(NB: only when there's more than one input frequency)- You can also provide your own Power-spectrum data, if you have worked it out using another method.
psd=None
The powerspectrum. Needs to be a numpy array with dimensions: (epochs, channels, frequency)freqs=None
The frequencys at which the powerspectrum was evaluated. Needs to be a one-dimensional numpy array.
The resulting data has the following attributes:
stimulation
: a data structure with the following attributes:stimulation.frequencies
,stimulation.power
,stimulation.snr
harmonics
,subharmonics
,intermodulations
: non-linear combination of your input stimulus frequencies, all with the attributes:_.frequencies
,_.power
,_.snr
,_.order
psd
: the Power-spectrumfreqs
: the frequencies at which the psd was evaluated
And the following methods:
plot_psd()
: Plot the power spectrumplot_snr()
: Plot the SNR spectrumsave(filename)
: Saves anhdf5
file that can be loaded withssvepy.load_ssvep(filename)
1
More to come.
1: This package currently uses hierarchical data files (hdf5) because it seems to lend itself to the different data stored in ssvep classes, but I know it's less than ideal to have different data structures from MNE. I'm still thinking about improvements.