p3k - yet another offline ERP analysis tool

From BCI2000 and OpenVibe P300 Speller. Based on mne-python

• Supported bci software
  • BCI2000 (BCI2kReader by @markusadamek)
  • OpenVibe
• Preprocessing features
  • REST infinity rereferencing
  • artifact subspace reconstruction (meegkit by @nbara)
  • current source density (CSD)
  • Artifact rejection channel/trial based
• ERP visualization
  • Target vs Non-target plots and topographic maps
  • signed r-square heatmaps (wyrm by @bbci)
• Classification
  • cross-fold shrinkage LDA
• Sample Data
  • OpenVibe P300 provided in ./data_sample

signed r-square maps	offline classification

Requirements

• OpenViBE ( for converting to gdf)
• python 3.7+
• If you want to use Artifact Subspace Reconstruction you must manually install
  • pip install "git+https://github.com/nbara/python-meegkit"
  • pip install statsmodels pyriemann

Install via pip

pip install p3k

or Install from git

• git clone https://github.com/lokinou/p3k_offline_analysis.git
• cd p3k_offline_analysis
• create an anaconda environment conda env create -f environment.yml python=3.8.1
• activate the environment conda activate p3k
• If you want to use Artifact subspace reconstrunction you must install this
  • pip install "git+https://github.com/nbara/python-meegkit"
  • pip install statsmodels pyriemann
• Install the p3k package pip install .
• Finally, check that p3k works, this should trigger no error python -c "import p3k"

Usage

If you are trying to modify from sources, make sure in the first lines of P300Analysis.py that DEVELOP = True to make sure python loads the current source files and not the package installe with pip located in site-packages.

Test the sample data

from p3k.P300Analysis import run_analysis
run_analysis()

BCI2000 data

Put the file(s) inside a folder

from p3k.P300Analysis import run_analysis
from p3k.params import ParamData

# Define the path to data parameter
p_data = ParamData(data_dir='./data_bci2k')

# run the analysis
run_analysis(param_data=p_data)

If the electrode names were not defined in the dat files, you must specify them manually

from p3k.params import ParamChannels
p_channels = ParamChannels(cname=['Fz','FC1','FC2','C1','Cz','C2','P3','Pz','P4','Oz'])
run_analysis(..., param_channels=p_channels)

OpenVibe data

Check my tutorial to convert .ov to .gdf

OpenVibe to gdf conversion does not carry channel names, and P300 Speller description, we must define them here

from p3k.P300Analysis import run_analysis
from p3k.params import ParamChannels, ParamData, SpellerInfo

# channel
p_channels = ParamChannels(cname=['Fz','FC1','FC2','C1','Cz','C2','P3','Pz','P4','Oz'])

# P300 speller description
speller_info = SpellerInfo(nb_stimulus_rows=7, nb_stimulus_cols=7, nb_seq=10)

# gdf file location
p_data = ParamData(data_files=r'./data_ov')

# run the analysis
run_analysis(param_data=p_data, param_channels=p_channels, speller_info=speller_info)

Changing any parameter

If not initialized or passed to run_analysis() default parameters apply. You can change them very easily:

from p3k.P300Analysis import run_analysis
from p3k.params import ParamData, ParamPreprocessing, ParamArtifacts, ParamEpochs, ParamLDA, ParamInterface, DisplayPlots, SpellerInfo

p_data = ParamData(data_files='./data')

# Change the length of the ERP window and baseline
p_epoch = ParamEpochs(time_epoch=(-0.5, 0.8), time_baseline=(-.1, 0))

# Use artifact subspace reconstruction for noisy data, and select another bandpass
p_preproc = ParamPreprocessing(apply_ASR=True, bandpass=(.5, 30))

# Change the number of cross fold to match the number of trials (e.g 8)
p_lda = ParamLDA(nb_cross_fold=8)

# Select which plots to display
p_plots = DisplayPlots(butterfly_topomap=True)

# Visualize a few of those parameters
print(p_epoch)
print(p_plots)

# Launch the analysis
run_analysis(param_data=p_data, param_epoch=p_epoch, param_preprocessing=p_preproc, param_lda=p_lda, param_plots=p_plots)

Output

By default, figures are saved into ./out/<name_first_datafile>/*

Accessing the notebook

• Follow the instructions to "Install from git"

• move to the current repository folder cd %USERPROFILE%\Desktop\p3k_offline_analysis

• activate the environment conda activate p3k

• execute the notebook: jupyter lab p300_analysis.ipynb

  • if jupyter lab crashes (win32api error), reinstall it from conda conda install pywin32 jupyterlab BCI2kReader

  • if jupyter lab does not want to work yet, use jupyter notebook instead by executing jupyter notebook p300_analysis.ipynb