How to apply baseline methods to MNE preprocessed raw EEG signals?

Question

I am new at EEG preprocessing and classification. I have followed Clemens Brunner's blog https://cbrnr.github.io/2018/01/29/removing-eog-ica/ as a tutorial for MNE.

This is how I have preprocessed and singled out all the individual trials for all subjects in the dataset BCI Competition IV Dataset 2a. The dataset can be found here: http://bnci-horizon-2020.eu/database/data-sets

ch_names = ['Fz', 'FC3', 'FC1', 'FCz', 'FC2', 'FC4', 'C5', 'C3', 'C1', 'Cz',
        'C2', 'C4', 'C6', 'CP3', 'CP1', 'CPz', 'CP2', 'CP4', 'P1', 'Pz',
        'P2', 'POz']

mat = loadmat('A01T.mat')

for j in range(6):

    timelist = mat['data'][0][j+3][0][0][1]    //this gives starting of each event
    timelist = list(timelist)
    timelist.append(np.array([96735], dtype='int32'))    //length of eeg for single channel is added
    timelist = np.array(timelist)

    actionlist = mat['data'][0][j+3][0][0][2]    //these are the labels

    eeg = ((mat["data"][0][j+3][0][0][0]*10e-6).T)[:22]
    raw = mne.io.RawArray(eeg, info)
    raw.set_montage("standard_1020")
    raw.filter(1, 30)

    raw_temp = raw.copy()
    ica = mne.preprocessing.ICA(method='infomax', fit_params=dict(extended=True))
    ica = ica.fit(raw_temp, picks=['eeg'])
    ica.detect_artifacts(raw_temp)
    raw = ica.apply(raw)
    trial = raw.get_data()

    label = []
    train = []

    for k in range(48):
        trial_temp = trial[:, timelist[k][0]:timelist[k+1][0]]
        train.append(trial_temp)
        label.append(actionlist[k][0] - 1)

The file is saved in the shape of 22 channels and corresponding measures for the next 7-8 seconds. Frequency is 250Hz.

How do I apply baseline methods such as SVM to this preprocessed data?

Also, how do I calculate the power of the signals using FFT or any other method?

Answer 1

MNE has a fantastic website with a lot of documentation and many tutorial examples. Those examples include how to access machine learning classifiers in scikit-learn (to play with SVMs) as well as the methods for getting / plotting the power, extracting frequency components with FFT. You should definitely check out the website.

• Alex