I have a dataset that consists of source estimated data of MEG brain signals.

I need to extract the different frequency band features (i.e., alpha, beta, gamma, etc) from them.

What steps/procedure should I take?

My data consists of 1D numpy array for each brain region.

From a little search, it seems I have to take fourier transform first. But I couldn't understand why I should use fourier transform and what to do after that.

Information about source estimated data can be found here.

I want to use python to calculate them.

Thanks in advance...


1 Answer 1


MEG data is non-stationary and FFT can provide a crude approximation on clean data at best. Instead I'd recommend time-frequency analysis, like STFT or CWT.

CWT is favored as it adjusts its resolution to better discriminate higher frequencies in time, and lower frequencies in frequency, on logscale (which is appropriate for brain waves). Afterwards one can apply ridge extraction to extract independent components as 1D frequency vs time arrays. CWT and STFT can both be enhanced by synchrosqueezing, which studied have applied to EEG.


Ridge extraction example

EEG example:

enter image description here


  1. ssqueezepy - CWT, STFT, synchrosqueezing
  2. EEG synchrosqueezing
  3. I'd recommend learning some SP basics, as it'll save much time and hassle in the long run; I've made a list here.


FFT offers a simpler but limited approach: algorithm below will estimate M most dominant frequencies. Improve accuracy by splitting up input and feeding separately.

import numpy as np

def est_freqs(x, M=3, T=1, smoothing=None):
    xf = np.abs(np.fft.rfft(x))
    # to avoid picking from around the same bin
    if smoothing not in (0, 1):
        if smoothing is None:
            smoothing = max(len(x) // 500, 2)
        # ensure we can reshape
        xf = np.pad(xf, [0, smoothing - len(xf) % smoothing])
        xfs = xf.reshape(-1, smoothing).mean(axis=1)
        xfs = xf
    # sort descending
    idxs = list(range(len(xfs)))
    xf_idxs_sort = sorted(zip(list(xfs), idxs), key=lambda x: x[0], reverse=True)
    idxs_sort = [a[1] for a in xf_idxs_sort]    
    # map back to un-smoothed and account for `T`
    idxs_sort = np.round(len(x) / len(xfs) / 2 * np.array(idxs_sort) / T

    return idxs_sort[:M]

fs = 400         # sampling frequency [Hz]
T  = 3           # duration [sec]
noise_std = 1    # WGN standard deviation
freqs = [4, 28]  # frequencies to simulate
amps  = [3,  2]  # their amplitudes

N = int(fs * T)
t = np.linspace(0, T, N, endpoint=False)
x = np.zeros(N)
for f, a in zip(freqs, amps):
    x += a * np.cos(2*np.pi * f * t)
x += noise_std * np.random.randn(N)

print(est_freqs(x, T=T, M=len(freqs)))
>>> [4, 28]
  • $\begingroup$ Thank you very much for your explanation. $\endgroup$
    – Kadaj13
    Commented Jul 8, 2021 at 9:50
  • $\begingroup$ What about wavelet transform? Which is the best to use? $\endgroup$
    – Kadaj13
    Commented Jul 8, 2021 at 9:51
  • $\begingroup$ @Kadaj13 I'd compare Tx, Wx, *_ = ssq_cwt(x, ('gmw', {'beta': 60})) with beta=20 and 90, see which one best captures time and frequency components -- examples. After the (wavelet) transform I'd also recommend taking log - see lecture. (for SSQ one would first transform Wx and then do SSQ, in separate steps) $\endgroup$ Commented Jul 8, 2021 at 14:09

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