mne_nirs.preprocessing.scalp_coupling_index_windowed

mne_nirs.preprocessing.scalp_coupling_index_windowed(raw, time_window=10, threshold=0.1, l_freq=0.7, h_freq=1.5, l_trans_bandwidth=0.3, h_trans_bandwidth=0.3, verbose=False)

Compute scalp coupling index for each channel and time window.

As described in [1] and [2]. This method provides a metric of data quality along the duration of the measurement. The user can specify the window over which the metric is computed.

Parameters:

rawinstance of Raw

The haemoglobin data.

time_windownumber

The duration of the window over which to calculate the metric. Default is 10 seconds as in PHOEBE paper.

thresholdnumber

Values below this are marked as bad and annotated in the raw file.

l_freqfloat | None

For FIR filters, the lower pass-band edge; for IIR filters, the lower cutoff frequency. If None the data are only low-passed.

h_freqfloat | None

For FIR filters, the upper pass-band edge; for IIR filters, the upper cutoff frequency. If None the data are only high-passed.

l_trans_bandwidthfloat | str

Width of the transition band at the low cut-off frequency in Hz (high pass or cutoff 1 in bandpass). Can be “auto” (default) to use a multiple of l_freq:

min(max(l_freq * 0.25, 2), l_freq)

Only used for method='fir'.

h_trans_bandwidthfloat | str

Width of the transition band at the high cut-off frequency in Hz (low pass or cutoff 2 in bandpass). Can be “auto” (default in 0.14) to use a multiple of h_freq:

min(max(h_freq * 0.25, 2.), info['sfreq'] / 2. - h_freq)

Only used for method='fir'.

verbosebool | str | int | None

Control verbosity of the logging output. If None, use the default verbosity level. See the logging documentation and mne.verbose() for details. Should only be passed as a keyword argument.

Returns:

rawinstance of Raw

The Raw data. Optionally annotated with bad segments.

scoresarray (n_nirs, n_windows)

Array of peak power values.

timeslist

List of the start and end times of each window used to compute the peak spectral power.

References

[1]

Pollonini L et al., “PHOEBE: a method for real time mapping of optodes-scalp coupling in functional near-infrared spectroscopy” in Biomed. Opt. Express 7, 5104-5119 (2016).

[2]

Hernandez, Samuel Montero, and Luca Pollonini. “NIRSplot: a tool for quality assessment of fNIRS scans.” Optics and the Brain. Optical Society of America, 2020.

Examples using mne_nirs.preprocessing.scalp_coupling_index_windowed

Signal Quality Evaluation

Signal Quality Evaluation