Deliberate Differences from MATLAB PREP

Although PyPREP aims to be a faithful reimplementation of the original MATLAB version of PREP, there are a few places where PyPREP has deliberately chosen to use different defaults than the MATLAB PREP.

To override these differerences, you can set the matlab_strict parameter for PrepPipeline, Reference, or NoisyChannels to True in order to match the original PREP’s internal math.

Differences in Signal Detrending

In the PREP pipeline, trends (i.e., slow drifts in EEG baseline signal) are temporarily removed from the data prior to adaptive line-noise removal as well as prior to bad channel detection via NoisyChannels, which occurs at multiple points during robust re-referencing. This is done to improve the accuracy of both of these processes, which are sensitive to influence from trends in the signal.

In MATLAB PREP, the default method of trend removal is to use EEGLAB’s pop_eegfiltnew, which creates and applies an FIR high-pass filter to the data. MNE’s mne.filter.filter_data() offers similar functionality, but with two key differences:

  1. MNE’s method of FIR filter design has minor differences, resulting in slightly lower FIR filter orders than EEGLAB for the same input values (e.g. 845 instead of EEGLAB’s 847).

  2. EEGLAB’s pop_eegfiltnew only applies the filter to the signal forwards, resulting in minor phase shift in the filtered signal. By contrast, MNE defaults to applying the filter both forwards and backwards, eliminating any phase shift from the filtering process.

As a result of these differences, NoisyChannels values also differ slightly (on the order of ~0.002) for RANSAC correlations between the filtering methods.

Because MNE’s filtering code is faster and technically preferable (due to the lack of phase shift) PyPREP defaults to using mne.filter.filter_data() for high-pass trend removal. However, for exact numeric equivalence, PyPREP has a basic re-implementation of EEGLAB’s pop_eegfiltnew in Python that produces identical results to MATLAB PREP’s removeTrend when the matlab_strict parameter is set to True.

Differences in RANSAC

During the “find-bad-by-RANSAC” step of noisy channel detection (see find_bad_by_ransac()), PREP does the following steps to identify channels that aren’t well-predicted by the signals of other channels:

  1. Generates a bunch of random subsets of currently-good channels from the data (50 samples by default, each containing 25% of the total EEG channels in the dataset).

  2. Uses the signals and spatial locations of those channels to predict what the signals will be at the spatial locations of all the other channels, with each random subset of channels generating a different prediction for each channel (i.e., 50 predicted signals per channel by default).

  3. For each channel, calculates the median predicted signal from the full set of predictions.

  4. Splits the full data into small non-overlapping windows (5 seconds by default) and calculates the correlation between the median predicted signal and the actual signal for each channel within each window.

  5. Compares the correlations for each channel against a threshold value (0.75 by default), flags all windows that fall below that threshold as ‘bad’, and calculates the proportions of ‘bad’ windows for each channel.

  6. Flags all channels with an excessively high proportion of ‘bad’ windows (minimum 0.4 by default) as being ‘bad-by-RANSAC’.

With that in mind, here are the areas where PyPREP’s defaults deliberately differ from the original PREP implementation:

Use of random seeds

In MATLAB PREP, the random seed used for RANSAC is always 435656, which is set just before random channel sampling occurs. This means that every run of RANSAC will result in identical random samples of channels given the same input, and will produce similar random samples of channels if a channel or two are removed between iterations.

Conversely, PyPREP defaults to setting an initial random state for the whole pipeline, meaning that RANSAC’s random channel picks will differ between consecutive runs during robust re-referencing or bad channel detection. This approach has the benefit of better randomness, but may also lead to more variability in PREP results between different seed values. More testing is required to determine which approach produces better results.

Note that to match MATLAB PREP exactly when the matlab_strict parameter is set to True, the random seed 435656 must be used.

Calculation of median estimated signal

In MATLAB PREP, the median signal in step 3 is calculated by sorting the different predictions for each EEG sample/channel from low to high and then taking the value at the middle index for each. The relevant lines of MATLAB PREP’s findNoisyChannels.m are reproduced below:

function rX = calculateRansacWindow(XX, P, n, m, p)
    YY = sort(reshape(XX*P, n, m, p),3);
    YY = YY(:, :, round(end/2));
    rX = sum(XX.*YY)./(sqrt(sum(XX.^2)).*sqrt(sum(YY.^2)));

The first line of the function generates the full set of predicted signals for each RANSAC sample, and then sorts the predicted values for each channel / timepoint from low to high. The second line calculates the index of the middle value (round(end/2)) and then uses it to take the middle slice of the sorted array to get the median predicted signal for each channel.

Because this logic only returns the correct result for odd numbers of samples, the current function will instead return the true median signal across predictions unless strict MATLAB equivalence is requested.

Correlation of predicted vs. actual signals

In MATLAB PREP, RANSAC channel predictions are correlated with actual data in step 4 using a non-standard method: essentially, it uses the standard Pearson correlation formula but without subtracting the channel means from each channel before calculating sums of squares. This is done in the last line of the calculateRansacWindow function reproduced above:

rX = sum(XX.*YY)./(sqrt(sum(XX.^2)).*sqrt(sum(YY.^2)));

For readability, here’s the same formula written in Python code:

SSxx = np.sum(xx ** 2)
SSyy = np.sum(yy ** 2)
rX = np.sum(xx * yy) / (np.sqrt(SSxx) * np.sqrt(SSyy))

Because the EEG data will have already been filtered to remove slow drifts in baseline before RANSAC, the signals correlated by this method will already be roughly mean-centered. and will thus produce similar values to normal Pearson correlation. However, to avoid making any assumptions about the signal for any given channel / window, PyPREP defaults to normal Pearson correlation unless strict MATLAB equivalence is requested.

Differences in Robust Referencing

During the robust referencing part of the pipeline, PREP tries to estimate a “clean” average reference signal for the dataset, excluding any channels flagged as noisy from contaminating the reference. The robust referencing process is performed using the following logic:

  1. First, an initial pass of noisy channel detection is performed to identify channels bad by NaN values, flat signal, or low SNR: the data is then average-referenced excluding these channels. These channels are subsequently marked as “unusable” and are excluded from any future average referencing.

  2. Noisy channel detection is performed on a copy of the re-referenced signal, and any newly detected bad channels are added to the full set of channels to be excluded from the reference signal.

  3. After noisy channel detection, all bad channels detected so far are interpolated, and a new estimate of the robust average reference is calculated using the mean signal of all good channels and all interpolated bad channels (except those flagged as “unusable” during the first step).

  4. A fresh copy of the re-referenced signal from Step 1 is re-referenced using the new reference signal calculated in Step 3.

  5. Steps 2 through 4 are repeated until either two iterations have passed and no new noisy channels have been detected since the previous iteration, or the maximum number of reference iterations has been exceeded (default: 4).

Exclusion of dropout channels

In MATLAB PREP, dropout channels (i.e., channels that have intermittent periods of flat signal) are detected on each iteration of the reference loop, but are currently not factored into the full set of “bad” channels to be interpolated. By contrast, PyPREP will detect and interpolate any bad-by-dropout channels detected during robust referencing.

Bad channel interpolation

MATLAB PREP uses EEGLAB’s internal eeg_interp method of spherical spline interpolation for interpolating identified bad channels during robust reference estimation and (if enabled) immediately after the robust reference signal is applied in order to remove any remaining detected bad channels once referencing is complete.

However, eeg_interp’s method of spherical interpolations differs quite a bit numerically from MNE’s implementation as well as the interpolation method used by MATLAB PREP for RANSAC predictions, both of which are numerically identical and based directly on the formulas in Perrin et al. (1989) 1. eeg_interp seems to use a modified variation of the Perrin et al. method, but diverges in a number of ways that are not clearly documented or cited in the code.

To keep with the more established method of spherical interpolation and stay consistent with the interpolation code used in RANSAC, PyPREP defaults to using MNE’s interpolate_bads() method for interpolation during and following robust referencing. However, for full numeric equivalence with MATLAB PREP, PyPREP will use a Python reimplementation of eeg_interp instead when the matlab_strict parameter is set to True.



Perrin, F., Pernier, J., Bertrand, O. and Echallier, JF. (1989). Spherical splines for scalp potential and current density mapping. Electroencephalography Clinical Neurophysiology, Feb; 72(2):184-7.