I.4: Preprocessing Tools

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Tutorial Outline
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Preprocessing tools

The upper portion of the Tools menu may be used to call three data preprocessing routines:

Changing the data sampling rate

The most common use for Tools > Change sampling rate is to reduce the sampling rate to save memory and disk storage. A pop_resample.m window pops up, asking for the new sampling rate. The function uses Matlab resample() (in the Signal Processing toolbox-- if you do not have this toolbox, it will use the slow Matlab function griddata). Do not use this function here, since the tutorial EEG dataset is already at an acceptable sampling rate.

Filtering the data

To remove linear trends, it is often desirable to high-pass filter the data.

KEY STEP 6: Remove linear trends.

We recommend filtering continuous EEG data, before epoching or artifact removal, although epoched data can also be filtered with this function (each epoch being filtered separately). Filtering the continuous data minimizes the introduction of filtering artifacts at epoch boundaries. Select Tools > Filter the data > Basic FIR filter (new, default), enter 1 (Hz) as the Lower edge frequency, and press OK.
Pop eegfiltnew 1hz.jpg
A pop_newset.m window will pop up to ask for the name of the new dataset. We choose to modify the dataset name and to overwrite the parent dataset by checking the Overwrite parent checkbox, then pressing the OK button.
Figure42 pop newset.jpg
Note that if high-pass and low-pass cutoff frequencies are BOTH selected, the filtering routine may not work. To avoid this problem, we recommend first applying the low-pass filter and then, in a second call, the high-pass filter (or vice versa).

Another common use for bandpass filtering is to remove 50-Hz or 60-Hz line noise. The filtering option in EEGLAB, eegfilt.m, uses linear finite impulse response (FIR) filtering. If the Matlab Signal Processing Toolbox is present, it uses the Matlab routine filtfilt(). This applies the filter forward and then again backward, to ensure that phase delays introduced by the filter are nullified. If the Matlab Signal Processing toobox is not present, EEGLAB uses a simple filtering method involving the inverse fourrier transform.

A infinite impulse response (IIR) filter plug-in is also distributed as a plug-in to EEGLAB. Once the plug-in is installed ( see how to install a plug-in here), it can be accessed from the menu item Tools > Filter the data > Short IIR filter . This functionality uses the same graphical interface as the FIR filtering option described above. Although IIR filters usually introduce different phase delays at different frequencies, this is compensated for by again applying filtering in reverse using Matlab function filtfilt(). In practice, we suggest you test the use of this IIR filter, as it is stronger (and shorter) than FIR filters.

If you apply filtering and continue to work with the updated data set, check that the filter has been applied by selecting menu item Plot > Channel spectra and maps to plot the data spectra. You might notice that filtered-out frequency regions might show 'ripples', unavoidable but hopefully acceptable filtering artifacts. (Note: There is much more to be learned about filtering, and more filtering options available in Matlab itself).

Re-referencing the data

What is re-referencing and why re-reference

The reference electrode used in recording EEG data is usually termed the 'common' reference for the data -- if all the channels use this same reference. Typical recording references in EEG recording are one mastoid (for example, TP10 in the 10-20 System, the electrode colored red in the picture below), linked mastoids (usually, digitally-linked mastoids, computed post hoc, the vertex electrode (Cz), single or linked earlobes, or the nose tip. Systems with active electrodes (e.g. BIOSEMI Active Two), may record data reference-free. In this case, a reference be must be chosen post hoc during data import. Failing to do so will leave 40 dB of unnecessary noise in the data!

There is no 'best' common reference site. Some researchers claim that non-scalp references (earlobes, nose) introduce more noise than a scalp channel reference though this has not been proven to our knowledge. If the data have been recorded with a given reference, they can usually be re-referenced (inside or outside EEGLAB) to any other reference channel or channel combination.


Converting data, before analysis, from fixed or common reference (for example, from a common earlobe or other channel reference) to 'average reference' is advocated by some researchers, particularly when the electrode montage covers nearly the whole head (as for some high-density recording systems). The advantage of average reference rests on the fact that outward positive and negative currents, summed across an entire (electrically isolated) sphere, will sum to 0 (by Ohm's law). For example, in the figure below a tangentially-oriented electrical source is associated with a positive inward current to the left (here, blue) and an opposing outward negative current to the right (red). If the current passing through the base of the skull to the neck and body is assumed to be negligible (for instance, because of low conductance of the skull at the base of the brain), one may assume that the sum of the electric field values recorded at all (sufficiently dense and evenly distributed) scalp electrodes is always 0 (the average reference assumption).

The problem with this assumption is that true average reference data would require the distribution of electrodes to be even over the head. This is not usually the case, as researchers typically place more electrodes over certain scalp areas, and fewer (if any) on the lower half of the head surface. As a consequence, an average reference result using one montage may not be directly comparable to an average reference result obtained using another montage.


Below, we detail the process of transforming data to 'average reference'. Note that in this process, the implied activity time course at the former reference electrode may be calculated from the rest of the data (so the data acquires an additional channel - though not an additional degree of freedom!). Also note that if the data were recorded using nose tip or ear lobe electrodes, you should not include these reference electrodes when computing the average reference in (1) (below), Thus, in the example below the dividing factor (in (2)) would be 64 instead of 65. Note that in localizing sources using the EEGLAB DIPFIT plug-in, 'average reference' will be used internally (without user input).

The choice of data reference does color (literally) the plotted results of the data analysis. For example, plots of mean alpha power over the scalp must have a minimum at the reference channel, even if there are in fact alpha sources just below and oriented toward the reference channel! However, no (valid) reference can said to be wrong - rather, each reference can be said to give another view of the data. However, the nature of the reference needs to be taken into account when evaluating (or, particularly, comparing) EEG results.


For ICA decomposition (covered later in the tutorial), the selection of reference is not so important. This is because changing the reference only amounts to making a linear transformation of the data (in mathematical terms, multiplying it by a fixed re-referencing matrix), a transformation to which ICA should be insensitive. In practice, we have obtained results of similar quality from data recorded and analyzed with mastoid, vertex, or nose tip reference.

We advise recording eye channels (conventionally four channels, two for vertical eye movement detection and two for horizontal eye movement detection) using the same reference as other channels, instead of using bipolar montages. One can always recover the bipolar montage activity by subtracting the activities of the electrode pairs. We term these channels 'peri-ocular EEG' channels since what they record is not exclusively electro-oculographic (EOG) signals, but also includes e.g. prefrontal EEG activities.

ICA can be used to decompose data from either average reference, common reference, or bipolar reference channels -- or from more than one of these types at once. However, plotting single scalp maps requires that all channels use either the same common reference or the same average reference. Robert Oostenveld advises that peri-ocular channel values, even in ICA component maps, may best be omitted from inverse source modeling using simple head models, since these are apt to poorly model the conductance geometry at the front of the head.

Specify reference and re-reference the data

We will now describe how to specify the reference electrode(s) in EEGLAB and to (optionally) re-reference the data

Exploratory Step: Re-reference the Data.

Select Tools > Re-reference the data to convert the dataset to average reference by calling the pop_reref.m function. When you call this menu item for the first time for a given dataset, the following window pops up.
Figure43 pop rerefgui.jpg
The (sample) data above were recorded using a mastoid reference. Since we do not wish to include this reference channel (neither in the data nor in the average reference), we do not click the Add current reference channel in data check-box. (Do click this check-box when the recording reference was on the scalp itself). The box Data are referenced to one site (default) should remain checked.

Now, press the OK button: the re-referencing window below appears.
Figure42 pop newset.jpg
Press the OK button to compute the average reference. This step will then be recorded in the main EEGLAB window (not shown). As in the previous step, a dialogue box will appear asking for the name of the new dataset. Save the re-referenced data to a new dataset or hit cancel, as the new reference is not used in the following sections.

After the data have been average referenced, calling the Tools > Re-reference the data menu still allows re-referencing the data to any channel or group of channels (or undoing an average reference transform -- as long as you chose to include the initial reference channel in the data when you transformed to average reference).

Note that the re-referencing function also re-references the stored ICA weights and scalp maps, if they exist.

Re-referencing data can be more complicated. For instance, if you recorded data referenced to Cz and want to re-reference the data to linked mastoid. Now you want to add Cz back to your data under the average reference assumption (the assumption that the average of all electrode is 0). The first step is to compute average reference and declare Cz as the reference in the channel editor. In the channel editor, references are placed after all the data channels (note that for reference the checkbox "data channel" is unchecked since these are not actual data channels). To declare a reference, go to the last channel and press the Append button. An empty channel is created.

Pop reref4.png

Fill up the channel label (enter "Cz" in the "Channel label" edit box) and enter the position of the channel if you have it. For instance, you may enter the X, Y, Z locations and press the XYZ -> Polar & Sph. to convert the 3-D Cartesian coordinates to polar and spherical coordinates. If you do not have the electrode location, you may simply press the Look up locs button to automatically look it up based on the 10-20 channel label (note that this will look up location for all electrodes).

Pop reref3.png

Then press the Set reference pushbutton to set the reference to all channels to Cz (Cz need to be typed into the checkbox and the channel range needs to be entered manually as well).

Pop reref5.png

Press OK to validate your new reference channel, and go back to the re-referencing interface. Now click on the Retain old reference button.

Pop reref6.png

You may now select electrode "Cz" and press OK.

Pop reref7.png

Then press OK to actually re-reference your data. This is the first step. If you actually want to re-reference your data to linked mastoid, you will need to call the re-referencing interface once more and select both mastoids as your new reference.

The reason for this overly complex procedure is that the reference channel can have a location and that this location needs to be declared in the channel editor so it can be plotted along with other channels.

The next tutorial section deals with extracting data epochs from continuous or epoched datasets.

Re-reference to multiple channels

Say you collected data with reference M1 (mastoid) and want to process your data using linked mastoid (M1 and M2) as reference. The process is as follow:

  • Specify M1 as reference as described in the previous section and compute average reference while keeping electrode M1 (how to keep the reference channel is also described in the previous section)
  • Re-reference a second time the data selecting both electrodes M1 and M2 as reference (you may then either select to keep the reference channels or have them deleted)

Arrow.small.left.gif (MT) I.3: Plotting Channel Spectra and Maps
Tutorial Outline
(MT) I.5: Extracting Data Epochs Arrow.small.right.gif