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Selecting a head model

There are several steps required for source localization. First, choosing a head model, which defines different regions of conductivities. Second, choosing a source model: The source model is the type of source you will use. This may be a single dipole, which position you optimize. This could also be a distributed model, with one dipole per brain voxel, such as when using Loreta. The source model is independent of the head model. Third, you will perform inverse source localization and plot the source results.

This section deals with the first step only of choosing a head model and aligning it with your electrode locations. Other steps are described in subsequent sections of the tutorial.

Table of contents

Setting up DIPFIT head model

In this section, we use the tutorial dataset after extracting data epochs. Select menu item File and press sub-menu item Load existing dataset. Select the tutorial file “eeglab_data_epochs_ica.set” located in the “sample_data” folder of EEGLAB. Then press Open.

Before running DIPFIT, we must select some input parameters. Select the EEGLAB menu item Tools → Locate dipoles using DIPFIT → Head model and settings to modify DIPFIT settings. This will pop up the window below:

The top edit box, Model (click to select), specifies the type of head model – spherical model, template boundary element model (BEM), or custom model. The spherical head model uses four spherical surfaces (skin, skull, CSF, cortex) to model the head. The BEM model is composed of three 3-D surfaces (skin, skull, cortex) extracted from the MNI (Montreal Neurological Institute) canonical template brain also used in Statistical Parametric Mapping (SPM). The BEM model is more realistic than the four concentric spheres model and will return more accurate results. The spherical head model is kept for backward compatibility purposes and should not be used for publication.

For this example, select Boundary element model. Clicking on the model name updates some of the fields below the dropdown menu:

  • The entry Head model file contains the head model parameters (surface information, conductances, etc…). These are MATLAB files and may be edited. See the FieldTrip documentation for more information on the head model files.
  • The edit box Matrix to align chan. locs with head model is automatically updated to align the current electrode coordinates with the current head model. We co-registered the MNI average brain MRI with landmark electrode positions. For the average MRI image, we used a publicly available average brain image (average of 152 T1-weighted stereotaxic volumes made available by the ICBM project) from the MNI database (Montreal Neurological Institute (MNI), Quebec). Co-registration of the MNI brain and the standard EEG landmarks was accomplished automatically using fiducials and the Cz (vertex) electrode position, then slightly adjusted manually. In our case, it is not ideal, as it is better to use electrode locations compatible with the head model (see next section). The automatic update of the transformation matrix is not always performed, and sometimes you may need to align electrode coordinates and the head model manually, as explained in a later section.
  • The entry Associated MRI file for plotting contains the name of the MRI image to use for plotting. You may enter a custom or individual subject MR image file, assuming this file has first been normalized to the MNI brain. The SPM software will take a raw subject MRI as input and normalize it to the MNI brain template.
  • The entry Associated channel locations if any contains the name of the template channel location file associated with the head model. This information is critical, as your dataset channel location file may be different from the template. If so, a co-registration transform is required to align your channel locations using the template locations associated with the model.
  • Edit box Channel to omit channels from dipole fitting. By pressing “”, a list of channels appears that allows users to exclude eye channels (or other, possibly non-head channels) from the dipole fitting procedure. For example, non-scalp channels should be removed prior to running dipole fitting. We advise excluding peri-ocular channel values from inverse source models because of poor conductance model geometry at the front of the head.

Next is the coregistration, which is explained in detail in the following sections.

Avoiding co-registration by choosing appropriate channel locations

It is ideal if your channel locations are the same as the ones associated with the head model. In the dataset we are using here, the channel locations are in the spherical coordinate system, while we want to use a BEM head model. If all your electrode locations are within the International 10-20 System (which is the case here), you may use the standard channel coordinates associated with the head model. Close the current head model settings window and go to the channel editing window (select menu item Edit → Channel location). The resulting channel editor window is shown below:


Press the Look up locs to look up your channel locations (by matching the channel labels) in the template channel location file. Select Use MNI coordinate file for the BEM DIPFIT model.

Press Ok on the window above and the channel editor window. Then go back to the head model settings using the Tools → Locate dipoles using DIPFIT → Head model and settings menu item. The window below will pop up. You can see that the matrix to align the electrode coordinate to the head model (edit box Matrix to align chan. locs with head model) mainly contains -pi/2 (-1.5708), which correspond to a 90-degree rotation in the axial plane (also known as the transverse or horizontal plane). This is because EEGLAB assumes that the nose direction is along a specific axis, while the head model uses a different convention. The Talairach transformation matrix, a vector comprised of nine fields [shiftx shifty shiftz pitch roll yaw scalex scaley scalez], is organized as follow:

  • The first 3 numbers [shiftx shifty shiftz] are the offset (in millimeters) along the x, y, and z axes. When equal to 0, no shift is applied.
  • The next 3 numbers [pitch roll yaw] are rotations along different planes in radian. Yaw means rotation in the horizontal plane around the z axis. Pitch and Roll are rotations around the x and y axes, respectively. When equal to 0, no rotation is applied.
  • The last 3 numbers [scalex scaley scalez] are scaling factors along the x, y, and z axes. When equal to 1, no scaling is applied.

In this case, the only alignment required is a 90-degree rotation between the electrode coordinates and the coordinate system of the head model. In case no co-registration/alignment is required, you may also select the No coreg checkbox.

Important note: If you change your channel locations, make sure to go back to DIPFIT settings to update the coordinate transformation settings.

Manual coregistration or fine-tuning of coregistration

If you are using channel locations and/or labels not in the International 10-20 System – for example, scanned electrode positions or some commercial high-density electrode cap file – you will need to align or co-register your electrode locations with the selected head model. The coregistration interface does not automatically allow you to align your electrode locations to the head model. Instead, it allows you to automatically align your electrode locations to matching template electrode locations associated with the head model.

Again, use the Tools → Locate dipoles using DIPFIT → Head model and settings menu item. Click on Manual coreg. in the DIPFIT settings window. A window appears. Change the resize values to 1.5 for all axes to see the electrodes (we are undoing the alignment for illustrative purposes).

Here, the electrode locations are plotted on the head model. Each small red or green sphere indicates an electrode location, with fiducial locations (conventionally, the nasion and ear canal centers) drawn as slightly bigger and darker spheres.

Use the Warp button to align and scale your electrode locations (green) so that it becomes best aligned with the template electrode locations (brown) associated with the head model.

A channel correspondence window will pop up:


The channel labels from your dataset electrode structure are shown in the right column, while the left column shows channel labels from the template channel file associated with the head model. Arrows in both columns indicate electrodes with the same labels in the other column. If your channels’ labels do not correspond to the International 10-20 System labels used in the template montage, press the Pair channels button and choose the nearest channel to each of your dataset channels in the template montage.

When you press Ok, the function will perform the optimal linear 3-D warp (translation, rotation, and scaling) to align your channel montage to the template montage associated with the head model. The result will be shown in the channel montage window (see below). You may press the Labels on button to toggle the display of your channels’ label (green) or the template channels associated with the head model (red). You may also restrict the display to subsets of channels using the Electrodes buttons.

Manual fine-tuning: To finely tune the alignment manually, repeatedly edit the values in the edit boxes, which correspond to the [shiftx shifty shiftz pitch roll yaw scalex scaley scalez] transformation mentioned previously. The resulting co-registration window should look something like this:


If you want to retain your modifications, press Ok to update the DIPFIT settings window. This will display the resulting Talairach transformation matrix in the edit box Matrix to align chan. locs with head model. In this specific case, you may press the Cancel button in the coregistration interface since no further alignment was necessary (we performed coregistration for illustrative purposes on a dataset that did not require further alignment). Then press Ok in the DIPFIT settings window and proceed to localization in the next section of the tutorial.

Note about fiducials: Your channel structure may contain standard fiducial locations (nasion and pre-auricular points). If you import a channel file with fiducial locations into the channel editor, give them the standard fiducial channel type FID, and they will be stored in the channel information structure, EEG.chaninfo. This will also be done automatically if your fiducials have the standard names, Nz (nasion), LPA (left pre-auricular point), and RPA (right pre-auricular point ). There is also considerable confusion about fiducials, and we have created new fiducial labels in an attempt to disambiguate exact fiducial locations (see this slide). Note that fiducial locations are stored outside the standard channel location structure, EEG.chanlocs, for compatibility with other EEGLAB plotting functions.

Thereafter, fiducial locations will appear in the channel co-registration window (above) and may be used (in place of location-matched scalp channels) to align your electrode montage to the template locations associated with the head model. Use the Align fiducials button to do this.

Head model and custom MRI

When plotting dipole sources in the next section of the tutorial, you may plot the head model head surface and the MRI.


In this case, we are using the tutorial data and the standard BEM model described in the previous sections. The BEM head model mesh was extracted from the average MRI used for plotting, so the alignment is perfect. When using participants’ MRI and transformed them to MNI space (for example, using SPM), this allows checking the alignment between the MRI and the head model.

It is also possible to compute extract 3-D meshes from your participants’ MRI and use them to create head models as described in this Fieldtrip tutorial. If you have a custom head model, use the dropdown menu Custom model files from other template or individual subject in the head model settings. A custom head model for MEG is also possible and described in the next section of the tutorial.