Spatial Localization of 3D Scanned EEG Electrodes with MeshLab

Joel P Diaz-Fong, Jordana Glouberman, Agatha Lenartowicz

Published: 2024-04-20 DOI: 10.17504/protocols.io.261geo8zjl47/v1

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Abstract

This protocol outlines step-by-step instructions for utilizing Meshlab's PickPoints tool to facilitate spatial localization of electroencephalogram (EEG) electrodes from 3D scanned head models. These include mesh models created from structured-light/infrared, photogrammetry, and LiDAR scanners, to name a few.

Before start

Download the latest version of the MeshLab software using the installer found on their website (www.meshlab.net) or download their source code directly from GitHub (https://github.com/cnr-isti-vclab/meshlab). For 3D scanning sample data, please visit: https://osf.io/87av2/

Steps

3D Scanning Setup

Participant Preparation

There are a few necessary steps to ensure that the participant is prepared in a way that guarantees a good quality scan. This includes:

1.1.

Fiducial Visibility

Identify Key Fiducials. Determine the anatomical landmarks (fiducials) to be used for coordinate registration (e.g., bridge of the nose, ears).
Ensure Unobstructed View. Instruct participants to remove any accessories or items that may obstruct the visibility of fiducials during the scan. Also, verify that the bridge of the nose and ears are clearly visible in the final 3D mesh model.

1.2.

Electrode Visibility

Check Electrode Placement. Verify the correct placement of electrodes on the participant's scalp according to the EEG system used. Ensure that no electrodes are obstructed by hair or any other objects.
Tuck Away Hair. Advise participants to ensure all strands of hair are neatly tucked away from the scanner's field of view of the electrodes.

1.3.

Reduce Reflective Surfaces

Identify Reflective Surfaces. Identify any reflective surfaces in the scanning environment that may impact electrodes visibility.
Apply Non-Reflective Coverings. Use non-reflective stickers or a wax marker to cover reflective surfaces, especially those in close proximity to the electrodes.

Import Mesh Model

Import the Mesh Model

After acquiring a 3D mesh model, open the MeshLab software and import the 3D mesh file.

Software

Value	Label
MeshLab	NAME
https://github.com/cnr-isti-vclab/meshlab	REPOSITORY
Visual Computing Lab - ISTI - CNR	DEVELOPER
https://www.meshlab.net/	LINK
2022.02	VERSION

Note

In case you do not have a 3D model, please use the dataset below for practice.

2.1.

Import mesh

To do so, select File > Import Mesh…

Note

The MeshLab software can import several types of 3D triangular mesh files.obj, .ply, .stl, .3ds, etc.

2.2.

Optional: Optional : Once the file is imported into the software, remove the trackball to get a better view of the mesh model.

Select View > Show Trackball
Unselect Show Trackball to remove the trackball

Imported mesh model with overlaid trackball

Spatial Localization

Open the PickPoints Tool PickPoints Tool

Once the model is imported into the MeshLab software, you can begin to localize the fiducial and electrode coordinates with the PickPoints tool.
To start, find the PickPoints icon in the toolbar or select Edit > PickPoints
PickPoints Icon

Note

PickPoints Window When first opening the PickPoints tool, the window will initially be empty. The Point Name Name should correspond to the electrodes you are trying to localize.

3.1.

Enter Point Names or load an existing template

Before you start selecting points on the mesh, manually enter each electrode label as a Point Name (see 5.2 about saving templates).
If you have an existing template, go to Template Controls , select Load and choose the .pptpl template file.

Note

PickPoints Window with Template

An example of a loaded template. The Point Name now includes the three fiducial labels and the electrode labels for EGI's HydroCell EEG net.

Begin selecting points on the mesh

Locate the fiducial or electrode on the mesh model and right-click the location with your cursor. A green pin should appear at that location.
To rotate the mesh model, unselect PickPoints and rotate/drag the model with your curser. Once you've adjusted the model to the desired position, reselect PickPoints to continue.

After right-clicking the model, XYZ coordinate points should appear next to the Point Name, and the checkbox in the active column will be selected. The next row will automatically be highlight.

4.1.

Selecting the fiducials

As mentioned in 1.1, the fiducials (anatomical landmarks) should be determined beforehand. The fiducials should also be the same across all your scans for a given study.
For the example in this protocol, we select the nasion (NAS), the left helix-tragus junction (LHJ), and the right helix-tragus junction (RHJ).

4.2.

Selecting the electrodes

Select each of the electrodes, point by point, following the order of the Point Names column.
For a good approximation of the electrode location, try to select the point at the center of the electrode. The green pin should appear perpendicular to the scalp if the surface of the electrode is flat.

Save PickedPoints

Save electrode coordinates

Select Save at the upper right-hand corner of the PickPoints tool.

Note

Coordinate points are saved as an XML formatted picked point (.pp ) file.

5.1.

Optional: Optional : save a snapshot

Snapshots of the mesh model with the green coordinate pins can be saved as an image file, which is useful for documenting the quality of mesh model and how the fiducials were defined for the selected coordinate points.
Go to File > Save snapshot
Example snapshot of the mesh model with all the selected points. The model texture (or surface detail) can be removed for anonymity.

5.2.

Optional: Optional : save the template of Point Names so the electrode labels can be loaded for processing multiple participants

Under Template Controls , select Save . Templates are saved as a .pptpl filetype.

Extract Coordinates

Finally, the coordinates should be extracted from the PickedPoints file and converted to a preferred format.

6.1.

Convert PickedPoints XML file to text

Extract coordinates from XML file and convert them to text.

6.2.

Convert coordinates to a standard space

The coordinates that are extracted from the PickedPoints file are typically the same unit of measurement and coordinate space as the mesh model. Use the fiducials as a reference point to convert the coordinate space to a standard format.