7. Visualization

Context

In the final step of the electrode reconstruction process, Lead-DBS offers a wide variety of options for electrode visualisation.
Lead-DBS allows you to choose the space in which you want to visualize the electrodes: the standard MNI space and the native space of the patient. If the latter is selected, the selected MNI atlas will be wrapped to the native patient space using an inversion of the transformation matrix that was generated during the process of normalization and which wrapped our patient image to the MNI space.
We can also visualise the atlas to define how and which target regions should be displayed. Here, Lead-DBS offers an impressive collection of subcortical atlases.
One atlas has been specifically created for Lead-DBS called the “Distal atlas.” This atlas precisely matched the MNI template, which other atlases usually do not. Moreover, it also offers you a parcellated STN and GPi (parcellated into sensorimotor and other functional areas through fibre tracking).
Lead-DBS also offers to visualize the volume of tissue activated (VTA) by the electric field and fibres activated by this VTA (fibres stem from a normative connectome).

How to

1. Rendering 2D Images

After a successful reconstruction, you can obtain 2D images of each contact at its location. To select this option, the box Write out 2D must be checked within the Lead-DBS main window.

The 2D images are based on the localization obtained during the reconstruction and the manual correction. They help to better understand how the electrode contacts relate to the surrounding brain structures.

Certain features can be changed to enhance the understanding of the structures surrounding the contacts:
- Labels and colors: Specific brain areas are labeled and colored for easier identification. The labels can be turned off or on by checking the Label box. The color of the contour can also be selected from a pop-up window.
- Bounding box: Determines the final size of the 2D image.
Images are stored as .png files within the patient folder and are named according to the electrode and the plane they belong.

2. Rendering the 3D Scene

If you set the Render 3D button in the Lead-DBS main window and press the Run (Image 1) button, the Lead-DBS 3D viewer pops up and renders the reconstructed electrodes and the atlas components in the main window.
This figure can be rotated in 3D using the built-in MATLAB 3D rotation tool and atlas components can be hidden (and shown back again) by pressing the corresponding colored checkboxes in the secondary toolbar of the viewer (press the alt-key to hide/show all atlases of the set – this only works if no other tool, such as the MATLAB 3D rotation tool is selected).
In the 3D viewer, there are various icons in the tool strip. You can set:

Show Electrode: For each electrode shown, there is a toggle button with which you can show or hide it. If no other tool is active (e.g. the MATLAB 3D rotation tool), you can additionally press the alt-button to show/hide all electrodes at once. This is helpful when visualizing groups of patients in Lead Group.
Electrode labels: Shows/hides the patient names at the top of each electrode displayed. This is especially helpful when visualizing groups of patients in Lead Group.
Add trajectory: To add a trajectory to simulate, for instance, surgery.
Stimulation Control Figure: This button opens the stimulation settings window. Using this window, you can estimate VTAs.
Slice Control Figure: Opens the anatomy control figure which can be used to add x-, y- and z-slices of an MR image to the scene. You can choose to visualize the MNI template, the pre-/post-op MR images of the current patient or a different image. This control figure can also be used only to show a 2D-like slice of the current scene in the x-, y- or z-axis.
MER Control Figure: Perform MER analysis if you have microelectrode recordings. Helpful for instance to note the entry and exit of the subthalamic nucleus.
Connectivity Visualization: To perform connectivity analysis with, for instance, a VTA seed.
Cortical Reconstruction Visualization: Displays the cortex.
Different options to set lighting, save screenshots or set the default view.
Save video: Use this button to export a video of the current scene. This is done based on preferences set in ea_prefs.m.
The colored squares denote atlas components or added objects. You can add objects such as ROI, and tracts either through drag and drop or 'Add Objects' in the menu bar.

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How to

1. Rendering 2D Images

After a successful reconstruction, you can obtain 2D images of each contact at its location. To select this option, the box Write out 2D must be checked within the Lead-DBS main window.

The 2D images are based on the localization obtained during the reconstruction and the manual correction. They help to better understand how the electrode contacts relate to the surrounding brain structures.

Certain features can be changed to enhance the understanding of the structures surrounding the contacts:

Labels and colors: Specific brain areas are labeled and colored for easier identification. The labels can be turned off or on by checking the Label box. The color of the contour can also be selected from a pop-up window.
Bounding box: Determines the final size of the 2D image.

Images are stored as .png files within the patient folder and are named according to the electrode and the plane they belong.

2. Rendering the 3D Scene

If you set the Render 3D button in the Lead-DBS main window and press the Run (Image 1) button, the Lead-DBS 3D viewer pops up and renders the reconstructed electrodes and the atlas components in the main window.

This figure can be rotated in 3D using the built-in MATLAB 3D rotation tool and atlas components can be hidden (and shown back again) by pressing the corresponding colored checkboxes in the secondary toolbar of the viewer (press the alt-key to hide/show all atlases of the set – this only works if no other tool, such as the MATLAB 3D rotation tool is selected).

In the 3D viewer, there are various icons in the tool strip. You can set:

Show Electrode: For each electrode shown, there is a toggle button with which you can show or hide it. If no other tool is active (e.g. the MATLAB 3D rotation tool), you can additionally press the alt-button to show/hide all electrodes at once. This is helpful when visualizing groups of patients in Lead Group.

Electrode labels: Shows/hides the patient names at the top of each electrode displayed. This is especially helpful when visualizing groups of patients in Lead Group.

Add trajectory: To add a trajectory to simulate, for instance, surgery.

Stimulation Control Figure: This button opens the stimulation settings window. Using this window, you can estimate VTAs.

Slice Control Figure: Opens the anatomy control figure which can be used to add x-, y- and z-slices of an MR image to the scene. You can choose to visualize the MNI template, the pre-/post-op MR images of the current patient or a different image. This control figure can also be used only to show a 2D-like slice of the current scene in the x-, y- or z-axis.

MER Control Figure: Perform MER analysis if you have microelectrode recordings. Helpful for instance to note the entry and exit of the subthalamic nucleus.

Connectivity Visualization: To perform connectivity analysis with, for instance, a VTA seed.

Cortical Reconstruction Visualization: Displays the cortex.

Different options to set lighting, save screenshots or set the default view.

Save video: Use this button to export a video of the current scene. This is done based on preferences set in ea_prefs.m.

The colored squares denote atlas components or added objects. You can add objects such as ROI, and tracts either through drag and drop or 'Add Objects' in the menu bar.