2D - 3D visualization

Help Guide - Views

---

The Toolbar - visualization controls

In the window toolbar, you will find several buttons to modify the visualization.

Zoom In and Zoom out control the zoom on the clicked image.

Pan allows to move the visualization area in a drag and drop interactive manner.

Rotate 3D is only used with 3D images to change the point of view. However, in rendered images, this doesn't change the light source, so you may notice dark areas. To update the light source, use the Refresh (R) button on the 3D view.

Data Cursor allows you to get a voxel or pixel value. MRI and CT are normalized from 0 to 1.

Change colormap will alternate colormap: Gray or Jet/Parula. Colormaps are useful in particular for looking in the Thresholded voxels view.

Reset 2D plots resets zoom and pan in three 2D slices view.

Crosshair toggles the visualization of a green cross in the 2D slices view. The crosshair shows the actual slices view.

Toggle layout Changes the layout for your convenience. Three different views are available.

Layout 1 - 2D views of the CT and MR images, 3D plot of the brain surfaces and electrodes, and 3D view of the thresholded CT voxels

Layout 2 - 2D views of the CT and MR images, and 3D plot of the brain surfaces and electrodes

Layout 3 - 2D views of the CT and MR images

Take snapshot Generate a screenshot of the current window in .jpg, .png, .tif, .bmp or .eps file format.

---

3D views of intracranial electrodes and brain surfaces

Example images of Native space brain surface obtained from Freesurfer. Pial and Smooth Cortical Envelope (SCE) surfaces can be plotted. Additionally, you can choose to plot with or without the parcellation information (annotation files). You can click on a desired surface coordinate to change the current 2D slices view.

3D view controls

Transparency The vertical slider allows you to control the transparency of the surfaces
Changing the transparency allows you to see the depth electrodes easily.

Left and Right checkboxes allow you to select what brain pial hemisphere to view.
L SCE and R SCE checkboxes allow you to select what Smooth Cortical Envelope (SCE) hemisphere to view.
Conn checkbox allows showing connections among electrodes
Labels checkbox shows electrodes labels
Parcel checkbox enables the parcellation view of the pial surface
Refresh (R) button will reset the light source.

---

2D views of MRI and CT images merged

Use lateral sliders or the mouse wheel to move along slices.
You can also left -lick on a desired coordinate to change the current slices view.
Important note: Disable the Rotate3D on the toolbar to be able to change the 2D view coordinates.

2D view controls

Visualization window sliders The first two sliders allow you to control the maximum and minimum value of the visualization window. Values above the maximum will look burned, values below minimum will look dark.

Elec (Electrodes) checkbox allows you to visualize or not the localized electrodes. By default, grid electrodes are plotted in red color, and depth electrodes are plotted in blue color.

Plan (Planning) checkbox allows you to visualize or not the planned/simulated electrodes. By default, planning/simulated electrodes are plotted in green color.

Col (Collapse) checkbox allows you to visualize the orthogonal projection of each electrode in the current slice. If unselected, only electrodes in the current coordinate +/- 1mm will be shown.

Parc (Parcellation) checkbox enables the view of the parcellation atlas.

Edge checkbox allows you to see the edges of the CT images overlayed on top of the MR. In this view mode, it is easier to check the coregistration.

CT-MRI visualization ratio sliders control the ratio of CT / MRI visualized. For example, CT and MR only:

Coordinates Panel

The second row of the panel shows the current voxel coordinate in the Anatomical coordinate system. This coordinate is not affected by LAS or RAS convention.
This is the coordinate system in "real", "individual", or "patient" space.
Important: All electrodes or target coordinates exported/imported from/to iElectrodes are in the Anatomical coordinate system.

Images are automatically transformed to RAS (right anterior superior) convention for display purposes. In most cases, you don't need to worry about this unless you are working in the matrix space for specific reasons. The first row of the panel shows the current voxel coordinates (i, j, k) in the data matrix in the RAS convention, so differences may appear in this coordinate when compared to other software. For images in LAS x coordinates are inverted (L to R).

---

3D view of thresholded voxels from CT

Controls for the Thresholded 3D view are explained in [Localization and labeling of intracranial electrodes]

---

Back to [Home]
Previous: [Load images] - Next: [Localization and labeling of intracranial electrodes]