3D view

You can use FSLeyes to view your images and meshes in 3D using the Views3D view menu item.

_images/3d_view_volume_example.png

3D view interaction

You can interact with the 3D view in the following ways:

  • Click and drag to rotate the view

  • Middle-click, or hold down the ⌥ key and click, to pan the view

  • Hold down the ⌘ or ⌃ and spin the mouse wheel to zoom in and out.

To reset the view, click on the reset_zoom_icon button on the toolbar.

3D overlay display settings

The FSLeyes 3D view can display volumetric images, and surface meshes. As with the ortho and lightbox views, you can open the overlay display settings by clicking on the gear_icon button.

Mesh overlays

_images/3d_view_mesh_example.png

The 3D display settings for mesh overlays are much the same as the 2D display settings. You can choose different variants of the same mesh via the Surface definition setting, and you can display data on the surface via the Vertex data setting.

The default behaviour, when you are colouring a mesh with some vertex data, is for the colours to be interpolated (smoothed) across the mesh surface. However, if you are viewing discrete data (e.g. anatomical labels), and/or wish to display the mesh with flat, unsmoothed colours, you can toggle the Flat shading option.

Volume overlays

FSLeyes uses a volumetric ray-casting algorithm to display 3D images. The 3D display settings pane in the overlay display panel (accessed via the gear_icon button) contains settings which allow you achieve higher quality rendering by controlling the ray casting algorithm.

_images/3d_view_volume_display_settings.png

It is generally advisable to change the Interpolation setting to Linear or Spline, unless you wish to achieve a Minecraft-style voxel effect.

The following settings can be used to control the ray-casting:

  • Blending This setting controls the extent to which adjacent samples along each ray are blended together.

  • Number of samples This setting controls how many samples are taken through the volume. A higher number of samples will result in a better quality rendering.

  • Quality This setting controls the resolution of the final rendering. Setting it to 100% will render the result at the display resolution. Reducing this setting will improve the rendering speed - a useful strategy is to reduce the quality, experiment with the other display settings until you are happy, and then increase the quality for the final rendering.

Volume clipping

The 3D display settings pane also contains options to control volume clipping.

_images/3d_view_volume_clipping.png

Volume overlays can be clipped by up to five clipping planes. A clipping plane is a flat plane which can be used to divide a volume into two parts - the part of the volume on one side of the plane will be shown, and the part on the opposite side will be hidden.

When more than one clipping plane is active, their effect is combined according to the Clipping mode setting - the default behaviour is to hide the parts of the volume which fall within the intersection of the active planes. You can also choose to hide areas of the volume according to the union, or the complement of the active planes.

When you change the Number of clipping planes setting, a set of additional controls will appear for each clipping plane that you add. The following settings allow you to control each clipping plane:

  • Clip position This setting controls the position of the plane, as a proportion of the image.

  • Clip rotation This setting (also known as the azimuth) controls the rotation of the plane about the vertical axis.

  • Clip Z angle This setting (also known as the incline) controls the rotation of the plane with respect to a horizontal plane.