Getting Started

  • Open the tutorial.vtk file that you downloaded previously using File>Open.

  • To the left should be a hierarchy menu inside the Pipeline Browser.

  • Click on the eye icon, which currently should be closed, to the left of "tutorial.vtk", so that the eye opens, as shown by the images on the right.

An outline of the image stack should now show up on a render window in the middle of the screen.

Volume rendering a stack of images

  • One of the toolbars at the top of the window should contain a drop-down menu that currently has "Outline" selected

  • Change the view from outline to volume.

  • At this point, you might be prompted with a pop-up telling you that "this will change the representation type to volume." Select yes to changing the rendering of the data.

  • You can utilize the color map editor to edit the transfer function for the volume rendering

  • If the color map editor is not there you can view it by going to View > Color Map Editor

  • By adding points and editing the graph on the color map you can change the opacity of varying densities of the image stack

Extracting an Isosurface (Polygonal Data)

  • In order to extract the isosurface click on the contour button on the top menu (highlighted below)

  • If the contour option isn’t available, click apply in the lower properties menu.

  • A new file should show up in the pipeline browser named “Contour1”

  • Change the view to just show the new contour by closing the eye next to "tutorial.vtk", and opening the eye next to "Contour1"

  • This creates a polygonal mesh of the specified density within the volume rendering

  • To change the density that is used to create the isosurface:

    • Go into the properties menu

    • Change the value within the menu to the desired density

  • In order to capture the small vessel structure in the mesh, change the value to 115

Explore Other Options

  • Smoothing

    • Filters > Alphabetical > Smooth

  • Animation

    • View > Animation View

  • Extracting the Volume/Surface area values

    • Filters > Alphabetical > Integrate Variables (can be very slow...)