The Volume Visualization Plugin

Table of Contents

• Overview
• Enable Volume Rendering
  • Loading an image into the application
  • Enable Volumerendering
  • The LOD & GPU checkboxes
• Applying premade presets
  • Internal presets
  • Saving and loading custom presets
• Interactively create transferfunctions
  • Threshold
  • Bell
• Customize transferfunctions in detail
  • Choosing grayvalue interval to edit
  • Grayvalue -> Opacity
  • Grayvalue -> Color
  • Grayvalue and Gradient -> Opacity

Icon of the Volume Visualization Plugin

Overview

The Volume Visualization Plugin is a basic tool for visualizing three dimensional medical images. MITK provides generic transfer function presets for medical CT data. These functions, that map the gray-value to color and opacity, can be interactively edited. Additionally, there are controls to quickly generate common used transfer function shapes like the threshold and bell curve to help identify a range of grey-values.

Enable Volume Rendering

Loading an image into the application

Load an image into the application by

• dragging a file into the application window.
• selecting file / load from the menu.

Volume Visualization imposes following restrictions on images:

• It has to be a 3D-Image Scalar image, that means a normal CT or MRT.
• 3D+T are supported for rendering, but the histograms are not computed.
• Also be aware that volume visualization requires a huge amount of memory. Very large images may not work, unless you use the 64bit version.

Enable Volumerendering

Select an image in datamanager and click on the checkbox left of "Volumerendering". Please be patient, while the image is prepared for rendering, which can take up to a half minute.

The LOD & GPU checkboxes

Volume Rendering requires a lot of computing resources including processor, memory and graphics card.

To run volume rendering on smaller platforms, enable the LOD checkbox (level-of-detail rendering). Level-of-detail first renders a lower quality preview to increase interactivity. If the user stops to interact a normal quality rendering is issued.

The GPU checkbox tries to use computing resources on the graphics card to accelerate volume rendering. It requires a powerful graphics card and OpenGL hardware support for shaders, but achieves much higher frame rates than software-rendering.

Applying premade presets

Internal presets

There are some internal presets given, that can be used with normal CT data (given in Houndsfield units). A large set of medical data has been tested with that presets, but it may not suit on some special cases.

Click on the "Preset" tab for using internal or custom presets.

• "CT Generic" is the default transferfunction that is first applied.
• "CT Black&White" does not use any colors, as it may be distracting on some data.
• "CT Cardiac" tries to increase detail on CTs from the heart.
• "CT Bone" emphasizes bones and shows other areas more transparent.
• "CT Bone (Gradient)" is like "CT Bone", but shows from other organs only the surface by using the gradient.
• "MR Generic" is the default transferfunction that we use on MRT data (which is not normalized like CT data).
• "CT Thorax small" tries to increase detail.
• "CT Thorax large" tries to increase detail.

Saving and loading custom presets

After creating or editing a transferfunction (see Customize transferfunctions in detail or Interactively create transferfunctions), the custom transferfunction can be stored and later retrieved on the filesystem. Click "Save" (respectively "Load") button to save (load) the threshold-, color- and gradient function combined in a single .xml file.

Interactively create transferfunctions

Beside the possibility to directly edit the transferfunctions (Customize transferfunctions in detail), a one-click generation of two commonly known shapes is given.

Both generators have two parameters, that can be modified by first clicking on the cross and then moving the mouse up/down and left/right.

The first parameter "center" (controlled by horizontal movement of the mouse) specifies the gravalue where the center of the shape will be located.

The second parameter "width" (controlled by vertical movement of the mouse) specifies the width (or steepness) of the shape.

Threshold

Click on the "Threshold" tab to active the threshold function generator.

A threshold shape begins with zero and raises to one across the "center" parameter. Lower widths results in steeper threshold functions.

Bell

Click on the "Bell" tab to active the threshold function generator.

A threshold shape begins with zero and raises to one at the "center" parameter and the lowers agains to zero. The "width" parameter correspondens to the width of the bell.

Customize transferfunctions in detail

Choosing grayvalue interval to edit

To navigate across the grayvalue range or to zoom in some ranges use the "range"-slider.

All three function editors have in common following:

• By left-clicking a new point is added.
• By right-clicking a point is deleted.
• By left-clicking and holding, an exisiting point can be dragged.
• By pressing arrow keys, the currently selected point is moved.
• By pressing the "DELETE" key, the currently selected point is deleted.
• Between points the transferfunctions are linear interpolated.

There are three transferfunctions to customize:

Grayvalue -> Opacity

grayvalues will be mapped to opacity.

An opacity of 0 means total transparent, an opacity of 1 means total opaque.

Grayvalue -> Color

grayvalues will be mapped to color.

The color transferfunction editor also allows by double-clicking a point to change its color.

Grayvalue and Gradient -> Opacity

Here the influence of the gradient is controllable at specific grayvalues.