Diffusion Tensor Image(DTI) Volumes

Scuba2 can view DTI volume slices with varying levels of detail and opacities. Each voxel contains a tensor pointing in the direction of the major eigenvector, also encoded by the color:

Brightness is weighted by fractional anisotropy(FA), where brighter tensors indicate high FA and dimmer tensors indicate low FA.

Loading Volumes

After launching scuba2, load a DTI volume by:

  1. Go to File->Load DTI... This will open a file browsing window.

  2. Navigate to the directory containing your tensor data. Make sure that the following volumes are in the same directory: fa, eigenvals, eigenvec1, eigenvec2, eigenvec3.
  3. Select the fa volume and click Open.

This will load your DTI volume as slices of tensors.

Display Options

In the Display Layer you have two modes of interaction, 2D and 3D. Both modes display slices of the diffusion tensor volume and enable you to move through the X, Y, and Z slices. You can switch between 2D and 3D mode by selecting either the 2D or 3D radio buttons in the View panel. In the 2D and 3D mode you can configure the following:

The following keys can be used:

2D Mode

In 2D mode (default), in the Display Mode Controls, you can click on the X, Y, or Z buttons to switch view planes. You can move through the slices by sliding the scroll bar or entering in the slice number. In 2D mode, the mouse can be used for navigating the data in the following manner:

3D Mode

In 3D mode, you can modify all three view planes without switching between them using the buttons. In the Layer panel, you have the following additional options:

In 3D mode, the mouse can be used for navigating the data in the following manner: