Updated for release version: 1.0.16-alpha

This page introduces the Volume Panel, which provides an interface for users to load 3D images (here called Volume3Ds), specify colour maps, visualize in 2D and 3D, define masks, etc.

Introduction

A 3D volume is essentially a regular grid defined in R3, with values associated with each grid coordinate. This is a way to represent data from a variety of modalities, including: magnetic resonance imaging (MRI), positron emission tomography (PET), and 3D geophysical surveys. The Volume Panel provides an interface to load such data into memory, defining the data type and dimensions, and to visualize it in 2D or 3D.

Defining and Loading Volume Data

This section describes how to define an load data into a 3D volume object. The relevant panel sections are: Grid, Geometry, and Data, as shown below.

Grid

The Grid section defines the current Volume for the panel; to define a new volume, "<-New Volume->" should be selected from the "Shape" drop-down box, and the shape set into which the new volume will be placed is defined by the "Set" drop-down box.

Geometry

The Geometry section defines the geometric dimensions of the Volume, including its origin point, its spatial dimensions, and its S, T, and R basis vectors (where, for a volume orthogonal to standard Euclidean space, S is analogous with X, T with Y, and S with Z). Changes to these values can be applied to the shape using the "Apply Changes" button.

Data

The Data section first displays the data dimensions of the Volume (how the grid is arranged along the three dimensions), and then lists the current vertex data columns in the selected Volume. This list contains four columns:

1. Current column

Only one row can be checked, and this row is the current column. If the volume is not being rendered as a composite, this is the column which will be used to render. The current column is used to fill the Data Type box, and the values in the Intensity and Histogram categories.

2. Show in composite

If checked, this image will be used to render a composite image, if the "Render as composite" box is checked (this corresponds to the "IsComposite" attribute of the Volume.

3. Column

The name of the column for this row.

4. Alpha

This slider bar determines the alpha level for composite rendering. Left is more transparent, right is more opaque.

The order of the rows in this table determines the order in which the data columns will be rendered as a composite image. Top-most data columns will be rendered last; i.e., they will appear on top. This order can be changed with the "Move up" and "Move down" buttons.

The Data Type drop-down box displays the data type of the current column. If this is changed for the current data column, it must be applied (see next).

The "Create Volume / Add Column" and "Update Current" check boxes determine the action to perform on a new or current volume.

Create Volume

If the Shape drop-down box is set to "<-New Volume->", only this check box will be available. This indicates that the current action will be to create a new volume object with the specified parameters. The relevant action button will read "Create".

Add Column

If the Shape drop-down box is set to an existing shape, checking this box means the next action will be to add a new data column with the same data dimensions as the current volume. The relevant action button will read "Add Column".

Update Current

If the Shape drop-down box is set to an existing shape, you also have the option of updating the current data column. The relevant action button will read "Update".

There follow three buttons which define the creating of a new volume or addition of a data column to an existing volume:

Zeros

This button defines a new grid of zeros. Clicking it with bring up an input box which allows the user to name the new volume or data column into which the zeros will be placed.

Volume File

This button brings up the Volume File Dialog (see section below), which allows the user to locate a volume file to load, as well as the initial colour map and alpha state.

Image Stack

This button allows the user to define a stack of image files as the source for the new volume or data column. [NB: this option is not implemented as of mgui-alpha-1.0.16].

The final two buttons are: "Delete", which deletes the current volume entirely; and the action button, which will display different text as described above. This button completes the relevant action: either to create a new volume, add a new data column, or update the current data column.

Volume File Dialog

Visualization of a Volume

This section describes how the Volume Panel can be used to define the way a volume is visualized. The relevant panel sections are: Intensity, Histogram, and Attributes.

Intensity

Histogram

Attributes

Masking

Tutorials

Working with volumes: Guides you through the process of loading and visualizing a volume, including a composite volume.