TutorialPlanesVisualization

Planes Visualization Tutorial

Summary

This plugin is a good starting point to understand vIST/e usage easily. Although vIST/e has a modular structure, all of the loaded datasets and the products of plugins are available to all the other plugins that might need to process or display them.

The Planes plugin can be used to visualize scalar volumes and/or DTI volumes using three orthogonal cross-section planes. The three planes are added to the 3D view, and each is added to one of the three 2D views. When visualizing a scalar volume, the scalar values are mapped to pixel colors through a look-up table. DTI volumes can be visualized used the RGB-method, which directly maps the main eigenvector of the DTI tensor to RGB values. In addition, these RGB values can be weighted using a scalar volume (i.e., the three RGB values are multiplied by a scalar). Linear interpolation of the pixels of the cross-planes is enabled by default, but can be disabled. Planes can be moved and turn on or off individually. This is one of the most essential plugins, and is a recommended part of most profiles.

Plugin Type

Plugin Type	Description
GUI	This plugin has a Graphical User Interface.
Consumer	This plugin consumes data.
Visualization	This plugin can visualize data.
Advanced	This plugin has advanced functionality.

Related Plugins

Plugins	Description
DTI Reader and NIfTI Reader	Used to read in DTI volumes.
DTI Measures	Used to convert DTI volumes to volumes that can be visualized by this plugin (eigensystem and DTI measures).
ROI Edit	Uses the current position of the three planes to correctly position the ROIs.
GPU Glyphs	Shows glyphs on the X-plane after reading in a DTI volume.
Transfer Function and Transfer Function Reader	Edit and load the look-up tables used to color the planes for scalar volumes.

Input Data Types

Data Type	Description
Scalar Volume	Can be visualized using a look-up table. Can be loaded from an external file, or computed by one of the other plugins (like the DTI Measures plugin). Can also be used as a weighting volume when visualizing a DTI volume using the RGB coloring method
Eigensystem Volume	Computed from a DTI volume by the DTI Measures plugin. Contains eigenvectors and -values of the DTI tensors. Used for the RGB coloring, which maps the main eigenvector to RGB color values.
Transfer Functions	Look-up table used to color the planes for scalar volumes. A built-in, black-to-white transfer function is selected by default.

Output Data Types

Data Type	Description
Seed Points	A set of seed points is created for each plane, containing the positions of all voxels in the plane (for its current position). This can for example be used by the GPU Glyphs plugin, to show glyphs on the current plane.
Plane Actors	These three data sets contain information about each of the three planes. The ROI Edit plugin uses this information to correctly position Regions of Interest drawn by the user.

GUI Controls

GUI Control	Description
Scalar Volume LUT	Select to visualize a scalar volume using a look-up table.
Scalar Volume	Scalar volume visualized by the planes.
Look-Up Table / Transfer Function	Look-up table used to color the planes.
Diffusion Tensors (RGB)	Select to visualize a DTI volume using the RGB coloring method.
DTI Volume	DTI volume visualized by the planes.
Weighting Scalar Volume	Optional scalar volume used to weigh the RGB values.

GUI Control	Description
Sagittal (X), Coronal (Y) and Axial (Z)	Slider and spin box are used to control the positions of the planes.
Visible	Show or hide individual planes.
Linear Interpolation	Turn linear interpolation of the plane textures on or off. Interpolated planes generally look smoother, but do not allow for inspection of individual voxels.

Screenshots

DTI volume visualized using the RGB coloring method, and weighted using its Fractional Anisotropy scalar volume.

The same DTI volume, but without scalar weighting.

The same DTI volume, but with linear interpolation of the planes turned off.

The Fractional Anisotropy scalar volume of the DTI volume, mapped through the default black-to-white transfer function.

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FA scalar volume is calculated from the loaded DTI automatically. Then Plane Visualisation plugin uses the FA scalar volume as scalar weighting image.

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DTI and HARDI Glyphs Displayed together. GPU Glyphs Plugin is used.

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Glyph type Selection on the GPU Glyphs GUI