Voxel display

Summary

Doc_BoxAlgorithm_VoxelDisplay.png
  • Plugin name : Voxel display
  • Version : 1.0
  • Author : Vincent Delannoy
  • Company : INRIA/IRISA
  • Short description : Displays brain activity as voxels
  • Documentation template generation date : Dec 30 2016
  • WARNING : this box has been marked as UNSTABLE by the developer. It means that its implementation may be incomplete or that the box can only work under well known conditions. It may possibly crash or cause data loss. Use this box at your own risk, you've been warned.

Description

This plugin uses a 3D grid of voxels to display brain activity sources in real time. The incoming matrix stream is assumed to contain the activation levels of each voxel in the form of value triplets. In addition, a semi-transparent face mesh can be displayed on top of the voxel grid to provide orientation cues to the viewer. Different settings allow to configure the way brain activity is depicted on screen.

This plugin is still a work in progress, and there's room for improvement in execution speed as well as functionalities. Some of its current limitations are mentioned in this documentation.

Inputs

1. Voxel activity levels

Voxel activity matrix. Its size should be 3 times the voxel count, for an [x,y,z] triplet is assumed to describe the dipole reconstructed at the location of each voxel. The vector provides the orientation of the dipole while its norm gives its activation level.

  • Type identifier : Streamed matrix (0x544a003e, 0x6dcba5f6)

Settings

1. Voxels filename

Voxel grid filename. This file should be in "OpenViBE Matrix" file format.

  • Type identifier : Filename (0x330306dd, 0x74a95f98)
  • Default value : [ ]

Online visualisation settings

Online options include :

  • Modify Color : voxel activation thresholds are mapped to voxel colors. A "standard" color scale (13 steps ranging from yellow to red) is used for now and cannot be modified.
  • Modify Transparency : voxel activation thresholds are mapped to voxel transparency factors. A unique transparency computation scheme is implemented for now, where transparency ranges from 1 (least activated voxels) to 0 (most activated voxels).
  • Modify Scale : voxel activation thresholds are mapped to voxel scale factors. A unique scale computation scheme is implemented for now, where the minimum scale factor is applied to the least activated voxels, the maximum scale factor is applied to the most activated voxels, and a linear interpolation is performed in between those levels.
  • Min Scale Factor : specifies the scale factor to apply to the least activated voxels
  • Max Scale Factor : specifies the scale factor to apply to the most activated voxels
  • Min Display Threshold Boundary : can be alternatively set to '<' or '>'
  • Min Display Threshold : defines the minimum activation threshold. This threshold is normalized
  • Max Display Threshold Boundary : can be alternatively set to '>' or '<'
  • Max Display Threshold : defines the maximum activation threshold. This threshold is normalized

The previous 4 settings allow to specify which voxels are to be displayed.

To see extrema values, i.e. the least and most activated voxels, set the minimum display threshold boundary to '<' (the other boundary automatically swtiches to '>'). This will display voxels whose level is either lower than the minimum display threshold, OR higher than the maximum display threshold.

To see all other voxels, click the Min Display Threshold Boundary and set it to '>' (the other boundary automatically switches to '<'). This will display voxels whose level lies in [Min Display Threshold, Max Display Threshold].

  • Face Opacity : sets the opacity of the face mesh surrounding the voxels. This provides orientation cues
  • Animate Camera : this option triggers a slight movement of the camera and improves parallax
  • View All : resets the camera position so that it encompasses the whole 3D scene, facing the +Z side of its bounding box
voxeldisplay_toolbar.png
Voxel Display toolbar

Examples

Miscellaneous