Bender/Documentation/2.0/Modules/FEMWorkflow

Introduction

This module guides the user step-by-step into transforming a volume using a rigging, skinning and posing technique.

Details

Author: Julien Finet, Kitware
Contributor #1: Johan Andruejol, Kitware
Acknowledgements: This work is supported by the Air Force Research Laboratories.
Contact: Julien Finet

Use Cases

• 

  2mm labelmap volume loaded in workflow

• 

  Bone and Skin surfaces extracted from 2mm labelmap volume

• 

  Rigging

• 

  Volume Skinning

Parameters

Advanced properties

Advanced Workflow: Volume Render Labelmap: Select the volume/labelmap you want to render. The checkbox next to labelmap controls whether the rendering is done. Label(s): Specify the label(s) that will be rendered. Go To Volume Rendering: Opens the Volume Renderer menu. Read here the documentation on this module.

Advanced properties panel

1) Adjust Labelmap

A) Labelmap Simple workflow Volume: Select the volume/labelmap that you want to reposition. Read here the instructions to load data into Bender. Colors: Select the color transfer function to apply to the volume . It will The transfer function is used to Apply: Set the color transfer function to the volume. LPS<->RAS: Apply a (-1,-1, 1) transform to the volume. It can be used to apply the same coordinate system used by Bender to the volume. The "R,L,A,P,S,I" letters on the purple box in the 3D view represent the orientations "Right, Left, Anterior, Posterior, Superior, Inferior". Advanced workflow Go To Volumes: Go to the Volumes module to read volume information (such as its size, origin, spacing, scalar type, range...) and display properties (window/level, threshold, interpolation...) B) Merge labels Simple workflow Output Labelmap: Select the labelmap for which the labels will be merged together. Merge labels: Merge the Bone Label(s) and Skin Label(s) from Input Labelmap (into respectively Bone Label and Skin Label) and outputs the result in Output Labelmap. Advanced workflow Input Labelmap: Select the labelmap that needs label to be merge together. Set by default to the selected volume in A) Labelmap. Bone label(s): Choose the label(s) that will be merge into the Bone Label. They are automatically computed based on the input volume color table by looking for names containing "bone" and "vertebrae" in it. Bone label: Select the new label value of the Bone Label(s). Skin label(s): Choose the label(s) that will be merge into the Skin Label. They are automatically computed based on the input volume color table by looking for names containing "skin" in it. Bone label: Select the new label value of the Skin Label(s).

Adjust labelmap panel

2) Extract Bone and Skin

A) Bone Model Maker Simple workflow Output model hierarchy: . Generate bone model: Advanced workflow Label(s): Go To Models: Go To Model Maker: B) Skin model maker Simple workflow Output: Toggle skin visibility:. Generate skin model:. Advanced workflow Input Labelmap: Select the labelmap that needs label to be merge together. Set by default to the selected volume in A) Labelmap. Threshold:. Go To Models: Go To Grayscale Model Maker:

Extract bone and skin panel

3) Create armature

Rig armature panel

4) Compute weight

Skin volume panel

5) Pose armature

Pose armature panel

6) Pose labelmap

Pose labelmap panel