Visualization in MIPAV

http://mipav.cit.nih.gov

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Visualization in MIPAV

Alexandra Bokinsky, PhD

Geometric Tools, Inc.
Ruida Cheng
National Institutes of Health

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 3D Visualization Outline

• 3D Image Processing
• Volume rendering
• Surface extraction and rendering
• Advanced rendering techniques
• Visualization Applications in MIPAV
– Diffusion Tensor Visualization, ISO-Surface
rendering, virtual endoscopy.

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 Course Goals

• Know what 3D visualization capabilities are

available in MIPAV
• Familiar with the tools and user-interface
• Able to start creating visualizations
A Brief Introduction to 3D Medical Images
Superior

Posterior

Medical images taken of the human body are acquired or displayed

in three main orientations:

1.Coronal orientation: in a cross section (plane), for example, across

Anterior the shoulders, dividing the body into front and back halves
2.Sagittal orientation: in a cross section (plane), for example, down
the middle, dividing the body into left and right halves
3.Axial orientation: in a cross section (plane), perpendicular to the
long axis of the body, dividing the body into upper and lower halves
Inferior

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Axial Sagittal Coronal
 Voxel Thickness & Resolution
Image plane
X-Dimension(1st)

(0,0,0) (1,0,0) (1,0,0) (8,0,0)

(0,1,0) (1,1,0) X-Dim

(0,2,0)

Y-Dimension(2nd) Y-Dim

Z-Dim

(0,6,0) (8,6,0)

(8,6,3)
Voxels, of 3D clinical images,
are typically NOT isotropic.
voxel
Z-Dimension (3rd) This factor should be accounted
for in processing algorithms.

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3D Visualization

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 Launch
GPU-Based
Volume Renderer

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Orthogonal Plane View

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Volume Rendering

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 Volume Rendering

• Opacity filter
• Gradient magnitude filter
• Color Lookup Table
• Global opacity and blending
• 2D Histogram filters
• Clipping and Sculpting Volumes
Select Volume View
Opacity Filter

Voxel values that

Default Opacity
are opaque

Voxel values that

are transparent

Composite Modified Opacity

Gradient Magnitude Filter

GM Filter Off
Select Color Lookup Table
Adding Color

GM Filter On
Voxel values that
are white

Voxel values that

are black

GM Filter Off
 Volume Rendering Modes

Render mode panel

Composite

Set render mode

MIP

Digitally Reconstructed Radiograph

Surface
Modifying Global Opacity

Global Opacity = 1

Global Opacity < 1

2D Histogram Tool

GM Filter On

Two histogram filters

2D Histogram Tool
 Volume Clipping
Enable clipping

Axis-aligned clipping sliders

 Sculpturing Tool

User-draw sculpt region After volume sculpting

 Volume Rendering Demo

• Opacity filter
• Gradient magnitude filter
• Color Lookup Table
• Global opacity and blending
• 2D Histogram filters
• Clipping and Sculpting Volumes
 Creating and Rendering Surfaces

• Creating Surfaces
• Adding a surface to the viewer
• Color and material
• Smoothing and decimation
• Painting on surfaces
 Surface Extraction from 2D Viewer

Use the Paint Can tool to grow a

3D region of paint in the image.
 Surface Extraction from 2D Viewer

Algorithms ->Extract surface (marching cubes)

Extracts from a mask or VOI region.
 WYSIWYG Surface Extraction

Adjust the volume opacity.

Display the volume in Surface mode.
Press Extract Mesh Button
 WYSIWYG Surface Extraction

Save the mesh to a file.

Surface visible in slice view.
 VOI Surface Generation
Extract Mesh from VOI

VOI Toolbar.
Can draw and edit VOIs in the
orthogonal views.
VOI Surface Generation

Surface and VOIs

 Adding a Surface from File

Add Surface to view

Smooth Surface and
Surface Decimation

Solid, line, or point

Surface after smoothing.

Point cloud rendering.

Surface after decimation.

Painting on Surface
Multiple Surfaces

Brain tumor extracted separately.

 Creating and Rendering Surfaces

• Creating Surfaces
• Adding a surface to the viewer
• Color and material
• Smoothing and decimation
• Painting on surfaces
Saving Visualization Data
Record Animation
Save current parameters
 Advanced 3D Visualization

• Image Fusion
• 4D Volume Rendering
• 3D Stereo viewing
 Image Fusion

CT Image A PET Image B

Blend between images.

 4D Volume Rendering

Adjust time slice

continuous animation
Stereo View

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Applications of MIPAV 3D
Visualization
DTI Visualization

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DTI Visualization

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DTI Visualization

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DTI Visualization

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Visual Endoscopy Simulation

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 SVM based Automatic Prostate Segmentation on 3D
Center slice as
MRI images Automatic
Segmentation
the training base
on the rest slices

Training Classification Morphology

Haralick Edge
Edge
Texture Finding
Finding

Features
Features Features
Features
Gabor Extraction
Extraction Extraction
Extraction
Loading SVM
Fuzzy-C
Classification
Classification
Means Mask

SVM Linear,
SVM
SVM Linear
Linear
Non-linear
Non-linear Deform based
Classification
Classification
Regression Image
Image
morphology
Automatic 3D MRI
Segmentation Surface
Reconstruction 3D Visualization
…
Merged
3D Cloud 3D Printing
 OpenCL

Open Compute Language

Use the Graphics Processing Unit (GPU) as a
general massively parallel compute device.
Currently available for FFT
Soon to be available in other MIAPV Algorithms
 Visualization

Processing Macros/Plugins

Quantification Ubiquitous File writer

file reader

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