3d analysis for volumetric measurement

Sir Syed University Of Engineering & Technology

Biomedical Engineering Department

FINAL YEAR PROJECT REPORT

Project Title:

3D analysis for volumetric measurement

Presented by:

Name: GOHAR SHABBIR Roll No#: 2008-BM-106

Name: ASMA ELAHI Roll No#: 2008-BM-099

Supervised by:

Name: ENGR.KAMRAN HAMEED

Designation: Assistance Professor

BMED: DT-3

SSUET: Biomedical Engineering Department

Date of Completion:

DECEMBER-2011

Sir Syed University Of Engineering & Technology 1

Table of Contents

Summary:.....................................................................................................................................................3

List of Figures...............................................................................................................................................4

List of Tables................................................................................................................................................4

1. CHAPTER 1:INTROUCTION AND METHADOLOGY

1.1. Introduction:................................................................................................................................6

1.1.1.Historical Background:..............................................................................................................6

1.1.2.Theoretical Investigation:..........................................................................................................6

1.1.3.Health Consequences:...............................................................................................................7

1.1.4.Working Principles:...................................................................................................................7

1.1.5.Calculations/Formulas:..............................................................................................................7

1.2. Usages in Biomedical Engineering:............................................................................................7

1.3. Design Methodology:...................................................................................................................8

1.3.1.Project Design In Phase:............................................................................................................8

1.3.1.1.Project Design In 1st Phase:...........................................................................................8

1.3.1.2.Project Design In 2nd Phase:..........................................................................................9

1.3.1.2.1.Modeling And Shading:.................................................................................9

1.3.1.2.2.Lightening:...................................................................................................16

1.3.1.2.3.Animation Setting:.......................................................................................17

1.3.1.3.Project Design In 3rd Phase:........................................................................................18

1.3.1.3.1.Rendering.....................................................................................................18

1.3.1.4.Project Design In 4th Phase:........................................................................................20

1.3.1.4.1.Animation:....................................................................................................20

1.3.5.Project Representation:............................................................................................................20

1.3.5.1.Over All Block Diagram:...........................................................................................21


2. CHAPTER 2 : SOFTWARE AND METHODS

1.4. Material & Method:............................................................................................................................23

2.1.1.Software:.................................................................................................................................23

1.4.1.1.Autodesk ® Maya ® 8.0.............................................................................................23

1.4.1.2.Adobe ® AfterEffects ®CS5.5...................................................................................23

2.1.2.Methods:..................................................................................................................................23

2.1.2.1.1st phase:......................................................................................................................23

2.1.2.2.2nd phase:.....................................................................................................................24

2.1.2.3.3rd Phase:.....................................................................................................................25

2.1.2.4.4th phase:......................................................................................................................25

3. CHAPTER 3: RESULT

3.1.Result of Project...................................................................................................................................27

4. CHAPTER 4: DISCUSSION

4.1. Discussion...................................................................................................................................30

4.1.2. 1st phase:.................................................................................................................................30

4.1.3.2nd phase:.........................................................................................................314.1.4.3rd phase:

..........................................................................................................................................................32

4.1.5.4th phase:..................................................................................................................................32

4.2. Problem encountered:....................................................................................................................33

4.3.Improvement for future:.................................................................................................................33

5. CHAPTER 5: CONCLUSION

5.1. Project:........................................................................................................................................35

5.2. Step of project:...........................................................................................................................35

References...................................................................................................................................................36

List of Abbreviations.................................................................................................................................37


Summary:

Our project entitled “3D analysis for volumetric measurement” which is based on 3D modeling.

3D modeling is the procedure of developing 3Dmodel using specialized software. It is a process of

creating a wireframe model that represents a three dimensional object. A three dimensional model is

created using a set of points in 3D space, which are connected by various geometric data such as lines,

and curved surfaces.[1]

The main idea of the project is making a 3D models which are used for 3D measurement, volume

calculation, surgical and treatment planning, surgical simulation, and 3D rapid prototyping applications.

3D rendering is performed via Autodesk® Maya® 8.0.Autodesk® Maya® 3D animation software

delivers an end-to-end creative workflow with comprehensive tools for animation, modeling, simulation,

visual effects, rendering, match moving, and compositing on a highly extensible production platform.[2]

The volumetric measurement was performed by measuring the tumor's length at each axis by using the

measurement tool in Autodesk® Maya® 8.0.

After rendering and measurement, the Adobe® After Effects® CS5.5 was used for or compiling rendered

image sequences or animation. This project can be use professionally after advancement by training and

collaboration with C++ like other softwares currently use by the medical industry such as 3D-DOCTOR.

This project is a prototype but it can be use at professional level after further development and training.

Great knowledge is gathered through the project as a used in the field of medical imaging.


List of Figures

FIGURE 1.1 AUTODESK® MAYA® [2]....................................................................................................8

FIGURE 1.2 BOX MODELING...................................................................................................................9

FIGURE 1.3 SKIN SHADE........................................................................................................................10

FIGURE 1.4 WIRE FRAME WITH SKIN SHADE...................................................................................10

FIGURE 1.5 CROSS SECTIONAL VIEW................................................................................................11

FIGURE 1.6 POLY MODELING 1............................................................................................................11



FIGURE 1.9 EXTRUSION MODELING...................................................................................................13

FIGURE 1.10 COLOURS SHADE.............................................................................................................14

FIGURE 1.11 COLORS AND MAPPING..................................................................................................14

FIGURE 1.12 SYMMETRY.......................................................................................................................15

FIGURE 1.13 WIRE FRAME SHOWING TUMOR..................................................................................15

FIGURE 1.14 DUPLICATE OR SYMMETRY THE HALF MODELED HEAD.....................................16

FIGURE 1.15 RENDER SETTING............................................................................................................17

FIGURE 1.16 PREFERENCES...................................................................................................................18

FIGURE 1.17 BATCH RENDERING........................................................................................................19

FIGURE 1.18 SCRIPT EDITOR.................................................................................................................19

FIGURE 1.19 BLOCK DIAGRAM OF PROJECT....................................................................................21

FIGURE 3.1.1 TUMOR IN BRAIN............................................................................................................27

FIGURE 3.1.2 DIMENSIONS OF TUMOR...............................................................................................27

FIGURE 3.1.3 TUMOR’S VOLUME.........................................................................................................28

FIGURE 4.1 BLOCK DIAGRAM OF PHASE 1........................................................................................30

FIGURE 4.2 BLOCK DIAGRAM OF 2ND PHASE..................................................................................31

FIGURE 4.3 BLOCK DIAGRAM PHASE 3..............................................................................................32

FIGURE 4.4 BLOCK DIAGRAM OF PHASE 4........................................................................................32

List of Tables

Table 1.1......................................................................................................................................................28


1. Chapter 1:

INTRODUCTION

&

METHODOLOGY


1.1. Introduction:

Our project is based on 3D rendering, which render the image making a 3D model by using

Autodesk® Maya® 8.0.

3D modeling is the procedure of developing 3Dmodel using specialized software. It is a process

of creating a wireframe model that represents a three dimensional object. A three dimensional

model is created using a set of points in 3D space, which are connected by various geometric

data such as lines, and curved surfaces. [1]

Autodesk® Maya® 3D animation software delivers an end-to-end creative workflow with

comprehensive tools for animation, modeling, simulation, visual effects, rendering, match

moving, and compositing on a highly extensible production platform. [2]

1.1.1. Historical Background:

Various powerful softwares have been developed to visualize data. Computer generated

imagery can be categorized into several different types: 2D, 3D, and animated graphics.

As technology has improved, 3D modeling have become more common, but 2D

computer graphics are still widely used. Computer graphics has emerged as a sub-field of

computer science which studies methods for digitally synthesizing and manipulating

visual content. Over the past decade, other specialized fields have been developed like

information visualization, and scientific visualization more concerned with "the

visualization of three dimensional phenomena (architectural, meteorological, medical,

biological, etc.), where the emphasis is on realistic renderings of volumes, surfaces,

illumination sources, and so forth, perhaps with a dynamic (time) component". [3]

1.1.2. Theoretical Investigation:

3D rendering is the 3D graphics process of automatically converting wire frame models

into 2D images with 3D photorealistic. 3D-DOCTOR is the production of ABLE

SOFTWARE CORP performs 3D rendering also the measurement of any

pathology. Also in used in Singapore for learning purpose.


http://en.wikipedia.org/wiki/Photorealism

http://en.wikipedia.org/wiki/Wire_frame_model

http://en.wikipedia.org/wiki/3D_computer_graphics

http://en.wikipedia.org/wiki/Biological_Data_Visualization

http://en.wikipedia.org/wiki/Three-dimensional_space

http://en.wikipedia.org/wiki/Scientific_visualization

http://en.wikipedia.org/wiki/Information_visualization

1.1.3. Health Consequences:

There are some health consequences where rendering is used.

3D reconstructions: Volume rendering, surface rendering, and 3D MIP

Volumetric analysis: Tumor volume measurements, organ volume measurements

Cardiac examinations: Ejection fraction calculation, flow quantification.

Dental and craniofacial reconstructions.

1.1.4. Working Principles:

The working principle of our project is based on software name Autodesk® Maya®

8.0.

We also performed animation by Adobe® After Effects® CS5.5 which is used for

compiling rendered image sequences or animation.

1.1.5. Calculations / Formulas:

Calculate the volume of tumor by using this formula.

34×π ×

x2×y2×z2

Formula 1

1.2. Usages in Biomedical Engineering:

It is use for study purpose. Study the image on various angles.

3D visualization of tumors demonstrates anatomic relationships to surrounding structures

which may be important in diagnosis and treatment planning.


1.3. Design Methodology:

Following are the step used to design the project.

Planning.

Modeling and shading.

Animation Setting.

Lightening.

Rendering.

Animation.

1.3.1. Project Design In Phases:

We divide our project in four phases.

Phase 1: Planning

Phase 2: Modeling and shading, lighting and animation setting.

Phase 3: Rendering.

Phase 4: Animation

1.3.1.1. Project Design In 1 st Phases:

In 1st phase of project is based on our planning that all process is perform in

Autodesk® Maya® 8.0 software.

Autodesk® Maya® 3D animation software delivers an end-to-end creative

workflow with comprehensive tools for animation, modeling, simulation, visual

effects, rendering, match moving, and compositing on a highly extensible

production platform. [2]


FIGURE 1.1 AUTODESK® MAYA® [2]

9

1.3.1.2. Project Design In 2 nd Phase:

In 2nd phase we are perform Modeling and shading, lighting and animation setting.

1.3.1.2.1. Modeling And Shading:

First was used the box modeling technique. It involves working on each

vertex (pixel in 3D).

Box modeling is a form of modeling in which a rough draft or

approximation of the final desired model is created. A smoothing

operation or subdivisions are then used to add the desired refinement. It is

a quick modeling method, especially compared to editing each individual

vertex but it can be difficult to get the desired results because of the

uniformity of the smoothing operations. [4]


FIGURE 1.2 BOX MODELING

1

FIGURE 1.3 SKIN SHADE

FIGURE 1.4 WIRE FRAME WITH SKIN SHADE

The wireframe model is being shaded with the human skin texture using

the shader. Shading addresses how different types of scattering are

distributed across the surface (i.e., which scattering function applies

where). Descriptions of this kind are typically expressed with a program

called a shader.


FIGURE 1.5 CROSS SECTIONAL VIEW

Partially modeled for symmetry and mapped the image texture.

Symmetrical models are usually taken in half so that it can be symmetric

and then weld. Texture mapping is a process in which a defined texture

or image is wrapped around a 3d object. Texture mapping ensures that all

the right things happen as rendered.

FIGURE 1.6 POLY MODELING 1




Brain modeling is performed using box modeling. This modeling

technique is called poly modeling.

Poly Modeling is one of the most common modeling techniques. It is

easy to use, but it consumes a lot of time and effort as your required to

copy the existing edges to make new ones and then align the vertex of

new edges to the blueprint.[4]


FIGURE 1.9 EXTRUSION MODELING

Model is further detailed by extruding of faces. This is performed by

pulling and pushing of small wireframe boxes.

Extrusion modeling is that starts from a two dimensional shape

(polygon) that resembles an orthographic view of the desired subject.

Geometry is then extruded from this shape to match a perpendicular

orthographic view. [4]


FIGURE 1.10 COLOURS SHADE

FIGURE 1.11 COLORS AND MAPPING

Color is assigned to the different lobes and regions of the brain by

material editor. Generally, the Material Editor provides functions to

create and edit materials and maps.

A material is data that assign to the surface or faces of an object so that

it appears a certain way when rendered. Materials affect the color of

objects, their glossiness, their opacity, and so on. The images or

procedural effects you assign to materials are called maps. Maps can be


assign to most of the components that make up a material. Materials that

contain one or more images or procedural maps are called mapped

materials. [4]

FIGURE 1.12 SYMMETRY

FIGURE 1.13 WIRE FRAME SHOWING TUMOR


FIGURE 1.14 DUPLICATE OR SYMMETRY THE HALF MODELED HEAD.

1.3.1.2.2. Lightening:

When render a scene using the mental ray renderer, an area Omni light

emits light from a spherical or cylindrical volume, rather than from a

point source. With the default scan line renderer, the area Omni light

behaves like any other standard Omni light. [5]

Two Omni lights are used, each at the right and the left.


1.3.1.2.3. Animation Setting:

FIGURE 1.15 RENDER SETTING

Image format that is being used is Targa (tga). TARGA is a graphics file

format. It is intended for professional computer image synthesis and

video editing with PCs. TARGA is an acronym for True vision

Advanced Raster Graphics Adapter; TGA is an initialize for True vision

Graphics Adapter. The compression method used in Targa images

performs poorly when compressing images with many color variations,

such as digital photos, but works well for textures and simpler images.

Therefore, it is best for video rendering. [6]


http://en.wikipedia.org/wiki/Initialism

http://en.wikipedia.org/wiki/Graphics_file_format_summary


FIGURE 1.16 PREFERENCES

Frames are usually set according to shots. Therefore, for normal

circumstances 24 frames per second were used.

1.3.1.3. Project Design In 3 rd Phase:

3rd phase is based on rendering.

1.3.1.3.1. Rendering

Rendering is to execute something in image or video form for any 3D

application. Rendering is performed on mental ray technology.

Mental ray 3D rendering software enables to produce high-volume, high-

quality renderings for today’s complex visualization productions in less

time. With accelerated performance, enhanced quality, support for

advanced shaders, and extended use of open file formats, mental ray

offers a faster solution for high-volume rendering tasks. [4]


FIGURE 1.17 BATCH RENDERING

Instead of frame rendering batch rendering is performed. Batch rendering

is the process of rendering out maya scene files without using the

interface. It allows starting renders, as well as changing some of the

attributes of the rendering software. It is basically image sequence

rendering.

FIGURE 1.18 SCRIPT EDITOR

Total 440 frames are formed after approximately 4 hours of rendering.

The rendering is viewed from script editor.


1.3.1.4. Project Design In 4 th Phase:

Our last phase is performed animation.

1.3.1.4.1. ANIMATION:

All the image sequences that are formed after the rendering are compiled

in Adobe® After Effects® CS5.5 to make animation of 3 minutes

and 36 seconds. The animation is exported in a video format to

view on media player.

Image sequences are compiling in adobe after effects. Color correction. Adding texts

1.3.2. Project Representation:

Over All Block Diagram


1.3.2.1. Over All Block Diagram:

FIGURE 1.19 BLOCK DIAGRAM OF PROJECT


Box Modeling Shader Image

Mapping

Poly Modeling Extrusion Material

Editor

Symmetry Rendering Volumetric Measurement

TextingAnimation

2

2. CHAPTER 2

SOFTWARE

&

METHODS


1.4.Material & Method:

Our project is based on software so as such no materials are used in.

1.1.1. Software:

Following softwares are used in our project.

Autodesk® Maya® 8.0

Adobe® After Effects® CS5.5

1.4.1.1. Autodesk® Maya® 8.0

Autodesk® Maya® 3D animation software delivers an end-to-end creative

workflow with comprehensive tools for animation, modeling, simulation, visual

effects, rendering, match moving, and compositing on a highly extensible

production platform. [2]

By Autodesk® Maya® we performed modeling, shading, lightning, and

rendering

1.4.1.2. Adobe® After Effects® CS5.5

Adobe® After Effects® CS5.5 was used for or compiling rendered image

sequences or animation.

1.1.2. Methods:

1.1.2.1. 1 st phase:

The planning is performed in 1st phase.

Planning:

Our project is based on our planning that all process is perform in

Autodesk® Maya® 8.0 software.


1.1.2.2. 2 nd phase:

The following work performed in 2nd phase.

Modeling and shading.

Animation Setting.

Lightening.

Modeling and shading:

In modeling we used 3 types of modeling (box modeling, poly modeling, and

extrusion modeling).

Partially modeled are used for symmetry and mapped the image. The

wireframe model is being shaded with the human skin texture using the

shader. Color is assigned to the different lobes and regions of the brain by

material editor.

Animation setting:

Image format that is being used is Targa (tga). TARGA is a graphics file

format. It is intended for professional computer image synthesis and video

editing with PCs. [6]

Frames are usually set according to shots. Therefore, for normal

circumstances 24 frames per second are used.

Lightning:

Two Omni lights are used, each at the right and the left.

Point light casts rays of light evenly in every direction from a point. Point

lights are sometimes used for simulating Omni directional light sources, such

as light bulbs. [5]




1.1.2.3. 3 rd Phase:

The 3rd phase is based on rendering.

Rendering:

Rendering is to execute something in image or video form for any 3D

application. Rendering is performed on mental ray technology. Instead of

frame rendering batch rendering is performed. Batch rendering is the process

of rendering out maya scene files without using the interface. It allows

starting renders, as well as changing some of the attributes of the rendering

software. It is basically image sequence rendering. [4]

Total 440 frames are formed after approximately 4 hours of rendering. The

rendering is viewed from script editor.

1.1.2.4. 4 th phase:

In last phase we make animation by using 2nd software

Animation :

All the image sequences that are formed after the rendering are compiled in

Adobe® After Effects® CS5.5 to make animation of 3 minutes and 36

seconds. The animation is exported in a video format to view on media

player.


3. CHAPTER 3

RESULT


1.2.Result of Project

In our project we performed the rendering and then the volumetric measurement of the tumor in

the brain. Following figures show the tumor in the brain.

FIGURE 3.1.20 TUMOR IN BRAIN

The volumetric measurement was performed by measuring the tumor's length at each axis by

using the measurement tool in Autodesk® Maya® 8.0.following figure also show the detailed

dimension of the tumor.

FIGURE 3.1.21 DIMENSIONS OF TUMOR


At 1 cm scaling the tumor’s dimensions are at each axis:

Axis Dimensionsx 0.998078cmy 0.816101cmz 0.453776cm

Table 3.1.1

As the tumor is elliptical therefore, by using following formula:

34×π×

x2×y2×z2

Tumor Volume = 0.108 cm3

FIGURE 3.1.22 TUMOR’S VOLUME


2. CHAPTER 4:

DISCUSSION


4.1. Discussion

3D analysis is a three dimensional model which is created using a set of points in 3D space,

which are connected by various geometric data such as lines, and curved surfaces. [1] 3D

rendering is performed via Autodesk® Maya® 8.0. The volumetric measurement was performed

by measuring the tumor's length at each axis by using the measurement tool in Autodesk®

Maya® 8.0 and the Adobe® After Effects® CS5.5 was used for or compiling rendered image

sequences or animation.

2.1.1. 1 st phase:

FIGURE 4.23 BLOCK DIAGRAM OF PHASE 1

Discussion:

In 1st phase process is performed using box modelling technique in which we worked on

each vertex (pixel in 3d). Human skin shade is formed on the wire frame. We can make

any shade (shader) or texture on any 3d geometry such as metal, wood, leather, plastic etc

.

We divided the model in half. Actually, symmetrical models are taken in half so that we

duplicate the half model then weld the two models.


Box Modelling

Shader

Mapping

3

2.1.2. 2 nd phase:

FIGURE 4.24 BLOCK DIAGRAM OF 2ND PHASE

Discussion:

In 2nd phase the brain modeling was performed by poly modeling which was detailed

further by extruding faces. Colors were assigned through material editor.


Poly Modeling

Extrusion

Material Editor

Symmetry

3

2.1.3. 3 rd phase:

FIGURE 4.25 BLOCK DIAGRAM PHASE 3

Discussion:

In 3rd phase rendering was performed through mental ray technology at 24 frames per

second.

1.4.2. 4 th phase:

FIGURE 4.26 BLOCK DIAGRAM OF PHASE 4


Rendering

Volumetric Measurement

Texting

Animation

3

Discussion:

In 4th phase, volumetric measurement was made by the using formula and the Adobe®

After Effects® CS5.5 was used for or compiling rendered image sequences or animation.

4.2. Problem encountered:

There were lot of problems encountered during the project as initially; we did not have the

awareness of the software used Autodesk® Maya® but as we progress, we get familiar with the

tools and able to use them.

4.3. Improvement for future:

This project can be use professionally after advancement by training and collaboration with C++

like other softwares currently use by the medical industry such as 3D-DOCTOR.


3. CHAPTER 5:

CONCLUSION


5.1. Project:

This project is a prototype but it can be use at professional level after further development and

training. A great deal of information and knowledge is gathered thorough the project as to use in

the field of medical science, specifically in the field of medical imaging.

5.2. Step of project:

Our project is complete in four phases which is discussed above. The following steps were

followed to complete the project.

1. Planning.2. Modeling.3. Animation Setting.4. Lightening.5. Rendering.6. Animation.

All above steps also discussed in above chapter.


References

[1]."3D Scanning Advancements in Medical Science". Konica Minolta. Retrieved 24 October 2011.

[2] Sangeetha Johari. "Hindu Goddesses : Maya - Hindu Goddess". sanatansociety.org. Retrieved 2010-

12-10.

[3] Michael Friendly (2008). "Milestones in the history of thematic cartography, statistical graphics, and

data visualization"

[4] Maya documentation: packaged with Alias Maya, http://www.alias.com/eng/index.shtml

[5] In slico book Jason Sharpe, Charles J. Lumsden, Nicholas Woolridge - 2008 - Computers.

[6] "Truevision TGAª — FILE FORMAT SPECIFICATION — Version 2.0"


http://www.math.yorku.ca/SCS/Gallery/milestone/milestone.pdf

http://www.math.yorku.ca/SCS/Gallery/milestone/milestone.pdf

List of Abbreviations

MIP maximum intensity projection

TARGA Truevision Advanced Raster Graphics Adapter;

Cm centimeter

cm3 cubic centimeters

TGA Truevision Graphics Adapter


3d analysis for volumetric measurement

Documents

project design

d measurement

d analysis

step of project

project representation

rd phase

nd phase

th phase