The University of Sydney Slide 1

HOUSEKEEPING

The University of Sydney Slide 2

Announcements

– Blackboard should now be visible to all students

– Lecture slides:

– All 2015 lectures are available for those who want to prepare early

– Will attempt to update slides by Monday (definitely available Thursday onwards)

– Simpleware ScanIP is now available on all PC Lab computers

Group projects

– Please send group lists to Paul

– Imaging is available from our office (but you’re still free to use your own)

– If interested in lab access for validation, please let us know by week 4

– Reports:

– Group reports for UGs (approx. 80 pages)

– Individual reports for PGs (approx. 40 pages)

The University of Sydney Slide 3

Tips for a Successful Project

– Exercise in project planning

– Establish your aims and scope early on

– Informal summary presentation next week

– Distribute the workload according to strengths

– Pull your weight (i.e. don’t be “that guy”)

– Have redundancies in case of “missing” group members

– Plan ahead to validate the model

“If you reach for the stars, you might not quite get one, but you

won’t end up with a handful of mud, either.”

~ Leo Burnett

The University of Sydney Slide 4

IMAGE PROCESSING

Presented by

Dr Paul Wong

AMME4981/9981

Semester 1, 2016

Lecture 2

The University of Sydney Slide 5

Required Inputs

Geometry

• What does it look like?

Material properties

• What is it made of?

Loads

• What forces is it subjected to?

Boundary conditions

• What is happening at the system boundary?

The University of Sydney Slide 6

Workflow for Biomedical Problems

1. Data acquisition

• Scan region of interest

• Obtain material properties for tissues and implants

• Estimate expected loads

2. Solid modelling

• Convert image stacks into a virtual replica

• Combine with CAD model of prosthesis

3. Finite element analysis

• Generate appropriate mesh

• Characterise interaction between anatomy and prosthesis

• Verify simulation results and prosthesis design

The University of Sydney Slide 7

SEGMENTATION & RECONSTRUCTION

The University of Sydney Slide 8

Objective

– To replicate the geometry of

the region of interest in silico

– Prosthesis is typically

modelled using CAD

– Anatomy can also be made in

CAD, but this is not ideal…

REGION OF INTEREST

Prosthesis Anatomy

The University of Sydney Slide 9

Organic Shapes

– Organic structures typically have

complex geometries

– Irregular shape, non-uniform

curves

– No symmetry

– Multiple parts and interfaces

– Differences between

individuals

– Anatomy should be reconstructed

from scans

– Higher accuracy

– Enables patient-specific

studies

The University of Sydney Slide 10

CT Scan of Proximal Femur

The University of Sydney Slide 11

Typical Workflow

Import image stack

Separate into different tissue types

or parts

Apply smoothing

filter and/or fit curves

Create surface model

Generate solid model

The University of Sydney Slide 12

Commercial Software

VSG Amira

– User friendly interface

– Easy to learn

– Some very handy selection tools

are unique to Amira

– Excellent real-time visualisation

options

– Meshing often requires manual

adjustment

The University of Sydney Slide 13

Commercial Software

Materialise Mimics

– Highest degree of user control

– Very powerful tools

– CE and FDA 510(k) market

clearance

– Not very user friendly

– Extremely expensive

The University of Sydney Slide 14

Commercial Software

Simpleware ScanIP

– 50 student licences, available in all PC Labs

– FDA 510(k) market clearance

– How to learn the software:

– “Basic segmentation from CT: Proximal femur”(Chapter 7, Simpleware Tutorial Guide)

– “Import and positioning of CAD implant: Proximal femur”(Chapter 8, Simpleware Tutorial Guide)

– Chapters 4-7, Simpleware Reference Guide

– Just try something and see what happens

The University of Sydney Slide 15

Typical Workflow

Import image stack

Separate into different tissue types

or parts

Apply smoothing

filter and/or fit curves

Create surface model

Generate solid model

The University of Sydney Slide 16

ScanIP User Interface

The University of Sydney Slide 17

Segmentation

The University of Sydney Slide 18

Selection Tools

– Selection tools add voxels to masks

NAME FUNCTION COMMENTS

Paint Selects voxels manually Only use this if all others are insufficient, or for

touch-ups

Threshold Selects voxels based on

luminance range

Use if tissues have significantly different grey

values in the image

Flood fill Selects voxels based on

connectivity

There are a few variations:

• Left click, inside volume – Keeps connected

voxels only

• Left click, outside volume – Fills gaps

• Right click, inside volume – Removes all

connected voxels

• Right click, outside volume – Removes cavities

The University of Sydney Slide 19

Smoothing

– Usually required because:

– Imaging rarely distinguishes tissues perfectly

– Manual slice-by-slice processing is difficult to align

– The dataset may have image artefacts

– Organic structures are generally smooth

– Misalignment creates jagged surfaces

– Not ideal for meshing

– Can result in stress concentrations and singularities at FEA stage that are not representative of real-world behaviour

The University of Sydney Slide 20

Filters

– Filters are used to manipulate a pre-existing mask

TYPE FUNCTION COMMENTS

Smoothing Removes jagged edges

and surfaces

Small features tend to be lost, so test

different amounts of smoothing (start small) to

balance smoothness with geometric accuracy

(i.e. to retain sufficient fine detail)

Morphological Manipulates size and

shape

There are a few variations:

• Dilate – Grows selected region

• Erode – Shrinks selected region

• Open – Removes small islands

(i.e. erode then dilate)

• Close – Removes small cavities

(i.e. dilate then erode)

The University of Sydney Slide 21

Surface vs Volume Models

Surface models

– Only define the outside shell of an

object

– Most systems achieve this using

non-uniform rational B-splines

(NURBS)

– Not fully-defined

Volume models

– Solid models define the entire

volume of an object

– e.g. Solidworks models

– Representation is unambiguous

The University of Sydney Slide 22

Dimensionality in Modelling

DIMENSION GEOMETRY MESH

0 Point Node

1 Curve Line element

2 Surface Shell element

3 Body Volume element

The University of Sydney Slide 23

Visualisation

– Fast preview

– Renders approximate volume in 3D viewer (using voxels from masks)

– May not represent segmentation accurately

– Model preview

– Creates and renders complete surface model (i.e. using triangles in 3D space)

– Can be exported for volume meshing in other programs

The University of Sydney Slide 24

Meshing

– Full model

– Generates and renders volume model and/or (non-conformal) NURBS surfaces

– Requires masks to be added to a model object

– Export options can be accessed through “Model setup”

ATTRIBUTE +FE GRID +FE FREE

Robustness Excellent; can mesh virtually

any geometry

Good, but can fail with

complex geometries

Mesh size Very large Medium; depends on

refinement settings

Mesh time Short Longer

FEA solution time Long Shorter

The University of Sydney Slide 25

Tips & Tricks

– Think in terms of layers (a la Photoshop)

– Can perform Boolean operations

– Can import multiple backgrounds

– Learn the keyboard and mouse shortcuts

– There is an undo button (5 actions by default)

– Don’t forget to backup SIP files

– “filename-v2.1” vs “filename-v2-draft-FINAL-realFinal”

– If in doubt, check the help guides

The University of Sydney Slide 26

COMING UP…

The University of Sydney Slide 27

Next Week

– Group project updates

– Each group to give an informal short talk about their chosen topic

– Expect up to 2 minutes with 1-2 slides

The University of Sydney Slide 28

TO THE LABS!