View
2
Download
0
Category
Preview:
Citation preview
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!
Recommended