Mapping, registration and atlases
IMAGE workshop breakout group
Members of group
•
•
•
•
•
•
•
Derek Hill, London
Richard Baldock, Edinburgh
Dave Berry, Edinburgh
Tilak Ratnanather, Baltimore
Xavier Pennec, Nice
Denise Ecklund, Edinburgh
Vincent Breton, Clermont Ferrand
Aims of breakouts
• To generate written report about issues
• Make recommendations for future work
• Highlight areas that might benefit from
future research funding
• Make links with industrial activity
• Facilitate international collaboration
Breakout group sub-headings
• How do we make image registration grid services
intraoperable?
• Can the grid provide a technology push?
• How should we represent mappings?
• Should we use grid-services for a major cross
validation of algorithms?
• How can, or should,atlases be shared?
• How could these services be used commercially
(eg: for drug discovery)
• What user interaction is required?
• Statistics of mappings
• How do we make image registration grid
services intraoperable?
– Do we need to devise an abstract model for
these services?
• Eg: what is a spatial transformation
• ITK is going some of the way in this direction and
illustrates some of the difficulties
• Can the grid provide a technology push
– New techniques that simultaneously analysis
cohorts
– Treating time better
– User interaction
• How should we represent mappings?
– Definition of coordinate systems
– Representing diffeomorphisms and other types
of mappings
– Do we need an ontology?
• Should we use grid-services for a major cross
validation of algorithms?
– Compare with 1995 retrospective registration
evaluation project which used ftp for international
multicentre collaboration
– Do you need a “gold standard” to do this?
– Could we share the necessary data internationally?
• Two approaches:
– Test algorithms against standard data including
sensitivity to data perturbations
– Test data against algorithms
• Who would pay for CPU cycles?
• Compare results of new algorithms with those of
established algorithms eg: SPM
• How can, or should, atlases be shared?
– Component data for atlas
– Algorithms that form part of atlas
• We need to carefully define what we mean
by an atlas
– Is there an agreed definition for a static atlas?
– Is it an evolving representation of the state of
knowledge
• How could these services be used
commercially (eg: for drug discovery)
– Regulatory approval?
– The grid could provide access to established
validated algorithms
– Mechanisms for licensing s/w on a per-use
basis.
User interface
• A user interface will be needed to interact with the
algorithm
– Set parameters, use best practice parameters
– Customize to application
– Interact with the registration process, eg: to add prior
knowledge about corresponding features
• Tutorials
• Visualization of results: how do we visualize
mappings (application specific)
• Mapping statistics
– Statistics on deformations might be part of an
atlas
How do we overlap with other
groups
• Visualization and data exploration
– We need visualization tools for interaction and viewing
results/metrics
• Image analysis, measurement and query
– How do we use queries to reason with mappings
generated by regn. algorithms?
– Metrics from mappings
– Metrics from registered images
• Data management, metadata, ontologies,
provenance
– We obviously need all of this stuff!
Issue of generalization
• Almost all headings in “registration” could
be applied to other image analysis
techniques eg: segmentations
Future work of this group
• Select sub-headings for detailed discussions
leading to recommendations
• What is easy to do, not easy to do, or dependent
on other activity?
• Can we identify the state-of-the-art in these areas?
• Can we facilitate international collaboration?
• Link our aspirations to the current state of grid
technology
A registration test bed
?
• Registration is a core technology in medical
image analysis
• There is no one algorithm that solves all
problems
• There continues to be substantial algorithm
development
• Registration needs to fit into many different
image analysis workflows
Scenario 1
• Prototyping a new application
–
–
–
–
New sort of data
New question
Want to find the right algorithm
Grid can be used to do large scale comparison
of different algorithms
Scenario 2
• “Production” image registration service
– Provides easy use for customers
• Application scientists eg: clinical research fellow
• Companies (eg: pharma)
• Healthcare organisations
Scenario 3
• Cross validation
– Grid services providing image registration
– Reference datasets
– Definition of how to to add a new registration service
or new data
– Can be used by researchers to compare algorithms prior
to publication
– Challenges to compare algorithms on new problems,
eg: one brought by a pharma company, new algorithms
Scenario 0
• To build a grid application to enable comparison
of registration algorithms
• Limited grid demonstrator
– Loose collaboration of resources, algorithms and
researchers
– At least 3 algorithms
– At least 3 data repositories (?include pathology)
– At least 3 compute resources
– At least 3 research teams
– Demonstrate expandability, heterogeneity
Obstacles
• Image file formats
– We could use the DICOM core fields
• Access to grid infrastructure
– Hardware
– Support and training to set it up
• Architecture
– Coordination
– Portal
– registry
More Obstacles
• Transformation format
– Could initially provide tutorial, example standard
transformation, i/o libraries
– Should we have a minimum subset of data eg: vector
field of resolution of original target image
– Origins etc…
• How do you quantify differences between
algorithms?
• Security and confidentiality
– We would start with anonymised data for which
suitable consent had been obtained
Way forward
• We want to keep it small so that things can
happen for scenario 0.
• We could keep it small by proposing it is
initially done with no funding.
• This needs to be application lead
• The primary aim is to answer scientific
questions about image registration
Partners and Roles
• INRIA linux cluster,
– already has a PhD student working on parallellising
registration algorithm,
– could probably generate interest in putting this on the grid.
• KCL & Imperial (IXI)
– Already implementing registration service
• NESC
– Could assist with registry and portal (a month or so of effort
to do something)
• Hopkins
• Supercomputer on the grid running registration
• Others to give global coverage
Timetable
• Set up email list – Sept 2003
• Invite key application groups to meeting at
MICCAI 2003, Montreal in November 2003
• Initial demonstration of concept, and
description of project for eHealth in January
2004
• Need a grid technology support from NESC
and Clermont Ferrand