Projects:RegistrationImprovement

Registration Improvements

This page will describe registration improvements made within Slicer3 to improve the usability and robustness of registration algorithms so they may be used in an interactive clinical setting.

Key Contributors

• Kitware: Casey Goodlett with consultation from Will Schroeder and Stephen Aylward
• BWH: Ron Kikinis, Dominik Meier, Andriy Fedorov

RegisterImages Algorithm

• ITK Metrics used: MattesMutualInformation
• Optimizer: OnePlusOne Evolutionary Optimizer followed by FRPR in fletcher reeves mode
• Transform Types: Rigid transform VersorRigid3DTransform, Affine transform AffineTransform, B-spline transform BSplineDeformableTransform
• Initialization types, details on landmark-based initialization

A user should typically one of the Pipeline methods (PipelineRigid, PipelineAffine, PipelineBspline) as these will run Initalization -> Rigid -> Affine -> Bspline to the specified level. These are run in order to convergence or maximum # of iterations. Within each pipeline step there is a two stage optimization. First the evolution optmizer is run to stochastically chose a starting location for optimization. After this the FRPR optimizer is used. Currently multi-resolution optimization is only used in the bspline level.

Improvement Ideas

• Use multi-resolution at all stages
  • Both multi-resolution and the sequence of calls with increasing DOF could be implemented as a single recursive scheme. The caller provides an array of DOF and a matching array of resolution levels, which is processed by recursive calls with the first/last element taken from the list. A simulation Matlab program and example is here: Projects:RegistrationImprovement:RecursiveScheme
  • The GUI can list the many combination as a single list of checkboxes for increasing DOF. The full list would be 3,6,7,9,12,b . The checked boxes provide the input string for the recursive call. Media:DOFHierarchy_GUI.jpg‎
• The prestage to affine maybe should be similarity not rigid (based on assumption that its hard to optimize rotation without scale change).
• Learn from FSL flirt to make an extensive test of a grid of possible rotations to get a good initialization for rotations.
• Ability to specify masks that are used to limit were samples are drawn (this should ultimately be both a label image or a user drawn box)

Timeline of contributions

September 22, 2009

Committed ability to use a label image to act as a mask for drawing samples for image match calculation.

September 11, 2009

Merge two new modules that present a simplified view of RegisterImages into Slicer3 to show up in Modules Menu hierarchy Menu hierarchy screenshot

September 9, 2009

Sync default parameters between GUI and command line version of RegisterImages

August 21, 2009

Initial Project Meeting

August 18, 2009

• Link landmark initalization with fiducials framework in Slicer3
• Link transform save and load with TransformIO in Slicer3

Links

• Project describing improvements to multi-threading of ITK Metrics and initial version of RegisterImages ITK_Registration_Optimization
• Initial Project Meeting

Registration Documentation

Efforts re. documentation, use case collection, user perspectives, troubleshooting etc. will be consolidated here: Projects:RegistrationDocumentation Suggested are 4 classes of documentation support:

1. Reference Manual, discussing each feature/parameter/button in detail. Preferred formats: Slicer Wiki, maybe PDF
2. User Manuals, discussing the main functionality from a case-point of view, formats: Slicer Wiki, PowerPoint.
3. Background Tutorials, explaining the basics of registration, formats: PowerPoint
4. Training Video Tutorials, formats: video files (quicktime, WMV, mp4 , Flash), optimized for streaming or download

Training Video Tutorials

• An example of the features/character of a video tutorial is here: Media:VideoTutorialDemo_v1_0.mov
• video tutorials have become a popular and widespread form to document GUI interactions, particularly tutorials
• they can have almost the quality of direct tutoring
• they are compact in length and filesize (because the changes are local and small over time, MPEG compression is very effective with little quality loss), which makes them ideal for online distribution
• movie viewing capability is mainstream, i.e. all OS will have this capability, viewers can be downloaded for free
• the audio track can provide main instructions, motivation, commentary and an abundance of detail information at the right juncture, something very difficult to provide in other formats without overloading a tutorial
• the step by step interaction is captured unambiguously. We do not spend a lot of time and space in showing slides with screen captures.
• since they are easy to make and great software is inexpensive, potential use even for developer communication can be considered, e.g. to document complex bugs
• they have a low usage threshold, i.e. users are more inclined to watch a video than to dig through a power point presentation
• they are not all that useful for reference or main documentation material, e.g. a tutorial on main registration concepts is probably still better in PPT.

Ideas Linked to Developent Efforts

• direct links to Reference Manual from Widget tooltips?