ITK Registration Optimization

Goals

There are two components to this research

1. Identify registration algorithms that are suitable for non-rigid registration problems that are indemic to NA-MIC
2. Develop implementations of those algorithms that take advantage of multi-core and multi-processor hardware.

Algorithmic Requirements and Use Cases

• Requirements
  1. relatively robust, with few parameters to tweak
  2. runs on grey scale images
  3. has already been published
  4. relatively fast (ideally speaking a few minutes for volume to volume).
  5. not patented
  6. can be implemented in ITK and parallelized.

• Use-cases
  1. Intersubject mapping example data set (Kilian)
  2. fMRI to hi-res brain morphology mapping example data set (Steve Pieper)
  3. DTI: components of the diffusion tensor DTI-non-rigid (Sylvain)

Hardware Platform Requirements and Use Cases

• Requirements
  1. Shared memory
  2. Single and multi-core machines
  3. Single and multi-processor machines
  4. AMD and Intel - Windows, Linux, and SunOS

• Use-cases
  1. Intel Core2Duo
  2. Intel quad-core Xeon processors (?)
  3. 6 CPU Sun, Solaris 8 (SPL: vision)
  4. 12 CPU Sun, Solaris 8 (SPL: forest and ocean)
  5. 16 core Opteron (SPL: john, ringo, paul, george)
  6. 16 core, Sun Fire, AMDOpteron (UNC: Styner)

Data

• NA-MIC MIDAS collection for this project

Workplan

Establish testing and reporting infrastructure

1. Identify timing tools
   1. Cross platform and multi-threaded
   2. Timing and profiling
   • Status
     1. Instrumenting modular tests
        • Extending itk's cross-platform high precision timer
        • Adding thread affinity to ensure valid timings
        • Adding method for increasing process priority
     2. Profiling complete registration solutions for use cases
        • Using CacheGrind on single and multi-core linux systems
2. Develop performance dashboard for collecting results
   1. Each test will report time and accuracy to a central server
   2. The performance of a test, over time, for a given platform can be viewed on one page
   3. The performance of a set of tests, at one point in time, for all platforms can be viewed on one page
   • Status
     1. BatchMake database communication code being isolated
     2. Performance dashboard web pages being designed

Develop tests

1. Develop modular tests
   • Status
     1. Developed itkCheckerboardImageSource so no IO required
     2. Developed
2. Develop complete registration solutions for use cases
   • Status
     1. Centralized data and provide easy access
     2. Identified relevant registration algorithms
        • rigid, affine, bspline, multi-level bspline, and Demons'
        • normalized mutual information, mean squared difference, and cross correlation
     3. Developing traditional ITK-style implementations

Compute performance on target platforms

• Ongoing

Benchmarks

All tests cout two values

• the time required
• an measure of the error (0 = no error; 1 = 100% error)

Tests being developed and suggested parameter settings

1. LinearInterpTest <numThreads> <dimSize> <factor> [<outputImage>]
   • NumThreads = 1, 2, 4, and #OfCoresIf>4
   • DimSize = 100, 200 (i.e., 100^3 and 200^3 images)
   • Factor = 1.5, 2, 3 (i.e., producing up to 600^3 images)
   • = 24 tests (approx time on dual-core for all tests = 1.5 minutes)
2. BSplineInterpTest <numThreads> <dimSize> <factor> [<outputImage>]
   • NumThreads = 1, 2, 4, and #OfCoresIf>4 (for every platform)
   • DimSize = 100, 200 (meaning: 100^3 and 200^3 images)
   • Factor = 1.5, 2, 3 (thereby producing up to 600^3 images)
   • = 24 tests (approx time on dual-core for all tests = ??)
3. SincInterpTest <numThreads> <dimSize> <factor> [<outputImage>]
4. BSplineTransformLinearInterpTest <numThreads> <dimSize> <numNodesPerDim> [<outputImage>]
5. MeanReciprocalSquaredDifferenceMetricTest
6. MeanSquaresMetricTest
7. NormalizedCorreltationMetricTest
8. GradientDifferentMetricTest
9. MattesMutualInformationMetricTest
10. MutualInformationMetricTest
11. NormalizedMutualInformationMetricTest
12. MutualInformationHistogramMetricTest
13. NormaalizedMutualInformationHistogramMetricTest

Related Pages

• Non Rigid Registration
• Slicer3:Performance_Analysis
• User:Barre/ITK Registration Optimization

Performance Measurement

• Intel's VTune for Linux ($)
• TAU
• Threadmon: Thread usage/blockage
• TotalView ($)
• PerfSuite (POSIX Threads)
• GProf work-around for multi-threaded apps
• References on multi-threaded profiling and code optimization
  • General C++ performance optimization
  • Multi-threaded performance measurement (pdf document)
  • Wikipedia - General performance analysis