ITK Registration Optimization

Quick Links

1. Dashboard for this project
2. Dashboard for BatchMake
3. Batchboard (nightly experiment results) for this project

Results and Publications

1. Aylward, Stephen; Jomier, Julien; Barre, Sebastien; Davis, Brad; Ibanez, Luis, "Optimizing ITK’s Registration Methods for Multi-processor, Shared-Memory Systems." MICCAI Open Source and Open Data Workshop, 2007 (Download PDF)

• One remaining, high priority task is to complete the integration of the new, threaded, registration methods into ITK. Luis and Sebastien have adapted the new methods to be 100% backward compatible with ITK's existing classes. This is a major effort involving approximately 50,000 lines of new code and over 400 new tests in ITK. The new registration framework is going to be significantly better tested as well as significantly faster than the existing ITK registration framework. Once it is ported, helper-classes will be added to ITK, and modules using those helper classes will be distributed with Slicer. We have chosen to spend the time to integrate with ITK because it will serve the broader community, it will benefit from the support of the broader community, it will avoid having to incorporate another SVN checkout into Slicer's build process, and it will keep us from having to maintain and monitor separate dashboards for this effort.

Goals

There are two components to this research

1. Identify registration algorithms that are suitable for non-rigid registration problems that are endemic 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
     • Example data (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, Visual Studio 8, Windows Vista (Kitware: redwall)
  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

• Now distributed with CVS

Workplan

Establish testing and reporting infrastructure

1. Identify timing tools
   1. Cross platform and multi-threaded
   2. Timing and profiling
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

Develop tests

1. Develop modular tests
2. Develop complete registration solutions for use cases

ITK Optimization

• Target bottlenecks
  • Multi-thread metric calculation
    • Initial target is MattesMutualInformationImageToImageMetric
  • Optimize code
    • Sacrifice some memory and algorithm initialization speed to gain algorithm operation speed increases
    • Call multi-threaded functions when possible
• Integrate metrics with transforms and interpolators for tailored performance

MattesMutualInformationImageToImageMetric

Optimizations Employed

• GetValue
  • Added multi-threading to GetValue function
    • Partitions the samples - thereby distributes the computation of the transforms and interpolations across threads
    • Added the pre-computation of the FixedImageMarginalPDF for the sample to reduce the need for the thread mutex lock
      • Required the concept of an AdjustedFixedImageMarginalPDF that is updated when a fixed image voxel does not map into the moving image and thereby isn't valid for the current computations. By only updating when samples are missed, mutex lock to update a cross-thread data structure is needed less often.
    • Each thread now has its own copy of the joinPDF. After threads complete, jointPDFs from each thread are summed. This eliminates mutex from the main loop over samples.
    • SUMMARY: Speedup on a dual-core system is about 30% (reduction in computation time) when using linear transform and linear interpolation and about 45% when using bspline transform and bspline interpolation.
  • Algorithm optimization (aside from adding multi-threading)
    • None at this level. Will be done for transforms and interpolators.
• GetDerivative
  • Following the same convention as used with GetValue

Modular tests

All tests send two values to performance dashboards

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

Tests being developed and their parameter spaces

1. NearestNeighborInterpTest <numThreads> <dimSize> <factor> [<outputImage>]
2. LinearInterpTest <numThreads> <dimSize> <factor> [<outputImage>]
3. BSplineInterpTest <numThreads> <dimSize> <factor> <bSplineOrder> [<outputImage>]
4. SincInterpTest <numThreads> <dimSize> <factor> [<outputImage>]
   • Uses the Welch window function
5. BSplineTransformLinearInterpTest <numThreads> <dimSize> <numNodesPerDim> <bSplineOrder> [<outputImage>]
   • 3 nodes are also added outside of the image for interpolation
6. MeanSquaresImageToImageMetricTest <numThreads> <dimSize> <iterations>
7. CorrelationCoefficientHistogramMetricTest <numThreads> <dimSize> <iterations>
8. NormalizedCorreltationImageToImageMetricTest <numThreads> <dimSize> <iterations>
9. MattesMutualInformationImageToImageMetricTest <numThreads> <dimSize> <numSamples> <iterations>
   • MattesMutualInformationMetric defaults to BSpline interpolator - this test overrides to use nearest neighbor interpolation
10. MutualInformationImageToImageMetricTest <numThreads> <dimSize> <numSamples> <iterations>
11. NormalizedMutualInformationHistrogramMetricTest <numThreads> <dimSize> <iterations>

SECOND GENERATION TEST

• Computes runtime for GetValue, GetDerivative, and GetValueAndDerivative for standard ITK implementation and for the optimized version being developed. Also computes difference (if any) between their answers and reports as an error measure

Larger tests

These are top down tests that implement registration tasks as a user would. These tests are run on real medical image data. The goal is to use these larger, realistic tests to focus our optimization effort.

• AlignMomentsTest <fixed image> <moving image> [number of threads] [transformed moving image] [post-registration difference image] [pre-registration difference image]
• AlignRigidMSETest <fixed image> <moving image> [number of threads] [number of iterations] [transformed moving image] [post-registration difference image] [pre-registration difference image]
• AlignRigidMMITest <fixed image> <moving image> [number of threads] [number of iterations] [transformed moving image] [post-registration difference image] [pre-registration difference image]

Events

• April 6, 2007: TCon
• April 12, 2007: TCon
• April 18, 2007: TCon
• May 1, 2007: TCon
• June 27, 2007: NAMIC Programmers' Week

Related Pages

• Non Rigid Registration
• Slicer3:Performance_Analysis
• User:Barre/ITK Registration Optimization
• Testing and ITK Backward Forward Compatibility

Performance Measurement

• LTProf - simple profilter for Windows - Shareware
• 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