ITK Registration Optimization
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Contents
Goals
There are two components to this research
- Identify registration algorithms that are suitable for non-rigid registration problems that are indemic to NA-MIC
- Develop implementations of those algorithms that take advantage of multi-core and multi-processor hardware.
Algorithmic Requirements and Use Cases
- Requirements
- relatively robust, with few parameters to tweak
- runs on grey scale images
- has already been published
- relatively fast (ideally speaking a few minutes for volume to volume).
- not patented
- can be implemented in ITK and parallelized.
- Use-cases
- Intersubject mapping example data set (Kilian)
- fMRI to hi-res brain morphology mapping example data set (Steve Pieper)
- DTI: components of the diffusion tensor DTI-non-rigid (Sylvain)
- Related NA-MIC wiki pages
Performance Requirements and Use Cases
- Requirements
- Single and multi-core machines
- Single and multi-processor machines
- AMD and Intel - Windows, Linux, and SunOS
- Use-cases
- <list specific machines here>
Data
Workplan
- Quantify current performance and bottlenecks
- Identify timing tools (cross platform, multi-threaded)
- For each use-case
- Centralized data and provide easy access
- Identify relevant registration algorithm(s)
- Develop traditional ITK-style implementations
- Develop timing tests using implementations and data
- Across use-cases
- Identify ITK classes/functions common to implementations (e.g., interpolation/resampling)
- Develop timing tests specific to these common sub-classes
- Compute performance on multiple platforms
Progress Highlights
- Quantify current performance and bottlenecks
- Identify timing tools
- We have chosen TAU for the performance quantification tool
- Summary of select performance quantification tools is available here
- Identify timing tools
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