[Insight-users] Questions about Image Registration with ITK 4.1.0

[Lydia Hellrung]

Hi ITK-list, 

I have some questions about doing registration with the quite new ITK 4. The story is quite long, so I try to clarify with steps:

(1) Used equipment

MAC PRO with 2x 2.26 GHZ and 8GB RAM
ITK 4.1.0 build as release without v3 compatibility
Xcode compiler llvmgcc42


(2) History of our work

- implemented multithreaded Registration algorithm for fMRI structural and functional data with ITK3.20.1 in Review code version
- coreg of structural and anatomical uses: prealign of the images, 
     VersorRigid3D transform; RegularGradientStepOptimizer; LinearInterpolator and MattesMutualInformationMetric
  -> took 15 seconds to find registration

- normalization to mni uses 3-step registration: prealign of the images, 
   (a) VersorRigid3D transform; RegularGradientStepOptimizer; LinearInterpolator and MattesMutualInformationMetric
   (b) Affine transform; RegularGradientStepOptimizer; LinearInterpolator and MattesMutualInformationMetric
   (b) BSpline transform; LBFGSOptimizer; LinearInterpolator and MattesMutualInformationMetric

   -> took 3 min to find registration


(3) Migration to ITK4
 
- worked through migration guides and adapted API 
- special handling for bspline transform found and implemented as described in guide
- using same parameter set for algorithms
- RESULTS: (a) less good registration results 
           (b) and disastrous runtimes with 114 sec for coreg and 14 min (!!) for normalization

(4) Questions now 

a) What are possible reasons for the tremendous increase in runtime? It still runs multithreaded on 16 kernels!
b) Is there anything else to be aware of when migrating to ITK4? 
c) In documentation we found several new ...v4 classes/modules and these are described as new and especially for 'high-dimensional transforms'. There's no example to find for these and trying to use them just come up with compiler messages about missing functions in these classes, like SetNumberOfThreads. Is there any example and what's the advantage of these classes?


Thanks in advance for any help and hints
Lydia

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Max Planck Institute for Human Cognitive and Brain Sciences
Lydia Hellrung	               e-mail: hellrung at cbs.mpg.de
Stephanstraße 1a               http://www.cbs.mpg.de/~hellrung
04103 Leipzig, Germany         Phone: +49-341-9940-2431 Fax: -2221
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