Did you try other optimizers in the v4 case? On Apr 17, 2014 1:37 PM, "Ghayoor, Ali" <[email protected]> wrote:
> 2160 parameters in each test. > > Thanks, > Ali > > From: brian avants <[email protected]> > Date: Thursday, April 17, 2014 at 12:33 PM > To: Ali Ghayoor <[email protected]> > Cc: Nicholas Tustison <[email protected]>, "Johnson, Hans J" < > [email protected]>, ITK <[email protected]> > Subject: Re: [ITK-dev] [ITK] Potential BSpline registration problems with > ITKv4 > > how many parameters are being optimized in each case? > > > brian > > > > > On Thu, Apr 17, 2014 at 1:22 PM, Ghayoor, Ali <[email protected]>wrote: > >> Hello all, >> >> I did a double check on the command line parameters and the code >> changes in v3 and v4 implementations. Basically same metric and optimizer >> is used for both implementations, and their parameters are set the same. >> Metric —> MattesMutualInformationImageToImageMetric(v4) >> Optimizer —> LBFGSBOptimizer(v4) >> >> Also, in ITKv4 based implementation, one level registration (with >> shrink factor 1 and smoothing sigma 0) is used that is the closest >> circumstance to what happens in ITKv3. >> Only notice that two implementations use different BSpline transform >> types too. >> >> In v3 implementation, a BSplineDeformableTransformType is used that is >> initialized by a BSplineDeformableTransformInitializer, and its bulk >> transform is initialized by the input initial transform. >> >> However, v4 implementation utilizes a BSplineTransformType that its >> parameters (origin, physicalDomain, meshSize and direction) are set >> directly. Also, the input initial transform is set directly to the >> registration filter as the moving initial transform. >> >> Moreover, I repeated my experiments on the >> “BRAINSFitTest_BSplineOnlyRescaleHeadMasks” test that does just one >> stage BSpline registration. (Previous test was performing two linear stages >> before the BSpline stage). >> >> This test was passed successfully in ITKv3 in very short times: >> >> ITKv3: release type -> passed in 13 seconds >> ITKv3: debug type -> passed in 102 seconds >> >> Also, it was passed successfully in ITKv4 when 4 cores were used and >> was failed by timeout when just 1 core was used: >> >> ITKv4: release type -> passed in 17 minutes (when 4 cores are used) >> ITKv4: release type -> failed by timeout (>30 mins) (when 1 core is used) >> >> >> Thank you, >> Ali >> >> >> >> From: Nicholas Tustison <[email protected]> >> Date: Thursday, April 17, 2014 at 8:07 AM >> To: "Johnson, Hans J" <[email protected]> >> Cc: Ali Ghayoor <[email protected]>, ITK <[email protected]> >> >> >> Subject: Re: [ITK-dev] [ITK] Potential BSpline registration problems >> with ITKv4 >> >> Very interesting find, Ali. Thanks. Please keep us >> informed of what you find. It would be nice if a fix >> could help us improve the general timing issues that >> we’ve discussed previously with ITKv4. >> >> >> >> On Apr 17, 2014, at 9:00 AM, Johnson, Hans J <[email protected]> >> wrote: >> >> There was not supposed to be. The intention was to do the minimal >> number of changes to allow the same results to occur in ITKv4 instead of >> ITKv3. No new features or changes were specified. >> >> Ali did this work, so he will need to double check, but upon quick >> review it looks like a simple refactoring from one framework to the other. >> >> Hans >> >> >> From: Nick Tustison <[email protected]> >> Date: Thursday, April 17, 2014 at 7:54 AM >> To: Hans Johnson <[email protected]> >> Cc: ITK <[email protected]> >> Subject: Re: [ITK-dev] [ITK] Potential BSpline registration problems >> with ITKv4 >> >> Hans, >> >> Are there any implementation differences between the two testing >> programs, e.g. different metric class versions? >> >> Thanks, >> Nick >> >> On Apr 17, 2014, at 8:24 AM, Bradley Lowekamp <[email protected]> >> wrote: >> >> Hans, >> >> >> >> I have see a single per-pixel dynamic memory/malloc cause a 10X >> performance penalty. Also I have found apple Instruments easy for >> diagnosing this bottle neck. This is one possibility among many. >> >> Good luck tracking down the issue. >> >> Brad >> >> On Apr 16, 2014, at 9:10 PM, Johnson, Hans J <[email protected]> >> wrote: >> >> FYI >> >> Ali Ghayoor did the following experiments on >> "BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks" test. >> >> 1) In one of my old build directories, I ran the >> "BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks" test in BRIANSFitv3 >> (that uses ITKv3 registration framework). The test was passed successfully >> in both release and debug types, and it took: >> >> 22 second in release >> 88 second in debug >> >> 2) I built NAMICExternalProject on my system in release type and ran >> the above BSpline test in BRAINSTools. The test was passed successfully >> again, but the run time in ITKv4 is tremendously longer than the time that >> test takes in ITKv3. The test took: >> >> 18 minutes using 4 cores >> 22 minutes using 1 core (In this case the environmental variable "NSLOTS" >> is set to 1). >> >> ================================== >> Basically trying to replicate in ITKv4 the same registration processes of >> ITKv3. >> >> Hans >> >> >> ------------------------------ >> Notice: This UI Health Care e-mail (including attachments) is covered by >> the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is >> confidential and may be legally privileged. If you are not the intended >> recipient, you are hereby notified that any retention, dissemination, >> distribution, or copying of this communication is strictly prohibited. >> Please reply to the sender that you have received the message in error, >> then delete it. 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