[ITK-dev] [ITK] Potential BSpline registration problems with ITKv4

Thu Apr 17 13:39:24 EDT 2014

Did you try other optimizers in the v4 case?
On Apr 17, 2014 1:37 PM, "Ghayoor, Ali" <ali-ghayoor at uiowa.edu> wrote:

>  2160 parameters in each test.
>
>  Thanks,
> Ali
>
>   From: brian avants <stnava at gmail.com>
> Date: Thursday, April 17, 2014 at 12:33 PM
> To: Ali Ghayoor <ali-ghayoor at uiowa.edu>
> Cc: Nicholas Tustison <ntustison at gmail.com>, "Johnson, Hans J" <
> hans-johnson at uiowa.edu>, ITK <insight-developers at itk.org>
> 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 <ali-ghayoor at uiowa.edu>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 <ntustison at gmail.com>
>> Date: Thursday, April 17, 2014 at 8:07 AM
>> To: "Johnson, Hans J" <hans-johnson at uiowa.edu>
>> Cc: Ali Ghayoor <ali-ghayoor at uiowa.edu>, ITK <insight-developers at itk.org>
>>
>>
>> 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 <hans-johnson at uiowa.edu>
>> 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 <ntustison at gmail.com>
>> Date: Thursday, April 17, 2014 at 7:54 AM
>> To: Hans Johnson <hans-johnson at uiowa.edu>
>> Cc: ITK <insight-developers at itk.org>
>> 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 <blowekamp at mail.nih.gov>
>> 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 <hans-johnson at uiowa.edu>
>> 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.  Thank you.
>> ------------------------------
>>  _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-developers
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/cgi-bin/mailman/listinfo/community
>>
>>
>>  _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-developers
>>
>>
>>
>>
>> ------------------------------
>> 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.  Thank you.
>> ------------------------------
>>
>>
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-developers
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-developers/attachments/20140417/f89c9815/attachment.html>