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

Thu Apr 17 13:33:24 EDT 2014

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://public.kitware.com/pipermail/community/attachments/20140417/8f8ee208/attachment-0002.html>
-------------- next part --------------
_______________________________________________
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