[Elastix] Running multi-metric registration

M.Staring at lumc.nl M.Staring at lumc.nl
Fri Apr 5 09:10:57 CEST 2013


Hi Jihun,

Try reducing your step size. My rule of thumb is that the stepsize multiplied by the metric gradient should be in the order of 1.

Marius

From: elastix-bounces at bigr.nl [mailto:elastix-bounces at bigr.nl] On Behalf Of Jihun Kim
Sent: donderdag 4 april 2013 21:35
To: elastix at bigr.nl
Subject: Re: [Elastix] Running multi-metric registration

Sorry that I did not attach this file.

Regards,
Jihun
--
Jihun Kim
Ph. D. candidate
Mechanical Engineering
University of Michigan, Ann Arbor
734-276-7167

On Thu, Apr 4, 2013 at 3:27 PM, Jihun Kim <jihun at umich.edu<mailto:jihun at umich.edu>> wrote:
Dear Elastix-subscribers,

I am trying to run multi-metric registration with AdvancedMeanSquares and TransformRigidityPenalty. I attached a parameter file to run a registration. I have got the following a command window message:

=====Message Begins======================================================================================
elastix is started at Thu Apr 04 15:20:05 2013.

elastix runs at: Jihun-PC
  Windows 7, Service Pack 1 (Build 7601)
  with 3956 MB memory, and 4 cores @ 2393 MHz.
-------------------------------------------------------------------------

Running elastix with parameter file 0: "D:\elastix\hncbm8\ct7\staring-ms\Parameters.txt".

Current time: Thu Apr 04 15:20:05 2013.
Reading the elastix parameters from file ...

Installing all components.
InstallingComponents was successful.

ELASTIX version: 4.600
Command line options from ElastixBase:
-f        D:\hncbm8\fect1-7.mhd
-m        D:\hncbm8\ct7.mhd
-fMask    unspecified, so no fixed mask used
-mMask    unspecified, so no moving mask used
-out      D:\elastix\hncbm8\ct7\staring-ms/
-p        D:\elastix\hncbm8\ct7\staring-ms\Parameters.txt
-priority unspecified, so NORMAL process priority
-threads  unspecified, so all available threads are used
Command line options from TransformBase:
-t0       D:\hncbm8\ct7toct1.txt
WARNING: The parameter "BSplineTransformSplineOrder", requested at entry number 0, does not exist at all.
  The default value "3" is used instead.
WARNING: The parameter "UseCyclicTransform", requested at entry number 0, does not exist at all.
  The default value "false" is used instead.

Reading images...
Reading images took 489 ms.

Reading the elastix parameters from file ...

Initialization of all components (before registration) took: 43 ms.
Preparation of the image pyramids took: 2882 ms.

Resolution: 0
WARNING: The parameter "ShowExactMetricValue", requested at entry number 0, does not exist at all.
  The default value "false" is used instead.
WARNING: The parameter "CheckNumberOfSamples", requested at entry number 0, does not exist at all.
  The default value "true" is used instead.
WARNING: The parameter "ShowExactMetricValue", requested at entry number 0, does not exist at all.
  The default value "false" is used instead.
WARNING: The parameter "CheckNumberOfSamples", requested at entry number 0, does not exist at all.
  The default value "true" is used instead.
Setting the fixed masks took: 0 ms.
Setting the moving masks took: 0 ms.
WARNING: The parameter "UseRelativeWeights", requested at entry number 0, does not exist at all.
  The default value "false" is used instead.
WARNING: The parameter "NumberOfSamplesForSelfHessian", requested at entry number 0, does not exist at all.
  The default value "100000" is used instead.
WARNING: The parameter "SelfHessianSmoothingSigma", requested at entry number 0, does not exist at all.
  The default value "1" is used instead.
WARNING: The parameter "SelfHessianNoiseRange", requested at entry number 0, does not exist at all.
  The default value "1" is used instead.
WARNING: The parameter "MaximumNumberOfSamplingAttempts", requested at entry number 0, does not exist at all.
  The default value "0" is used instead.
Elastix initialization of all components (for this resolution) took: 2 ms.
Initialization of AdvancedMeanSquares metric took: 0 ms.
Initialization of TransformRigidityPenalty term took: 0 ms.
1:ItNr 2:Metric 2:Metric0 2:Metric1 3:StepSize 4:||Gradient0|| 4:||Gradient1|| 4:||Gradient|| Metric-LC Metric-OC Metric-PC Time0[ms] Time1[ms] Time[ms] ||Gradient-LC|| ||Gradient-OC|| ||Gradient-PC||
SGD
elxTemplate
0 13224.394736 13224.394736 0.000000 7457.268480 593.852296 0.000000 593.852296 0.0000000000 0.0000000000 0.0000000000 103 115 295 0.0000000000 0.0000000000 0.0000000000
Time spent in resolution 0 (ITK initialisation and iterating): 0.333 s.
Stopping condition: Error in metric.

itk::ExceptionObject (0178FA88)
Location: "ElastixTemplate - Run()"
File: d:\src4\elastix_sources_v4.6\src\common\costfunctions\itkAdvancedImageToImageMetric.hxx
Line: 628
Description: itk::ERROR: AdvancedMeanSquaresMetric(03ABCAB0): Too many samples map outside moving image buffer: 0 / 5000

Error occurred during actual registration.

Errors occurred!
=====Message Ends======================================================================================

Following the instruction given in FAQ, I applied an initial transform but I don't know what to try further. I am wondering if you could give me some suggestions.
Thanks very much.

Regards,
Jihun
--
Jihun Kim
Ph. D. candidate
Mechanical Engineering
University of Michigan, Ann Arbor
734-276-7167<tel:734-276-7167>

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