[Insight-users] BSpline Transformation and binary images

[Luis Ibanez]

Hi Serena,

Thanks a lot for tracking this down.

Your findings are quite interesting.

The three lines of code that you have indicated are indeed performing
incorrect computations, in the case where of number of bins is == 2.

I'm preparing a patch for this class,

Insight/Code/Algorithms/
itkMattesMutualInformationImageToImageMetric.txx

and its multi-threaded version:

Insight/Code/Review/
itkOptMattesMutualInformationImageToImageMetric.txx

that will cast properly the variable m_NumberOfHistogramBins
to the type OffsetValueType (which is signed).

We need to run this in a couple of experimental builds first,
and then we should put together a test that exercises this
metric on a binary image.


Again, Thanks for tracking this issue,
and pointing to the location of the problem in the code.


About your second question:

A typical registration process with images that are of size 100^3
pixels,  should take more than 30 minutes in a modern computer.

Are you seeing any output from the Command observer ?
Something is certainly wrong with the process.

Also, please not that the call

       get_num_evaluations()

is not quite equivalent, to number of Iterations.

In the case of the Amoeba optimizer, what
happens is that the Metric may be computed multiple
times in the process of computing a single Iteration
of the optimizer.  The method get_num_evaluations
tells you how many times the metric was evaluated
in the last iteration of the optimizer, not how many
iterations have been used by the optimizer.


      Regards,


             Luis


-------------------------------------------------------------------
On Thu, Oct 15, 2009 at 2:49 PM, Serena Fabbri <fabbri at u.washington.edu> wrote:
>
> Hi Luis,
>
> I have taken a look to itkMattesMutualInformationImageToImageMetric, and the
> problems seem to be:
> -line 241 (Initialize):  m_NumberOfHistogramBins is unsigned long and the
> value of brackets expression is (-2). It can not be assigned.
> -line 677 (ComputeFixedImageParzenWindowIndices): same problem and besides
> pindex is unsigned int and it can not be (-1) the correct value.
> -line 758 (GetValue): same problem and again movingImageParzenWindowindex is
> unsigned int and it can not be (-1).
>
> I am not sure that to do a cast is ok because after the cast (line 682
> ComputeFixedImageParzenWindowIndices),  (*iter).FixedimageParzenWindowIndex
> will be 1 and 2 and they (at least 2) can not be indexes  for
> m_FixedImageMarginalPDF (line 767 GetValue) because the dimension of this
> array is the number of the bin (=2).
>
> Do you agree with me?
>
>
> Now I am running Cardinality Metric with Amoeba optmizer and BSpline
>  Transformation.
> My image are (80;80;101) pixelsize and (4;4;1)mm spacing.
>
> I have set
>        simplexDelta.Fill( 5.0 );
>        optimizer->AutomaticInitialSimplexOff();
>        optimizer->SetInitialSimplexDelta( simplexDelta );
>        optimizer->SetParametersConvergenceTolerance( 2 );
>        optimizer->SetFunctionConvergenceTolerance(1);
>        optimizer->SetMaximumNumberOfIterations( 200 );
>
> I'd like to ask you how long the registration task can be, because it
> started 2 days ago and it is still running.
> Besides I have put optimizer->GetOptimizer()->get_num_evaluations() in
> observer code but it doesn't work. How can I do to visualize the number of
> iteration during the process?
>
>
> Thank you for any info.
>
> Serena.
>
>
>
>
>
> On Mon, 12 Oct 2009, Luis Ibanez wrote:
>
>> Hi Serena,
>>
>> I believe Hans Johnson reported a while ago that this
>> metric implementation had a bug that make it unsuitable
>> for registering binary images.
>>
>> (My mistake for suggesting to use this metric for this
>> case without having tried).
>>
>> Your options at this point are:
>>
>>
>>           A) Help us debug the metric   :-)
>>
>>
>>           B) Use the Cardinality Metric instead.
>>                itkMatchCardinalityImageToImageMetric.h
>>
>>
>> Please let us know what would be your preference,
>>
>>
>>    Thanks
>>
>>
>>           Luis
>>
>>
>> -----------------------------------------------------------------
>> On Mon, Oct 12, 2009 at 7:23 PM, Serena Fabbri <fabbri at u.washington.edu>
>> wrote:
>>>
>>> Hi All,
>>>
>>> I am trying to register binary images of the head using Non Rigid
>>> Registration. They are (80;80;101) pixelsize and (4;4;1)mm spacing.
>>>
>>> I use Mattes-MI, LBFGSB, NearestNeighbor interpolator and BSpline
>>> Transformation.
>>> After reading the email
>>> http://www.itk.org/pipermail/insight-users/2007-November/024178.html
>>>
>>> I set 2 bin and 10% of statistic for MI and I have got this message:
>>>
>>> Starting Registration
>>> ExceptionObject caught !
>>>
>>> itk::ExceptionObject (0x1900fb0)
>>> Location: "void
>>> itk::MattesMutualInformationImageToImageMetric<TFixedImage,
>>> TMovingImage>::GetValueAndDerivative(typename
>>> itk::ImageToImageMetric<TFixedImage, TMovingImage>::ParametersType&,
>>> typename itk::ImageToImageMetric<TFixedImage,
>>> TMovingImage>::MeasureType&,
>>> typename itk::ImageToImageMetric<TFixedImage,
>>> TMovingImage>::DerivativeType&) const [with TFixedImage = main(int,
>>> char**)::FixedImageType, TMovingImage = main(int,
>>> char**)::MovingImageType]"
>>> File: /Users/InsightToolkit-
>>> 3.10.0/Code/Algorithms/itkMattesMutualInformationImageToImageMetric.txx
>>> Line: 1160
>>> Description: itk::ERROR:
>>> MattesMutualInformationImageToImageMetric(0x1900260): Fixed image
>>> marginal
>>> PDF summed to zero
>>>
>>> I have increased the statistic until 30% and I get the same error.
>>> Is it possible that BSpline Transformation is not suitable for binary
>>> images
>>> registration?
>>>
>>> Any suggestion will be appreciate.
>>>
>>> Thanks.
>>>
>>> Serena.
>>>
>>>
>>>
>>>
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>>
>
>
>