[Insight-users] BSpline Transformation and binary images

Serena Fabbri fabbri at u.washington.edu
Thu Oct 22 14:44:19 EDT 2009 

Hi Luise,

This is great, I will try the correct MMI!!

Regarding the Observer: good idea, thank you for the suggestion.

For the registration task:
I am using:
Cardinality Metric with Amoeba optmizer,  BSpline  Transformation and NearestNeighbor Interpolator
My binary images are (80;80;101) pixelsize and (4;4;1) mm spacing and (13;13;13) nodes Bspline grid.


Thank you again for any advice.
Serena.




On Thu, 22 Oct 2009, Luis Ibanez wrote:

> Hi Serena,
>
>
> The code in
>
>     Insight/Code/Algorithms
>
> has already been fixed.
>
> --
>
> I'm still working  on patching the one in
>
>      Insight/Code/Review
>
> This is described in :
>
>     http://public.kitware.com/Bug/view.php?id=9745
>
> ---
>
>
> Regarding the Observer:
>
> The number of iterations, can actually be provided
> by introducing a counter in the observer itself and
> counting events.
>
> ---
>
>
> The time that you report is unusually long for registering
> an image of that size.
>
> How many samples are you using in MattesMI  ?
>
>
>    Please let us know,
>
>
>           Thanks
>
>
>                Luis
>
>
> --------------------------------------------------------------------------------
-------------
> On Thu, Oct 22, 2009 at 1:12 PM, Serena Fabbri <fabbri at u.washington.edu> wrote:
>>
>>
>> Hi Luise,
>>
>> I am glad that my suggestions were useful for you.
>> When the MMI code will be fixed, do you write an email?
>>
>> Yes, I get output from  optimizer->GetCachedValue() This instruction is
>> inside the observer code. The registration runs but it is very slow, my
>> computer is new......so what could it be wrong in my Registration task?
>> I am using (13;13;13) nodes Bspline grid.
>>
>> I have read the the Amoeba optimizer documentation again and I have not
>> found a function to obtain the number of iteration. Am I wrong?
>>
>>
>> Thank again for your help.
>>
>>
>> Serena.
>>
>>
>>
>>
>>
>> On Tue, 20 Oct 2009, Luis Ibanez wrote:
>>
>>> 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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>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>>
>

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