[Insight-users] BSpline Transformation and binary images
Luis Ibanez
luis.ibanez at kitware.com
Thu Oct 22 14:11:00 EDT 2009
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.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> 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-users
>>>>>
>>>>
>>>
>>>
>>>
>>
>
>
>
>
More information about the Insight-users
mailing list