[Insight-users] Initializing a BSplineTransform in ITK 4.4
Nick Tustison
ntustison at gmail.com
Thu Aug 1 10:09:53 EDT 2013
Hi Frank,
I don't see anything immediately. I can't work on it now but will most likely get to
it this weekend. I'll also take your code and, after we figure out what's going on,
add it as a test in using the b-spline transform with the new framework since
we currently don't have one (outside of our ANTs tool).
Nick
On Jul 31, 2013, at 11:10 AM, Frank Preiswerk <frank.preiswerk at unibas.ch> wrote:
> Hi Nick,
>
> I have noticed that the error is not thrown if I do not set the initial transform for the moving image via registrationMethod->SetMovingInitialTransform (although the optimizer then produces a constant error value and the registration simply iterates without altering the deformation field - I don't know if this is an unrelated problem).
>
> My setup is simple, i.e. no multi-resolution involved. I'm doing essentially this:
>
> typedef itk::BSplineTransform< PixelType, ImageDimension > TransformType;
> typedef itk::MeanSquaresImageToImageMetricv4< ImageType, ImageType > MetricType;
> typedef itk::GradientDescentOptimizerv4 OptimizerType;
> typedef itk::ImageRegistrationMethodv4< ImageType, ImageType, TransformType > RegistrationMethodType;
> typedef itk::RegistrationParameterScalesFromPhysicalShift< MetricType > ScalesEstimatorType;
>
> MetricType::Pointer metric = MetricType::New();
>
> OptimizerType::Pointer optimizer = OptimizerType::New();
> optimizer->SetNumberOfIterations( 200 );
> optimizer->SetDoEstimateLearningRateOnce( true );
> optimizer->SetMinimumConvergenceValue( 1e-16 );
> optimizer->SetConvergenceWindowSize( 20 );
> optimizer->SetMaximumStepSizeInPhysicalUnits( 2 );
>
> ScalesEstimatorType::Pointer scalesEstimator = ScalesEstimatorType::New();
> scalesEstimator->SetMetric( metric );
> scalesEstimator->SetTransformForward( true );
> optimizer->SetScalesEstimator( scalesEstimator );
> optimizer->SetDoEstimateScales( true );
>
> RegistrationMethodType::Pointer registrationMethod = RegistrationMethodType::New();
> registrationMethod->SetOptimizer( optimizer );
> registrationMethod->SetFixedImage( fixedImage );
> registrationMethod->SetMovingImage( movingImage );
> registrationMethod->SetFixedInitialTransform( initialFixedTransform );
> registrationMethod->SetMovingInitialTransform( initialMovingTransform );
> registrationMethod->SetNumberOfLevels( 1 );
> registrationMethod->SetMetric( metric );
> registrationMethod->SetMetricSamplingStrategy( RegistrationMethodType::NONE );
>
>
>
>
> The initial transforms are initialized like this:
>
> TransformType::PhysicalDimensionsType fixedPhysicalDimensions;
> TransformType::MeshSizeType meshSize;
> for( unsigned int i=0; i < ImageDimension; i++ )
> {
> fixedPhysicalDimensions[i] = fixedImage->GetSpacing()[i] *
> static_cast<double>(
> movingImage->GetLargestPossibleRegion().GetSize()[i] - 1 );
> }
> unsigned int SplineOrder = 3;
> unsigned int numberOfGridNodesInOneDimension = 5;
> meshSize.Fill( numberOfGridNodesInOneDimension - SplineOrder );
> initialMovingTransform->SetTransformDomainOrigin( movingImage->GetOrigin() );
> initialMovingTransform->SetTransformDomainPhysicalDimensions( fixedPhysicalDimensions );
> initialMovingTransform->SetTransformDomainMeshSize( meshSize );
> initialMovingTransform->SetTransformDomainDirection( movingImage->GetDirection() );
> TransformType::ParametersType initialMovingParameters( initialMovingTransform->GetNumberOfParameters() );
> initialMovingParameters.Fill(0.0);
> initialMovingTransform->SetParameters(initialMovingParameters);
>
>
> Thanks for the link to the relevant ANTs class. I took a look at the relevant lines but it didn't help me either.
>
> Many thanks,
> Frank
>
>
>
>
>
> On 07/31/2013 01:21 PM, Nick Tustison wrote:
>> Hi Frank,
>>
>> I'm cc'ing the insight users list as others might be interested.
>>
>> How are you setting up the registration? In case you were interested, we have
>> a pretty comprehensive application which ties in all the new registration stuff
>> in a single application. In it, we set up the B-spline transform which you can
>> view at
>>
>> https://github.com/stnava/ANTs/blob/master/Examples/itkantsRegistrationHelper.hxx
>>
>> starting at line 1896.
>>
>> Nick
>>
>> On Jul 31, 2013, at 4:45 AM, Frank Preiswerk <frank.preiswerk at unibas.ch> wrote:
>>
>>> Hi Nick,
>>>
>>> I have adapted my code to work with the new ITKv4 classes. For the affine registration this worked well. But for the BSplineTransform, I get the following error during optimization:
>>>
>>> /usr/local/include/ITK-4.4/itkImageToImageMetricv4GetValueAndDerivativeThreaderBase.hxx:258:
>>> Exception in GetValueAndDerivativeProcessPoint:
>>> /usr/local/include/ITK-4.4/itkBSplineBaseTransform.h:282:
>>> itk::ERROR: BSplineTransform(0x384cb00): ComputeJacobianWithRespectToPosition not yet implemented for BSplineTransform
>>>
>>> I use GradientDescentOptimizerv4 and MeanSquaresImageToImageMetricv4 and also tried substituting them with QuasiNewtonOptimizerv4 and MattesMutualInformationImageToImageMetricv4 but to no avail.
>>>
>>> Sorry to bother you but I could not find any examples on the web that shows how the BSplineTransform can be used in the new framework.
>>>
>>> Many thanks!
>>> Frank
>>>
>>>
>>>
>>>
>>> On 07/30/2013 04:09 PM, Nick Tustison wrote:
>>>> Hi Frank,
>>>>
>>>> I don't think that anybody on the registration team has tried to use the composite
>>>> transform with the old registration framework. I'm not even sure that it would work
>>>> as both the optimization and metrics are completely separate between ITKv3 and
>>>> ITKv4. In suggesting the use of the CompositeTransform class, I didn't catch that
>>>> you were sticking with ITKv3. Sorry about that.
>>>>
>>>> There was some earlier work by Torsten and Marius & Stefan who gave us some
>>>> ideas for the current composite transform. Perhaps one of those contributions would
>>>> fit your needs.
>>>>
>>>> http://www.insight-journal.org/browse/publication/143
>>>> http://www.insight-journal.org/browse/publication/91
>>>>
>>>> Also, I would be remiss if I didn't at least proselyte concerning the utility of the new
>>>> registration framework. There's quite a few advantages in addition to the composite
>>>> transform:
>>>>
>>>> http://www.itk.org/Wiki/ITK/Release_4/Why_Switch_to_ITKv4#New_Registration_Framework
>>>>
>>>> Nick
>>>>
>>>>
>>>> On Jul 30, 2013, at 7:35 AM, Frank Preiswerk <frank.preiswerk at unibas.ch> wrote:
>>>>
>>>>> Hi Nick,
>>>>>
>>>>> I have a few additional questions and I would be very glad if you could help me getting on the right track.
>>>>>
>>>>> Your suggestion to use the CompositeTransform guided me to the new registration framework. I have played around a bit and now I'm unsure which version to use.
>>>>>
>>>>> First of all, in ImageRegistrationMethodv4 there is a method SetMovingInitialTransform that probably does exactly what I need. As far as I understand it, one can achieve the same with the old framework by using CompositeTransform like this:
>>>>>
>>>>> compositeTransform->AddTransform(affineTransform); // the output from the prior affine step
>>>>> compositeTransform->AddTransform(bsplineTransform);
>>>>> compositeTransform->SetOnlyMostRecentTransformToOptimizeOn(); // activate the bspline transform for the next optimization
>>>>> registration->SetTransform( compositeTransform );
>>>>>
>>>>> Is this the way how to properly use CompositeTransform in the old registration framework? And is my assumption correct that SetMovingInitialTransform would be sufficient when using the new framework?
>>>>>
>>>>> Thanks a lot for your efforts,
>>>>> Frank
>>>>>
>>>>>
>>>>>
>>>>> On 07/29/2013 12:16 PM, Nick Tustison wrote:
>>>>>> You should try using the composite transform
>>>>>>
>>>>>> http://www.itk.org/Doxygen/html/classitk_1_1CompositeTransform.html
>>>>>>
>>>>>> Nick
>>>>>>
>>>>>> On Jul 29, 2013, at 4:49 AM, Frank Preiswerk <frank.preiswerk at unibas.ch> wrote:
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I'm writing a program that performs image registration by first computing an
>>>>>>> affine transformation followed by a bspline deformation. The bspline
>>>>>>> registration should be initialized with the output of the affine
>>>>>>> registration.
>>>>>>>
>>>>>>> I'm using ITK 4.4. The example DeformableRegistration15.cxx intends to do
>>>>>>> the above but it seems that the BSplineTransform is actually not initialized
>>>>>>> with the output of the affine step, as already reported earlier:
>>>>>>> http://www.itk.org/pipermail/insight-users/2012-May/044623.html
>>>>>>>
>>>>>>> ITK 3's BSplineDeformableTransform had a method SetBulkTransform to concat
>>>>>>> the bspline transform with another transform, but in ITK 4's
>>>>>>> BSplineTransform this method was removed. So the question remains how to
>>>>>>> properly initialize a BSplineTransform with an affine (or any other)
>>>>>>> registration output.
>>>>>>>
>>>>>>> Computing the parameters of the bspline transform by applying the affine
>>>>>>> transform to the grid nodes is an option. But something like
>>>>>>> SetBulkTransform would be much more convenient.
>>>>>>>
>>>>>>> I'm thankful for any hints.
>>>>>>>
>>>>>>> Regards,
>>>>>>> Frank
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Initializing-a-BSplineTransform-in-ITK-4-4-tp7583607.html
>>>>>>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
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>>>>> --
>>>>> Frank Preiswerk, Senior Researcher
>>>>> Medical Image Analysis Center (MIAC)
>>>>> University of Basel c/o University Hospital Basel
>>>>> Spitalstrasse 21
>>>>> CH-4031 Basel
>>>>> Switzerland
>>>>>
>>>>> Tel: +41 61 265 96 58
>>>>> Fax: +41 61 265 96 68
>>>>> Office:Schanzenstrasse 46, Room 321
>>>>>
>>>
>>>
>>> --
>>> Frank Preiswerk, Senior Researcher
>>> Medical Image Analysis Center (MIAC)
>>> University of Basel c/o University Hospital Basel
>>> Spitalstrasse 21
>>> CH-4031 Basel
>>> Switzerland
>>>
>>> Tel: +41 61 265 96 58
>>> Fax: +41 61 265 96 68
>>> Office:Schanzenstrasse 46, Room 321
>>
>
>
> --
> Frank Preiswerk, Senior Researcher
> Medical Image Analysis Center (MIAC)
> University of Basel c/o University Hospital Basel
> Spitalstrasse 21
> CH-4031 Basel
> Switzerland
>
> Tel: +41 61 265 96 58
> Fax: +41 61 265 96 68
> Office:Schanzenstrasse 46, Room 321
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