[Insight-users] White Output after Rigid Registration

[Luis Ibanez]

Hi Andy,

Thanks for the additional information.

The following lines in your code are suspicious:


a:  resamTransform->SetParameters( transform->GetParameters() );
b:  resamTransform->SetMatrix( transform->GetRotationMatrix() );
c:  resamTransform->SetOffset( transform->GetOffset() );


If you use line (a) you shouldn't do (b) and (c).
The SetParameters() method should take care of all the
initialization of the transform.

You should use only line (a) and in the form:

   resamTransform->SetParameters(
       registration->GetLastTransformParameters() );

In order to double check the content of the transform,
you could add

      resamTransform->Print( std::cout );




   Regards,


      Luis

-----------------
Andy Eow wrote:
> Hi Luis,
> 
> I'm using 3D Slicer to visualize the volume. The actual values in the 
> volume are all the same ... hence I don't think the problem is with 
> visualizing. I'm guessing there's something I'm not setting right in the 
> registration process. Pls advise. Thanks!
> 
> Cheers,
> Andy
> 
> ----- Original Message ----- From: "Luis Ibanez" <luis.ibanez at kitware.com>
> To: "Andy Eow" <vtkitk at hotmail.com>
> Cc: <insight-users at itk.org>
> Sent: Wednesday, September 29, 2004 11:54 AM
> Subject: Re: [Insight-users] White Output after Rigid Registration
> 
> 
>> Hi Andy,
>>
>> What are you  using for visualizing your resampled moving image ?
>>
>> When you say that the output is "white", did you verified the
>> actual values in the output image ?
>>
>> Please let us know.
>>
>>
>>    Thanks
>>
>>
>>      Luis
>>
>>
>> -----------------
>> Andy Eow wrote:
>>
>>> Hi,
>>>  I'm trying to perform a straightforward rigid registration in 3D 
>>> using sample code from the MultiResMIRegistration application. The 
>>> transform parameters after registration are as follows for my MRI (T1 
>>> & T2) dataset: [0.61162, 0.0627385, 0.0105601, 0.78859, 1.63678, 
>>> -0.662944, 0.223458]. However, I suspect my post registration 
>>> resampling is not working because the resulting volume from that is 
>>> completely white. Attached is the exact code that I'm running. Any 
>>> advice is appreciated. Thanks!!!
>>>  VolumeType::Pointer MakeSymmetrical( VolumeType::Pointer fixedVol, 
>>> VolumeType::Pointer movingVol ) {
>>>   typedef itk::ChangeInformationImageFilter< VolumeType > CentererType;
>>>   typedef itk::NormalizeImageFilter< VolumeType, VolumeType > 
>>> NormalizerType;
>>>   typedef itk::QuaternionRigidTransform< double > TransformType;
>>>   typedef itk::QuaternionRigidTransformGradientDescentOptimizer 
>>> OptimizerType;
>>>   typedef itk::MutualInformationImageToImageMetric< VolumeType, 
>>> VolumeType > MetricType;
>>>   typedef itk::LinearInterpolateImageFunction< VolumeType, double > 
>>> InterpolatorType;
>>>   typedef itk::RecursiveMultiResolutionPyramidImageFilter< 
>>> VolumeType, VolumeType > FixedImagePyramidType;
>>>   typedef itk::RecursiveMultiResolutionPyramidImageFilter< 
>>> VolumeType, VolumeType > MovingImagePyramidType;
>>>   typedef itk::MultiResolutionImageRegistrationMethod< VolumeType, 
>>> VolumeType > RegistrationType;
>>>   typedef itk::FixedArray< unsigned int, 3 > ShrinkFactorsArray;
>>>   typedef itk::Array< unsigned int > UnsignedIntArray;
>>>   typedef itk::Array< double > DoubleArray;
>>>   typedef itk::AffineTransform< double, 3 > AffineTransformType;
>>>   typedef AffineTransformType::ScalarType CoordRepType;
>>>   typedef itk::LinearInterpolateImageFunction< VolumeType, 
>>> CoordRepType > ResampleInterpolatorType;
>>>   typedef itk::ResampleImageFilter< VolumeType, VolumeType > 
>>> ResamplerType;
>>>  // Parameters
>>>   unsigned short noOfLevels = 1;
>>>   double translationScale = 1.0;
>>>   double movingVolStdDev = 0.4;
>>>   double fixedVolStdDev = 0.4;
>>>   unsigned short noOfSpatialSamples = 50;
>>>   DoubleArray learningRates = DoubleArray( noOfLevels );
>>>   learningRates.Fill( 1e-4 );
>>>   UnsignedIntArray noOfIterations = UnsignedIntArray( noOfLevels );
>>>   noOfIterations.Fill( 2500 );
>>>   ShrinkFactorsArray fixedVolShrinkFactors;
>>>   fixedVolShrinkFactors.Fill( 1 );
>>>   ShrinkFactorsArray movingVolShrinkFactors;
>>>   movingVolShrinkFactors.Fill( 1 );
>>>  // Fixed Volume
>>>   CentererType::Pointer centerer =  CentererType::New();
>>>   centerer->CenterImageOn();
>>>   centerer->SetInput( fixedVol );
>>>  NormalizerType::Pointer normalizer = NormalizerType::New(); 
>>> normalizer->SetInput( centerer->GetOutput() );
>>>   ITK_TRY_MACRO( normalizer->Update() );
>>>   VolumeType::Pointer tFixedVol = normalizer->GetOutput();
>>>  // Moving Volume
>>>   CentererType::Pointer centerer2 =  CentererType::New();
>>>   centerer2->CenterImageOn();
>>>   centerer2->SetInput( movingVol );
>>>  NormalizerType::Pointer normalizer2 = NormalizerType::New(); 
>>> normalizer2->SetInput( centerer2->GetOutput() );
>>>   ITK_TRY_MACRO( normalizer2->Update() );
>>>   VolumeType::Pointer tMovingVol = normalizer2->GetOutput();
>>>  // Setup the registrator
>>>   TransformType::Pointer transform = TransformType::New();
>>>   RegistrationType::ParametersType transformInitialParameters = 
>>> RegistrationType::ParametersType( transform->GetNumberOfParameters() );
>>>   transformInitialParameters.Fill( 0.0 );
>>>   transformInitialParameters[3] = 1.0;
>>>  OptimizerType::Pointer optimizer = OptimizerType::New();
>>>   OptimizerType::ScalesType scales( 
>>> transform->GetNumberOfParameters() );
>>>   scales.Fill( 1.0 );
>>>   for ( int i = 4; i < 7; i++ )
>>>     scales[i] = translationScale;
>>>   optimizer->SetScales( scales );
>>>   optimizer->MaximizeOn();
>>>  MetricType::Pointer metric = MetricType::New();
>>>   metric->SetMovingImageStandardDeviation( movingVolStdDev );
>>>   metric->SetFixedImageStandardDeviation( fixedVolStdDev );
>>>   metric->SetNumberOfSpatialSamples( noOfSpatialSamples );
>>>  FixedImagePyramidType::Pointer fixedImagePyramid = 
>>> FixedImagePyramidType::New();
>>>   fixedImagePyramid->SetNumberOfLevels( noOfLevels );
>>>   fixedImagePyramid->SetStartingShrinkFactors( 
>>> fixedVolShrinkFactors.GetDataPointer() );
>>>  MovingImagePyramidType::Pointer movingImagePyramid = 
>>> MovingImagePyramidType::New(); movingImagePyramid->SetNumberOfLevels( 
>>> noOfLevels );
>>>   movingImagePyramid->SetStartingShrinkFactors( 
>>> movingVolShrinkFactors.GetDataPointer() );
>>>  InterpolatorType::Pointer interpolator = InterpolatorType::New();
>>>  RegistrationType::Pointer registration  = RegistrationType::New();
>>>   registration->SetTransform( transform );
>>>   registration->SetOptimizer( optimizer );
>>>   registration->SetMetric( metric );
>>>   registration->SetInterpolator( interpolator );
>>>   registration->SetFixedImagePyramid( fixedImagePyramid );
>>>   registration->SetMovingImagePyramid( movingImagePyramid );
>>>   registration->SetFixedImage( tFixedVol );
>>>   registration->SetMovingImage( tMovingVol );
>>>   registration->SetNumberOfLevels( noOfLevels );
>>>   registration->SetInitialTransformParameters( 
>>> transformInitialParameters );
>>>   registration->SetFixedImageRegion( tFixedVol->GetBufferedRegion() );
>>>   ITK_TRY_MACRO( registration->StartRegistration() );
>>>   MESSAGE( "Transform Parameters (post-reg): " << 
>>> transform->GetParameters() );
>>>   MESSAGE( "Rotation (post-reg): " << transform->GetRotation() );
>>>   MESSAGE( "Translation (post-reg): " << transform->GetTranslation() );
>>>  // Setup the resampler
>>>   AffineTransformType::Pointer resamTransform = 
>>> AffineTransformType::New();
>>>   resamTransform->SetIdentity();
>>>   resamTransform->SetParameters( transform->GetParameters() );
>>>   resamTransform->SetMatrix( transform->GetRotationMatrix() );
>>>   resamTransform->SetOffset( transform->GetOffset() );
>>>  ResampleInterpolatorType::Pointer resamInterpolator = 
>>> ResampleInterpolatorType::New();
>>>  ResamplerType::Pointer resampler = ResamplerType::New();
>>>   resampler->SetInput( tMovingVol );
>>>   resampler->SetTransform( resamTransform );
>>>   resampler->SetInterpolator( resamInterpolator );
>>>   resampler->SetSize( tFixedVol->GetLargestPossibleRegion().GetSize() );
>>>   resampler->SetOutputOrigin( tFixedVol->GetOrigin() );
>>>   resampler->SetOutputSpacing( tFixedVol->GetSpacing() );
>>>   resampler->SetDefaultPixelValue( 0 );
>>>   ITK_TRY_MACRO( resampler->Update() );
>>>  return resampler->GetOutput();
>>> }
>>>  Cheers,
>>> Andy
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Insight-users mailing list
>>> Insight-users at itk.org
>>> http://www.itk.org/mailman/listinfo/insight-users
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