# m\_UseSequentialSampling error while performing registration of two 3D images of same modality

**URL:** <https://discourse.itk.org/t/m-usesequentialsampling-error-while-performing-registration-of-two-3d-images-of-same-modality/1728>\
**Category:** Beginner Questions\
**Tags:** registration\
**Created:** [April 2, 2019, 7:39am UTC](https://discourse.itk.org/t/m-usesequentialsampling-error-while-performing-registration-of-two-3d-images-of-same-modality/1728 "2019-04-02T07:39:58Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![EE18D504\_SINDHURA\_C](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b3f665/32.png) [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Post date:** [April 2, 2019, 7:39am UTC](https://discourse.itk.org/t/m-usesequentialsampling-error-while-performing-registration-of-two-3d-images-of-same-modality/1728/1 "2019-04-02T07:39:58Z")

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I am trying to execute the code from following page for my registration  
I removed all this exception handling code …as I am not much aware of it. and tried executing. the error comes while executing registration-\>update() and it takes to error at m\_UseSequentialSampling. How to resolve this? please help me. I have uploaded screenshots also.

 ![image](https://discourse.itk.org/uploads/default/original/1X/c61d648bf5c21a155cd65b458b809d4e4e5fe5b7.png)  
 ![image](https://discourse.itk.org/uploads/default/original/1X/1d20604b3ca1185a459414b181610b22d7be1335.png)

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**Author:** ![EE18D504\_SINDHURA\_C](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b3f665/32.png) [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Post date:** [April 2, 2019, 10:56am UTC](https://discourse.itk.org/t/m-usesequentialsampling-error-while-performing-registration-of-two-3d-images-of-same-modality/1728/2 "2019-04-02T10:56:45Z")

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I tried with the data available in ITK

- brainweb1e1a10f20.mha
- brainweb1e1a10f20Rot10Tx15.mha  
I get this error when regestration is performing. How can I rectify this? what does this error mean?  
 ![image](https://discourse.itk.org/uploads/default/original/1X/1a6430ae743fa209e3896e1de76c4b225f08557b.png)

(edited After sometime)  
Now i got to know that, for my input images, if i define dimension as 2 instead of 3, My code runs without any error and i am getting registration output image for one slice.  
Why is it happening? do i need to declare anything else when playing with 3D images??

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**Author:** ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Post date:** [April 2, 2019, 4:12pm UTC](https://discourse.itk.org/t/m-usesequentialsampling-error-while-performing-registration-of-two-3d-images-of-same-modality/1728/3 "2019-04-02T16:12:54Z")

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You did not post the code you are using. And [DeformableRegistration7](https://itk.org/Doxygen45/html/Registration_2DeformableRegistration7_8cxx-example.html) is already 3D.

And the problem was line 387, the `resize` call which allocates memory. VisualStudio usually points to the next line instead of the one which causes the crash.

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**Author:** ![EE18D504\_SINDHURA\_C](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b3f665/32.png) [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Post date:** [April 2, 2019, 4:20pm UTC](https://discourse.itk.org/t/m-usesequentialsampling-error-while-performing-registration-of-two-3d-images-of-same-modality/1728/4 "2019-04-02T16:20:49Z")

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please find the following code

```
#include "itkImageRegistrationMethod.h"
#include "itkMeanSquaresImageToImageMetric.h"
#include "itkTimeProbesCollectorBase.h"
#include "itkMemoryProbesCollectorBase.h"
#include "itkBSplineTransform.h"
#include "itkLBFGSBOptimizer.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkResampleImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkSquaredDifferenceImageFilter.h"

int main()
{

    const unsigned int ImageDimension = 3;
typedef float PixelType;
typedef itk::Image< PixelType, ImageDimension > FixedImageType;
typedef itk::Image< PixelType, ImageDimension > MovingImageType;
const unsigned int SpaceDimension = ImageDimension;
const unsigned int SplineOrder = 3;
typedef double CoordinateRepType;
typedef itk::BSplineTransform<
	CoordinateRepType,
	SpaceDimension,
	SplineOrder > TransformType;

typedef itk::LBFGSBOptimizer OptimizerType;
typedef itk::MeanSquaresImageToImageMetric<
	FixedImageType,
	MovingImageType > MetricType;
typedef itk::LinearInterpolateImageFunction<
	MovingImageType,
	double > InterpolatorType;
typedef itk::ImageRegistrationMethod<
	FixedImageType,
	MovingImageType > RegistrationType;
MetricType::Pointer metric = MetricType::New();
OptimizerType::Pointer optimizer = OptimizerType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
RegistrationType::Pointer registration = RegistrationType::New();
registration->SetMetric(metric);
registration->SetOptimizer(optimizer);
registration->SetInterpolator(interpolator);

TransformType::Pointer transform = TransformType::New();
registration->SetTransform(transform);

typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
FixedImageReaderType::Pointer fixedImageReader = FixedImageReaderType::New();
MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();
fixedImageReader->SetFileName("C:\\VISUAL STUDIO\\projects\\bspline3dregistration1\\bin\\Debug\\brainweb1e1a10f20.mhd");
movingImageReader->SetFileName("C:\\VISUAL STUDIO\\projects\\bspline3dregistration1\\bin\\Debug\\brainweb1e1a10f20Rot10Tx15.mhd");
FixedImageType::ConstPointer fixedImage = fixedImageReader->GetOutput();
registration->SetFixedImage(fixedImage);
registration->SetMovingImage(movingImageReader->GetOutput());
fixedImageReader->Update();
FixedImageType::RegionType fixedRegion = fixedImage->GetBufferedRegion();
registration->SetFixedImageRegion(fixedRegion);

typedef TransformType::RegionType RegionType;
unsigned int numberOfGridNodes = 8;
TransformType::PhysicalDimensionsType fixedPhysicalDimensions;
TransformType::MeshSizeType meshSize;
TransformType::OriginType fixedOrigin;
for (unsigned int i = 0; i < SpaceDimension; i++)
{
	fixedOrigin[i] = fixedImage->GetOrigin()[i];
	fixedPhysicalDimensions[i] = fixedImage->GetSpacing()[i] *
		static_cast<double>(
			fixedImage->GetLargestPossibleRegion().GetSize()[i] - 1);
}
meshSize.Fill(numberOfGridNodes - SplineOrder);
transform->SetTransformDomainOrigin(fixedOrigin);
transform->SetTransformDomainPhysicalDimensions(
	fixedPhysicalDimensions);
transform->SetTransformDomainMeshSize(meshSize);
transform->SetTransformDomainDirection(fixedImage->GetDirection());
typedef TransformType::ParametersType ParametersType;
const unsigned int numberOfParameters =
	transform->GetNumberOfParameters();
ParametersType parameters(numberOfParameters);
parameters.Fill(0.0);
transform->SetParameters(parameters);

registration->SetInitialTransformParameters(transform->GetParameters());

std::cout << "Intial Parameters = " << std::endl;
std::cout << transform->GetParameters() << std::endl;

OptimizerType::BoundSelectionType boundSelect(transform->GetNumberOfParameters());
OptimizerType::BoundValueType upperBound(transform->GetNumberOfParameters());
OptimizerType::BoundValueType lowerBound(transform->GetNumberOfParameters());
boundSelect.Fill(0);
upperBound.Fill(0.0);
lowerBound.Fill(0.0);
optimizer->SetBoundSelection(boundSelect);
optimizer->SetUpperBound(upperBound);
optimizer->SetLowerBound(lowerBound);
optimizer->SetCostFunctionConvergenceFactor(1e+12);
optimizer->SetProjectedGradientTolerance(1.0);
optimizer->SetMaximumNumberOfIterations(500);
optimizer->SetMaximumNumberOfEvaluations(500);
optimizer->SetMaximumNumberOfCorrections(5);

itk::TimeProbesCollectorBase chronometer;
itk::MemoryProbesCollectorBase memorymeter;
std::cout << std::endl << "Starting Registration" << std::endl;
try
{
	memorymeter.Start("Registration");
	chronometer.Start("Registration");
	registration->Update();
	chronometer.Stop("Registration");
	memorymeter.Stop("Registration");
	std::cout << "Optimizer stop condition = "
		<< registration->GetOptimizer()->GetStopConditionDescription()
		<< std::endl;
}
catch (itk::ExceptionObject & err)
{
	std::cerr << "ExceptionObject caught !" << std::endl;
	std::cerr << err << std::endl;
	return EXIT_FAILURE;
}
OptimizerType::ParametersType finalParameters =
	registration->GetLastTransformParameters();
std::cout << "Last Transform Parameters" << std::endl;
std::cout << finalParameters << std::endl;
// Report the time taken by the registration
chronometer.Report(std::cout);
memorymeter.Report(std::cout);
// Software Guide : BeginCodeSnippet
transform->SetParameters(finalParameters);
// Software Guide : EndCodeSnippet
typedef itk::ResampleImageFilter<
	MovingImageType,
	FixedImageType > ResampleFilterType;
ResampleFilterType::Pointer resample = ResampleFilterType::New();
resample->SetTransform(transform);
resample->SetInput(movingImageReader->GetOutput());
resample->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
resample->SetOutputOrigin(fixedImage->GetOrigin());
resample->SetOutputSpacing(fixedImage->GetSpacing());
resample->SetOutputDirection(fixedImage->GetDirection());
resample->SetDefaultPixelValue(100);
typedef unsigned char OutputPixelType;
typedef itk::Image< OutputPixelType, ImageDimension > OutputImageType;
typedef itk::CastImageFilter<
	FixedImageType,
	OutputImageType > CastFilterType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
CastFilterType::Pointer caster = CastFilterType::New();
writer->SetFileName("C:\\VISUAL STUDIO\\projects\\bspline3dregistration1\\bin\\Debug\\outputimage1.mhd");
caster->SetInput(resample->GetOutput());
writer->SetInput(caster->GetOutput());
try
{
	writer->Update();
}
catch (itk::ExceptionObject & err)
{
	std::cerr << "ExceptionObject caught !" << std::endl;
	std::cerr << err << std::endl;
	return EXIT_FAILURE;
}
 }
```

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**Author:** ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Post date:** [April 2, 2019, 4:29pm UTC](https://discourse.itk.org/t/m-usesequentialsampling-error-while-performing-registration-of-two-3d-images-of-same-modality/1728/5 "2019-04-02T16:29:38Z")

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[std::bad\_alloc](https://en.cppreference.com/w/cpp/memory/new/bad_alloc) means that your computer does not have enough memory for what you are trying to do. Try closing other programs, increasing virtual memory size, and changing your pixel type from `float` to `unsigned char` (_brainweb1e1a10f20.mha_ has UCHAR type, so you don’t need float for that input).

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**Author:** ![EE18D504\_SINDHURA\_C](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b3f665/32.png) [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Post date:** [April 2, 2019, 5:37pm UTC](https://discourse.itk.org/t/m-usesequentialsampling-error-while-performing-registration-of-two-3d-images-of-same-modality/1728/6 "2019-04-02T17:37:42Z")

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I tried as you said. But no use. My system has 16 GB RAM. I tried giving maximum allocation. But no use. Any other idea?

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**Author:** ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Post date:** [April 2, 2019, 5:48pm UTC](https://discourse.itk.org/t/m-usesequentialsampling-error-while-performing-registration-of-two-3d-images-of-same-modality/1728/7 "2019-04-02T17:48:43Z")

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Try setting [metric sampling percentage](https://itk.org/Doxygen/html/classitk_1_1ImageRegistrationMethodv4.html#a9705f26f83cdb36c397496a46c7234e1) lower (e.g. 0.05, or 0.01). You can also try reducing `numberOfGridNodes` from 8 to 4. You should also use [memory profiler](https://docs.microsoft.com/en-us/visualstudio/profiling/profiling-feature-tour?view=vs-2017#analyze-memory-usage) to narrow down the problem.