# User:Ramirez

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## Tuning Parameters

### Optimizers

"[...] In order to get some insight on how to tune the parameters for your optimization, probably the best thing to do is to study the characteristics of the Metric when computed over your images. Please find attached a small program that allows you to explore the values of the metric using a translation transform. You want to plot these values in order to get a feeling on the level of noise of the Metric, the presence of local minima, and the overall reproducibility of the Metric function itself. (you will have to convert the dimension to 3D, since the example was configured for 2D)

Please run this program first using the *same* input image as fixed and moving images, and let the translation be evaluated for a range that is close to 1/2 of the image extent (physical extent in millimeters).

Plot the values using your favorite plotting program. (anything from GNUPlot to Excel).

For examples on how these plot will look like, please take a look at the course in Image Registration:

```    http://www.cs.rpi.edu/courses/spring04/imagereg/
```

In particular, look at lectures 8 and 9.

[...] It is not productive to fight with the registration + optimization until you find a way of generating relatively smooth Metric plots. Note that this is just an exercise on learning how to tune the parameters. Once you figure out the parameters, you will not need to plot the Metric anymore.

Make sure that origin and spacing are correctly set in your images before you start computing all these metric plots."

```#include "itkImage.h"
#include "itkImageFileWriter.h"
#include "itkMattesMutualInformationImageToImageMetric.h"
#include "itkTranslationTransform.h"
#include "itkLinearInterpolateImageFunction.h"

int main( int argc, char * argv[] )
{
if( argc < 3 )
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << "  fixedImage  movingImage" << std::endl;
return 1;
}

const     unsigned int   Dimension = 2;
typedef   unsigned char  PixelType;

typedef itk::Image< PixelType, Dimension >   ImageType;
typedef itk::Image< PixelType, Dimension >   ImageType;

try
{
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception catched !" << std::endl;
std::cerr << excep << std::endl;
}

typedef itk::MattesMutualInformationImageToImageMetric< ImageType, ImageType >  MetricType;

MetricType::Pointer metric = MetricType::New();

typedef itk::TranslationTransform< double, Dimension >  TransformType;

TransformType::Pointer transform = TransformType::New();

typedef itk::LinearInterpolateImageFunction<
ImageType, double >  InterpolatorType;

InterpolatorType::Pointer interpolator = InterpolatorType::New();

metric->SetInterpolator( interpolator );
metric->SetTransform( transform );

metric->SetNumberOfHistogramBins( 20 );
metric->SetNumberOfSpatialSamples( 10000 );

transform->SetIdentity();

metric->SetFixedImage(  fixedImage  );
metric->SetMovingImage( movingImage );

metric->SetFixedImageRegion(  fixedImage->GetBufferedRegion()  );

try
{
metric->Initialize();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception catched !" << std::endl;
std::cerr << excep << std::endl;
return -1;
}

MetricType::TransformParametersType displacement( Dimension );

int rangex = 50;
int rangey = 50;

for( int dx = -rangex; dx <= rangex; dx++ )
{
for( int dy = -rangey; dy <= rangey; dy++ )
{
displacement[0] = dx;
displacement[1] = dy;
const double value = metric->GetValue( displacement );

std::cout << dx << "   "  << dy << "   " << value << std::endl;
}
}

std::cout << std::endl;

return 0;
}```

Optimizer->SetScales()

The rule of thumb is to figure out how much each one of those parameters will change for your registration, and then rescale that range to [-1:1].

In the case that you know the anticipated range of translations and rotations,

"[...]if you are doing 2D rigid you will have a 2D transform with three parameters:

```     Tx  translation in millimeters along X
Ty  translation in millimeters along Y
```

and you anticipate that your images need a correction of the order of 10 to 50 millimeters in translation and 0.01 to 0.1 radians in rotation, then you should put scales:

```     scale[0] = 1/50;     scale for Tx
scale[1] = 1/50;     scale for Ty
scale[2] = 1/0.1;    scale for Rotation
```

Of course, those will be just "good values to start with". You will still need to refine them according to the behavior of the optimizer."

In the case that you do not know the anticipated range of translations and rotations,

"[...]the recommendation for the scaling of translation parameters versus rotation parameter is to use a factor proportional to the diagonal length of the image.

For your case the, you have 100 pixels with 1 mm / pixel, therefore the physical extent of your image is

```       100mm  X  100mm  X 100mm
```

The diagonal the image bounding box is

```         sqrt(3) * 100 mm
```

```             173.2
```

and extra factor of 10X is usually useful, so you should probably try a factor of

```    1.0 / ( 10 x 173.2 )  =  1.0 / 1732.0
```

You could use this same factor for the three components of the translation or you could estimate independent factor for each component in the way it is done in the VolView plugin.

Note that this factors are not expected to be computed precisely. Their purpose is simply to bring the rotational and translational parameters to a similar numerical scale.

By default, they are quite disproportionate since rotation are in radians, therefore in a range about -1:1, while translations are in millimeters, and for an image of 100mm you probably can expect translations as large as 50mm."

In short,

"[...]for an 3D AffineTransform, you get 12 parameters: the first 9 are the coefficients of the matrix (representing rotation, scale and shearing) the last 3 are the components of a translation vector. You want then to provide an array of 12 values with the first 9 being =1.0 and the last three being on the range of 1.0 / the image size (in millimeters)."

"[...]There is no magic recipe for selecting one. You probably want to start experimenting with a small value (e.g. 0.01) and plot the metric evaluations during the registration process. If you observe that the metric values are fairly monotonic, that means that you can safely increment the step length. Such an increment has the advantage of reducing the time required to reach an extrema of the cost function (the image metric in this case). You could restart the registration with larger values of the step length, as long as you don't observe a noisy and/or erratic behavior on the Metric values.

Step length issues are discussed in the course material from the "Image Registration Techniques" course at RPI.

```  http://www.cs.rpi.edu/courses/spring04/imagereg/
```

for example in lecture 9:

```  http://www.cs.rpi.edu/courses/spring04/imagereg/lecture09.ppt"
```

## Use Cases

### PET-CT Registration

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