SimpleElastix

https://simpleelastix.readthedocs.io
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SimpleElastix is a medical image registration library that provides state-of-the-art image...
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### Example Point File

Source: https://simpleelastix.readthedocs.io/PointBasedRegistration.html

An example of a valid point file using world coordinates.

```plaintext
point
3
102.8 -33.4 57.0
178.1 -10.9 14.5
180.4 -18.1 78.9


```

--------------------------------

### Register images with SimpleElastix in Python

Source: https://simpleelastix.readthedocs.io/

Performs image registration between a fixed and moving image using the sitk.Elastix function.

```python
import SimpleITK as sitk
resultImage = sitk.Elastix(sitk.ReadImage("fixedImage.nii"), sitk.ReadImage("movingImage.nii"))
```

--------------------------------

### Point Set File Format

Source: https://simpleelastix.readthedocs.io/PointBasedRegistration.html

Specifies the format for point set text files, which can be in VTK pointdata legacy format or elastix's own format with a 'pts' extension. 'index' is for pixel coordinates, 'point' for world coordinates.

```plaintext
<index, point>
<number of points>
point1 x point1 y [point1 z]
point2 x point2 y [point2 z]


```

--------------------------------

### Add CorrespondingPointsEuclideanDistanceMetric to Parameter Map

Source: https://simpleelastix.readthedocs.io/PointBasedRegistration.html

Append 'CorrespondingPointsEuclideanDistanceMetric' to the list of metrics in the parameter map. This metric must be specified last due to elastix constraints.

```python
import SimpleITK as sitk

parameterMap = sitk.GetDefaultParameterMap("bspline")
parameterMap["Metric"].append("CorrespondingPointsEuclideanDistanceMetric")

```

--------------------------------

### Perform Rigid Registration with EulerTransform

Source: https://simpleelastix.readthedocs.io/RigidRegistration.html

Uses the default rigid parameter map to align a moving image to a fixed image via rotation and translation.

```python
import SimpleITK as sitk

elastixImageFilter = sitk.ElastixImageFilter()
elastixImageFilter.SetFixedImage(sitk.ReadImage("fixedImage.nii"))
elastixImageFilter.SetMovingImage(sitk.ReadImage("movingImage.nii"))
elastixImageFilter.SetParameterMap(sitk.GetDefaultParameterMap("rigid"))
elastixImageFilter.Execute()
sitk.WriteImage(elastixImageFilter.GetResultImage())
```

--------------------------------

### Warp Point Set with SimpleTransformix

Source: https://simpleelastix.readthedocs.io/PointBasedRegistration.html

Applies a computed transformation to a point set using SimpleTransformix. The input points are in the fixed image domain and warped to the moving image domain. The moving image is required to infer point set dimensionality.

```python
import SimpleITK as sitk

fixedImage = sitk.ReadImage("fixedImage.nii")
movingImage = sitk.ReadImage("movingImage.nii")

# Compute the transformation
elastixImageFilter = sitk.ElastixImageFilter()
elastixImageFilter.SetFixedImage(fixedImage)
elastixImageFilter.SetMovingImage(movingImage)
elastixImageFilter.Execute()

# Warp point set. The transformed points will be written to a file named
# outputpoints.txt in the output directory determined by SetOutputDirectory()
# (defaults to working directory). The moving image is needed for transformix
# to correctly infer the dimensionality of the point set.
transformixImageFilter = sitk.TransformixImageFilter()
transformixImageFilter.SetTransformParameterMap(elastixImageFilter.GetTransformParameterMap())
transformixImageFilter.SetFixedPointSetFileName("fixedPointSet.pts")
transformixImageFilter.Execute()


```

--------------------------------

### Add CorrespondingPointsEuclideanDistanceMetric to ElastixImageFilter

Source: https://simpleelastix.readthedocs.io/PointBasedRegistration.html

Add the 'CorrespondingPointsEuclideanDistanceMetric' to all metrics in the ElastixImageFilter object with a single call.

```python
import SimpleITK as sitk

elastixImageFilter = sitk.ElastixImageFilter()
elastixImageFilter.AddParameter( "Metric", "CorrespondingPointsEuclideanDistanceMetric" )

```

--------------------------------

### Add CorrespondingPointsEuclideanDistanceMetric to a Specific Parameter Map

Source: https://simpleelastix.readthedocs.io/PointBasedRegistration.html

Add the 'CorrespondingPointsEuclideanDistanceMetric' to a specific parameter map within the ElastixImageFilter. Assumes at least two parameter maps exist.

```python
elastixImageFilter.AddParameter( 1, "Metric", "CorrespondingPointsEuclideanDistanceMetric" )

```
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