Elastix

Class: NodeElastixProcessor

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Uses elastix to register images using specified parameters. It requires at least one fixed and one moving image as input, and will output the moving image registered and resampled to the fixed image coordinate system.

The default registration method is rigid multimodal registration using mutual information. To change it, click the Edit Parameters button in the node settings panel or double-click on the Elastix node in the process window. The parameters are saved with the Registration (Elastix) node in the workflow (.ice-file). Parameters can also be imported from a .txt file from within the Parameter editor.

There are a multitude of different settings and parameters that can be changed to achieve a wide variety of registrations and results. We have written a separate article to exemplify and describe some possible settings, and for even further information, we refer the user to the elastix homepage and their manual.

Inputs

The inputs are dynamic, and the ones listed below are just the default settings.

Fixed

The fixed input image to register to.

Type: Image4DFloat, Required, Single

Moving 1

The moving input image that will be registered.

Type: Image4DFloat, Required, Single

Outputs

Out 1

The registered moving image.

Type: Image4DFloat

Settings

Input

Number of Moving Images Integer

Specifies the number of moving images to be registered to one or more fixed images.

Use Initial Transform Boolean

Input an initial transform (Transformix Parameter data type) that is applied to the moving image before registration starts.

Use Fixed Masks Boolean

Creates input(s) for fixed mask(s). If used, the sampler draws the required number of samples from within the valid region of the fixed image.

Use Moving Masks Boolean

Creates input(s) for moving mask(s). If used, the sampler will discard any samples drawn from outside the valid region of the moving image.

Use Multiple Fixed Images Boolean

Register all moving images to separate fixed images.

Multi Metric Boolean

Use this option to register a set of moving and fixed images using different metrics simultaneously. A metric need to be specified for each set of images.

Number of Auxiliary Images Integer

Sets the number of auxiliary images. To use them enter the name of the auxiliary image into your parameters file.

Output

Transformix Transforms Boolean

Creates an output for the Transformix Parameters of the resulting registration.

Output Affine Transforms Boolean

Creates an output for affine transforms. This is a Data data type output, which gives the augmented affine transformation matrix, as well as the Euler angles.

Parameters

Parameters Text

Parameters for the registration.

Processing

2D/2D Registration Boolean

If set the images will be treated as having two dimensions. This is uesful when trying to register single slice images.

Note: For this to work you need to change FixedImageDimension and MovingImageDimension to 2 in your parameters. Z position and rotation of all images will be discarded.

Single Thread Boolean

If selected only one instance of elastix will be used by this node.

References

See also

Image registration

Keywords: Registration