Get Elastix Parameters

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Get Elastix Parameters as a Structure. The Elastix registration is governed by a set of Elastix Parameters, describing e.g. the metric, transforms and so on. This is usually set in the Elastix node settings. The settings parameters can also be represented as a Structure. This allows the user to change specific aspects of the registration e.g. when batching, or by some property of the input images.

Outputs

Output

The output Elastix Parameters.

Type: Struct

Settings

Parameter Source

Source Selection

Set the source of the output parameters.

Values: Settings, Load Parameter File, Parameters Editor

Paramter File Filepath

Load parameter file from disk.

Templates Selection

Use a predefined template to generate the output.

Values: Affine (Affine Matrix), Affine (Rot+Shear+Scale+Trans), Non-Rigid, Rigid Time Series, Rigid

Editor Elastix Parameters

Use the Parameter Editor to generate the output Parameters.

Components

Transform Selection

Choose which transform to use.

Values: Translation, Rigid, Similarity, Affine, Affine (R+H+S+T), BSplines

Metric Selection

Choose which metric to use.

Values: Mean Squares Difference, Normalized Correlation Coefficient, Mutual Information, Normalized Mutual Information, Kappa Statistics

Transform Settings

BSplines Grid Spacing [mm] Numbers

Set the resolution of the Bsplines grid in [mm].

Metric Settings

Number of Bins Integers

Set the number of bins used by the metric. Be mindful of intensity outliers in the input image, e.g. a metallic implant in a CT image which has significantly higher intensity than the tissue. Such images can be clipped before registering to improve the registration quality.

Bending Penalty Boolean

Use bending energy penalty. See elastix documentation for further information.

Penalty Weight Numbers

Set the relative weights of the metrics.

Sampler Settings

Number of Samples Integers

Set the number of samples to calculate the metric for.

Number of Sampling Attempts Integers

A certain fraction of valid samples (i.e. samples that are within the moving image buffer) are required to give a valid result. If a valid results is not obtained, the sampler will try again for the number of times specified.

Fraction of Valid Samples Numbers

Specify the number of valid samples (i.e. samples that are within the moving image buffer) required for a valid result.

Pyramid Settings

Pyramid Steps Integer

Set the number of downsampling steps to use in the registration.

Fixed Pyramid Scaling Integers

Set the downsampling divisor for each pyramid step, specified as a Numeric Array of integers.

Moving Pyramid Scaling Integers

Set the downsampling divisor for each pyramid step, specified as a Numeric Array of integers.

Fixed Sampling Selection

Set the sampling strategy for the fixed image pyramid.

Values: Smoothing and Downsampling, Smoothing, Downsampling

Moving Sampling Selection

Set the sampling strategy for the moving image pyramid.