How to access velocity/update field from DiffeomorphicDemonsRegistrationFilter?

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Summary

The DiffeomorphicDemonsRegistrationFilter in SimpleITK is used for deformable registration, but it only returns the final displacement field. However, accessing the internal velocity/update field is crucial for certain applications. This article explores the root cause of this limitation and provides a solution to access the velocity field.

Root Cause

The DiffeomorphicDemonsRegistrationFilter uses a diffeomorphic formulation that computes the velocity field internally, but it is not directly accessible through the Execute() method. The main reasons for this are:

  • The velocity field is used to compute the displacement field through an exponential map.
  • The DiffeomorphicDemonsRegistrationFilter is designed to return the displacement field, which is the primary output of the registration process.

Why This Happens in Real Systems

In real-world systems, the velocity field is often required for:

  • Computing deformation metrics, such as the Jacobian determinant.
  • Analyzing the registration process, including the convergence of the algorithm.
  • Visualizing the deformation, which can be useful for quality control and debugging.

Real-World Impact

The inability to access the velocity field can have significant impacts, including:

  • Limited analysis capabilities, making it difficult to understand the registration process.
  • Inaccurate deformation metrics, which can lead to incorrect conclusions.
  • Reduced quality control, making it challenging to detect registration errors.

Example or Code

import SimpleITK as sitk

# Create a DiffeomorphicDemonsRegistrationFilter
demons = sitk.DiffeomorphicDemonsRegistrationFilter()

# Set the parameters
demons.SetNumberOfIterations(300)
demons.SetStandardDeviations(1.0)
demons.SetMaximumUpdateStepLength(2.5)
demons.SetSmoothDisplacementField(True)
demons.SetSmoothUpdateField(True)

# Execute the registration
displacement_field = demons.Execute(fixed_image, moving_image)

# To access the velocity field, you can use the GetUpdateField() method
# However, this method is not available in the DiffeomorphicDemonsRegistrationFilter
# One possible solution is to use the DemonsRegistrationFilter instead
demons = sitk.DemonsRegistrationFilter()
demons.SetNumberOfIterations(300)
demons.SetStandardDeviations(1.0)
demons.SetMaximumUpdateStepLength(2.5)
demons.SetSmoothDisplacementField(True)
demons.SetSmoothUpdateField(True)

# Execute the registration
displacement_field = demons.Execute(fixed_image, moving_image)

# Get the update field (velocity field)
update_field = demons.GetUpdateField()

How Senior Engineers Fix It

Senior engineers can fix this issue by:

  • Using alternative registration filters, such as the DemonsRegistrationFilter, which provides access to the update field.
  • Implementing custom registration algorithms, which can provide more control over the registration process and access to internal fields.
  • Using other libraries or frameworks, such as ITK or scikit-image, which may provide more flexibility and access to internal fields.

Why Juniors Miss It

Junior engineers may miss this issue because:

  • Lack of experience with registration algorithms and their internal workings.
  • Insufficient understanding of the diffeomorphic formulation and its requirements.
  • Overreliance on high-level APIs, which may not provide access to internal fields or parameters.