uniGradICON Howto

Welcome to the uniGradICON Howto. On this page, we will show some code snippets using uniGradICON.

How to compute the Jacobian determinant map from the transformation

import itk
transform_file = ""
fixed_img_file = ""
transform = itk.transformread(transform_file)[0]
jacob = itk.displacement_field_jacobian_determinant_filter(
    itk.transform_to_displacement_field_filter(
        transform,
        reference_image=itk.imread(fixed_img_file),
        use_reference_image=True
    )
)
itk.imwrite(jacob, "transform_jacob.nii.gz")

How to compute the log of Jacobian determinant map from the transformation

import itk
transform_file = ""
fixed_img_file = ""
transform = itk.transformread(transform_file)[0]
jacob = itk.displacement_field_jacobian_determinant_filter(
    itk.transform_to_displacement_field_filter(
        transform,
        reference_image=itk.imread(fixed_img_file),
        use_reference_image=True
    )
)
log_jacob = itk.LogImageFilter.New(jacob)
log_jacob.Update()
log_jacob = log_jacob.GetOutput()

itk.imwrite(jacob, "transform_jacob.nii.gz")
itk.imwrite(log_jacob, "transform_log_jacob.nii.gz")