pymerlin.reg.versor3D_registration

pymerlin.reg.versor3D_registration(fixed_image_fname, moving_image_fname, moco_output_name=None, fixed_output_name=None, fixed_mask_fname=None, reg_par_name=None, iteration_log_fname=None, opt_range=[0.017453292519943295, 10], init_angle=0, init_axis=[0, 0, 1], relax_factor=0.5, winsorize=None, threshold=None, sigmas=[0], shrink=[1], metric='MS', learning_rate=5, convergence_window_size=10, convergence_value=1e-06, min_step_length=1e-06, nit=250, verbose=2)[source]

Multi-scale rigid body registration

ITK registration framework inspired by ANTs which performs a multi-scale 3D versor registratio between two 3D volumes. The input data is provided as .h5 image files.

Default values works well. Mask for the fixed image is highly recommended for ZTE data with head rest pads visible.

Note that the outputs of the registration is are versor and translation vectors. The versor is the vector part of a unit normalised quarterion. To get the equivalent euler angles use pymerlin.utils.versor_to_euler.

Parameters

  • fixed_image_fname (str) – Fixed file (.h5 file)

  • moving_image_fname (str) – Moving file (.h5 file)

  • moco_output_name (str, optional) – Output moco image as nifti. Defaults to None.

  • fixed_output_name (str, optional) – Output fixed image as nifti. Defaults to None.

  • fixed_mask_name (str, optional) – Mask for fixed image. Defaults to None

  • reg_par_name (str, optional) – Name of output parameter file. Defaults to None.

  • iteration_log_fname (str, optional) – Name for output log file. Defaults to None.

  • opt_range (list, optional) – Expected range of motion [deg,mm]. Defaults to [1 rad, 10 mm].

  • init_angle (float, optional) – Initial angle for registration. Defaults to 0

  • init_axis (array, optional) – Direction of intial rotation for registration. Defaults to [0,0,1]

  • relax_factor (float, optional) – Relaxation factor for optimizer, factor to decrease step length by. Defaults to 0.5.

  • winsorize (list, optional) – Limits for winsorize filter. Defaults to None.

  • threshold (float, optional) – Lower value for threshold filter. Defaults to None.

  • sigmas (list, optional) – Smoothing sigmas for multi-scale registration. Defaults to [0].

  • shrink (list, optional) – Shring factors for multi-scale registration. Defaults to [1].

  • metric (str, optional) – Image metric for registrationn (MI/MS). Defaults to ‘MS’.

  • learning_rate (float, optional) – Initial step length. Defaults to 5.

  • convergence_window_size (int, optional) – Length of window to calculate convergence value. Defaults to 10.

  • convergence_value (float, optional) – Convergence value to terminate registration. Defaults to 1E-6.

  • min_step_length (float, optional) – Minimum step length, after which the registration terminates. Defaults to 1E-6,

  • nit (int, optional) – Maximum number of iterations per scale. Defaults to 250.

  • verbose (int, optional) – Level of debugging (0/1/2). Defaults to 2.

Returns

Registration object, Registration history, Name of output file with correction factors

Return type

(itk.ImageRegistrationMethodv4, dict, str)