dipy_align_syn#

Usage#

dipy_align_syn [OPTIONS] static_image_files moving_image_files

Input Parameters#

  • static_image_files

    Path of the static image file.

  • moving_image_files

    Path to the moving image file.

General Options#

  • --prealign_file

    The text file containing pre alignment information via an affine matrix. (default: )

  • --inv_static

    Apply the inverse mapping to the static image. (default: False)

  • --level_iters

    The number of iterations at each level of the gaussian pyramid. (default: (10, 10, 5))

  • --metric

    The metric to be used. metric available: cc (Cross Correlation), ssd (Sum Squared Difference), em (Expectation-Maximization). (default: cc)

  • --mopt_sigma_diff

    Metric option applied on Cross correlation (CC). The standard deviation of the Gaussian smoothing kernel to be applied to the update field at each iteration. (default: 2.0)

  • --mopt_radius

    Metric option applied on Cross correlation (CC). the radius of the squared (cubic) neighborhood at each voxel to be considered to compute the cross correlation. (default: 4)

  • --mopt_smooth

    Metric option applied on Sum Squared Difference (SSD) and Expectation Maximization (EM). Smoothness parameter, the larger the value the smoother the deformation field. (default 1.0 for EM, 4.0 for SSD) (default: 0.0)

  • --mopt_inner_iter

    Metric option applied on Sum Squared Difference (SSD) and Expectation Maximization (EM). This is number of iterations to be performed at each level of the multi-resolution Gauss-Seidel optimization algorithm (this is not the number of steps per Gaussian Pyramid level, that parameter must be set for the optimizer, not the metric). Default 5 for EM, 10 for SSD. (default: 0)

  • --mopt_q_levels

    Metric option applied on Expectation Maximization (EM). Number of quantization levels (Default: 256 for EM) (default: 256)

  • --mopt_double_gradient

    Metric option applied on Expectation Maximization (EM). if True, the gradient of the expected static image under the moving modality will be added to the gradient of the moving image, similarly, the gradient of the expected moving image under the static modality will be added to the gradient of the static image. (default: True)

  • --mopt_step_type

    Metric option applied on Sum Squared Difference (SSD) and Expectation Maximization (EM). The optimization schedule to be used in the multi-resolution Gauss-Seidel optimization algorithm (not used if Demons Step is selected). Possible value: (‘gauss_newton’, ‘demons’). default: ‘gauss_newton’ for EM, ‘demons’ for SSD. (default: )

  • --step_length

    the length of the maximum displacement vector of the update displacement field at each iteration. (default: 0.25)

  • --ss_sigma_factor

    parameter of the scale-space smoothing kernel. For example, the std. dev. of the kernel will be factor*(2^i) in the isotropic case where i = 0, 1, …, n_scales is the scale. (default: 0.2)

  • --opt_tol

    the optimization will stop when the estimated derivative of the energy profile w.r.t. time falls below this threshold. (default: 1e-05)

  • --inv_iter

    the number of iterations to be performed by the displacement field inversion algorithm. (default: 20)

  • --inv_tol

    the displacement field inversion algorithm will stop iterating when the inversion error falls below this threshold. (default: 0.001)

Output Options#

  • --out_dir

    Directory to save the transformed files. (default: current directory)

  • --out_warped

    Name of the warped file. (default: warped_moved.nii.gz)

  • --out_inv_static

    Name of the file to save the static image after applying the inverse mapping. (default: inc_static.nii.gz)

  • --out_field

    Name of the file to save the diffeomorphic map. (default: displacement_field.nii.gz)

References#

Garyfallidis, E., M. Brett, B. Amirbekian, A. Rokem, S. Van Der Walt, M. Descoteaux, and I. Nimmo-Smith. Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics, 1-18, 2014.

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