dipy_align_affine#

Usage#

dipy_align_affine [OPTIONS] static_image_files moving_image_files

Input Parameters#

  • static_image_files

    Path to the static image file.

  • moving_image_files

    Path to the moving image file.

General Options#

  • --transform

    'com': center of mass; 'trans': translation; 'rigid': rigid body; 'rigid_isoscaling': rigid body + isotropic scaling, 'rigid_scaling': rigid body + scaling; 'affine': full affine including translation, rotation, shearing and scaling.

  • --nbins

    Number of bins to discretize the joint and marginal PDF.

  • --sampling_prop

    Number ([0-100]) of voxels for calculating the PDF. None implies all voxels.

  • --metric

    Similarity metric for gathering mutual information.

  • --level_iters

    The number of iterations at each scale of the scale space. level_iters[0] corresponds to the coarsest scale, level_iters[-1] the finest, where n is the length of the sequence.

  • --sigmas

    Custom smoothing parameter to build the scale space (one parameter

    for each scale).

  • --factors

    Custom scale factors to build the scale space (one factor for each

    scale).

  • --progressive

    Enable/Disable the progressive registration.

  • --save_metric

    If true, quality assessment metric are saved in ‘quality_metric.txt’.

  • --static_vol_idx

    1D array representing indices of axis=-1 of a 4D static input volume. From the command line use something like 3 4 5 6. From script use something like [3, 4, 5, 6]. This input is required for 4D volumes.

  • --moving_vol_idx

    1D array representing indices of axis=-1 of a 4D moving input volume. From the command line use something like 3 4 5 6. From script use something like [3, 4, 5, 6]. This input is required for 4D volumes.

Output Options#

  • --out_dir

    Directory to save the transformed image and the affine matrix

    (default current directory).

  • --out_moved

    Name for the saved transformed image.

  • --out_affine

    Name for the saved affine matrix.

  • --out_quality

    Name of the file containing the saved quality metric.

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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