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. (default: affine)

• --nbins

  Number of bins to discretize the joint and marginal PDF. (default: 32)

• --sampling_prop

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

• --metric

  Similarity metric for gathering mutual information. (default: mi)

• --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. (default: (10000, 1000, 100))

• --sigmas

  Custom smoothing parameter to build the scale space (one parameter for each scale). (default: (3.0, 1.0, 0.0))

• --factors

  Custom scale factors to build the scale space (one factor for each scale). (default: (4, 2, 1))

• --progressive

  Enable/Disable the progressive registration. (default: True)

• --save_metric

  If true, quality assessment metric are saved in ‘quality_metric.txt’. (default: False)

• --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. (default: None)

• --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. (default: None)

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. (default: moved.nii.gz)

• --out_affine

  Name for the saved affine matrix. (default: affine.txt)

• --out_quality

  Name of the file containing the saved quality metric. (default: quality_metric.txt)

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.