dipy_correct_motion#

Usage#

dipy_correct_motion [OPTIONS] input_files bvalues_files bvectors_files

Input Parameters#

  • input_files

    Path to the input volumes. This path may contain wildcards to process multiple inputs at once.

  • bvalues_files

    Path to the bvalues files. This path may contain wildcards to use multiple bvalues files at once.

  • bvectors_files

    Path to the bvectors files. This path may contain wildcards to use multiple bvectors files at once.

General Options#

  • --b0_threshold

    Threshold used to find b0 volumes. (default: 50)

  • --bvecs_tol

    Threshold used to check that norm(bvec) = 1 +/- bvecs_tol b-vectors are unit vectors (default: 0.01)

  • --level_iters

    The number of iterations at each level of the Gaussian pyramid. (default: (1000, 500, 100))

  • --metric

    Similarity metric. Supported values are 'mi' for mutual information and 'cc' for local cross-correlation. (default: mi)

  • --nbins

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

  • --sampling_prop

    Proportion of voxels used to calculate the PDF for the mutual information metric. Must be in the interval (0, 1]. None uses all voxels. (default: None)

  • --radius

    Neighborhood radius for local cross-correlation. (default: 4)

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_bvecs

    Name for the saved reoriented b-vectors. (default: moved.bvec)

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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