dipy_correct_biasfield#

Synopsis#

Correct bias field.

Usage#

dipy_correct_biasfield [OPTIONS] input_files

Input Parameters#

  • input_files

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

General Options#

  • --bval

    Path to the b-value file. (default: None)

  • --bvec

    Path to the b-vector file. (default: None)

  • --method

    Bias field correction method. Choose from:
    • ‘n4’: DeepN4 bias field correction. See [1] for more details.

    • ‘b0’: B0 bias field correction via normalization.

    ‘n4’ method is recommended for T1-weighted images where ‘b0’ method is recommended for diffusion-weighted images. (default: n4)

  • --threshold

    Threshold for cleaning the final correction field in DeepN4 method. (default: 0.5)

  • --use_cuda

    Use CUDA for DeepN4 bias field correction. (default: False)

  • --verbose

    Print verbose output. (default: False)

Output Options#

  • --out_dir

    Output directory. (default: current directory)

  • --out_corrected

    Name of the corrected volume to be saved. (default: biasfield_corrected.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.