dipy_fit_gqi#

Synopsis#

Workflow for Generalized Q-Sampling Imaging (GQI)

See [1] for further details about the method.

Usage#

dipy_fit_gqi [OPTIONS] input_files bvalues_files bvectors_files mask_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 bvalues files. This path may contain wildcards to use multiple bvalues files at once.

  • mask_files

    Path to the input masks. This path may contain wildcards to use multiple masks at once.

General Options#

  • --method

    Method used to compute the ODFs. It can be ‘standard’ or ‘gqi2’. (default: gqi2)

  • --sampling_length

    The maximum length of the sampling fibers. (default: 1.2)

  • --normalize_peaks

    If True, the peaks are normalized to 1. (default: False)

  • --sphere_name

    Sphere name on which to reconstruct the fODFs. (default: None)

  • --b0_threshold

    Threshold used to find b0 volumes. (default: 50.0)

  • --bvecs_tol

    Bvecs should be unit vectors. (default: 0.01)

  • --sh_order_max

    Maximum spherical harmonics order (l) used in the SFM fit. (default: 8)

  • --relative_peak_threshold

    Only return peaks greater than relative_peak_threshold * m where m is the largest peak. (default: 0.5)

  • --min_separation_angle

    The angle tolerance between directions. (default: 25)

  • --parallel

    Whether to use parallelization in peak-finding. (default: False)

  • --extract_pam_values

    Save or not to save pam volumes as single nifti files. (default: False)

  • --num_processes

    If parallel is True, the number of subprocesses to use (default: None)

Output Options#

  • --out_dir

    Output directory. (default: current directory)

  • --out_pam

    Name of the peaks volume to be saved. (default: peaks.pam5)

  • --out_shm

    Name of the spherical harmonics volume to be saved. (default: shm.nii.gz)

  • --out_peaks_dir

    Name of the peaks directions volume to be saved. (default: peaks_dirs.nii.gz)

  • --out_peaks_values

    Name of the peaks values volume to be saved. (default: peaks_values.nii.gz)

  • --out_peaks_indices

    Name of the peaks indices volume to be saved. (default: peaks_indices.nii.gz)

  • --out_gfa

    Name of the generalized FA volume to be saved. (default: gfa.nii.gz)

  • --out_sphere

    Sphere vertices name to be saved. (default: sphere.txt)

  • --out_b

    Name of the B Matrix to be saved. (default: B.nii.gz)

  • --out_qa

    Name of the Quantitative Anisotropy to be saved. (default: qa.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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