dipy_fit_qball#

Synopsis#

Constant Solid Angle.

See [1] for further details about the method.

Usage#

dipy_fit_qball [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 bvectors files. This path may contain wildcards to use multiple bvectors files at once.

  • mask_files

    Path to the input masks. This path may contain wildcards to use multiple masks at once. (default: No mask used)

General Options#

  • --method

    Method to use for the reconstruction. Can be one of the following: ‘csa’ for Constant Solid Angle reconstruction ‘qball’ for Q-Ball reconstruction ‘opdt’ for Orientation Probability Density Transform reconstruction (default: csa)

  • --smooth

    The regularization parameter of the model. (default: 0.006)

  • --min_signal

    During fitting, all signal values less than min_signal are clipped to min_signal. This is done primarily to avoid values less than or equal to zero when taking logs. (default: 1e-05)

  • --assume_normed

    If True, clipping and normalization of the data with respect to the mean B0 signal are skipped during mode fitting. This is an advanced feature and should be used with care. (default: False)

  • --b0_threshold

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

  • --bvecs_tol

    Threshold used so that norm(bvec)=1. (default: 0.01)

  • --sphere_name

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

  • --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 minimum distance between directions. If two peaks are too close only the larger of the two is returned. (default: 25)

  • --sh_order_max

    Spherical harmonics order (l) used in the CSA fit. (default: 8)

  • --parallel

    Whether to use parallelization in peak-finding during the calibration procedure. (default: False)

  • --extract_pam_values

    Whether 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 multiprocessing.cpu_count()). If < 0 the maximal number of cores minus num_processes + 1 is used (enter -1 to use as many cores as possible). 0 raises an error. (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_sphere

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

  • --out_gfa

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

  • --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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