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dipy_fit_csd
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usage: dipy_fit_csd [-h] [--b0_threshold float] [--bvecs_tol float]
                     [--roi_center [int [int ...]]] [--roi_radius int]
                     [--fa_thr float] [--frf [float [float ...]]]
                     [--extract_pam_values] [--sh_order int]
                     [--odf_to_sh_order int] [--parallel]
                     [--nbr_processes int] [--out_dir str] [--out_pam str]
                     [--out_shm str] [--out_peaks_dir str]
                     [--out_peaks_values str] [--out_peaks_indices str]
                     [--out_gfa str]
                     input_files bvalues_files bvectors_files mask_files

Constrained spherical deconvolution

positional arguments:
  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)

optional arguments:
  -h, --help            show this help message and exit
  --b0_threshold float  Threshold used to find b=0 directions
  --bvecs_tol float     Bvecs should be unit vectors. (default:0.01)
  --roi_center [int [int ...]]
                        Center of ROI in data. If center is None, it is assumed that it is the center of the volume with shape `data.shape[:3]` (default None)
  --roi_radius int      radius of cubic ROI in voxels (default 10)
  --fa_thr float        FA threshold for calculating the response function (default 0.7)
  --frf [float [float ...]]
                        Fiber response function can be for example inputed as 15 4 4 (from the command line) or [15, 4, 4] from a Python script to be converted to float and multiplied by 10**-4 . If None the fiber response function will be computed automatically (default: None).
  --extract_pam_values  Save or not to save pam volumes as single nifti files.
  --sh_order int        Spherical harmonics order (default 6) used in the CSA fit.
  --odf_to_sh_order int
                        Spherical harmonics order used for peak_from_model to compress the ODF to spherical harmonics coefficients (default 8)
  --parallel            Whether to use parallelization in peak-finding during the calibration procedure. Default: False
  --nbr_processes int   If `parallel` is True, the number of subprocesses to use (default multiprocessing.cpu_count()).

output arguments(optional):
  --out_dir str         Output directory (default input file directory)
  --out_pam str         Name of the peaks volume to be saved (default 'peaks.pam5')
  --out_shm str         Name of the spherical harmonics volume to be saved (default 'shm.nii.gz')
  --out_peaks_dir str   Name of the peaks directions volume to be saved (default 'peaks_dirs.nii.gz')
  --out_peaks_values str
                        Name of the peaks values volume to be saved (default 'peaks_values.nii.gz')
  --out_peaks_indices str
                        Name of the peaks indices volume to be saved (default 'peaks_indices.nii.gz')
  --out_gfa str         Name of the generalized FA volume to be saved (default 'gfa.nii.gz')

References: 
.. [1] Tournier, J.D., et al. NeuroImage 2007. Robust determination of   the fibre orientation distribution in diffusion MRI: Non-negativity   constrained super-resolved spherical deconvolution.
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.