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dipy_fit_ivim
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usage: dipy_fit_ivim [-h] [--split_b_D int] [--split_b_S0 int]
                     [--b0_threshold int] [--save_metrics [str [str ...]]]
                     [--out_dir str] [--out_S0_predicted str]
                     [--out_perfusion_fraction str] [--out_D_star str]
                     [--out_D str]
                     input_files bvalues_files bvectors_files mask_files

Workflow for Intra-voxel Incoherent Motion reconstruction and for computing IVIM metrics. Performs a IVIM reconstruction on the files by 'globing' ``input_files`` and saves the IVIM metrics in a directory specified by ``out_dir``.

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 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. (default: No mask used)

optional arguments:
  -h, --help            show this help message and exit
  --split_b_D int       Value to split the bvals to estimate D for the two-stage process of fitting (default 400)
  --split_b_S0 int      Value to split the bvals to estimate S0 for the two-stage process of fitting. (default 200)
  --b0_threshold int    Threshold value for the b0 bval. (default 0)
  --save_metrics [str [str ...]]
                        List of metrics to save. Possible values: S0_predicted, perfusion_fraction, D_star, D (default [] (all))

output arguments(optional):
  --out_dir str         Output directory (default input file directory)
  --out_S0_predicted str
                        Name of the S0 signal estimated to be saved (default: 'S0_predicted.nii.gz')
  --out_perfusion_fraction str
                        Name of the estimated volume fractions to be saved (default 'perfusion_fraction.nii.gz')
  --out_D_star str      Name of the estimated pseudo-diffusion parameter to be saved (default 'D_star.nii.gz')
  --out_D str           Name of the estimated diffusion parameter to be saved (default 'D.nii.gz')

References: 
.. [Stejskal65] Stejskal, E. O.; Tanner, J. E. (1 January 1965).                "Spin Diffusion Measurements: Spin Echoes in the                Presence of a Time-Dependent Field Gradient". The                Journal of Chemical Physics 42 (1): 288.                Bibcode: 1965JChPh..42..288S. doi:10.1063/1.1695690.
.. [LeBihan84] Le Bihan, Denis, et al. "Separation of diffusion               and perfusion in intravoxel incoherent motion MR               imaging." Radiology 168.2 (1988): 497-505.
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.