[–bval_threshold float] [–save_metrics [str [str …]]] [–laplacian_weighting float] [–radial_order int] [–out_dir str] [–out_rtop str] [–out_lapnorm str] [–out_msd str] [–out_qiv str] [–out_rtap str] [–out_rtpp str] [–out_ng str] [–out_perng str] [–out_parng str] data_files bvals_files bvecs_files small_delta big_delta
Workflow for fitting the MAPMRI model (with optional Laplacian regularization). Generates rtop, lapnorm, msd, qiv, rtap, rtpp, non-gaussian (ng), parallel ng, perpendicular ng saved in a nifti format in input files provided by data_files and saves the nifti files to an output directory specified by out_dir.
In order for the MAPMRI workflow to work in the way intended either the Laplacian or positivity or both must be set to True.
data_files Path to the input volume. bvals_files Path to the bval files. bvecs_files Path to the bvec files. small_delta Small delta value used in generation of gradient table of provided bval and bvec. big_delta Big delta value used in generation of gradient table of provided bval and bvec.
show this help message and exit
Threshold used to find b=0 directions (default 0.0)
Regularize using the Laplacian of the MAP-MRI basis (default True)
Constrain the propagator to be positive. (default True)
Sets the b-value threshold to be used in the scale factor estimation. In order for the estimated non-Gaussianity to have meaning this value should set to a lower value (b<2000 s/mm^2) such that the scale factors are estimated on signal points that reasonably represent the spins at Gaussian diffusion. (default: 2000)
List of metrics to save. Possible values: rtop, laplacian_signal, msd, qiv, rtap, rtpp, ng, perng, parng (default:  (all))
Weighting value used in fitting the MAPMRI model in the Laplacian and both model types. (default: 0.05)
Even value used to set the order of the basis (default: 6)
Output directory (default: input file directory)
Name of the rtop to be saved
Name of the norm of Laplacian signal to be saved
Name of the msd to be saved
Name of the qiv to be saved
Name of the rtap to be saved
Name of the rtpp to be saved
Name of the Non-Gaussianity to be saved
Name of the Non-Gaussianity perpendicular to be saved
Name of the Non-Gaussianity parallel to be saved
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.