ReconstMAPMRIFlow
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.
Parameters
- data_files : string
- Path to the input volume.
- bvals_files : string
- Path to the bval files.
- bvecs_files : string
- Path to the bvec files.
- small_delta : float
- Small delta value used in generation of gradient table of provided
bval and bvec.
- big_delta : float
- Big delta value used in generation of gradient table of provided
bval and bvec.
- b0_threshold : float, optional
- Threshold used to find b=0 directions (default 0.0)
- laplacian : bool, optional
- Regularize using the Laplacian of the MAP-MRI basis (default True)
- positivity : bool, optional
- Constrain the propagator to be positive. (default True)
- bval_threshold : float, optional
- 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)
- save_metrics : variable string, optional
- List of metrics to save.
Possible values: rtop, laplacian_signal, msd, qiv, rtap, rtpp,
ng, perng, parng
(default: [] (all))
- laplacian_weighting : float, optional
- Weighting value used in fitting the MAPMRI model in the laplacian
and both model types. (default: 0.05)
- radial_order : unsigned int, optional
- Even value used to set the order of the basis
(default: 6)
- out_dir : string, optional
- Output directory (default: input file directory)
- out_rtop : string, optional
- Name of the rtop to be saved
- out_lapnorm : string, optional
- Name of the norm of laplacian signal to be saved
- out_msd : string, optional
- Name of the msd to be saved
- out_qiv : string, optional
- Name of the qiv to be saved
- out_rtap : string, optional
- Name of the rtap to be saved
- out_rtpp : string, optional
- Name of the rtpp to be saved
- out_ng : string, optional
- Name of the Non-Gaussianity to be saved
- out_perng : string, optional
- Name of the Non-Gaussianity perpendicular to be saved
- out_parng : string, optional
- Name of the Non-Gaussianity parallel to be saved