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_file 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_file : string
Path to the input volume.
data_bvals : string
Path to the bval files.
data_bvecs : 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
Regularize using the Laplacian of the MAP-MRI basis (default True)
positivity : bool
Constrain the propagator to be positive. (default True)
bval_threshold : float
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 : list of strings
List of metrics to save. Possible values: rtop, laplacian_signal, msd, qiv, rtap, rtpp, ng, perng, parng (default: [] (all))
laplacian_weighting : float
Weighting value used in fitting the MAPMRI model in the laplacian and both model types. (default: 0.05)
radial_order : unsigned int
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