dipy_fit_mapmri

Usage

dipy_fit_mapmri [-h] [–b0_threshold float] [–laplacian] [–positivity] [–bval_threshold float] [–save_metrics [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.

Positional Arguments

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.

options:

-h, --help

show this help message and exit

--b0_threshold float

Threshold used to find b0 volumes.

--laplacian

Regularize using the Laplacian of the MAP-MRI basis.

--positivity

Constrain the propagator to be positive.

--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.

–save_metrics [str …]

List of metrics to save. Possible values: rtop, laplacian_signal, msd, qiv, rtap, rtpp, ng, perng, parng

--laplacian_weighting float

Weighting value used in fitting the MAPMRI model in the Laplacian and both model types.

--radial_order int

Even value used to set the order of the basis.

Output Arguments(Optional)

--out_dir str

Output directory. (default: current directory)

--out_rtop str

Name of the rtop to be saved.

--out_lapnorm str

Name of the norm of Laplacian signal to be saved.

--out_msd str

Name of the msd to be saved.

--out_qiv str

Name of the qiv to be saved.

--out_rtap str

Name of the rtap to be saved.

--out_rtpp str

Name of the rtpp to be saved.

--out_ng str

Name of the Non-Gaussianity to be saved.

--out_perng str

Name of the Non-Gaussianity perpendicular to be saved.

--out_parng str

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.