dipy_fit_ivim

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.