ReconstDkiFlow

Workflow for Diffusion Kurtosis reconstruction and for computing DKI metrics. Performs a DKI reconstruction on the files by ‘globing’ input_files and saves the DTI metrics in a directory specified by out_dir.

Parameters

input_files : string
Path to the input volumes. This path may contain wildcards to process multiple inputs at once.
bvalues : string
Path to the bvalues files. This path may contain wildcards to use multiple bvalues files at once.
bvectors : string
Path to the bvalues files. This path may contain wildcards to use multiple bvalues files at once.
mask_files : string
Path to the input masks. This path may contain wildcards to use multiple masks at once. (default: No mask used)
b0_threshold : float, optional
Threshold used to find b=0 directions (default 0.0)
save_metrics : variable string, optional
List of metrics to save. Possible values: fa, ga, rgb, md, ad, rd, mode, tensor, evec, eval (default [] (all))
out_dir : string, optional
Output directory (default input file directory)
out_dt_tensor : string, optional
Name of the tensors volume to be saved (default: ‘dti_tensors.nii.gz’)
out_dk_tensor : string, optional
Name of the tensors volume to be saved (default ‘dki_tensors.nii.gz’)
out_fa : string, optional
Name of the fractional anisotropy volume to be saved (default ‘fa.nii.gz’)
out_ga : string, optional
Name of the geodesic anisotropy volume to be saved (default ‘ga.nii.gz’)
out_rgb : string, optional
Name of the color fa volume to be saved (default ‘rgb.nii.gz’)
out_md : string, optional
Name of the mean diffusivity volume to be saved (default ‘md.nii.gz’)
out_ad : string, optional
Name of the axial diffusivity volume to be saved (default ‘ad.nii.gz’)
out_rd : string, optional
Name of the radial diffusivity volume to be saved (default ‘rd.nii.gz’)
out_mode : string, optional
Name of the mode volume to be saved (default ‘mode.nii.gz’)
out_evec : string, optional
Name of the eigenvectors volume to be saved (default ‘evecs.nii.gz’)
out_eval : string, optional
Name of the eigenvalues to be saved (default ‘evals.nii.gz’)
out_mk : string, optional
Name of the mean kurtosis to be saved (default: ‘mk.nii.gz’)
out_ak : string, optional
Name of the axial kurtosis to be saved (default: ‘ak.nii.gz’)
out_rk : string, optional
Name of the radial kurtosis to be saved (default: ‘rk.nii.gz’)

References

[1]Tabesh, A., Jensen, J.H., Ardekani, B.A., Helpern, J.A., 2011. Estimation of tensors and tensor-derived measures in diffusional kurtosis imaging. Magn Reson Med. 65(3), 823-836
[2]Jensen, Jens H., Joseph A. Helpern, Anita Ramani, Hanzhang Lu, and Kyle Kaczynski. 2005. Diffusional Kurtosis Imaging: The Quantification of Non-Gaussian Water Diffusion by Means of Magnetic Resonance Imaging. MRM 53 (6):1432-40.