dipy_fit_csd

Usage

dipy_fit_csd [-h] [–b0_threshold float] [–bvecs_tol float]

[–roi_center [int [int …]]] [–roi_radii int] [–fa_thr float] [–frf [float [float …]]] [–extract_pam_values] [–sh_order int] [–odf_to_sh_order int] [–parallel] [–nbr_processes int] [–out_dir str] [–out_pam str] [–out_shm str] [–out_peaks_dir str] [–out_peaks_values str] [–out_peaks_indices str] [–out_gfa str] input_files bvalues_files bvectors_files mask_files

Constrained spherical deconvolution

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 bvectors files. This path may contain wildcards to use multiple bvectors 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

--b0_threshold float

Threshold used to find b=0 directions

--bvecs_tol float

Bvecs should be unit vectors. (default:0.01)

–roi_center [int [int …]]

Center of ROI in data. If center is None, it is assumed that it is the center of the volume with shape data.shape[:3] (default None)

--roi_radii int

radii of cuboid ROI in voxels (default 10)

--fa_thr float

FA threshold for calculating the response function (default 0.7)

–frf [float [float …]]

Fiber response function can be for example inputed as 15 4 4 (from the command line) or [15, 4, 4] from a Python script to be converted to float and multiplied by 10**-4 . If None the fiber response function will be computed automatically (default: None).

--extract_pam_values

Save or not to save pam volumes as single nifti files.

--sh_order int

Spherical harmonics order (default 6) used in the CSA fit.

--odf_to_sh_order int

Spherical harmonics order used for peak_from_model to compress the ODF to spherical harmonics coefficients (default 8)

--parallel

Whether to use parallelization in peak-finding during the calibration procedure. Default: False

--nbr_processes int

If parallel is True, the number of subprocesses to use (default multiprocessing.cpu_count()).

Output Arguments(Optional)

--out_dir str

Output directory (default input file directory)

--out_pam str

Name of the peaks volume to be saved (default ‘peaks.pam5’)

--out_shm str

Name of the spherical harmonics volume to be saved (default ‘shm.nii.gz’)

--out_peaks_dir str

Name of the peaks directions volume to be saved (default ‘peaks_dirs.nii.gz’)

--out_peaks_values str

Name of the peaks values volume to be saved (default ‘peaks_values.nii.gz’)

--out_peaks_indices str

Name of the peaks indices volume to be saved (default ‘peaks_indices.nii.gz’)

--out_gfa str

Name of the generalized FA volume to be saved (default ‘gfa.nii.gz’)

References

1

Tournier, J.D., et al. NeuroImage 2007. Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution.

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.