dipy_fit_dsi

Usage

dipy_fit_dsi [-h] [–qgrid_size int] [–r_start float] [–r_end float] [–r_step float] [–filter_width float] [–normalize_peaks] [–extract_pam_values] [–parallel]

[–num_processes int] [–out_dir str] [–out_pam str] [–out_shm str] [–out_peaks_dir str] [–out_peaks_values str] [–out_peaks_indices str] input_files bvalues_files bvectors_files mask_files

Diffusion Spectrum Imaging (DSI) reconstruction workflow.

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.

options:

-h, --help

show this help message and exit

--qgrid_size int

has to be an odd number. Sets the size of the q_space grid. For example if qgrid_size is 17 then the shape of the grid will be (17, 17, 17).

--r_start float

ODF is sampled radially in the PDF. This parameters shows where the sampling should start.

--r_end float

Radial endpoint of ODF sampling

--r_step float

Step size of the ODf sampling from r_start to r_end

--filter_width float

Strength of the hanning filter

--normalize_peaks

Whether to normalize the peaks

--extract_pam_values

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

--parallel

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

--num_processes int

If parallel is True, the number of subprocesses to use (default multiprocessing.cpu_count()). If < 0 the maximal number of cores minus num_processes + 1 is used (enter -1 to use as many cores as possible). 0 raises an error.

Output Arguments(Optional)

--out_dir str

Output directory. (default current directory)

--out_pam str

Name of the peaks volume to be saved.

--out_shm str

Name of the spherical harmonics volume to be saved.

--out_peaks_dir str

Name of the peaks directions volume to be saved.

--out_peaks_values str

Name of the peaks values volume to be saved.

--out_peaks_indices str

Name of the peaks indices volume 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.