[–roi_center [int [int …]]] [–roi_radius 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
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)
show this help message and exit
Threshold used to find b=0 directions
Bvecs should be unit vectors. (default:0.01)
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)
radius of cubic ROI in voxels (default 10)
FA threshold for calculating the response function (default 0.7)
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).
Save or not to save pam volumes as single nifti files.
Spherical harmonics order (default 6) used in the CSA fit.
Spherical harmonics order used for peak_from_model to compress the ODF to spherical harmonics coefficients (default 8)
Whether to use parallelization in peak-finding during the calibration procedure. Default: False
If parallel is True, the number of subprocesses to use (default multiprocessing.cpu_count()).
Output directory (default input file directory)
Name of the peaks volume to be saved (default ‘peaks.pam5’)
Name of the spherical harmonics volume to be saved (default ‘shm.nii.gz’)
Name of the peaks directions volume to be saved (default ‘peaks_dirs.nii.gz’)
Name of the peaks values volume to be saved (default ‘peaks_values.nii.gz’)
Name of the peaks indices volume to be saved (default ‘peaks_indices.nii.gz’)
Name of the generalized FA volume to be saved (default ‘gfa.nii.gz’)
References: ..  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.