ReconstCSDFlow

Constrained spherical deconvolution

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 bvectors files. This path may contain wildcards to use multiple bvectors 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
bvecs_tol : float, optional
Bvecs should be unit vectors. (default:0.01)
roi_center : variable int, optional
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_radius : int, optional
radius of cubic ROI in voxels (default 10)
fa_thr : float, optional
FA threshold for calculating the response function (default 0.7)
frf : variable float, optional
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 mutiplied by 10**-4 . If None the fiber response function will be computed automatically (default: None).
extract_pam_values : bool, optional
Save or not to save pam volumes as single nifti files.
sh_order : int, optional
Spherical harmonics order (default 6) used in the CSA fit.
odf_to_sh_order : int, optional
Spherical harmonics order used for peak_from_model to compress the ODF to spherical harmonics coefficients (default 8)
out_dir : string, optional
Output directory (default input file directory)
out_pam : string, optional
Name of the peaks volume to be saved (default ‘peaks.pam5’)
out_shm : string, optional
Name of the shperical harmonics volume to be saved (default ‘shm.nii.gz’)
out_peaks_dir : string, optional
Name of the peaks directions volume to be saved (default ‘peaks_dirs.nii.gz’)
out_peaks_values : string, optional
Name of the peaks values volume to be saved (default ‘peaks_values.nii.gz’)
out_peaks_indices : string, optional
Name of the peaks indices volume to be saved (default ‘peaks_indices.nii.gz’)
out_gfa : string, optional
Name of the generalise 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.