ReconstCSDFlow

Parameters

input_files : string

Path to the input volumes. This path may contain wildcards to process multiple inputs at once.

bvalues_files : string

Path to the bvalues files. This path may contain wildcards to use multiple bvalues files at once.

bvectors_files : 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