dipy_fit_sdt#
Synopsis#
Workflow for Spherical Deconvolution Transform (SDT)
See [1] for further details about the method.
Usage#
dipy_fit_sdt [OPTIONS] input_files bvalues_files bvectors_files mask_files
Input Parameters#
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 bvalues files. This path may contain wildcards to use multiple bvalues 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)
General Options#
--ratio
Ratio of the smallest to largest eigenvalue used in the response function estimation. If None, the response function will be estimated automatically. (default: None)
--roi_center
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
radii of cuboid ROI in voxels. (default: 10)
--fa_thr
FA threshold to compute the WM response function. (default: 0.7)
--sphere_name
Sphere name on which to reconstruct the fODFs. (default: None)
--sh_order_max
Maximum spherical harmonics order (l) used in the SDT fit. (default: 8)
--lambda_
Regularization parameter. (default: 1.0)
--tau
Diffusion time. (default: 0.1)
--b0_threshold
Threshold used to find b0 volumes. (default: 50.0)
--bvecs_tol
Bvecs should be unit vectors. (default: 0.01)
--relative_peak_threshold
Only return peaks greater than
relative_peak_threshold * m
where m is the largest peak. (default: 0.5)--min_separation_angle
The angle tolerance between directions. (default: 25)
--parallel
Whether to use parallelization in peak-finding. (default: False)
--extract_pam_values
Save or not to save pam volumes as single nifti files. (default: False)
--num_processes
If parallel is True, the number of subprocesses to use (default: None)
Output Options#
--out_dir
Output directory. (default: current directory)
--out_pam
Name of the peaks volume to be saved. (default: peaks.pam5)
--out_shm
Name of the spherical harmonics volume to be saved. (default: shm.nii.gz)
--out_peaks_dir
Name of the peaks directions volume to be saved. (default: peaks_dirs.nii.gz)
--out_peaks_values
Name of the peaks values volume to be saved. (default: peaks_values.nii.gz)
--out_peaks_indices
Name of the peaks indices volume to be saved. (default: peaks_indices.nii.gz)
--out_gfa
Name of the generalized FA volume to be saved. (default: gfa.nii.gz)
--out_sphere
Sphere vertices name to be saved. (default: sphere.txt)
--out_b
Name of the B Matrix to be saved. (default: B.nii.gz)
--out_qa
Name of the Quantitative Anisotropy to be saved. (default: qa.nii.gz)
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.