dipy_fit_csa

Synopsis

Constant Solid Angle.

See [1] for further details about the method.

Usage

dipy_fit_csa [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 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)

General Options

• --b0_threshold

  Threshold used to find b0 volumes.

• --bvecs_tol

  Threshold used so that norm(bvec)=1.

• --sphere_name

  Sphere name on which to reconstruct the fODFs.

• --relative_peak_threshold

  Only return peaks greater than relative_peak_threshold * m where m is the largest peak.

• --min_separation_angle

  The minimum distance between directions. If two peaks are too close only the larger of the two is returned.

• --sh_order_max

  Spherical harmonics order (l) used in the CSA fit.

• --parallel

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

• --extract_pam_values

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

• --num_processes

  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 Options

• --out_dir

  Output directory. (default current directory)

• --out_pam

  Name of the peaks volume to be saved.

• --out_shm

  Name of the spherical harmonics volume to be saved.

• --out_peaks_dir

  Name of the peaks directions volume to be saved.

• --out_peaks_values

  Name of the peaks values volume to be saved.

• --out_peaks_indices

  Name of the peaks indices volume to be saved.

• --out_sphere

  Sphere vertices name to be saved.

• --out_gfa

  Name of the generalized FA volume to be saved.

• --out_b

  Name of the B Matrix to be saved.

• --out_qa

  Name of the Quantitative Anisotropy to be saved.

References

[1]

Iman Aganj, Christophe Lenglet, and Guillermo Sapiro. ODF reconstruction in q-ball imaging with solid angle consideration. In 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, volume, 1398–1401. 2009. doi:10.1109/ISBI.2009.5193327.

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.