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

• --method

  Method to use for the reconstruction. Can be one of the following: ‘csa’ for Constant Solid Angle reconstruction ‘qball’ for Q-Ball reconstruction ‘opdt’ for Orientation Probability Density Transform reconstruction (default: csa)

• --smooth

  The regularization parameter of the model. (default: 0.006)

• --min_signal

  During fitting, all signal values less than min_signal are clipped to min_signal. This is done primarily to avoid values less than or equal to zero when taking logs. (default: 1e-05)

• --assume_normed

  If True, clipping and normalization of the data with respect to the mean B0 signal are skipped during mode fitting. This is an advanced feature and should be used with care. (default: False)

• --b0_threshold

  Threshold used to find b0 volumes. (default: 50.0)

• --bvecs_tol

  Threshold used so that norm(bvec)=1. (default: 0.01)

• --sphere_name

  Sphere name on which to reconstruct the fODFs. (default: None)

• --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 minimum distance between directions. If two peaks are too close only the larger of the two is returned. (default: 25)

• --sh_order_max

  Spherical harmonics order (l) used in the CSA fit. (default: 8)

• --parallel

  Whether to use parallelization in peak-finding during the calibration procedure. (default: False)

• --extract_pam_values

  Whether 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 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. (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_sphere

  Sphere vertices name to be saved. (default: sphere.txt)

• --out_gfa

  Name of the generalized FA volume to be saved. (default: gfa.nii.gz)

• --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

[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.