dipy_nifti2pam

Synopsis

Convert multiple nifti files to a single pam5 file.

Usage

dipy_nifti2pam [OPTIONS] peaks_dir_files peaks_values_files peaks_indices_files

Input Parameters

• peaks_dir_files

  Path to the input peaks directions volume. This path may contain wildcards to process multiple inputs at once.

• peaks_values_files

  Path to the input peaks values volume. This path may contain wildcards to process multiple inputs at once.

• peaks_indices_files

  Path to the input peaks indices volume. This path may contain wildcards to process multiple inputs at once.

General Options

• --shm_files

  Path to the input spherical harmonics volume. This path may contain wildcards to process multiple inputs at once.

• --gfa_files

  Path to the input generalized FA volume. This path may contain wildcards to process multiple inputs at once.

• --sphere_files

  Path to the input sphere vertices. This path may contain wildcards to process multiple inputs at once. If it is not define, default_sphere option will be used.

• --default_sphere_name

  Specify default sphere to use for spherical harmonics representation. This option can be superseded by sphere_files option. Possible options: [‘symmetric362’, ‘symmetric642’, ‘symmetric724’, ‘repulsion724’, ‘repulsion100’, ‘repulsion200’].

Output Options

• --out_dir

  Output directory (default input file directory).

• --out_pam

  Name of the peaks volume to be saved.

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.