dipy_fit_powermap

Synopsis

Workflow for generating anisotropic powermap from diffusion data.

This workflow generates an anisotropic powermap as introduced by Dell’Acqua et al.[1]. The anisotropic powermap can be used as a pseudo-T1 for tissue classification when a T1 image is not available. The anisotropic powermap is computed by extracting the anisotropic power from the spherical harmonic coefficients.

Usage

dipy_fit_powermap [OPTIONS] input_files bvalues_files bvectors_files mask_files

Input Parameters

• input_files

  Path to the input diffusion 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.

General Options

• --shm_files

  Path to the spherical harmonic coefficient files. This file may be a nifti file (shm.nii.gz) containing the SH coefficients or a pam file (*.pam5) containing the SH coefficients. (default: None)

• --sh_order_max

  Maximum spherical harmonic order. (default: 8)

• --b0_threshold

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

• --bvecs_tol

  Threshold used to check that norm(bvec) = 1 +/- bvecs_tol. (default: 0.01)

• --norm_factor

  The value to normalize the ap values. (default: 1e-05)

• --power

  The degree to which power maps are calculated. (default: 2)

• --non_negative

  Whether to rectify the resulting map to be non-negative. (default: True)

• --smooth

  The amount of smoothing to apply to the SH coefficients before computing the anisotropic powermap. This is a smoothing factor applied to the SH coefficients, which can help reduce noise in the resulting powermap. A value of 0.0 means no smoothing is applied. (default: 0.0)

• --sh_basis

  The spherical harmonic basis to use for the computation. (default: descoteaux07)

Output Options

• --out_dir

  Output directory. Default is current directory. (default: current directory)

• --out_powermap

  Name of the anisotropic powermap volume to be saved. (default: powermap.nii.gz)

References

[1]

Flavio Dell’Acqua, Luis Lacerda, Marco Catani, and Andrew Simmons. Anisotropic Power Maps: A diffusion contrast to reveal low anisotropy tissues from HARDI data. In Joint Annual Meeting ISMRM-ESMRMB 2014 SMRT 23rd Annual Meeting, volume. Milan, Italy, 2014. International Society for Magnetic Resonance in Medicine (ISMRM).

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.