dMRI-Lab 1.0
hydidsi2shodf.m File Reference

Functions

function hydidsi2shodf (in eapfile, in dtifile, in Qxfile, in Qyfile, in Qzfile, in latticefile, in shfile, in varargin)
 

Function Documentation

◆ hydidsi2shodf()

function hydidsi2shodf ( in eapfile,
in dtifile,
in Qxfile,
in Qyfile,
in Qzfile,
in latticefile,
in shfile,
in varargin )

Computes the SH coefficients of the ODF from a Cartesian sampling of the Ensemble Average Propagator (EAP) as computed with atti2hydidsi. To that end, the function:

  • Generates a set of evenly spaced directions in (half) the unit sphere, twice as the number of SH coefficients to fit.
  • ANALYTICALLY computes the value of the following integral at each unit direction u: int_{q=0}^{infinity} q * (-1/4/pi^2) * Laplacian{E}(q*u) dq according to the HYDI-DSI representation (NOTE: this is done by the mex function hydidsiQIntegrals_).
  • NUMERICALLY fits the first SH coefficients up to order L to the previously sampled signal.
  • ANALYTICALLY computes the Funk-Radon transform of the signal by multiplying its SH coefficients by the FRT eigenvalues.
    Parameters
    eapfileA regular sampling of the positive, unit mass Ensemble Average Propagator estimated with atti2hydidsi.
    dtifileThe diffusion tensor estimation at each voxel
    Qxfile,Qyfile,QzfileThe estimated bandwidths of the q-space signal along each dimension. They are necessary to interpret the computed eap.
    shfileA string specifying the file to save the SH coefficients of the ODF at each imaged voxel. (As passed to atti2hydidsi):
    latticefileThe radii of the lattice at each voxel. This is useful in case this parameter is automatically determined instead of fed as an input argument.
    vararginOptional arguments passed as -name value pairs (e.g. -wlsit 5).
    Returns
    - shfile: The SH coefficients of the ODF at each imaged voxel.
    Mandatory Inputs:

eapfile: A regular sampling of the positive, unit mass Ensemble Average Propagator estimated with atti2hydidsi.

  • dtifile: The diffusion tensor estimation at each voxel
  • Qxfile, Qyfile, Qzfile: The estimated bandwidths of the q-space signal along each dimension.
  • shfile: A string specifying the file to save the SH coefficients of the ODF at each imaged voxel.
  • latticefile: The radii of the lattice at each voxel. This is useful in case this parameter is automatically determined instead of fed as an input argument.
  • varargin: Optional arguments passed as -name value pairs (e.g. -wlsit 5).

Optional Arguments General Optional Parameters:

  • L: an even integer with the maximum order of the SH to be used (default: 8).
  • ADC0: estimated diffusivity of free water at body temperature (Diso). Should use the same as in atti2micro (default: 3.0e-3). rescale: whether (true) or not (false) re-normalize the final SH coefficients so that the DC component exactly equals 1/sqrt(4*pi) (so that the ODF exactly integrates to 1) (default: true).
  • mask: a MxNxP array of logicals. Only those voxels where mask is true are processed, the others are filled with isotropic ODFs (default: all trues).
  • maxthreads: (only for POSIX systems) the maximum number of threads used by mex functions (default: automatically determined).

Example:

hydidsi2shodf eapfile.nii dtifile.nii Qxfile.nii Qyfile.nii Qzfile.nii latticefile.nii shfile.nii -mask mask_file.nii
function hydidsi2shodf(in eapfile, in dtifile, in Qxfile, in Qyfile, in Qzfile, in latticefile, in shfile, in varargin)
Note
This is the simplest use case
See also
hydidsi2shodf