dMRI-Lab 1.0
atti2apa.m File Reference

Functions

function atti2apa (in dwifile, in gifile, in bifile, in pafile, in varargin)
 

Function Documentation

◆ atti2apa()

function atti2apa ( in dwifile,
in gifile,
in bifile,
in pafile,
in varargin )

Computes the (apparent) Propagator Anisotropy (PA) according to a mono-exponential model for single-shell acquisitions as described in AMURA:

                               atti(u,b) = exp(-b*D_0(u)),

where D_0(u) is the Apparent Diffusion Coefficient measured at b=b0 for each direction 'u' within the unit sphere. The PA is defined in terms of the 'angle' between the true attenuation signal and its isotropic counterpart, which in AMURA is modeled as that with a homogeneous Diffusion Coefficente: D_iso = mean{D_0(u)}.

Parameters
dwifileA string specifying the file containing the diffusion-weighted images.
gifileA string specifying the file containing the gradient directions.
bifileA string specifying the the corresponding b-values of each entry in gi.
Note
for the AMURA model to make sense, all bi should be similar, otherwise the sampling scheme is a multi-shell and a differente model (such as MiSFIT) should be used. Alternatively, bi can be a single scalar describing the acquired shell.
Parameters
pafileA string specifying the file to save the computed PA.
vararginOptional arguments passed as -name value pairs.
Returns
- mufile: The computed PA.

Mandatory Inputs:

  • dwifile: A string specifying the file containing the diffusion-weighted images.
  • gifile: A string specifying the file containing the gradient directions.
  • bifile: A string specifying the file containing the b-values.
  • pafile A string specifying the file to save the computed PA.
  • varargin: Optional arguments passed as -name value pairs.

Optional Arguments - General parameters:

  • mask: a MxNxP array of logicals. Only those voxels where mask is true are processed, the others are filled with zeros (default: all trues).
  • epsilon: to improve the contrast of the raw PA, a gamma correction is usually performed with the form:
                              pa = pa0^(3*epsilon)/(1-3*pa0^epsilon+3*pa0^(2*epsilon));
    

Use empty brackets, [], to avoid this correction and work with the raw PA (default: 0.4).

Parameters related to SH computations:

  • L: an even integer with the maximum order of the SH to be used (default: 8).
  • lambda: the Laplace-Beltrami regularization parameter for the linear least squares problem of fitting SH coefficients (
    Note
    the order L used for SH is internally computed) (default 0.001).
    Sanity checks on the attenuation signal:
  • tl, tu: the lower and upper thresholds, respectively, defining the range the atti will lay within, so that tl should be close to 0 and tu should be close to 1 (default: 1.0e-7, 1-1.0e-7).

Example:

atti2apa dwifile.nii gifile.bvec bifile.bval pafile.nii -mask mask_file.nii
function atti2apa(in dwifile, in gifile, in bifile, in pafile, in varargin)
See also
atti2apa