dMRI-Lab 1.0
mapl2atti.m File Reference

Functions

function mapl2atti (in maplfile, in dtifile, in gifile, in bifile, in attifile, in varargin)
 

Function Documentation

◆ mapl2atti()

function mapl2atti ( in maplfile,
in dtifile,
in gifile,
in bifile,
in attifile,
in varargin )

Given the coefficients of the MAP-MRI expansion, reconstruct the corresponding attenuation signal, according to the model described by Ozarslan et al:

  Ozarslan E, Koay CG, Shepherd TM, Komlosh ME, Irfanoglu MO, Pierpaoli C, Basser PJ. "Mean apparent propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure". 
  Neuroimage. 2013 Sep; 78:16-32.

This function does the converse job of atti2mapl.

Parameters
maplfileThe MAPL coefficients, where: K = (Nmax+2)(Nmax+4)(2*Nmax+3)/24 for some even integer Nmax>=0.
dtifileThe estimated tensor model at each voxel.
gifileA string specifying the file containing the gradient directions.
bifileA string specifying the file containing the b-values.
attifileA string specifying the file to save the values reconstructed for the attenuations signal at each of the MxNxP voxels within the FOV.
vararginOptional arguments passed as -name value pairs (e.g. -wlsit 5).
Returns
- attifile: The values reconstructed for the attenuations signal at each of the MxNxP voxels within the FOV.

Mandatory Inputs:

  • maplfile The MAPL coefficients.
  • dtifile The estimated tensor model at each voxel.
  • gifile A string specifying the file containing the gradient directions.
  • bifile A string specifying the file containing the b-values.
  • attifile A string specifying the file to save the values reconstructed for the attenuations signal at each of the MxNxP voxels within the FOV.
  • varargin: Optional arguments passed as -name value pairs.

Optional Arguments General Optional Parameters:

  • ADC0: estimated diffusivity of free water at body temperature. It is used to determine the lower and upper bounds of the eigenvalues of the dti and perform sanity checks (default: 3.0e-3).

Other General Options:

  • maxthreads: the algorithm is run as a multi-threaded mex. This is the maximum allowed number of threads, which can indeed be reduced if it exceeds the number of logical cores (default: the number of logical cores in the machine).
  • mask: a MxNxP array of logicals. Only those voxels where mask is true are processed, the others are filled with zeros (default: all trues).

Example:

mapl2atti maplfile.nii dtifile.nii gifile.bvec bifile.bval attifile.nii -mask mask_file.nii
function mapl2atti(in maplfile, in dtifile, in gifile, in bifile, in attifile, in varargin)
Note
This is the simplest use case
See also
mapl2atti