dMRI-Lab 1.0
mapl2index.m File Reference

Functions

function mapl2index (in maplfile, in dtifile, in indexfile, in varargin)
 

Function Documentation

◆ mapl2index()

function mapl2index ( in maplfile,
in dtifile,
in indexfile,
in varargin )

Given the coefficients of the MAP-MRI expansion, compute some related scalar indices, according to the model described by

  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.
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.
indexfileA string specifying the file to save the values of the desired scalar index at each of the MxNxP voxels within the FOV.
vararginOptional arguments passed as -name value pairs (e.g. -wlsit 5).
Returns
- indexfile: The values of the desired scalar index at each of the MxNxP voxels within the FOV.

Mandatory Inputs:

  • maplfile The MAPL coefficients.
  • dtifile The estimated tensor model at each voxel.
  • indexfile A string specifying the file to save the values of the desired scalar index 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).
  • tau: the effective diffusion time of the acquisition, in seconds, necessary to compute the indices (default: 35e-3). type: the particular index to be computed, a single char, one of:
    • 'o' for RTOP
    • 'a' for RTAP
    • 'p' for RTPP
    • 'd' for PA_DTI
    • 'g' for NG
    • 'e' for E(0)
    • 'm' for MSD
    • 'q' for QIV
    • 'l' for the energy of the Laplacian of E(q)
    • 'u' for the u0 describing the "most similar isotropic propagator" as in eq. (48) of Ozarslan's paper (default: 'o');

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:

mapl2index maplfile.nii dtifile.nii index.nii -mask mask_file.nii
function mapl2index(in maplfile, in dtifile, in indexfile, in varargin)
Note
This is the simplest use case
See also
mapl2index