dMRI-Lab 1.0
mapl2eap.m File Reference

Functions

function mapl2eap (in maplfile, in dtifile, in uifile, in rifile, in eapfile, in varargin)
 

Function Documentation

◆ mapl2eap()

function mapl2eap ( in maplfile,
in dtifile,
in uifile,
in rifile,
in eapfile,
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.

This function is used to reconstruct the values of P(R) from a MAPL model fitted with 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.
uifileA Gx3 matrix with the directions table, each row corresponding to a unit vector with the direction for which the EAP will be evaluated.
rifileA Gx1 vector with the distances to the origin corresponding to each of the G directions described above.
Note
that {ui,ri} describe a samplig of the R-space (EAP domain) in spherical coordinates.
Parameters
eapfileA string specifying the file to save the values reconstructed for the EAP at each of the MxNxP voxels within the FOV.
Note
G will match the number of entries in the directions table ui.
Parameters
vararginOptional arguments passed as -name value pairs (e.g. -tau 70.0e-3).
Returns
- eapfile: The values reconstructed for the EAP at each of the MxNxP voxels within the FOV.

Mandatory Inputs:

  • maplfile The MAPL coefficients.
  • dtifile The estimated tensor model at each voxel.
  • uifile A Gx3 matrix with the directions table, each row corresponding to a unit vector with the direction for which the EAP will be evaluated.
  • rifile A Gx1 vector with the distances to the origin corresponding to each of the G directions described above.
  • eapfile A string specifying the file to save the values reconstructed for the EAP 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: 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:

mapl2eap maplfile.nii dtifile.nii uifile.nii rifile.nii eapfile.nii -mask mask_file.nii
function mapl2eap(in maplfile, in dtifile, in uifile, in rifile, in eapfile, in varargin)
Note
This is the simplest use case
See also
mapl2eap