mapl2odf.m File Reference

Functions
function	mapl2odf (in maplfile, in dtifile, in uifile, in odffile, in varargin)

Function Documentation

mapl2odf()

function mapl2odf	(	in	maplfile,
		in	dtifile,
		in	uifile,
		in	odffile,
		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 Phi(u) from a MAPL model fitted with atti2mapl.

Parameters

maplfile	The MAPL coefficients, where: K = (Nmax+2)(Nmax+4)(2*Nmax+3)/24 for some even integer Nmax>=0.
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.
odffile	A string specifying the file to save the values reconstructed for the ODF at each of the MxNxP voxels within the FOV.

Note

G will match the number of entries in the directions table ui.

Parameters

varargin

Optional arguments passed as -name value pairs (e.g. -tau 70.0e-3).

Returns

- odffile: 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.
• odffile A string specifying the file to save the values reconstructed for the ODF 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).
• contrast: the exponent of r in the radial integral that defines the ODF. With contrast=2, one gets the actual jacobian of the spherical coordinates, so that the ODF is the actual probability density function in the orientation space, as described by Tristan-Vega et al., NeuroImage (2009). With contrast=0, one gets the ODF described by Tuch for Q-Balls. For any other real value strictly greater than -1, one gets different contrasts (default: 2.0, i.e. actual probabilistic ODF).

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:

mapl2odf maplfile.nii dtifile.nii uifile.nii odffile.nii -mask mask_file.nii 

Note

This is the simplest use case

See also

mapl2odf