dMRI-Lab 1.0
hydidsi2atti.m File Reference

Functions

function hydidsi2atti (in eapfile, in dtifile, in latticefile, in Qxfile, in Qyfile, in Qzfile, in gifile, in bifile, in attifile, in varargin)
 

Function Documentation

◆ hydidsi2atti()

function hydidsi2atti ( in eapfile,
in dtifile,
in latticefile,
in Qxfile,
in Qyfile,
in Qzfile,
in gifile,
in bifile,
in attifile,
in varargin )

Predicts the value of the attenuation signal, according to the HYDI-DSI representation retrieved with the function atti2hydidsi, for a set of desired q-space locations specified by directions gi and b-values bi

Parameters
eapfileA regular sampling of the positive, unit mass Ensemble Average Propagator estimated with atti2hydidsi. To interpret this sampling, the following five input arguments (as returned by atti2hydidsi) are mandatory:
dtifileThe estimated tensor model at each voxel.
latticefileThe radii of the lattice at each voxel. This is useful in case this parameter is automatically determined instead of fed as an input argument.
Qxfile,Qyfile,QzfileThe estimated bandwidths of the q-space signal along each dimension. They are necessary to interpret the computed eap. Besides, you must provide the q-space points where the signal representation will be evaluated. THESE POINTS ARE NOT NECESSARILY THE SAME (BUT MIGHT BE) AS THOSE USED TO CALL atti2hydidsi:
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 attenaution signal predicted at each voxel
vararginOptional arguments passed as -name value pairs (e.g. -wlsit 5).
Returns
- attifile: The attenaution signal predicted at each voxel

Mandatory Inputs:

  • eapfile: A regular sampling of the positive, unit mass Ensemble Average Propagator estimated with atti2hydidsi.
  • dtifile: The estimated tensor model at each voxel.
  • latticefile: The radii of the lattice at each voxel.
  • Qxfile, Qyfile, Qzfile: The estimated bandwidths of the q-space signal along each dimension.
  • attifile: A string specifying the file to save the attenaution signal predicted at each voxel
  • varargin: Optional arguments passed as -name value pairs (e.g. -wlsit 5).

Optional Arguments General Optional Parameters:

  • tau: the effective diffusion time of the acquisition, necessary to determine the actual support of the q-space. THE SAME USED IN atti2hydidsi!!! (default: 35e-3).
  • 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).
  • 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:

hydidsi2atti eapfile.nii dtifile.nii latticefile.nii Qxfile.nii Qyfile.nii Qzfile.nii gifile.bvec bifile.bval -mask mask_file.nii
function hydidsi2atti(in eapfile, in dtifile, in latticefile, in Qxfile, in Qyfile, in Qzfile, in gifile, in bifile, in attifile, in varargin)
Note
This is the simplest use case
See also
hydidsi2atti