dMRI-Lab 1.0
hydidsi2index.m File Reference

Functions

function hydidsi2index (in eapfile, in latticefile, in Qxfile, in Qyfile, in Qzfile, in indexfile, in varargin)
 

Function Documentation

◆ hydidsi2index()

function hydidsi2index ( in eapfile,
in latticefile,
in Qxfile,
in Qyfile,
in Qzfile,
in indexfile,
in varargin )

Computes scalar diffusion indices from the Ensemble Average Propagator computed by atti2hydidsi, namely RTOP, RTPP, RTAP, and MSD.

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:
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.
indexfile
Qxfile,Qyfile,QzfileThe estimated bandwidths of the q-space signal along each dimension. They are necessary to interpret the computed eap.
  • varargin: Optional arguments passed as -name value pairs (e.g. -wlsit 5).
Returns
- indexfile

Mandatory Inputs:

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

Optional Arguments General Optional Parameters:

  • kind: string, one of 'rtop', 'rtpp', 'rtap', or 'msd', describing the actual index to coompute (default: 'rtop').
  • 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:

hydidsi2index eapfile.nii latticefile.nii Qxfile.nii Qyfile.nii Qzfile.nii indexfile.nii -mask mask_file.nii
function hydidsi2index(in eapfile, in latticefile, in Qxfile, in Qyfile, in Qzfile, in indexfile, in varargin)
Note
This is the simplest use case
See also
hydidsi2index