dMRI-Lab 1.0
micro2atti.m File Reference

Functions

function micro2atti (in shfile, in lparfile, in lperpfile, in ffile, in gifile, in bifile, in attifile, in varargin)
 

Function Documentation

◆ micro2atti()

function micro2atti ( in shfile,
in lparfile,
in lperpfile,
in ffile,
in gifile,
in bifile,
in attifile,
in varargin )

Reconstructs the attenuation signal E(q) (without the free water compartment) provided a microstructure model described by lpar and lperp and an ODF described by its SH coefficients. E(q) is evaluated at a multi-shell sampling with directions gi and b-values bi.

Parameters
shfileA string specifying the file containing the SH coefficients of the ODF at each voxel up to order L. Should be computed with micro2shodf.
lparfileA string specifying the file containing the parallel diffusivity at each voxel, estimated with atti2micro.
lperpfileA string specifying the file containing the traverse diffusivity at each voxel, estimated with atti2micro.
ffileA string specifying the file containing the partial volume fraction of intra-cellular water (should fulfill 0<=f<=1). If an empty array is passed, then f=1 for all voxels is assumed, so that ones(M,N,P) has the same effect as [].
gifileA string specifying the file containing the gradients table, each row must be a unit-norm direction.
bfileA string specifying the file containing the b-values describing a multi-shell sampling. This means bi should have few unique values (typically 2 to 4): length(unique(bi)) << length(bi).
attifileA string specifying the file to save the attenuation signal.
vararginOptional arguments passed as -name value pairs (e.g. -ADC0 3.0e-3).
Returns
- attifile: The attenuation signal reconstructed at the desired points.

Mandatory Inputs:

  • shfile: A string specifying the file containing the SH coefficients of the ODF at each voxel up to order L.
  • lparfile: A string specifying the file containing the parallel diffusivity at each voxel, estimated with atti2micro.
  • lperpfile: A string specifying the file containing the traverse diffusivity at each voxel, estimated with atti2micro.
  • ffile: A string specifying the file containing the partial volume fraction of intra-cellular water (should fulfill 0<=f<=1). If an empty array is passed, then f=1 for all voxels is assumed, so that ones(M,N,P) has the same effect as [].
  • gifile: AA string specifying the file containing the gradients table, each row must be a unit-norm direction.
  • bfile: A string specifying the file containing the b-values describing a multi-shell sampling. This means bi should have few unique values (typically 2 to 4): length(unique(bi)) << length(bi).
  • attifile: A string specifying the file to save the attenuation signal.
  • varargin: Optional arguments passed as -name value pairs (e.g. -ADC0 3.0e-3).

Optional Arguments:

  • mask: a MxNxP array of logicals. Only those voxels where mask is true are processed, the others are filled with zeros.
  • bth: B-values that differ from each other less than this threshold are assumed to belong to the same shell (default: 1).
  • ADC0: Estimated diffusivity of free water at body temperature (default: 3.0e-3).
  • chunksz: Voxels processed together to improve performance (default: 100).

Examples:

micro2atti shfile.nii lambdaparfile.nii lambdaperpfile.nii ffile.nii gifile.bvec bifile.bval attifile.nii -mask mask_file.nii
function micro2atti(in shfile, in lparfile, in lperpfile, in ffile, in gifile, in bifile, in attifile, in varargin)
Note
This is the simplest use case
See also
micro2atti