D_iso = mean{D_0(u)}.
Computes the Diffusion Anisotropy (DiA) according to a mono-exponential model for single-shell acquisitions as described in AMURA:
atti(u,b) = exp(-b*D_0(u)),
where D_0(u) is the Apparent Diffusion Coefficient (ADC) measured at b=b0 for each direction 'u' within the unit sphere. The DiA is defined in terms of the 'angle' between the true ADC and its isotropic
- Parameters
-
dwifile | A string specifying the file containing the diffusion-weighted images. |
gifile | A string specifying the file containing the gradient directions. |
bifile | A string specifying the the corresponding b-values of each entry in gi. |
- Note
- for the AMURA model to make sense, all bi should be similar, otherwise the sampling scheme is a multi-shell and a differente model (such as MiSFIT) should be used. Alternatively, bi can be a single scalar describing the acquired shell.
- Parameters
-
diafile | A string specifying the file to save the computed DiA. |
varargin | Optional arguments passed as -name value pairs. |
- Returns
- - rtopfile: The computed DiA.
Mandatory Inputs:
- dwifile: A string specifying the file containing the diffusion-weighted images.
- gifile: A string specifying the file containing the gradient directions.
- bifile: A string specifying the file containing the b-values.
- diafile: A string specifying the file to save the computed DiA.
- varargin: Optional arguments passed as -name value pairs.
Optional Arguments - General parameters:
- mask: a MxNxP array of logicals. Only those voxels where mask is true are processed, the others are filled with zeros (default: all trues).
- epsilon: to improve the contrast of the raw DiA, a gamma correction is optionally performed with the form: Use empty brackets, [], to avoid this correction and work with the raw DiA (default: 0.4).
Parameters related to SH computations:
- L: the maximim order for the SH expansions used to represent spherical functions (default: 8).
- lambda: the Laplace-Beltrami regularization parameter for the linear least squares problem of fitting SH coefficients (
- Note
- the order L used for SH is internally computed) (default: 0.001).
Sanity checks on the attenuation signal:
- tl, tu: the lower and upper thresholds, respectively, defining the range the atti will lay within, so that tl should be close to 0 and tu should be close to 1 (default: 1.0e-7, 1-1.0e-7).
Example:
atti2dia dwifile.nii gifile.bvec bifile.bval dia.nii -mask mask_file.nii
function atti2dia(in dwifile, in gifile, in bifile, in diafile, in varargin)
D_iso = mean{D_0(u)}.
- See also
- atti2dia