Computes the (apparent) Return To Axis Probability 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 measured at b=b0 for each direction 'u' within the unit sphere.
- 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
-
rtapfile | A string specifying the file to save the computed RTAP. |
varargin | Optional arguments passed as -name value pairs. |
- Returns
- - rtapfile: The computed RTAP.
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.
- rtapfile: A string specifying the file to save the computed RTAP.
- 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).
Parameters related to SH computations:
- tensor: wether (true) or not (false) using a tensor model instead of a model-free ODF estimation to compute the maximum diffusion direction. Using a tensor estimation is usually more robust (default: true).
- 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).
Advanced parameters:
- tau: 1x1, the effective diffusion time of the dMRI sequence in miliseconds (default: 70.0e-3).
- chunksz: the evaluation of SH at desired directions is done by repeatedly calling GenerateSHMatrix. This is done chunk-by-chunk for efficiency (default: 256).
- clean: 1x1 double in the range [0,100]. This is a simple outlier rejection parameter to avoid out-of-range values: 0 means no outlier rejection is applied; >0 means outlier rejection is applied, the closer to 100 the more agressive (default: 50).
Example:
atti2artap dwifile.nii gifile.bvec bifile.bval rtapfile.nii -mask mask_file.nii
function atti2artap(in dwifile, in gifile, in bifile, in rtapfile, in varargin)
- See also
- atti2artap