dMRI-Lab 1.0
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Functions | |
function | atti2hydidsi (in dwifile, in gifile, in bifile, in eapfile, in dtifile, in latticefile, in Qxfile, in Qyfile, in Qzfile, in resfile, in laplfile, in loptfile, in varargin) |
function atti2hydidsi | ( | in | dwifile, |
in | gifile, | ||
in | bifile, | ||
in | eapfile, | ||
in | dtifile, | ||
in | latticefile, | ||
in | Qxfile, | ||
in | Qyfile, | ||
in | Qzfile, | ||
in | resfile, | ||
in | laplfile, | ||
in | loptfile, | ||
in | varargin ) |
Computes the Ensemble Average Propagator (eap) at a regular Cartesian lattice from a set of scattered q-space measurements (atti) using Hybrid Diffusion Imaging without q-space re-gridding. To that end, the R-space is first aligned with the eigenvectors of a tensor model (the z axis aligns with the maximum diffusion direction) and an appropriate lattice is designed so that the whole extent of the EAP is covered according to the computed eigenvalues. From this estimate, the q-space is cropped to avoid aliasing, meaning that some q-space samples might be discarded for some voxels. Accordingly, the tensor model estimated is necessary to interpret the computed eap (and it is returned by this function). The eap is estimated by solving a quadratic programming problem that involves the encoding matrix that relates q-space measurments to R-space Fourier coefficients (i.e. EAP samples).
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. |
eapfile | A string specifying the file to save the unrolled Cartesian samples of the eap. If the lattice has radii Nx x Ny x Nz, a grand total of Nl=(2*Nx+1)(2*Ny+1)*(2*Nz+1) samples would be needed. However, due to the antipodal symmetry of the eap we need just K=(Nl+1)/2. The samples are arranged as follows:
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dtifile | A string specifying the file to save the estimated tensor model at each voxel. |
latticefile | A string specifying the file to save the 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,Qzfile | Strings specifying the files to save estimated bandwidths of the q-space signal along each dimension. They are necessary to interpret the computed eap. |
resfile | A string specifying the file to save the residual of the QP problem at each voxel. |
laplfile | A string specifying the file to save the energy of the Laplacian at each voxel. |
loptfile | A string specifying the file to save the optimal value of lambda computed at each voxel (makes sense only if Generalized Cross Validation is used to optimally set the value of lambda at each voxel, see below). |
varargin | Optional arguments passed as -name value pairs (e.g. -wlsit 5). |
Mandatory Inputs:
Optional Arguments General Optional Parameters:
Other General Options:
Example: