This demo illustrates the basic use of the HYDI module, aimed at the model-free analysis of multi-shell data sets.
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This demo illustrates the basic use of the HYDI module, aimed at the model-free analysis of multi-shell data sets.
Compute the EAP at a Cartesian lattice
atti2hydidsi dwi.nii dwi.bvec dwi.bval eapfile.nii dtifile.nii latticefile.nii Qxfile.nii Qyfile.nii Qzfile.nii resfile.nii laplfile.nii loptfile.nii -mask dwi_mask.nii.gz
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)
Compute the standard measures
hydidsi2index eapfile.nii latticefile.nii Qxfile.nii Qyfile.nii Qzfile.nii indefile.nii -mask dwi_mask.nii.gz -kind rtop
function hydidsi2index(in eapfile, in latticefile, in Qxfile, in Qyfile, in Qzfile, in indexfile, in varargin)
hydidsi2index eapfile.nii latticefile.nii Qxfile.nii Qyfile.nii Qzfile.nii indefile.nii -mask dwi_mask.nii.gz -kind rtpp
hydidsi2index eapfile.nii latticefile.nii Qxfile.nii Qyfile.nii Qzfile.nii indefile.nii -mask dwi_mask.nii.gz -kind rtap
hydidsi2index eapfile.nii latticefile.nii Qxfile.nii Qyfile.nii Qzfile.nii indefile.nii -mask dwi_mask.nii.gz -kind msd
hydidsi2index eapfile.nii latticefile.nii Qxfile.nii Qyfile.nii Qzfile.nii indefile.nii -mask dwi_mask.nii.gz -kind mass
Plot the results
DWI reconstruction
hydidsi2atti eapfile.nii dtifile.nii latticefile.nii Qxfile.nii Qyfile.nii Qzfile.nii dwi.bvec dwi.bval attifile.nii -mask dwi_mask.nii.gz -tau 36.5e-3
function hydidsi2atti(in eapfile, in dtifile, in latticefile, in Qxfile, in Qyfile, in Qzfile, in gifile, in bifile, in attifile, in varargin)
Compute the ODFs
A simple sanity check...
hydidsi2shodf eapfile.nii dtifile.nii Qxfile.nii Qyfile.nii Qzfile.nii latticefile.nii shfile.nii -mask dwi_mask.nii.gz -L 8 -ADC0 3.0e-3
function hydidsi2shodf(in eapfile, in dtifile, in Qxfile, in Qyfile, in Qzfile, in latticefile, in shfile, in varargin)
Represent the field of ODFs