This demo illustrates the basic use of the MAPL module, aimed at the analysis of multi-shell data sets.
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This demo illustrates the basic use of the MAPL module, aimed at the analysis of multi-shell data sets.
Compute the MAP-MRI coefficients
atti2mapl dwi.nii.gz dwi.bvec dwi.bval maplfile.nii dtifile.nii loptfile.nii -mask dwi_mask.nii.gz -tl 1.0e-7 -tu 1-1.0e-7 -ADC0 ADC0 -lambda lambda -tau tau -constRad 5 -maxthreads 8
function atti2mapl(in dwifile, in gifile, in bifile, in maplfile, in dtifile, in loptfile, in varargin)
Compute some standard measures
mapl2index maplfile.nii dtifile.nii -mask dwi_mask.nii.gz -ADC0 ADC0 -tau tau -type g
function mapl2index(in maplfile, in dtifile, in indexfile, in varargin)
mapl2index maplfile.nii dtifile.nii -mask dwi_mask.nii.gz -ADC0 ADC0 -tau tau -type e
mapl2index maplfile.nii dtifile.nii -mask dwi_mask.nii.gz -ADC0 ADC0 -tau tau -type o
mapl2index maplfile.nii dtifile.nii -mask dwi_mask.nii.gz -ADC0 ADC0 -tau tau -type a
mapl2index maplfile.nii dtifile.nii -mask dwi_mask.nii.gz -ADC0 ADC0 -tau tau -type p
mapl2index maplfile.nii dtifile.nii -mask dwi_mask.nii.gz -ADC0 ADC0 -tau tau -type m
mapl2index maplfile.nii dtifile.nii -mask dwi_mask.nii.gz -ADC0 ADC0 -tau tau -type q
mapl2index maplfile.nii dtifile.nii -mask dwi_mask.nii.gz -ADC0 ADC0 -tau tau -type d
mapl2index maplfile.nii dtifile.nii -mask dwi_mask.nii.gz -ADC0 ADC0 -tau tau -type u
mapl2index maplfile.nii dtifile.nii -mask dwi_mask.nii.gz -ADC0 ADC0 -tau tau -type l
DWI reconstruction
mapl2atti maplfile.nii dtifile.nii dwi.bvec dwi.bval attifile.nii -mask dwi_mask.nii.gz
function mapl2atti(in maplfile, in dtifile, in gifile, in bifile, in attifile, in varargin)
EAP reconstruction and representation
The MAP-MRI coefficients can be used to recover the Ensemble Average Propagator as well for arbitrary points in the R-space described in spherical coordinates. For the purpose of this demo, we will choose a fixed distance from the origin and compute the value of the EAP in a densely sampled sphere with this radius. This way, we will get a spherical diffusion profile with information similar (but not equivalent) to that provided by ODF fields.
mapl2eap maplfile.nii dtifile.nii uifile.nii rifile.nii eapfile.nii -mask mask_file.nii
function mapl2eap(in maplfile, in dtifile, in uifile, in rifile, in eapfile, in varargin)
Computation of Orientation Ditribution Functions (ODFs)
The values of the ODF can be analytically retrieved for any arbitrary set of unit-directions from the MAPL coefficients. We will use the same set "ui" designed in the previous section, so that it suffices to call the corresponding function (you can play with the "contrast" parameter -always use values greater than -1- and check the results; the default value of 2.0 provides the actual probabilistic ODFs):
mapl2odf maplfile.nii dtifile.nii uifile.nii odffile.nii -mask mask_file.nii
function mapl2odf(in maplfile, in dtifile, in uifile, in odffile, in varargin)