Introduce new models

[Lestropie]

There will always be new diffusion models that could be introduced into the specification. The intention is for the framework of the specification to be sufficiently general and extensible to be possible to utilise directly for new models, though precedents such as filename suffix & model parameter dictionary can still be set by introducing that model into the specification.

This issue is intended to serve as a list of prospective models that could be introduced into the specification, and to link to relevant Issues / PRs as necessary. The Issue will additionally be used to stash content from models that have been removed from earlier drafts of the specification.

For each model, we ideally don't want to base the specification off of one specific software implementation; the proposal needs to be compatible with all softwares providing implementations of that model. So proposal for inclusion of any of these models will need to include a search and listing of all relevant softwares.

---

• [] Constant Solid Angle (CSA)
  Manuscript

• [] Diffusion Kurtosis Imaging (DKI)
  Manuscript

• [] Diffusion Spectrum Imaging (DSI)
  Manuscript

• [] Fiber ORientation Estimated using Continuous Axially Symmetric Tensors (FORECAST)
  Manuscript

• [] Free water DTI
  (Unsure whether this should be a "separate model", or whether it should be an integral part of the DTI model, with some instances simply failing to estimate the free water component)

• [] Mean Apparent Propagator MRI
  Manuscript

• [] NODDI
  Manuscript

• [] Q-Ball Imaging (QBI)
  Original manuscript
  SH version

• [] SHORE

• [] White Matter Tract Integrity (WMTI)
  Manuscript

[Lestropie]

Old draft contents for models removed in #40

Intrinsic model parameters

Model label	Full Name	Data representation
csa	Constant Solid Angle [Aganj2010]	Spherical harmonics image
dki	Diffusion Kurtosis Imaging [Jensen2005]	Single parameter vectors image with parameter name "all" with 21 volumes in the order: Dxx, Dxy, Dxz, Dyy, Dyz, Dzz, Wxxxx, Wyyyy, Wzzzz, Wxxxy, Wxxxz, Wxyyy, Wyyyz, Wxzzz, Wyzzz, Wxxyy, Wxxzz, Wyyzz, Wxxyz, Wxyyz, Wxyzz (D is the diffusion tensor, W is the kurtosis tensor) OR 6 diffusion tensor coefficients as parameter vectors image with parameter name "tensor"; 15 kurtosis tensor coefficients as parameter vectors image with parameter name "kurtosis"; Optional: estimated b=0 intensity as scalar image with parameter name "bzero"
dsi	Diffusion Spectrum Imaging [Wedeen2008],[Paquette2017]	Probability distribution functions
forecast	Fiber ORientation Estimated using Continuous Axially Symmetric Tensors [Zuchelli2017]	Spherical harmonics image
fwdti	Free water DTI [Hoy2015]	One parameter vectors image with parameter name "tensor", containing 6 volumes in the order: Dcxx, Dcxy, Dcxz, Dcyy, Dcyz, Dczz (Dc is the free-water-corrected diffusion tensor); One scalar image with parameter name "fwf" corresponding to the estimated free water fraction
mapmri	Mean Apparent Propagator MRI [Ozarslan2013]
noddi	Neurite Orientation Dispersion and Density Imaging [Zhang2012],[Daducci2015]	Three scalar images, with parameter names equal to {"icvf", "isovf", "od"} (ICVF is the “intracellular volume fraction” (also known as NDI); ISOVF is the "isotropic component volume fraction"; OD is the “orientation dispersion” (the variance of the Watson distribution; also known as ODI)); One 3-vectors image with parameter name "direction" to provide the estimated fibre orientation
qbi	Q-Ball Imaging [Tuch2004], [Hess2006]	Single amplitudes image OR Single spherical harmonics image
shore	Simple Harmonic Oscillator-based Re[construction and Estimation [Ozarslan2008]
wmti	White Matter Tract Integrity [Fieremans2011]	One parameter vectors image with parameter name "coeffs", with 33 volumes in the order: Dxx, Dxy, Dxz, Dyy, Dyz, Dzz, Wxxxx, Wyyyy, Wzzzz, Wxxxy, Wxxxz, Wxyyy, Wyyyz, Wxzzz, Wyzzz, Wxxyy, Wxxzz, Wyyzz, Wxxyz, Wxyyz, Wxyzz, Dhxx, Dhxy, Dhxz, Dhyy, Dhyz, Dhzz, Drxx, Drxy, Drxz, Dryy, Dryz, Drzz (D is the diffusion tensor and W is the kurtosis tensor); One scalar image with parameter name "awf", representing the estimated axonal water fraction

Input model parameters

• csa :

  • SphericalHarmonicOrder : value
  • Smoothing : value
  • Basis : value

• dsi :

  • GridSize : value
  • RStart : value
  • RStep : value
  • REnd : value
  • FilterWidth : value

• forecast :

  • Sphere : value
  • DecAlg : value
  • LambdaLb : value
  • SphericalHarmonicsOrder : value

• mapmri :

  • RadialOrder : value
  • LaplacianRegularization : bool
  • LaplacianWeighting : value
  • PositivityConstraint : bool
  • Tau : value
  • ConstrainE0 : value
  • PositiveConstraint : value
  • PosGrid : value
  • PosRadius : value
  • AnisotropicScaling : bool
  • EigenvalueThreshold : value
  • PosGrid : value
  • BvalThreshold : value
  • DTIScaleEstimation : bool
  • StaticDiffusivity : value

• noddi:

  • DPar : value
  • DIso : value
  • Lambda1 : value
  • Lambda2 : value

• shore :

  • RadialOrder : value
  • Zeta : value
  • LambdaN : value
  • LambdaL : value
  • Tau : value
  • ConstrainE0 : value
  • PositiveConstraint : value
  • PosGrid : value
  • PosRadius : value

Extrinsic model parameters

<parameter> value	Description	Data representation	Possible Model sources	Unit or scale
ak	Axial kurtosis	Scalar	{ dki, wmti }	Unitless
mk	Mean kurtosis	Scalar	{ dki, wmti }	Unitless
msd	Mean-Squared Displacement	Scalar	{ mapmri, shore }
pdf	Diffusion propagator	3-vectors
rk	Radial kurtosis	Scalar	{ dki, wmti }	Unitless
rtap	Return To Axis Probability	Scalar	{ mapmri }	Probability [0.0-1.0]
rtop	Return To Origin Probability	Scalar	{ shore }	Probability [0.0-1.0]
rtpp	Return To Plane Probability	Scalar	{ mapmri }	Probability [0.0-1.0]
tort	Tortuosity of extra-cellular space	Scalar	{ dki }

Demonstrative examples

• A NODDI fit:

  my_diffusion_pipeline/
      sub-01/
          dwi/
              sub-01_parameter-icvf_noddi.nii.gz
              sub-01_parameter-isovf_noddi.nii.gz
              sub-01_parameter-od_noddi.nii.gz
              sub-01_parameter-direction_noddi.nii.gz
              sub-01_parameter-direction_noddi.json
              sub-01_noddi.json
  

  Dimensions of NIfTI image "sub-01_parameter-icvf_noddi.nii.gz": IxJxK (scalar)
  Dimensions of NIfTI image "sub-01_parameter-isovf_noddi.nii.gz": IxJxK (scalar)
  Dimensions of NIfTI image "sub-01_parameter-od_noddi.nii.gz": IxJxK (scalar)
  Dimensions of NIfTI image "sub-01_parameter-direction_noddi.nii.gz": IxJxKx3 (3-vectors)

  Contents of file "sub-01_noddi.json" (common to all intrinsic model parameter images):

  {
      "Model": "Neurite Orientation Dispersion and Density Imaging (NODDI)",
      "ModelURL": "https://www.nitrc.org/projects/noddi_toolbox"
  }

  Contents of JSON file "sub-01_parameter-direction_noddi.json":

  {
      "OrientationRepresentation": "3vector",
      "ReferenceAxes": "???"
  }