Sections Q: Quantities

MRI sequence quantities

The items in this group are related to the MR sequence used to acquire the signal.

Code	Standardised name	Alternative names	Notation	Description	Standardised units	Reference
DIFFUSIONLEX:XXX	Diffusion time	--	$\mathrm{\Delta }$	The time interval between bi-polar diffusion encoding gradient	ms	--
DIFFUSIONLEX:XXX	Diffusion gradient duration	--	$\delta$	The duration of the diffusion encoding gradient	ms	--
DIFFUSIONLEX:XXX	Diffusion gradient strength	--	G	The strength of the diffusion encoding gradient	mT/m	--
DIFFUSIONLEX:XXX	b-value	--	b-value	A factor that reflects the strength and timing of the gradients used to generate diffusion-weighted images	s/mm²	--
DIFFUSIONLEX:XXX	Quantity not listed	--	--	This is a custom free-text item, which can be used if a quantity of interest is not listed. Please state a literature reference and request the item to be added to the lexicon for future usage.	[variable]	--

Diffusion tensor quantities

The items of this group are quantities related to diffusion of water (rate, directionality, orientation)

Code	OSIPI name	Alternative names	Notation	Description	OSIPI units	Reference
DIFFUSIONLEX:XXX	Apparent diffusion coefficient	(Trace)/3	ADC	The diffusion coefficient of water as observed in a diffusion-weighted MRI averaged over the three principal directions (i.e. the mean of the 3 tensor eignevalues). The "Apparent" describes the fact that water in biological tissues is hindered/restricted and hence appears lower than it would in a freely diffusing environment	mm²/s	--
DIFFUSIONLEX:XXX	Diffusion Tensor	--	D	A 3 x 3 symmetric tensor matrix containing elements (Dxx, Dxy, Dxz, etc) representing observed diffusion coefficients along different directions in anisotropic media.	mm²/s	--
DIFFUSIONLEX:XXX	Radial Diffusivity	--	$D_r$	The diffusion coefficient of water as observed in a diffusion-weighted MRI in a direction perpendicular to of an axonal fibre. Often used as a marker of axonal integrity.	mm²/s	--
DIFFUSIONLEX:XXX	Axial Diffusivity	--	$D_a$	The diffusion coefficient of water as observed in a diffusion-weighted MRI along parralel to the axis of an axonal fibre.	mm²/s	--
DIFFUSIONLEX:XXX	Fractional Anistropy	--	FA	A scalar value between 0 and 1 that describes the degree of anisotropy of a diffusion process. \($FA=\frac{\sqrt{({\lambda }_1-{\lambda }_2)+({\lambda }_2-{\lambda }_3)+({\lambda }_1-{\lambda }_3)}}{\sqrt{2}{\lambda }_1+{\lambda }_2+{\lambda }_3}$\)	n.a.	--

CL, CP, and CS: the linear, planar, and spherical shape measures. Mode of anisotropy (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163395/#:~:text=In%20diffusion%20MRI%2C%20magnetic%20field,areas)%20due%20to%20anisotropic%20diffusion.) | Q.DTI1.999 | Quantity not listed | -- | -- | This is a custom free-text item, which can be used if a quantity of interest is not listed. Please state a literature reference and request the item to be added to the lexicon for future usage. | [variable] | -- |

Tractography quantities

In this group quantities used to describe tractography are listed | Code | OSIPI name| Alternative names|Notation|Description|OSIPI units|Reference| | -- | -- | -- | -- | -- | -- | -- | Euler’s method (following the eigenvector or tangent for a fixed step size) -(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163395/#:~:text=In%20diffusion%20MRI%2C%20magnetic%20field,areas)%20due%20to%20anisotropic%20diffusion.)) second order Runge-Kutta (also known as the midpoint method, where the tangent is followed for half a step, then a new tangent is calculated at the midpoint of the interval and used to take the full step), fourth order Runge-Kutta (where the weighted average of four estimated tangents to the curve is used when taking each step) FACT Some related methods attempt to introduce “inertia” when tracking through regions of planar anisotropy (likely fiber crossings).

Structural connectivity quantities

In this group quantities used to describe structural connectivity are listed | Code | OSIPI name| Alternative names|Notation|Description|OSIPI units|Reference| | -- | -- | -- | -- | -- | -- | -- |

Microstructure quantities

In this group quantities used to describe tissue microstructure are listed | Code | OSIPI name| Alternative names|Notation|Description|OSIPI units|Reference| | -- | -- | -- | -- | -- | -- | -- | (https://www.frontiersin.org/articles/10.3389/fninf.2019.00064/full) IVIM, AxCaliber, NODDI Bingham-NODDI, the spherical mean-based SMT and MC-MDI, and spherical convolution-based single- and multi-tissue CSD SANDI NEXI DOC

Exchange quantities

In this group commonly used quantities relating to exchange of water across cell membranes are described. | Code | OSIPI name| Alternative names|Notation|Description|OSIPI units|Reference| | -- | -- | -- | -- | -- | -- | -- | | Q.PH1.010.[j] | Water exchange rate | k_in, k_out | k_w,j | Equilibrium water exchange rate between two compartments (e.g. k_{w, e → b}) | 1/s | -- | | Q.EX1.001 | Apparent exchange rate | -- | AXR | The apparent exchange rate of water across a membrane observed using filtered exchange imaging. \($AXR=k_{i}n+k_{o}ut$\). | 1/min | -- | | Q.EX1.001 | Filter efficiency | -- | $\sigma$ | The efficient of a diffusion filter. The ratio of diffusivity at very short mixing time with and without the diffusion filter in FEXI experiment | a.u. | -- | | Q.PH1.004 | Permeability surface area product of membrane | Extraction flow (FE) | PS | The volume of tissue plasma that is fully cleared of indicator in a unit of time by a unit tissue volume. | mL/min/100mL | -- | | Q.PH1.005 | Extraction fraction | -- | E | The fraction of indicator particles that is extracted from plasma in one pass through the vasculature. | -- | -- | | Q.PH1.008 | Volume transfer constant | Transfer constant | K^trans | The rate of indicator particle delivery from the blood plasma to the extravascular, extracellular volume per unit of tissue volume, per unit arterial plasma concentration. | 1/min | -- | | Q.PH1.015 | Maximum oxygen extraction fraction| -- | OEF^{max | Upper biophysical limit of the proportion of oxygen that can be extracted by tissue. | -- | --| | Q.PH1.999 | Quantity not listed | -- | -- | This is a custom free-text item, which can be used if a quantity of interest is not listed. Please state a literature reference and request the item to be added to the lexicon for future usage. | [variable] | -- |}

Biophysical quantities

In this group commonly used quantities relating to the bioiphysical properties of tissue are described. | Code | OSIPI name| Alternative names|Notation|Description|OSIPI units|Reference| | -- | -- | -- | -- | -- | -- | -- | fibre density neurite density myelin density microglial density neuronal density fibre orientation orientation complexity axon diameter cell size