Tissue Properties in pyAFQ#
This document lists some of the more common tissue property parameters available in pyAFQ, though not all of them. They are organized by the diffusion model they are derived from. Custom tissue properties can be imported, see How to add custom tissue properties from another pipeline. If there is a tissue property in DIPY not in pyAFQ, you can add it in AFQ/tasks/data.py, or post an issue.
DTI Model Parameters#
Parameter |
Description |
|---|---|
dti_fa (Fractional Anisotropy) |
Measures the directional dependence of water diffusion (0 = isotropic, 1 = fully anisotropic) |
dti_md (Mean Diffusivity) |
Average of the three eigenvalues, representing overall diffusion magnitude |
dti_ad (Axial Diffusivity) |
Largest eigenvalue (λ₁), representing diffusion parallel to fibers |
dti_rd (Radial Diffusivity) |
Average of the second and third eigenvalues (λ₂+λ₃)/2, representing diffusion perpendicular to fibers |
dti_ga (Geodesic Anisotropy) |
Similar to FA but based on Riemannian geometry |
dti_cfa (Color FA) |
FA map where colors represent principal diffusion direction (RGB = XYZ) |
dti_pdd (Principal Diffusion Direction) |
The dominant direction of diffusion (first eigenvector) |
dti_lt0 (Dxx) |
First element of diffusion tensor (left-right diffusion) |
dti_lt1 (Dyy) |
Second element of diffusion tensor (posterior-anterior diffusion) |
dti_lt2 (Dzz) |
Third element of diffusion tensor (inferior-superior diffusion) |
dti_lt3 (Dxy) |
Fourth element of diffusion tensor (xy plane relationship) |
dti_lt4 (Dxz) |
Fifth element of diffusion tensor (xz plane relationship) |
dti_lt5 (Dyz) |
Sixth element of diffusion tensor (yz plane relationship) |
Free-water DTI (FWDTI) Parameters#
Parameter |
Description |
|---|---|
fwdti_fa (Fractional Anisotropy) |
FA of the tissue compartment (excluding free water) |
fwdti_md (Mean Diffusivity) |
MD of the tissue compartment (excluding free water) |
fwdti_fwf (Free Water Fraction) |
Fraction of the signal attributed to free water diffusion |
DKI Model Parameters#
Parameter |
Description |
|---|---|
dki_fa (Fractional Anisotropy) |
FA derived from DKI tensor |
dki_md (Mean Diffusivity) |
MD derived from DKI tensor |
dki_mk (Mean Kurtosis) |
Average kurtosis over all directions |
dki_kfa (Kurtosis FA) |
Fractional anisotropy of the kurtosis tensor |
dki_ga (Geodesic Anisotropy) |
Geodesic anisotropy derived from DKI |
dki_rd (Radial Diffusivity) |
Radial diffusivity derived from DKI |
dki_ad (Axial Diffusivity) |
Axial diffusivity derived from DKI |
dki_rk (Radial Kurtosis) |
Kurtosis perpendicular to the main fiber direction |
dki_ak (Axial Kurtosis) |
Kurtosis parallel to the main fiber direction |
dki_awf (Axonal Water Fraction) |
Estimated fraction of water in the axonal compartment |
dki_kt0-dki_kt14 |
15 independent elements of the kurtosis tensor |
dki_lt0-dki_lt5 |
6 independent elements of the diffusion tensor |
Mean Signal DKI (MSDKI) Parameters#
Parameter |
Description |
|---|---|
msdki_msd (Mean Signal Diffusivity) |
Diffusivity derived from mean signal approach |
msdki_msk (Mean Signal Kurtosis) |
Kurtosis derived from mean signal approach |
CSD Model Parameters#
Parameter |
Description |
|---|---|
csd_apm (Anisotropic Power Map) |
Map of fiber orientation distribution function (fODF) power |
csd_ai (Anisotropic Index) |
Index of anisotropy derived from fODF |
GQ (Generalized Q-Sampling) Parameters#
Parameter |
Description |
|---|---|
gq_apm (Anisotropic Power Map) |
Power map from GQ sampling |
gq_ai (Anisotropic Index) |
Anisotropy index from GQ sampling |
gq_aso (Anisotropic Component) |
Anisotropic part of the ODF |
gq_iso (Isotropic Component) |
Isotropic part of the ODF |
OPDT (Orientation Probability Density Transform) Parameters#
Parameter |
Description |
|---|---|
opdt_apm (Anisotropic Power Map) |
Power map from OPDT |
opdt_ai (Anisotropic Index) |
Anisotropy index from OPDT |
opdt_gfa (Generalized FA) |
Generalized fractional anisotropy |