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Diffusion derivatives: Formatting
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- Fix use of superscripts in "Scalar maps" table.
- For "Units" field in tractography JSON file, list possible values in the same format as that used elsewhere in the document.
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@Lestropie
Lestropie committed Apr 24, 2019
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64 changes: 32 additions & 32 deletions src/05-derivatives/05-diffusion-derivatives.md
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Expand Up @@ -268,28 +268,28 @@ fields for the maps.

These maps are saved 3D NIfTI files (x,y,z). Some examples of such maps are as follows:

| `<parameter>` value | Description | Possible Model sources | Unit or scale |
| ------------------- | ------------------------------------------------------------------ | -----------------------------------------------------------------------------------| ----------------------- |
| FA | Fractional Anisotropy | DTI, DKI, WMTI (D, Dh, Dr) | Unitless \[0-1\] |
| MD | Mean diffusivity (also called apparent diffusion coefficient, ADC) | DTI, DKI, WMTI (D, Dh, Dr) | microns^2/ms ^1 |
| AD | Axial Diffusivity (also called parallel diffusivity) | DTI, DKI, WMTI (D, Dh, Dr) | microns^2/ms ^1 |
| RD | Radial Diffusivity (also called perpendicular diffusivity) | DTI, DKI, WMTI (D, Dh, Dr) | microns^2/ms ^1 |
| MODE | Mode of the tensor | DTI, DKI, WMTI (D, Dh, Dr) | |
| LINEARITY | Tensor linearity (Westin 1997) | DTI, DKI, WMTI (D, Dh, Dr) | |
| PLANARITY | Tensor planarity (Westin 1997) | DTI, DKI, WMTI (D, Dh, Dr) | |
| SPHERICITY | Tensor sphericity (Westin 1997) | DTI, DKI, WMTI (D, Dh, Dr) | |
| MK | Mean kurtosis | DKI, WMTI | Unitless |
| RK | Radial kurtosis | DKI, WMTI | Unitless |
| AK | Axial kurtosis | DKI, WMTI | Unitless |
| GFA | Generalized Fractional Anisotropy | CSA, CSD, SHORE, MAPMRI, Forecast (or any model that can be represented as an ODF) | Proportion \[0-1\] |
| FSUM | Sum of partial volume fractions of stick components | Ball-and-stick(s) | Volume fraction \[0-1\] |
| Fi | Volume fraction of stick i | Ball-and-stick(s) | Volume fraction \[0-1\] |
| D | Diffusivity | Ball-and-stick(s) | microns^2/ms ^1 |
| DSTD | Standard deviation of diffusivity | Ball-and-stick(s) | microns^2/ms |
| RTPP | Return to the plane probability | MAPMRI | Probability \[0-1\] |
| RTAP | Return to axis probability | MAPMRI | Probability \[0-1\] |

^1 For example, for free water in body temperature, the diffusivity in units of microns^2/ms should be approximately 3.0.
| `<parameter>` value | Description | Possible Model sources | Unit or scale |
| ------------------- | ------------------------------------------------------------------ | -----------------------------------------------------------------------------------| ----------------------------------- |
| FA | Fractional Anisotropy | DTI, DKI, WMTI (D, Dh, Dr) | Unitless \[0-1\] |
| MD | Mean diffusivity (also called apparent diffusion coefficient, ADC) | DTI, DKI, WMTI (D, Dh, Dr) | microns<sup>2<\sup>/ms <sup>1<\sup> |
| AD | Axial Diffusivity (also called parallel diffusivity) | DTI, DKI, WMTI (D, Dh, Dr) | microns<sup>2<\sup>/ms <sup>1<\sup> |
| RD | Radial Diffusivity (also called perpendicular diffusivity) | DTI, DKI, WMTI (D, Dh, Dr) | microns<sup>2<\sup>/ms <sup>1<\sup> |
| MODE | Mode of the tensor | DTI, DKI, WMTI (D, Dh, Dr) | |
| LINEARITY | Tensor linearity (Westin 1997) | DTI, DKI, WMTI (D, Dh, Dr) | |
| PLANARITY | Tensor planarity (Westin 1997) | DTI, DKI, WMTI (D, Dh, Dr) | |
| SPHERICITY | Tensor sphericity (Westin 1997) | DTI, DKI, WMTI (D, Dh, Dr) | |
| MK | Mean kurtosis | DKI, WMTI | Unitless |
| RK | Radial kurtosis | DKI, WMTI | Unitless |
| AK | Axial kurtosis | DKI, WMTI | Unitless |
| GFA | Generalized Fractional Anisotropy | CSA, CSD, SHORE, MAPMRI, Forecast (or any model that can be represented as an ODF) | Proportion \[0-1\] |
| FSUM | Sum of partial volume fractions of stick components | Ball-and-stick(s) | Volume fraction \[0-1\] |
| Fi | Volume fraction of stick i | Ball-and-stick(s) | Volume fraction \[0-1\] |
| D | Diffusivity | Ball-and-stick(s) | microns<sup>2<\sup>/ms <sup>1<\sup> |
| DSTD | Standard deviation of diffusivity | Ball-and-stick(s) | microns<sup>2<\sup>/ms |
| RTPP | Return to the plane probability | MAPMRI | Probability \[0-1\] |
| RTAP | Return to axis probability | MAPMRI | Probability \[0-1\] |

<sup>1<\sup> For example, for free water in body temperature, the diffusivity in units of microns<sup>2<\sup>/ms should be approximately 3.0.

### Directionally-encoded colour (DEC) maps

Expand Down Expand Up @@ -406,16 +406,16 @@ RECOMMENDED to appear within the "`Constraints`" field when "`TractographyClass`

RECOMMENDED to appear within the "`Parameters`" field when "`TractographyClass`" is "`local`":

| **Key name** | **Description** |
| ----------------- | -------------------------------------------------- |
| Units | "mm","norm" (applies to all within "`Parameters`") |
| StepSize | value |
| AngleCurvature | value (maximum angle per step) |
| RadiusCurvature | value (minimal radius of curvature) |
| MinimumLength | value |
| MaximumLength | value |
| IntegrationOrder | integer |
| Unidirectional | bool |
| **Key name** | **Description** |
| ----------------- | ---------------------------------------------------- |
| Units | {`mm`,`norm`} (applies to all within "`Parameters`") |
| StepSize | value |
| AngleCurvature | value (maximum angle per step) |
| RadiusCurvature | value (minimal radius of curvature) |
| MinimumLength | value |
| MaximumLength | value |
| IntegrationOrder | integer |
| Unidirectional | bool |

RECOMMENDED to appear within the "Seeding" field when `TractographyClass` is `local`:

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