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Diffusion derivatives: Further fixes for #205
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- Minor spelling & grammar fixes.
- In "scalar maps" section, expand out the different parameters to be derived from the ball-and-stick(s) model.
- Provide more accurate link to MRtrix3 tracks file format.
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@Lestropie
Lestropie committed Apr 24, 2019
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Expand Up @@ -32,7 +32,7 @@ Additional reserved JSON metadata fields:
| MotionCorrection | OPTIONAL. Boolean. Motion correction |
| EddyCurrentCorrection | OPTIONAL. Boolean. Eddy currents corrections |
| IntensityNormalizationMethod | OPTIONAL. String. Method (if any) used for intensity normalization |
| FieldInhomogeneityCorrection | OPTIONAL. Boolean. Correction for geometric distrotions arising from magnetic field inhomogeneity |
| FieldInhomogeneityCorrection | OPTIONAL. Boolean. Correction for geometric distortions arising from magnetic field inhomogeneity |
| GradientNonLinearityCorrection | OPTIONAL. String. Correction for non-linear gradients; allowed values: `none`, `geometry`, `gradients`, `geometry&gradients` |

## Diffusion Models (and input parameters)
Expand Down Expand Up @@ -71,7 +71,7 @@ version of the specification.
| `WMTI` | White matter tract integrity (Fieremans et al., 2011) | 4D image with Dxx, Dxy, Dxz, Dyy, Dyz, Dzz, Wxxxx, Wyyy, 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, AWF; where D is the diffusion tensor, W is the kurtosis tensor, AWF is the additional axonal water fraction parameter |
| `CSD` | Constrained Spherical Deconvolution (Tournier et al. 2007; Descoteaux et al. 2009) | 4D image with spherical harmonic (SH) coefficients (number of volumes and their ordering depends on the model maximal degree and basis set, specified in the sidecar) |
| `NODDI` | Neurite Orientation Dispersion and Density Imaging (Zhang et al. 2012, Daducci et al., 2015) | Three 3D images, with <parameter> equal to {`ICVF`,`OD`,`ISOVF`}: ICVF is the “intracellular volume fraction” (also known as NDI); OD is the “orientation dispersion” (the variance of the Bingham; also known as ODI); ISOVF is the isotropic component volume fraction (also known as IVF). Additionally a vector-valued map with the parameter name "`direction`" may provide the XYZ direction of the estimated fibre orientation. |
| `DSI` | Diffusion Spectrum Imaging (Wedeen et al. 2008; Paquette et al 2017) | DSI is generally used mostly to compute the diffusion ODF (Orientation Distribution Function). No parameters are generally returned, but an ODF can be saved as a map. |
| `DSI` | Diffusion Spectrum Imaging (Wedeen et al. 2008; Paquette et al 2017) | DSI is generally used to compute the diffusion ODF (Orientation Distribution Function). No parameters are generally returned, but an ODF can be saved as a map. |
| `CSA` | Constant solid angle (Aganj et al. 2010) | 4D image with SH coefficients (number of volumes and their ordering depends on the model maximal degree and basis set, specified in the side-car) |
| `SHORE` | Simple Harmonic Oscillator based Reconstruction and Estimation. (Ozarslan et al. 2008) | 4D image with basis coefficients depending on choice of basis. |
| `MAPMRI` | Mean Apparent Propagator MRI. (Ozarslan, 2013) | 4D image with basis coefficients depending on choice of basis. |
Expand Down Expand Up @@ -268,23 +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 (for example, for free water in body temperature, this should be approximately 3) |
| AD | Axial Diffusivity (also called parallel diffusivity) | DTI, DKI, WMTI (D, Dh, Dr) | microns^2/ms (for example, for free water in body temperature, this should be approximately 3) |
| RD | Radial Diffusivity (also called perpendicular diffusivity) | DTI, DKI, WMTI (D, Dh, Dr) | microns^2/ms (for example, for free water in body temperature, this should be approximately 3) |
| 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 \[0 - 1\] |
| INDEX | Scalar maps from bedpostx | FSUM (sum of partial volume fractions of the sticks)F_i (volume fraction of stick i)D (diffusivity)DSTD (std of diffusivity) | FSUM \[0 - 1\]F_i \[0 - 1\]D and DSTD microns^2/ms (for example, for free water in body temperature, this should be 3) |
| RTPP | Return to the plane probability | MAPMRI | Probability \[0 - 1\] |
| RTAP | Return to axis probability | MAPMRI | Probability \[0 - 1\] |
| `<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.

### Directionally-encoded colour (DEC) maps

Expand All @@ -307,7 +312,7 @@ tensor model is coloured according to the direction of the principal eigenvector

### Vector-valued maps

These maps are saved 4D NIfTI files (x,y,z, 3\*n), where each triplet of volumes
These maps are saved as 4D NIfTI files (x,y,z, 3\*n), where each triplet of volumes
encodes both a direction in 3D space and some quantitiative value (these are
sometimes referred to as "fixels"). The number of volumes in the image must be
3 times the maximal number of fixels that can appear in any voxel in the image
Expand Down Expand Up @@ -356,7 +361,7 @@ kept, or `subsampled50` if only 50% of the streamlines were kept.
### File formats

- [.trk - Diffusion Toolkit (+TrackVis)](https://web.archive.org/web/20190103230122/http://www.trackvis.org/docs/?subsect=fileformat)
- [.tck - MRtrix](https://web.archive.org/web/20190103230209/https://mrtrix.readthedocs.io/en/latest/getting_started/image_data.html)
- [.tck - MRtrix](https://web.archive.org/web/20190103230209/https://mrtrix.readthedocs.io/en/latest/getting_started/image_data.html#tracks-file-format-tck)

### JSON Metadata

Expand Down

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