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BEP016: Forced data representation specification #67

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BEP016: Forced data representation specification #67

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22 changes: 13 additions & 9 deletions src/05-derivatives/05-diffusion-derivatives.md
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Expand Up @@ -109,6 +109,10 @@ rather than the image data).
<source_keywords>[_space-<space>]_model-<label>_model.json
```

- Files "`<source_keywords>[_space-<space>]_model-<label>_param-<param*>_model.json`"
are REQUIRED to accompany each NIfTI file individually, as they MUST specify the
[data representation](#data-representations) used for each image.

- File "`<source_keywords>[_space-<space>]_model-<label>_model.json`"
provides basic model information and [input parameters](#paramdef-input).

Expand Down Expand Up @@ -338,15 +342,15 @@ in order to produce a [directionally-encoded colour](#data-dec),

### Orientation specification

| **Key name** | **Relevant [data representations](#data-representations)** | **Description** |
| --------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `AntipodalSymmetry` | [Spherical coordinates](#data-spherical), [3-vectors](#data-3vector), [spherical harmonics](#data-sh), [amplitudes](#data-amp), [parameter vectors](#data-param) | OPTIONAL. Boolean. Indicates whether orientation information should be interpreted as being antipodally symmetric. Assumed to be True if omitted. |
| `Directions` | [Amplitudes](#data-amp) | REQUIRED. List. Data are either [spherical coordinates (directions only)](#data-spherical) or [3-vectors](#data-3vector) with unit norm. Defines the dense directional basis set on which samples of a spherical function within each voxel are provided. |
| `FillValue` | [Spherical coordinates](#data-spherical), [3-vectors](#data-3vector) | OPTIONAL. Float; allowed values: { 0.0, NaN }. Value stored in image when number of discrete orientations in a voxel is fewer than the maximal number for that image. |
| `OrientationRepresentation` | All except [scalar](#data-scalar) | REQUIRED. String; allowed values: { `dec`, `unitspherical`, `spherical`, `unit3vector`, `3vector`, `sh`, `amp`, `param` }. The [data representation](#data-representations) used to encode orientation information within the NIfTI image. |
| `ReferenceAxes` | All except [scalar](#data-scalar) | REQUIRED. String; allowed values: { `ijk`, `xyz` }. Indicates whether the NIfTI image axes, or scanner-space axes, are used as reference axes for orientation information. |
| `SphericalHarmonicBasis` | [Spherical harmonics](#data-sh) | REQUIRED. String; allowed values: { `MRtrix3` }. Basis by which to define the interpretation of image values across volumes as spherical harmonics coefficients. |
| `SphericalHarmonicDegree` | [Spherical harmonics](#data-sh) | REQUIRED. Integer. Maximal degree of the spherical harmonic basis employed. |
| **Key name** | **Relevant [data representations](#data-representations)** | **Description** |
| --------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `AntipodalSymmetry` | [Spherical coordinates](#data-spherical), [3-vectors](#data-3vector), [spherical harmonics](#data-sh), [amplitudes](#data-amp), [parameter vectors](#data-param) | OPTIONAL. Boolean. Indicates whether orientation information should be interpreted as being antipodally symmetric. Assumed to be True if omitted. |
| `Directions` | [Amplitudes](#data-amp) | REQUIRED. List. Data are either [spherical coordinates (directions only)](#data-spherical) or [3-vectors](#data-3vector) with unit norm. Defines the dense directional basis set on which samples of a spherical function within each voxel are provided. |
| `FillValue` | [Spherical coordinates](#data-spherical), [3-vectors](#data-3vector) | OPTIONAL. Float; allowed values: { 0.0, NaN }. Value stored in image when number of discrete orientations in a voxel is fewer than the maximal number for that image. |
| `OrientationRepresentation` | All | REQUIRED (unless [scalar](#data-scalar) [model-derived parameters](#paramdef-derived)). String; allowed values: { `scalar`, `dec`, `unitspherical`, `spherical`, `unit3vector`, `3vector`, `sh`, `amp`, `param` }. The [data representation](#data-representations) used to encode orientation information within the NIfTI image. |
| `ReferenceAxes` | All except [scalar](#data-scalar) | REQUIRED. String; allowed values: { `ijk`, `xyz` }. Indicates whether the NIfTI image axes, or scanner-space axes, are used as reference axes for orientation information. |
| `SphericalHarmonicBasis` | [Spherical harmonics](#data-sh) | REQUIRED. String; allowed values: { `MRtrix3` }. Basis by which to define the interpretation of image values across volumes as spherical harmonics coefficients. |
| `SphericalHarmonicDegree` | [Spherical harmonics](#data-sh) | REQUIRED. Integer. Maximal degree of the spherical harmonic basis employed. |

If `AntipodalSymmetry` is True, then no constraints are imposed with respect
to the domain on the 2-sphere in which orientations may be specified;
Expand Down