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DWI models: Define "bvec" orientation reference #98

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Jun 5, 2024
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DWI models: Define "bvec" orientation reference #98

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DWI models: Define "bvec" orientation reference
Lestropie May 15, 2024
b093ac1
DWI models: Update bvec reference
Lestropie Jun 5, 2024
bda570f
Merge remote-tracking branch 'origin/bep-016' into bvec_reference_axes
Lestropie Jun 5, 2024
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18 changes: 13 additions & 5 deletions src/derivatives/05-diffusion-derivatives.md
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Expand Up @@ -127,7 +127,7 @@ see [parameter metadata](#parameter-metadata).
orthogonal to the zenith direction,
with value of 0.0 corresponding to the *first* reference axis
(see [parameter metadata](#parameter-metadata)),
increasing according to the right-hand rule about the zenith direction.
increasing toward the positive direction of the *second* reference axis.

Number of image volumes is equal to (3x*N*),
where *N* is the maximum number of discrete orientations in any voxel in the image.
Expand Down Expand Up @@ -290,12 +290,20 @@ Dictionary `"OrientationEncoding"` has the following reserved keywords:
| AntipodalSymmetry | [spherical coordinates](#encoding-spherical), [3-vectors](#encoding-3vector), [tensor](#encoding-tensor), [amplitudes](#encoding-amp), [spherical harmonics](#encoding-sh) | OPTIONAL. Boolean. Indicates whether orientation information should be interpreted as being antipodally symmetric. Assumed to be True if omitted. |
| EncodingAxis | All except [scalar](#encoding-scalar) | REQUIRED. Integer. Indicates the image axis (indexed from zero) along which image intensities should be interpreted as corresponding to orientation encoding. |
| FillValue | [Scalar](#encoding-scalar), [spherical coordinates](#encoding-spherical), [3-vectors](#encoding-3vector) | OPTIONAL. Float; allowed values: { 0.0, NaN }. Value stored in image when the number of discrete orientations in a given voxel is fewer than the maximal number for that image. |
| Reference | All except [scalar](#encoding-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. |
| Reference | All except [scalar](#encoding-scalar) | REQUIRED. String; allowed values: { `bvec`, `ijk`, `xyz` }. Defines the reference coordinate system against which orientation information is encoded (more below). |
| SphericalHarmonicBasis | [Spherical harmonics](#encoding-sh) | REQUIRED for `"Type": "sh"`; MUST NOT be specified otherwise. String. Options are: { `mrtrix3`, `descoteaux` }. Details are provided in the [spherical harmonics bases](#spherical-harmonics-bases) section. |
| SphericalHarmonicDegree | [Spherical harmonics](#encoding-sh) | OPTIONAL for `"Type": "sh"`; MUST NOT be specified otherwise. Integer. The maximal spherical harmonic order *l<sub>max</sub>*; the number of volumes in the associated NIfTI image must correspond to this value as per the relationship described in [spherical harmonics bases](#spherical-harmonics-bases) section. |
| TensorRank | [Tensor](#encoding-tensor) | REQUIRED for `"Type": "tensor"; MUST NOT be specified otherwise. Integer. Rank of tensor reporesentation. Specification currently only supports a value of 2. |
| Type | Any | REQUIRED. String. Specifies the type of orientation information (if any) encoded in the NIfTI image. Permitted values: { `scalar`, `dec`, `unitspherical`, `spherical`, `unit3vector`, `3vector`, `tensor`, `sh`, `amplitudes` }. |

Field `"OrientationEncoding"["Reference"]` MUST contain one of the following values:

| **Value** | **Interpretation** |
| --------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| bvec | The three spatial image axes; **unless** those axes form a right-handed coordinate system (that is, the 3x3 linear component of the NIfTI header transformation has a positive determinant), in which case the negative of the first axis orientation is the first reference. |
| ijk | The three spatial image axes define the orientation reference. |
| xyz | The "real" / "scanner" space axes, which are independent of the NIfTI image header transform, define the orientation reference. |

Dictionary `"ResponseFunction"` has the following reserved keywords:

| **Key name** | **Description** |
Expand Down Expand Up @@ -639,7 +647,7 @@ Contents of JSON file "`sub-01_model-bs_desc-mean_param-polar_dwimap.json`":
},
"OrientationEncoding": {
"EncodingAxis": 3,
"Reference": "ijk",
"Reference": "bvec",
"Type": "unitspherical"
}
}
Expand All @@ -665,7 +673,7 @@ Contents of JSON file "`sub-01_model-bs_desc-mean_param-vector_dwimap.json`":
},
"OrientationEncoding": {
"EncodingAxis": 3,
"Reference": "ijk",
"Reference": "bvec",
"Type": "unit3vector"
}
}
Expand Down Expand Up @@ -780,7 +788,7 @@ Contents of JSON file "`sub-01_model-bs_desc-merged_param-polar_dwimap.json`":
},
"OrientationEncoding": {
"EncodingAxis": 3,
"ReferenceAxes": "ijk",
"ReferenceAxes": "bvec",
"Type": "unitspherical"
}
}
Expand Down