diff --git a/src/derivatives/05-diffusion-derivatives.md b/src/derivatives/05-diffusion-derivatives.md index f059ac21..3cdcf8f9 100644 --- a/src/derivatives/05-diffusion-derivatives.md +++ b/src/derivatives/05-diffusion-derivatives.md @@ -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. @@ -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 *lmax*; 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** | @@ -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" } } @@ -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" } } @@ -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" } }