From eddad2289617ebaf20d43475dba2b299a41e0e50 Mon Sep 17 00:00:00 2001 From: Robert Smith Date: Fri, 7 Oct 2022 12:41:26 +1100 Subject: [PATCH] DWI derivatives: Make tensor a data representation --- src/05-derivatives/05-diffusion-derivatives.md | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/src/05-derivatives/05-diffusion-derivatives.md b/src/05-derivatives/05-diffusion-derivatives.md index f3e0813f..44d7b566 100644 --- a/src/05-derivatives/05-diffusion-derivatives.md +++ b/src/05-derivatives/05-diffusion-derivatives.md @@ -144,6 +144,18 @@ interpretation of that information; see [orientation specification](#orientation \[[Pajevic1999](#pajevic1999)\]. Image data MUST NOT contain negative values. +1. *Rank-2 tensor*: + + 4D image encoding coefficients of a rank-2 tensor. + If `"AntipodalSymmetry"` is `True` (or omitted), + then the image MUST contain six volumes, in the order: + *Dxx*, *Dxy*, *Dxz*, *Dyy*, *Dyz*, *Dzz. + If `"AntipodalSymmetry"` is `False`, + then the image MUST contain nine volumes, in the order: + *Dxx*, *Dxy*, *Dxz*, *Dyx*, *Dyy*, *Dyz, *Dzx*, *Dzy*, *Dzz. + (If `"ReferenceAxes"` is `"ijk"`, then the interpretation of the coefficients + above should be substituted accordingly) + 1. *Spherical coordinates*: 4D image where data across volumes within each voxel encode one or @@ -244,7 +256,7 @@ keywords for "`_param-`" fields, which are listed below. | ----------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `bs` | Ball-and-Stick(s) model \[[Behrens2003](#behrens2003)\],\[[Behrens2007](#behrens2007)\],\[[Jbabdi2012](#jbabdi2012)\] | One [spherical coordinates](#data-spherical) image with parameter name "`sticks`", providing both fibre volume fractions and orientations using polar angles;
Optional scalar images with parameter names {"`bzero`", "`dmean`", "`dstd`"} providing the model-estimated *b*=0 signal intensity, mean stick diffusivity, and standard deviation of stick diffusivities respectively | | `csd` | Constrained Spherical Deconvolution \[[Tournier2007](#tournier2007)\],\[[Descoteaux2009](#descoteaux2009)\],\[[Jeurissen2014](#jeurissen2014)\] | [Spherical harmonics](#data-sh) image
If a multi-tissue decomposition is performed, provide one individual 4D image per tissue, with "`_param-`" entity being an abbreviation of the tissue estimated by that particular ODF | -| `tensor` | Diffusion Tensor \[[Basser1994](#basser1994)\] | Single [parameter vectors](#data-param) image with no `param` entity with 6 volumes in the order: *Dxx*, *Dxy*, *Dxz*, *Dyy*, *Dyz*, *Dzz*
OR
Tensor coefficients as [parameter vectors](#data-param) image with parameter name "`tensor`";
Estimated *b*=0 intensity as [scalar](#data-scalar) image with parameter name "`bzero`" | +| `tensor` | Diffusion Tensor \[[Basser1994](#basser1994)\] | Single [tensor image](#data-tensor) with no `param` entity
OR
Tensor coefficients as [tensor image](#data-tensor) image with `param` entity ``tensor``;
Estimated *b*=0 intensity as [scalar image](#data-scalar) with `param` entity "`bzero`" | The JSON sidecar for the intrinsic diffusion model parameters may contain the following key/value pairs irrespective of the particular model: @@ -340,7 +352,7 @@ in order to produce a [directionally-encoded colour](#data-dec), | **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. | +| `AntipodalSymmetry` | [Tensor](#data_tensor), [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. | @@ -434,7 +446,7 @@ another. sub-01_model-tensor_model.json ``` - Dimensions of NIfTI image "`sub-01_model-tensor_param-tensor_model.nii.gz`": *I*x*J*x*K*x6 ([parameter vectors](#data-param)) + Dimensions of NIfTI image "`sub-01_model-tensor_param-tensor_model.nii.gz`": *I*x*J*x*K*x6 ([tensor image](#data-tensor)) Dimensions of NIfTI image "`sub-01_model-tensor_param-bzero_model.nii.gz`": *I*x*J*x*K* ([scalar](#data-scalar)) Dimensions of NIfTI image "`sub-01_model-tensor_param-fa_mdp.nii.gz`": *I*x*J*x*K* ([scalar](#data-scalar))