diff --git a/src/05-derivatives/05-diffusion-derivatives.md b/src/05-derivatives/05-diffusion-derivatives.md
index 54133e26..a6847f5f 100644
--- a/src/05-derivatives/05-diffusion-derivatives.md
+++ b/src/05-derivatives/05-diffusion-derivatives.md
@@ -54,17 +54,17 @@ Throughout this document, the term "parameter" is used to refer to
multiple distinct sources of information. The distinction between
these uses is defined thus:
-1. *Input* model parameter:
+1. *Input* parameter:
Value or non-numerical setting that influences the conformation
of the diffusion model to the empirical diffusion-weighted data.
-1. *Intrinsic* model parameter:
+1. *Model* parameter:
Value that is the direct result of fitting the diffusion model to the
empirical diffusion-weighted data.
-1. *Extrinsic* model parameter:
+1. Model-*derived* parameter:
Value that can be calculated directly from previously estimated
intrinsic model parameters, without necessitating reference to
@@ -72,8 +72,8 @@ these uses is defined thus:
For example, consider a diffusion tensor model fit: the number of
iterations in the optimisation algorithm would be an *input* parameter;
-the six unique diffusion tensor coefficients would be the *intrinsic*
-parameters; the Fractional Anisotropy (FA) would be an *extrinsic*
+the six unique diffusion tensor coefficients would be the *model*
+parameters; the Fractional Anisotropy (FA) would be a *model-derived*
parameter (as it is calculated from the diffusion tensor coefficients
rather than the image data).
@@ -83,47 +83,40 @@ rather than the image data).
/
sub-/
dwi/
- [_space-][_desc-]_param-_.nii[.gz]
- [_space-][_desc-]_param-_.nii[.gz]
- [_space-][_desc-]_.json
-
- [[_space-][_desc-]_param-_.nii[.gz]]
- [[_space-][_desc-]_param-_.json]
- [[_space-][_desc-]_param-_.nii[.gz]]
- [[_space-][_desc-]_param-_.json]
+ [_space-][_desc-]_param-_model.nii[.gz]
+ [_space-][_desc-]_param-_model.json
+ [_space-][_desc-]_param-_model.nii[.gz]
+ [_space-][_desc-]_param-_model.json
+ [_space-][_desc-]_model.json
+
+ [[_space-][_desc-]_param-_mdp.nii[.gz]]
+ [[_space-][_desc-]_param-_mdp.json]
+ [[_space-][_desc-]_param-_mdp.nii[.gz]]
+ [[_space-][_desc-]_param-_mdp.json]
```
-- Field "``" is a unique identifier corresponding to the particular
- diffusion model. If the particular diffusion model is one that is included
- in this specification, then the [prescribed model label](intrinsic-model-parameters)
- MUST be utilised; e.g. "`tensor`" for the diffusion tensor model.
-
-- Files "`[_space-][_desc-]_param-_.nii[.gz]`"
- provide data corresponding to the various [intrinsic](#paramdef-intrinsic) parameters
- of the model. In cases where [intrinsic](#paramdef-intrinsic) model parameters are all
- contained within a single image file, field "`_param-`" nevertheless MUST be
- included, with value "`all`"; e.g.:
+- Files "`[_space-][_desc-]_param- _model.nii[.gz]`"
+ provide data corresponding to the various requisite [model parameters](#paramdef-model).
+ In cases where *all* [model parameters](#paramdef-model) are contained within a single image
+ file, field "`_parameter-`" nevertheless MUST be included, with value "`all`"; e.g.:
```Text
/
sub-/
dwi/
- [_space-][_desc-]_param-all_.nii[.gz]
- [_space-][_desc-]_.json
+ [_space-][_desc-]_param-all_model.nii[.gz]
+ [_space-][_desc-]_model.json
```
-- File "`[_space-][_desc-]_.json`"
- provides basic model information and [input](#paramdef-input)
- model parameters.
+- File "`[_space-][_desc-]_model.json`"
+ provides basic model information and [input parameters](#paramdef-input).
-- OPTIONAL images "`[_space-][_desc-]_param-_.nii[.gz]`"
- may be defined, in order to provide additional [extrinsic](#paramdef-extrinsic)
- model parameters.
+- OPTIONAL images "`[_space-][_desc-]_param-_mdp.nii[.gz]`"
+ may be defined, in order to provide additional [model-derived parameters](#paramdef-derived).
-- OPTIONAL files "`[_space-][_desc-]_param-_.json`"
- may be defined to provide only information or parameters relevant to
- derivation of each relevant [extrinsic](#paramdef-extrinsic) model
- parameter image.
+- OPTIONAL files "`[_space-][_desc-]_param- _mdp.json`"
+ may be defined to provide information or parameters only relevant to
+ each relevant [model-derived parameter](#paramdef-derived).
### Data representations
@@ -139,8 +132,8 @@ interpretation of that information; see [orientation specification](#orientation
1. *Scalars* :
- Any model parameter image (whether [intrinsic](#paramdef-intrinsic) or
- [extrinsic](#paramdef-extrinsic)) where a solitary numerical value is
+ Any parameter image (whether [model](#paramdef-model) or
+ [model-derived](#paramdef-derived)) where a solitary numerical value is
defined in each 3D image voxel is referred to here as a "scalar" image.
1. *Directionally-Encoded Colours (DEC)* :
@@ -201,8 +194,8 @@ interpretation of that information; see [orientation specification](#orientation
Each 3-vector, once explicitly normalized, provides a direction
on the unit sphere; the *norm* of each 3-vector additionally encodes
- the magnitude of some model parameter, the nature of which MUST be
- indicated in the "`_param-*`" filename field.
+ the magnitude of some model or model-derived parameter, the nature of
+ which MUST be indicated in the "`_param-*`" filename field.
1. Directions only
@@ -237,15 +230,14 @@ interpretation of that information; see [orientation specification](#orientation
4D image containing, for every image voxel, data corresponding to some
set of model parameters, the names and order of which are defined within
- the [intrinsic](#paramdef-intrinsic) model parameters section.
+ the [model parameters](#paramdef-model) section below.
-### Intrinsic model parameters
+### Model parameters
-The following models are codified within the specification, and the model
-label should be used as the final field in the filename for storage of any
-intrinsic or extrinsic parameters. If a new model is used, common sense
-should be used to derive a name following the BIDS standard, and should
-ideally be integrated in a future version of the specification.
+The following models are codified within the specification. The model label
+should be included in the "`_desc-`" field in the filename for storage
+of both model and model-derived parameters. Some models necessitate reserved
+keywords for "`_parameter-`" fields, which are listed below.
| Model label | Full Name | [Data representation](#data-representations) |
| ----------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
@@ -319,7 +311,7 @@ Reserved keywords for models built into the specification are as follows:
- `RESTORESigma`: Float
-### Extrinsic model parameters
+### Model-derived parameters
| `` value | Description | [Data representation](#data-representations) | Possible Model sources | Unit or scale |
| ------------------- | ---------------------------------------------------------------------- | -------------------------------------------- | ---------------------- | -------------------------------------------------------------- |
@@ -435,11 +427,15 @@ another.
my_diffusion_pipeline/
sub-01/
dwi/
- sub-01_tensor.nii.gz
- sub-01_tensor.json
+ sub-01_desc-dti_param-tensor_model.nii.gz
+ sub-01_desc-dti_param-bzero_model.nii.gz
+ sub-01_desc-dti_param-fa_mdp.nii.gz
+ sub-01_desc-dti_model.json
```
- Dimensions of NIfTI image "`sub-01_tensor.nii.gz`": *I*x*J*x*K*x6 ([parameter vectors](#data-param))
+ Dimensions of NIfTI image "`sub-01_desc-dti_param-tensor_model.nii.gz`": *I*x*J*x*K*x6 ([parameter vectors](#data-param))
+ Dimensions of NIfTI image "`sub-01_desc-dti_param-bzero_model.nii.gz`": *I*x*J*x*K* ([scalar](#data-scalar))
+ Dimensions of NIfTI image "`sub-01_desc-dti_param-fa_mdp.nii.gz`": *I*x*J*x*K* ([scalar](#data-scalar))
Contents of JSON file:
@@ -461,20 +457,20 @@ another.
my_diffusion_pipeline/
sub-01/
dwi/
- sub-01_desc-wm_csd.nii.gz
- sub-01_desc-wm_csd.json
- sub-01_desc-gm_csd.nii.gz
- sub-01_desc-gm_csd.json
- sub-01_desc-csf_csd.nii.gz
- sub-01_desc-csf_csd.json
- sub-01_csd.json
+ sub-01_desc-csd_param-wm_model.nii.gz
+ sub-01_desc-csd_param-wm_model.json
+ sub-01_desc-csd_param-gm_model.nii.gz
+ sub-01_desc-csd_param-gm_model.json
+ sub-01_desc-csd_param-csf_model.nii.gz
+ sub-01_desc-csd_param-csf_model.json
+ sub-01_desc-csd_model.json
```
- Dimensions of NIfTI image "`sub-01_desc-wm_csd.nii.gz`": *I*x*J*x*K*x45 ([spherical harmonics](#data-sh))
- Dimensions of NIfTI image "`sub-01_desc-gm_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh))
- Dimensions of NIfTI image "`sub-01_desc-csf_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh))
+ Dimensions of NIfTI image "`sub-01_desc-csd_param-wm_model.nii.gz`": *I*x*J*x*K*x45 ([spherical harmonics](#data-sh))
+ Dimensions of NIfTI image "`sub-01_desc-csd_param-gm_model.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh))
+ Dimensions of NIfTI image "`sub-01_desc-csd_param-csf_model.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh))
- Contents of file "`sub-01_csd.json`" (common to all [intrinsic](#paramdef-intrinsic) model parameter images):
+ Contents of file "`sub-01_desc-csd_model.json`" (common to all [model parameters](#paramdef-model)):
```JSON
{
@@ -488,7 +484,7 @@ another.
}
```
- Contents of JSON file "`sub-01_desc-wm_csd.json`":
+ Contents of JSON file "`sub-01_desc-csd_param-wm_model.json`":
```JSON
{
@@ -503,7 +499,7 @@ another.
}
```
- Contents of JSON file "`sub-01_desc-gm_csd.json`":
+ Contents of JSON file "`sub-01_desc-csd_param_gm_model.json`":
```JSON
{
@@ -525,24 +521,27 @@ another.
my_diffusion_pipeline/
sub-01/
dwi/
- sub-01_desc-mean_param-bzero_bs.nii.gz
- sub-01_desc-mean_param-dmean_bs.nii.gz
- sub-01_desc-mean_param-dstd_bs.nii.gz
- sub-01_desc-mean_param-sticks_bs.nii.gz
- sub-01_desc-mean_param-sticks_bs.json
- sub-01_desc-merged_param-sticks_bs.nii.gz
- sub-01_desc-merged_param-sticks_bs.json
- sub-01_bs.json
+ sub-01_desc-bs_param-bzero_model.nii.gz
+ sub-01_desc-bs_param-bzero_model.json
+ sub-01_desc-bs_param-md_mdp.nii.gz
+ sub-01_desc-bs_param-md_mdp.json
+ sub-01_desc-bs_param-stdd_mdp.nii.gz
+ sub-01_desc-bs_param-stdd_mdp.json
+ sub-01_desc-bs_param-sticks_mdp.nii.gz
+ sub-01_desc-bs_param-sticks_mdp.json
+ sub-01_desc-bs_param-sticks_model.nii.gz
+ sub-01_desc-bs_param-sticks_model.json
+ sub-01_desc-bs_model.json
```
- Dimensions of NIfTI image "`sub-01_desc-mean_param-bzero_bs.nii.gz`": *I*x*J*x*K* ([scalar](#data-scalar))
- Dimensions of NIfTI image "`sub-01_desc-mean_param-dmean_bs.nii.gz`": *I*x*J*x*K* ([scalar](#data-scalar))
- Dimensions of NIfTI image "`sub-01_desc-mean_param-dstd_bs.nii.gz`": *I*x*J*x*K* ([scalar](#data-scalar))
- Dimensions of NIfTI image "`sub-01_desc-mean_param-sticks_bs.nii.gz`": *I*x*J*x*K*x9 ([spherical coordinates](#data-spherical), distance from origin encodes fibre volume fraction)
- Dimensions of NIfTI image "`sub-01_desc-merged_param-sticks_bs.nii.gz`": *I*x*J*x*K*x9x50 ([spherical coordinates](#data-spherical), distance from origin encodes fibre volume fraction; 50 bootstrap realisations)
+ Dimensions of NIfTI image "`sub-01_desc-bs_param-bzero_model.nii.gz`": *I*x*J*x*K* ([scalar](#data-scalar))
+ Dimensions of NIfTI image "`sub-01_desc-bs_param-ms_mdp.nii.gz`": *I*x*J*x*K* ([scalar](#data-scalar))
+ Dimensions of NIfTI image "`sub-01_desc-bs_param-stdd_mdp.nii.gz`": *I*x*J*x*K* ([scalar](#data-scalar))
+ Dimensions of NIfTI image "`sub-01_desc-bs_param-sticks_mdp.nii.gz`": *I*x*J*x*K*x9 ([spherical coordinates](#data-spherical), distance from origin encodes fibre volume fraction)
+ Dimensions of NIfTI image "`sub-01_desc-bs_param-sticks_model.nii.gz`": *I*x*J*x*K*x9x50 ([spherical coordinates](#data-spherical), distance from origin encodes fibre volume fraction; 50 bootstrap realisations)
- Contents of JSON files "`sub-01_desc-mean_param-sticks_bs.json`"
- and "`sub-01_desc-merged_param-sticks_bs.json`" (contents of two
+ Contents of JSON files "`sub-01_desc-bs_param-sticks_mdp.json`"
+ and "`sub-01_desc-bs_param-sticks_model.json`" (contents of two
files are identical):
```JSON
@@ -552,7 +551,7 @@ another.
}
```
- Contents of JSON file "`sub-01_bs.json`":
+ Contents of JSON file "`sub-01_desc-bs_model.json`":
```JSON
{