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BEP016: Adopt "model fit parameters" terminology
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In order to better disambiguate the various types of "parameters" defined, change "model parameters" to "model fit parameters".
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Lestropie committed Sep 13, 2022
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23 changes: 12 additions & 11 deletions src/05-derivatives/05-diffusion-derivatives.md
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Expand Up @@ -37,11 +37,12 @@ biological structure. A wide range of such models are available, each of
which has its own unique requirements with respect to:

- The [input](#paramdef-input) parameters required in order to
define / constrain the model;
define / constrain the way in which the model will be fit to the
empirical image data;

- The appropriate [data representations](#data-representations) utilised to
store information parameterised [by](#paramdef-intrinsic) or
[from](#paramdef-extrinsic) the model onto the filesystem;
store information parameterised [by](#paramdef-fit) or
[from](#paramdef-derived) the model onto the filesystem;

- The requirements for encapsulation and complete representation of
derived [orientation information](#orientation-specification), which is
Expand All @@ -59,7 +60,7 @@ these uses is defined thus:
Value or non-numerical setting that influences the conformation
of the diffusion model to the empirical diffusion-weighted data.

1. <a name="paramdef-model">*Model*</a> parameter:
1. <a name="paramdef-fit">Model *fit*</a> parameter:

Value that is the direct result of fitting the diffusion model to the
empirical diffusion-weighted data.
Expand All @@ -72,7 +73,7 @@ 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 *model*
the six unique diffusion tensor coefficients would be the *model fit*
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).
Expand All @@ -96,9 +97,9 @@ rather than the image data).
```

- Files "`<source_keywords>[_space-<space>]_model-<label>_param-<param*>_model.nii[.gz]`"
provide data corresponding to the various requisite [model parameters](#paramdef-model).
provide data corresponding to the various requisite [model fit parameters](#paramdef-fit).

In cases where *all* [model parameters](#paramdef-model) are contained within a single image
In cases where *all* [model fit parameters](#paramdef-fit) are contained within a single image
file, entity "`_param-`" MUST NOT be included; e.g.:
```Text
<pipeline_name>/
Expand Down Expand Up @@ -132,7 +133,7 @@ interpretation of that information; see [orientation specification](#orientation

1. <a name="data-scalar">*Scalars*</a>:

Any parameter image (whether [model](#paramdef-model) or
Any parameter image (whether [model fit](#paramdef-fit) 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.

Expand Down Expand Up @@ -230,7 +231,7 @@ 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 [model parameters](#paramdef-model) section below.
the [model fit parameters](#paramdef-fit) section below.

### Model parameters

Expand Down Expand Up @@ -330,7 +331,7 @@ Reserved keywords for models built into the specification are as follows:
| `rd` | Radial Diffusivity (also called perpendicular diffusivity) | [Scalar](#data-scalar) | { `tensor` } | \mu m<sup>2</sup>.ms<sup>-1</sup> <sup>[1](#diffusivity)</sup> |

While not explicitly included in the table above, *any* [scalar](#data-scalar)
[extrinsic](paramdef-extrinsic) parameter can theoretically be combined
[model-derived parameter](paramdef-derived) can theoretically be combined
with a separate source of orientation information from the diffusion model
in order to produce a [directionally-encoded colour](#data-dec),
[spherical coordinates](#data-spherical) or [3-vectors](#data-3vector) image.
Expand Down Expand Up @@ -470,7 +471,7 @@ another.
Dimensions of NIfTI image "`sub-01_model-csd_param-gm_model.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh))
Dimensions of NIfTI image "`sub-01_model-csd_param-csf_model.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh))
Contents of file "`sub-01_model-csd_model.json`" (common to all [model parameters](#paramdef-model)):
Contents of file "`sub-01_model-csd_model.json`" (common to all [model fit parameters](#paramdef-fit)):
```JSON
{
Expand Down

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