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Current state of the BEP (NOT FOR MERGING) #24

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7a58c97
ENH: Restore diffusion derivatives
effigies Aug 1, 2019
86facea
MAINT: Split out tractography
oesteban Sep 18, 2019
578079f
Merge pull request #9 from bids-standard/maint/split-tractography
arokem Sep 18, 2019
5ab7dc3
First commit for restructuring of DWI derivatives
Lestropie Jul 4, 2019
1beda57
BEP016: Small fixes, and try to get links to headers working
Lestropie Jul 16, 2019
1fd477c
BEP016: More updates of internal header links
Lestropie Jul 16, 2019
a462603
BEP016: Minor tweaks from first feedback round
Lestropie Aug 16, 2019
021cfd5
BEP016: Try to get links working within tables
Lestropie Aug 16, 2019
899a676
BEP016: More minor tweaking
Lestropie Aug 16, 2019
48c24dc
BEP016: Transpose SH volume count tables
Lestropie Aug 16, 2019
c092f48
BEP016: Provide example for parameter definitions
Lestropie Sep 11, 2019
7fe44f9
BEP016: Change to single-file diffusion models
Lestropie Sep 11, 2019
7eb44cb
BEP016: Initial explanation of filename
Lestropie Sep 11, 2019
4bc2b95
BEP016: File naming clarification
Lestropie Sep 11, 2019
f07489d
BEP016: Spelling fix
Lestropie Sep 11, 2019
5d14ffa
BEP016: Fix missing anchor links
Lestropie Sep 11, 2019
a804aeb
BEP016: Move orientation specification
Lestropie Sep 18, 2019
77a732f
Merge pull request #5 from bids-standard/dwi_derivatives_restructure
oesteban Sep 23, 2019
1a0f221
Merge remote-tracking branch 'upstream/master' into bep-016
effigies Jun 14, 2021
7210dd7
Merge remote-tracking branch 'bids-specification/master' into bep-016
Lestropie Nov 16, 2021
7227a75
BEP016: Revise SH description
Lestropie Nov 22, 2021
3c412f6
BEP016: Initial conformity to markdown formatting
Lestropie Nov 22, 2021
a5f4514
BEP016: More formatting conformity changes
Lestropie Nov 22, 2021
0dccc99
BEP016: More formatting conformity changes
Lestropie Nov 22, 2021
f237b8b
BEP016: Attempted fixes to table cell padding
Lestropie Nov 22, 2021
4c5e388
BEP016: Minor fix to tractography derivatives for CI pass
Lestropie Nov 22, 2021
3975051
Merge pull request #30 from bids-standard/remark_fixes
Lestropie Nov 22, 2021
b92e919
Merge branch 'bep-016' into sh_description_cherrypick
Lestropie Nov 22, 2021
158586f
BEP016: Modify nomenclature around MRtrix3 SH coefficients
Lestropie Nov 22, 2021
6ab7130
BEP016: Revise preprocessed DWI data example
Lestropie Nov 23, 2021
4c7b81b
BEP016: Remove SH Descoteaux placeholder
Lestropie Nov 30, 2021
80e19fe
BEP016: Remove majority of models
Lestropie Dec 1, 2021
beb7a16
BEP016: Formatting fix following removal of models
Lestropie Dec 1, 2021
8f18d91
Merge pull request #40 from bids-standard/remove_models
arokem Dec 1, 2021
29fde11
Merge pull request #37 from bids-standard/revise_preprocessed
francopestilli Dec 1, 2021
9ee4aa6
Merge pull request #28 from bids-standard/sh_description_cherrypick
francopestilli Dec 2, 2021
fcff8ac
BEP016: Strip out tractography content
Lestropie Dec 2, 2021
bab2900
Fixes a typo caught by codespell
arokem Dec 2, 2021
3874db9
Merge pull request #45 from bids-standard/typo-fix
Lestropie Dec 2, 2021
c9d2748
BEP016: Initial draft of common filename suffix "model"
Lestropie Dec 2, 2021
618ee5b
BEP016: Rename "dti" to "tensor"
Lestropie Dec 2, 2021
39fa5b0
Merge pull request #42 from bids-standard/strip_tractography
arokem Dec 8, 2021
844f9a5
Merge pull request #47 from bids-standard/rename_tensor
Lestropie Jan 11, 2022
4e03dc7
Rename "_parameter-" entity to "_param-"
Lestropie Aug 9, 2022
a83d607
DWI derivatives: Compulsory "parameter" entity
Lestropie Aug 9, 2022
ab05216
Merge pull request #51 from bids-standard/param_entity
Lestropie Aug 10, 2022
653766d
Merge remote-tracking branch 'origin/bep-016' into compulsory_paramet…
Lestropie Aug 10, 2022
c7cfbaf
DWI derivatives: Resolution between content changes
Lestropie Aug 10, 2022
46d3eb4
Merge remote-tracking branch 'origin/bep-016' into model_suffix
Lestropie Aug 16, 2022
d3bbb86
DWI derivatives: Fix tensor model example
Lestropie Aug 16, 2022
d86b7cd
DWI derivatives: "model" as entity
Lestropie Aug 16, 2022
e101e50
Merge pull request #46 from bids-standard/model_suffix
francopestilli Sep 12, 2022
2b7f88d
Merge branch 'bep-016' into compulsory_parameter_entity
Lestropie Sep 12, 2022
143d1cc
Merge pull request #52 from bids-standard/compulsory_parameter_entity
Lestropie Sep 12, 2022
d5bda6d
Merge branch 'bep-016' into model_entity
Lestropie Sep 12, 2022
ec50c47
Merge branch 'master' into bep-016
Lestropie Sep 12, 2022
e485551
Merge pull request #57 from bids-standard/model_entity
Lestropie Sep 12, 2022
a453274
DWI models: Restore renaming "dti" to "tensor"
Lestropie Sep 12, 2022
8ca6f53
Merge pull request #60 from bids-standard/restore_rename_tensor
Lestropie Sep 12, 2022
4746056
BEP016: Remove reference to old terminology
Lestropie Sep 13, 2022
4118ce0
Merge pull request #63 from bids-standard/revert_intrinsic
Lestropie Sep 13, 2022
c13031e
BEP016: Revert "_param-all"
Lestropie Sep 13, 2022
2b40cb7
Merge pull request #64 from bids-standard/no_paramall
Lestropie Sep 13, 2022
4489a0c
BEP016: Adopt "model fit parameters" terminology
Lestropie Sep 13, 2022
f4a7239
BEP016: Remove references to removed "pdf" data representation
Lestropie Sep 13, 2022
419b25f
Merge pull request #65 from bids-standard/model_fit_parameters
Lestropie Sep 13, 2022
ed53944
Merge pull request #66 from bids-standard/remove_pdf
Lestropie Sep 13, 2022
eddad22
DWI derivatives: Make tensor a data representation
Lestropie Oct 7, 2022
bcd768c
DWI derivatives: Fix ModelDescription in exemplars
Lestropie Oct 7, 2022
c1814fa
Merge pull request #75 from bids-standard/model_description
Lestropie Oct 7, 2022
3ece540
update based on current BIDS spec master
PeerHerholz Nov 10, 2022
2c4932f
Merge pull request #78 from PeerHerholz/update_specification
arokem Nov 14, 2022
235552a
Merge branch 'master' into bep-016
arokem Nov 14, 2022
53f7484
Merge branch 'master' into bep-016
arokem Nov 28, 2022
6da90d4
Merge branch 'master' into bep-016
PeerHerholz Apr 25, 2023
7994706
Adds the descoteaux 2007 convention.
arokem Apr 25, 2023
f7e6f43
Merge pull request #80 from arokem/adds_descoteaux
arokem Apr 25, 2023
2fa5940
Change from strange html encoding to "<" and ">"
arokem Apr 29, 2023
8dee2f0
Merge pull request #81 from arokem/adds_descoteaux
arokem Apr 29, 2023
dd8fe32
Fix codespell-detected British spellings.
arokem Apr 29, 2023
a0cadd3
Merge pull request #82 from arokem/fix-british-spellings
arokem Jun 27, 2023
9a68b41
Merge branch 'master' into bep-016
arokem Jun 28, 2023
7a605fd
Replace the latin "etc" with ellipses.
arokem Jun 28, 2023
ab2b4cd
Merge pull request #83 from arokem/fix-validation
arokem Jun 29, 2023
0a04ee6
Bump actions/checkout from 3 to 4
dependabot[bot] Sep 11, 2023
48a6a42
Merge branch 'master' into bep-016
arokem Mar 29, 2024
c6e50fc
Merge branch 'bep-016' into tensor_as_representation
Lestropie Apr 23, 2024
ab173a5
Merge pull request #74 from bids-standard/tensor_as_representation
Lestropie Apr 23, 2024
c62a2d7
BEP016: Major changes
Lestropie Apr 26, 2024
a2c35b8
BEP016: Fis JSON formatting in demonstrative examples
Lestropie Apr 26, 2024
8672cbe
Diffusion models: Forbid negative spherical coordinate radius
Lestropie Apr 26, 2024
7a123d5
Diffusion model derivatives: Spelling fixes
arokem May 1, 2024
1b50e3e
Merge pull request #92 from bids-standard/dwimap_and_no_inheritance
arokem May 14, 2024
148f9fa
Merge branch 'master' into bep-016
arokem May 14, 2024
4cf0723
Apply US spelling. Addresses current codespell CI failure.
arokem May 14, 2024
1317863
Markdown table linting
arokem May 14, 2024
77dbfbd
Get rid of a few latin phrases (i.e., "e.g.").
arokem May 14, 2024
156359a
DWI models: Define "bvec" orientation reference
Lestropie May 15, 2024
adb0e62
DWI models: Force presence of "param" entity
Lestropie May 15, 2024
2ac5549
DWI models: add "ParameterURL" metadata field
Lestropie May 15, 2024
4b8c56e
Merge remote-tracking branch 'origin/bep-016' into dependabot/github_…
Lestropie May 15, 2024
3bb9da0
Clarify metadata fields relevance (#102)
Lestropie May 15, 2024
9163f9d
Merge pull request #87 from bids-standard/dependabot/github_actions/a…
Lestropie May 15, 2024
9c3ceda
Merge pull request #97 from arokem/us-spelling
Lestropie May 15, 2024
73e4252
Merge branch 'bep-016' into metadata_parameterurl
arokem May 15, 2024
37b1bad
Merge pull request #101 from bids-standard/metadata_parameterurl
arokem May 15, 2024
c73cf54
Merge branch 'bep-016' into force_param_entity
arokem May 15, 2024
3f5f38d
Merge pull request #99 from bids-standard/force_param_entity
arokem May 15, 2024
e4df23c
Removes one more i.e.
arokem May 15, 2024
a26ccbd
Merge pull request #103 from arokem/one_more_latin
Lestropie May 15, 2024
900381c
BEP016: Utilize filesystem macro
Lestropie May 16, 2024
c531a0a
BEP016: Reformat demonstrative examples
Lestropie May 16, 2024
9cb1e09
BEP016: Don't use filesystem macros for templates
Lestropie May 17, 2024
f115ec4
BEP016: Comment filesystem macros
Lestropie May 17, 2024
1fb734f
Merge pull request #105 from bids-standard/filesystem_macros
Lestropie May 17, 2024
b093ac1
DWI models: Update bvec reference
Lestropie Jun 5, 2024
d56816d
Merge branch 'master' into bep-016
arokem Jun 5, 2024
bda570f
Merge remote-tracking branch 'origin/bep-016' into bvec_reference_axes
Lestropie Jun 5, 2024
1ce38c2
Merge pull request #98 from bids-standard/bvec_reference_axes
Lestropie Jun 5, 2024
edab0fd
Merge branch 'master' into bep-016
arokem Aug 20, 2024
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BEP016: Small fixes, and try to get links to headers working
Lestropie authored and oesteban committed Sep 18, 2019

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commit 1beda57186f7d61c8c7c17f46e80c8a9657f2923
180 changes: 91 additions & 89 deletions src/05-derivatives/05-diffusion-derivatives.md
Original file line number Diff line number Diff line change
@@ -3,7 +3,7 @@
## Preprocessed diffusion-weighted images

Multiple different versions of preprocessing can be stored for the same source
data. To distinguish them from each other, the `desc` fileneame keyword can be
data. To distinguish them from each other, the `desc` filename keyword can be
used. Details of preprocessing performed for each variation of the processing
should be included in the pipeline documentation.

@@ -84,16 +84,16 @@ which has its own unique requirements with respect to:
```

- File "`<source_keywords>[_space-<space>][_desc-<label>]_<model>.json`"
provides basic model information and [input model parameters].
provides basic model information and [input model parameters](#input-model-parameters).

- OPTIONAL file "`<source_keywords>[_space-<space>][_desc-<label>]_parameter-<extparam*>_<model>.json`"
provides only information or parameters relevant to derivation of the
relevant [extrinsic model parameter] based on prior estimates of
[intrinsic model parameters].
relevant [extrinsic model parameter](#extrinsic-model-parameters) based
on prior estimates of [intrinsic model parameters](#intrinsic-model-parameters).

- If all [intrinsic model parameters] are contained within a single image
file, field "`_parameter-*`" MUST be omitted (for intrinsic parameter
image only):
- If all [intrinsic model parameters](#intrinsic-model-parameters) are
contained within a single image file, field "`_parameter-*`" MUST be
omitted (for intrinsic parameter image only):

```Text
<pipeline_name>/
@@ -111,12 +111,12 @@ which has its own unique requirements with respect to:
solitary value is defined in each 3D image voxel is referred to here as a
"scalar" image.
1. Directionally-Encoded Colours (DEC)
1. Directionally-Encoded Colours
4D image with three volumes, intended to be interpreted as red, green
and blue colour intensities for visualisation
\[[Pajevic1999](#pajevic1999)\]. Image data MUST NOT contain negative
values.
values. Abbreviation "DEC" is regularly used to refer to such data.
1. Spherical coordinates
@@ -135,12 +135,13 @@ which has its own unique requirements with respect to:
1. Inclination / polar angle, in radians, relative to the zenith
direction being the positive direction of the *third* reference
axis (see [orientation specification]);
axis (see [orientation specification](#orientation-specification));
1. Azimuth angle, in radians, orthogonal to the zenith direction,
with value of 0.0 corresponding to the *first* reference axis
(see [orientation specification]), increasing according to the
right-hand rule about the zenith direction.
(see [orientation specification](#orientation-specification)),
increasing according to the right-hand rule about the zenith
direction.
Number of image volumes is equal to (3x*N*), where *N* is the maximum
number of discrete orientations in any voxel in the image.
@@ -166,11 +167,11 @@ which has its own unique requirements with respect to:
Number of image volumes is equal to (3x*N*), where *N* is the maximum
number of discrete orientations in any voxel in the image.
1. Spherical Harmonics (SH)
1. Spherical Harmonics
4D image where data across volumes within each voxel represent a
continuous function spanning the 2-sphere as coefficient values using a
spherical harmonic basis.
spherical harmonic (SH) basis.
Number of image volumes depends on the spherical harmonic basis employed,
and the maximal spherical harmonic degree *l<sub>max</sub>*.
@@ -184,27 +185,27 @@ which has its own unique requirements with respect to:
on the unit sphere along which samples for the function in each voxel
are provided.
1. Probability Distribution Functions (PDF)
1. Probability Distribution Functions
1. Parameter vectors
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 model parameters] section.
the [intrinsic model parameters](#intrinsic-model-parameters) section.
### Orientation specification
| **Key name** | **Relevant [data representations]** | **Description** |
| --------------------------- | ------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| `AntipodalSymmetry` | [Spherical coordinates], [3-vectors], [spherical harmonics], [amplitudes], [probability distribution functions], [parameter vectors] | OPTIONAL. Boolean. Indicates whether orientation information should be interpreted as being antipodally symmetric. Assumed to be True if omitted. If True, no constraints are imposed with respect to the domain on the 2-sphere in which orientations may be specified. |
| `Directions` | [Amplitudes] | REQUIRED. List. Data are either [spherical coordinates] ([directions only]) or [3-vectors] with unit norm. Defines the dense directional basis set on which samples of a spherical function within each voxel are provided. |
| `FillValue` | [Spherical coordinates], [3-vectors] | 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] | REQUIRED. String; allowed values: { `dec`, `unitspherical`, `spherical`, `unit3vector`, `3vector`, `sh`, `amp`, `param` }. The [data representation] used to encode orientation information. |
| `ReferenceAxes` | All except [scalar] | REQUIRED. String; allowed values: { `ijk`, `xyz` }. Indicates whether the NIfTI image axes, or scanner-space axes, are used as reference for orientation information. |
| `SphericalHarmonicBasis` | [Spherical harmonics (SH)] | REQUIRED. String; allowed values: { `MRtrix3`, `Descoteaux` }. Basis by which to define the interpretation of image values across volumes as spherical harmonic coefficients. |
| `SphericalHarmonicDegree` | [Spherical harmonics (SH)] | REQUIRED. Integer. Maximal degree of the spherical harmonic basis employed. |
| **Key name** | **Relevant [data representations]** | **Description** |
| --------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| `AntipodalSymmetry` | [Spherical coordinates](#spherical-coordinates), [3-vectors](#3-vectors), [spherical harmonics](#spherical-harmonics), [amplitudes](#amplitudes), [probability distribution functions](#probability-distribution-functions), [parameter vectors](#parameter-vectors) | OPTIONAL. Boolean. Indicates whether orientation information should be interpreted as being antipodally symmetric. Assumed to be True if omitted. If True, no constraints are imposed with respect to the domain on the 2-sphere in which orientations may be specified. |
| `Directions` | [Amplitudes] | REQUIRED. List. Data are either [spherical coordinates (directions only)](#directions-only) or [3-vectors](#3-vectors) with unit norm. Defines the dense directional basis set on which samples of a spherical function within each voxel are provided. |
| `FillValue` | [Spherical coordinates](#spherical-coordinates), [3-vectors](#3-vectors) | 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](#scalar) | REQUIRED. String; allowed values: { `dec`, `unitspherical`, `spherical`, `unit3vector`, `3vector`, `sh`, `amp`, `param` }. The [data representation](#data-representations) used to encode orientation information. |
| `ReferenceAxes` | All except [scalar](#scalar) | REQUIRED. String; allowed values: { `ijk`, `xyz` }. Indicates whether the NIfTI image axes, or scanner-space axes, are used as reference for orientation information. |
| `SphericalHarmonicBasis` | [Spherical harmonics](#spherical-harmonics) | REQUIRED. String; allowed values: { `MRtrix3`, `Descoteaux` }. Basis by which to define the interpretation of image values across volumes as spherical harmonic coefficients. |
| `SphericalHarmonicDegree` | [Spherical harmonics](#spherical-harmonics) | REQUIRED. Integer. Maximal degree of the spherical harmonic basis employed. |
#### Spherical Harmonics (SH) bases
#### Spherical Harmonics bases
- `MRtrix3`
@@ -272,21 +273,21 @@ 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.
| Model label | Full Name | [Data representation] |
| ----------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `bs` | Ball-and-Stick(s) model \[[Behrens2003](#behrens2003)\],\[[Behrens2007](#behrens2007)\],\[[Jbabdi2012](#jbabdi2012)\] | One [spherical coordinates] image with parameter name "`sticks`", providing both fibre volume fractions and orientations using polar angles;<br>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 |
| `csa` | Constant Solid Angle \[[Aganj2010](#aganj2010)\] | [Spherical harmonics (SH)] image |
| `csd` | Constrained Spherical Deconvolution \[[Tournier2007](#tournier2007)\],\[[Descoteaux2009](#descoteaux2009)\],\[[Jeurissen2014](#jeurissen2014)\] | [Spherical harmonics (SH)] image<br>If a multi-tissue decomposition is performed, provide one individual 4D image per tissue, with "`_desc-<desc>`" filename field being an abbreviation of the tissue estimated by that particular ODF |
| `dki` | Diffusion Kurtosis Imaging \[[Jensen2005](#jensen2005)\] | Single [parameter vectors] image with 21 volumes in the order: *D<sub>xx</sub>*, *D<sub>xy</sub>*, *D<sub>xz</sub>*, *D<sub>yy</sub>*, *D<sub>yz</sub>*, *D<sub>zz</sub>*, *W<sub>xxxx</sub>*, *W<sub>yyyy</sub>*, *W<sub>zzzz</sub>*, *W<sub>xxxy</sub>*, *W<sub>xxxz</sub>*, *W<sub>xyyy</sub>*, *W<sub>yyyz</sub>*, *W<sub>xzzz</sub>*, *W<sub>yzzz</sub>*, *W<sub>xxyy</sub>*, *W<sub>xxzz</sub>*, *W<sub>yyzz</sub>*, *W<sub>xxyz</sub>*, *W<sub>xyyz</sub>*, *W<sub>xyzz</sub>* (*D* is the diffusion tensor, *W* is the kurtosis tensor)<br>OR<br>6 diffusion tensor coefficients as [parameter vectors] image with parameter name "`tensor`";<br>15 kurtosis tensor coefficients as [parameter vectors] image with parameter name "`kurtosis`";<br>Optional: estimated *b*=0 intensity as scalar image with parameter name "`bzero`" |
| `dsi` | Diffusion Spectrum Imaging \[[Wedeen2008](#wedeen2008)\],\[[Paquette2017](paquette2017)\] | [Probability distribution functions (PDF)] | |
| `dti` | Diffusion Tensor Imaging \[[Basser1994](#basser1994)\] | Single [parameter vectors] image with 6 volumes in the order: *D<sub>xx</sub>*, *D<sub>xy</sub>*, *D<sub>xz</sub>*, *D<sub>yy</sub>*, *D<sub>yz</sub>*, *D<sub>zz</sub>*<br>OR<br>Tensor coefficients as [parameter vectors] image with parameter name "`tensor`";<br>Estimated *b*=0 intensity as [scalar] image with parameter name "`bzero`" |
| `forecast` | Fiber ORientation Estimated using Continuous Axially Symmetric Tensors \[[Zuchelli2017](#zuchelli2017)\] | [Spherical harmonics (SH)] image |
| `fwdti` | Free water DTI \[[Hoy2015](#hoy2015)\] | One [parameter vectors] image with parameter name "`tensor`", containing 6 volumes in the order: *Dc<sub>xx</sub>*, *Dc<sub>xy</sub>*, *Dc<sub>xz</sub>*, *Dc<sub>yy</sub>*, *Dc<sub>yz</sub>*, *Dc<sub>zz</sub>* (*Dc* is the free-water-corrected diffusion tensor);<br>One scalar image with parameter name "`fwf`" corresponding to the estimated free water fraction |
| `mapmri` | Mean Apparent Propagator MRI \[[Ozarslan2013](#ozarslan2013)\] | |
| `noddi` | Neurite Orientation Dispersion and Density Imaging \[[Zhang2012](#zhang2012)\],\[[Daducci2015](#daducci2015)\] | Three scalar images, with parameter names equal to {"`icvf`", "`isovf`", "`od`"} (ICVF is the “intracellular volume fraction” (also known as NDI); ISOVF is the "isotropic component volume fraction"; OD is the “orientation dispersion” (the variance of the Watson distribution; also known as ODI));<br>One [3-vectors] image with parameter name "`direction`" to provide the estimated fibre orientation |
| `qbi` | Q-Ball Imaging \[[Tuch2004](#tuch2004)\], \[[Hess2006](#hess2006)\] | Single [amplitudes] image<br>OR<br>Single [spherical harmonics (SH)] image |
| `shore` | Simple Harmonic Oscillator-based Reconstruction and Estimation \[[Ozarslan2008](#ozarslan2008)\] | |
| `wmti` | White Matter Tract Integrity \[[Fieremans2011](#fieremans2011)\] | One [parameter vectors] image with parameter name "`coeffs`", with 33 volumes in the order: *D<sub>xx</sub>*, *D<sub>xy</sub>*, *D<sub>xz</sub>*, *D<sub>yy</sub>*, *D<sub>yz</sub>*, *D<sub>zz</sub>*, *W<sub>xxxx</sub>*, *W<sub>yyyy</sub>*, *W<sub>zzzz</sub>*, *W<sub>xxxy</sub>*, *W<sub>xxxz</sub>*, *W<sub>xyyy</sub>*, *W<sub>yyyz</sub>*, *W<sub>xzzz</sub>*, *W<sub>yzzz</sub>*, *W<sub>xxyy</sub>*, *W<sub>xxzz</sub>*, *W<sub>yyzz</sub>*, *W<sub>xxyz</sub>*, *W<sub>xyyz</sub>*, *W<sub>xyzz</sub>*, *Dh<sub>xx</sub>*, *Dh<sub>xy</sub>*, *Dh<sub>xz</sub>*, *Dh<sub>yy</sub>*, *Dh<sub>yz</sub>*, *Dh<sub>zz</sub>*, *Dr<sub>xx</sub>*, *Dr<sub>xy</sub>*, *Dr<sub>xz</sub>*, *Dr<sub>yy</sub>*, *Dr<sub>yz</sub>*, *Dr<sub>zz</sub>* (*D* is the diffusion tensor and *W* is the kurtosis tensor);<br>One scalar image with parameter name "`awf`", representing the estimated axonal water fraction |
| Model label | Full Name | [Data representation](#data-representations) |
| ----------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `bs` | Ball-and-Stick(s) model \[[Behrens2003](#behrens2003)\],\[[Behrens2007](#behrens2007)\],\[[Jbabdi2012](#jbabdi2012)\] | One [spherical coordinates](#spherical-coordinates) image with parameter name "`sticks`", providing both fibre volume fractions and orientations using polar angles;<br>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 |
| `csa` | Constant Solid Angle \[[Aganj2010](#aganj2010)\] | [Spherical harmonics](#spherical-harmonics) image |
| `csd` | Constrained Spherical Deconvolution \[[Tournier2007](#tournier2007)\],\[[Descoteaux2009](#descoteaux2009)\],\[[Jeurissen2014](#jeurissen2014)\] | [Spherical harmonics](#spherical-harmonics) image<br>If a multi-tissue decomposition is performed, provide one individual 4D image per tissue, with "`_desc-<desc>`" filename field being an abbreviation of the tissue estimated by that particular ODF |
| `dki` | Diffusion Kurtosis Imaging \[[Jensen2005](#jensen2005)\] | Single [parameter vectors] image with 21 volumes in the order: *D<sub>xx</sub>*, *D<sub>xy</sub>*, *D<sub>xz</sub>*, *D<sub>yy</sub>*, *D<sub>yz</sub>*, *D<sub>zz</sub>*, *W<sub>xxxx</sub>*, *W<sub>yyyy</sub>*, *W<sub>zzzz</sub>*, *W<sub>xxxy</sub>*, *W<sub>xxxz</sub>*, *W<sub>xyyy</sub>*, *W<sub>yyyz</sub>*, *W<sub>xzzz</sub>*, *W<sub>yzzz</sub>*, *W<sub>xxyy</sub>*, *W<sub>xxzz</sub>*, *W<sub>yyzz</sub>*, *W<sub>xxyz</sub>*, *W<sub>xyyz</sub>*, *W<sub>xyzz</sub>* (*D* is the diffusion tensor, *W* is the kurtosis tensor)<br>OR<br>6 diffusion tensor coefficients as [parameter vectors](#parameter-vectors) image with parameter name "`tensor`";<br>15 kurtosis tensor coefficients as [parameter vectors](#parameter-vectors) image with parameter name "`kurtosis`";<br>Optional: estimated *b*=0 intensity as scalar image with parameter name "`bzero`" |
| `dsi` | Diffusion Spectrum Imaging \[[Wedeen2008](#wedeen2008)\],\[[Paquette2017](paquette2017)\] | [Probability distribution functions](#probability-distribution-functions) | |
| `dti` | Diffusion Tensor Imaging \[[Basser1994](#basser1994)\] | Single [parameter vectors](#parameter-vectors) image with 6 volumes in the order: *D<sub>xx</sub>*, *D<sub>xy</sub>*, *D<sub>xz</sub>*, *D<sub>yy</sub>*, *D<sub>yz</sub>*, *D<sub>zz</sub>*<br>OR<br>Tensor coefficients as [parameter vectors] image with parameter name "`tensor`";<br>Estimated *b*=0 intensity as [scalar](#scalar) image with parameter name "`bzero`" |
| `forecast` | Fiber ORientation Estimated using Continuous Axially Symmetric Tensors \[[Zuchelli2017](#zuchelli2017)\] | [Spherical harmonics](#spherical-harmonics) image |
| `fwdti` | Free water DTI \[[Hoy2015](#hoy2015)\] | One [parameter vectors](#parameter-vectors) image with parameter name "`tensor`", containing 6 volumes in the order: *Dc<sub>xx</sub>*, *Dc<sub>xy</sub>*, *Dc<sub>xz</sub>*, *Dc<sub>yy</sub>*, *Dc<sub>yz</sub>*, *Dc<sub>zz</sub>* (*Dc* is the free-water-corrected diffusion tensor);<br>One scalar image with parameter name "`fwf`" corresponding to the estimated free water fraction |
| `mapmri` | Mean Apparent Propagator MRI \[[Ozarslan2013](#ozarslan2013)\] | |
| `noddi` | Neurite Orientation Dispersion and Density Imaging \[[Zhang2012](#zhang2012)\],\[[Daducci2015](#daducci2015)\] | Three [scalar](#scalar) images, with parameter names equal to {"`icvf`", "`isovf`", "`od`"} (ICVF is the “intracellular volume fraction” (also known as NDI); ISOVF is the "isotropic component volume fraction"; OD is the “orientation dispersion” (the variance of the Watson distribution; also known as ODI));<br>One [3-vectors](#3-vectors) image with parameter name "`direction`" to provide the estimated fibre orientation |
| `qbi` | Q-Ball Imaging \[[Tuch2004](#tuch2004)\], \[[Hess2006](#hess2006)\] | Single [amplitudes](#amplitudes) image<br>OR<br>Single [spherical harmonics](#spherical-harmonics) image |
| `shore` | Simple Harmonic Oscillator-based Reconstruction and Estimation \[[Ozarslan2008](#ozarslan2008)\] | |
| `wmti` | White Matter Tract Integrity \[[Fieremans2011](#fieremans2011)\] | One [parameter vectors](#parameter-vectors) image with parameter name "`coeffs`", with 33 volumes in the order: *D<sub>xx</sub>*, *D<sub>xy</sub>*, *D<sub>xz</sub>*, *D<sub>yy</sub>*, *D<sub>yz</sub>*, *D<sub>zz</sub>*, *W<sub>xxxx</sub>*, *W<sub>yyyy</sub>*, *W<sub>zzzz</sub>*, *W<sub>xxxy</sub>*, *W<sub>xxxz</sub>*, *W<sub>xyyy</sub>*, *W<sub>yyyz</sub>*, *W<sub>xzzz</sub>*, *W<sub>yzzz</sub>*, *W<sub>xxyy</sub>*, *W<sub>xxzz</sub>*, *W<sub>yyzz</sub>*, *W<sub>xxyz</sub>*, *W<sub>xyyz</sub>*, *W<sub>xyzz</sub>*, *Dh<sub>xx</sub>*, *Dh<sub>xy</sub>*, *Dh<sub>xz</sub>*, *Dh<sub>yy</sub>*, *Dh<sub>yz</sub>*, *Dh<sub>zz</sub>*, *Dr<sub>xx</sub>*, *Dr<sub>xy</sub>*, *Dr<sub>xz</sub>*, *Dr<sub>yy</sub>*, *Dr<sub>yz</sub>*, *Dr<sub>zz</sub>* (*D* is the diffusion tensor and *W* is the kurtosis tensor);<br>One [scalar](#scalar) image with parameter name "`awf`", representing the estimated axonal water fraction |
The JSON sidecar for the intrinsic diffusion model parameters may contain
the following key/value pairs irrespective of the particular model:
@@ -317,8 +318,8 @@ field depends on the particular model used.
"`Parameters`" fields that may be applicable to multiple models:
| **Key name** | **Description** |
| ---------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| **Key name** | **Description** |
| ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| FitMethod | OPTIONAL. String. The optimisation procedure used to fit the intrinsic model parameters to the empirical diffusion-weighted signal. Options are: "`ols`" (Ordinary Least Squares); "`wls`" (Weighted Least Squares); "`iwls`" (Iterative Weighted Least Squares); "`nlls`" (Non-Linear Least Squares). |
| Iterations | OPTIONAL. Integer. The number of iterations used for any form of model fitting procedure where the number of iterations is a fixed input parameter. |
| OutlierRejection | OPTIONAL. Boolean. Value indicating whether or not rejection of outlier values was performed during fitting of the intrinsic model parameters. |
@@ -346,8 +347,8 @@ Reserved keywords for models built into the specification are as follows:
- Vector of floating-point values, where values correspond to the response function coefficient for each consecutive even zonal spherical harmonic degree starting from zero (in this case field "`Shells`" should contain a single integer value);
- Matrix of floating-point values: 1 row per unique *b*-value as listed in "`Shells`"; 1 column per even zonal spherical harmonic degree starting from zero; if there are a different number of non-zero zonal spherical harmonic coefficients for different *b*-values, these must be padded with zeroes such that all rows contain the same number of columns.
- `ResponseFunctionTensor`: Vector of 4 floating-point values: three tensor eigenvalues, then reference *b*=0 intensity
- `SphericalHarmonicBasis`: String. Options are: { `MRtrix3`, `Descoteaux` }. Details are provided in the [Spherical harmonics (SH) bases] section.
- `SphericalHarmonicDegree`: 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].
- `SphericalHarmonicBasis`: String. Options are: { `MRtrix3`, `Descoteaux` }. Details are provided in the [Spherical harmonics bases](#spherical-harmonics-bases) section.
- `SphericalHarmonicDegree`: 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](#spherical-harmonics).
- `Tissue`: String. A more verbose description for the tissue estimated via this specific ODF.
- `dsi` :
@@ -408,36 +409,37 @@ Reserved keywords for models built into the specification are as follows:
### Extrinsic model parameters
| `<parameter>` value | Description | [Data representation] | Possible Model sources | Unit or scale |
| ------------------- | ---------------------------------------------------------------------- | --------------------- | ----------------------------------------------- | -------------------------------------------------------------- |
| `ad` | Axial Diffusivity (also called parallel diffusivity) | Scalar | { `dki`, `dti`, `forecast`, `fwdti`, `wmti` } | \mu m<sup>2</sup>.ms<sup>-1</sup> <sup>[1](#diffusivity)</sup> |
| `ak` | Axial kurtosis | Scalar | { `dki`, `wmti` } | Unitless |
| `afdtotal` | Total Apparent Fibre Density (AFD) \[[Calamante2015](#calamante2015)\] | Scalar | { `csd` } | Unitless |
| `cl` | Tensor linearity \[[Westin1997](#westin1997)\] | Scalar | { `dki`, `dti`, `fwdti`, `wmti` } | |
| `cp` | Tensor planarity \[[Westin1997](#westin1997)\] | Scalar | { `dki`, `dti`, `fwdti`, `wmti` } | |
| `cs` | Tensor sphericity \[[Westin1997](#westin1997)\] | Scalar | { `dki`, `dti`, `fwdti`, `wmti` } | |
| `evec` | Eigenvector(s) | [3-vectors] | { `dki`, `dti`, `fwdti`, `wmti` } | \mu m<sup>2</sup>.ms<sup>-1</sup> <sup>[1](#diffusivity)</sup> |
| `fa` | Fractional Anisotropy \[[Basser1996](#basser1996)\] | Scalar | { `dki`, `dti`, `forecast`, `fwdti`, `wmti` } | Proportion \[0.0-1.0\] |
| `fsum` | Sum of partial volume fractions of stick components | Scalar | { `bs` } | Volume fraction \[0.0-1.0\] |
| `gfa` | Generalized Fractional Anisotropy \[[Tuch2004](#tuch2004)\] | Scalar | { `csa`, `csd`, `forecast`, `mapmri`, `shore` } | Proportion \[0.0-1.0\] |
| `md` | Mean diffusivity (also called apparent diffusion coefficient, ADC) | Scalar | { `dki`, `dti`, `forecast`, `fwdti`, `wmti` } | \mu m<sup>2</sup>.ms<sup>-1</sup> <sup>[1](#diffusivity)</sup> |
| `mk` | Mean kurtosis | Scalar | { `dki`, `wmti` } | Unitless |
| `mode` | Mode of the tensor | Scalar | { `dki`, `dti`, `fwdti`, `wmti` } | |
| `msd` | Mean-Squared Displacement | Scalar | { `mapmri`, `shore` } | |
| `pdf` | Diffusion propagator | [3-vectors] | | |
| `peak` | Direction(s) and amplitude(s) of ODF maximum (maxima) | [3-vectors] | { `csa`, `csd`, `forecast`, `shore` } | Same units as ODF |
| `rd` | Radial Diffusivity (also called perpendicular diffusivity) | Scalar | { `dki`, `dti`, `forecast`, `fwdti`, `wmti` } | \mu m<sup>2</sup>.ms<sup>-1</sup> <sup>[1](#diffusivity)</sup> |
| `rk` | Radial kurtosis | Scalar | { `dki`, `wmti` } | Unitless |
| `rtap` | Return To Axis Probability | Scalar | { `mapmri` } | Probability \[0.0-1.0\] |
| `rtop` | Return To Origin Probability | Scalar | { `shore` } | Probability \[0.0-1.0\] |
| `rtpp` | Return To Plane Probability | Scalar | { `mapmri` } | Probability \[0.0-1.0\] |
| `tort` | Tortuosity of extra-cellular space | Scalar | { `dki` } | |
While not explicitly included in the table above, *any* scalar extrinsic
parameter can theoretically be combined with a separate source of orientation
information from the diffusion model in order to produce a
[directionally-encoded colours (DEC)], [spherical coordinates] or
[3-vectors] image.
| `<parameter>` value | Description | [Data representation] | Possible Model sources | Unit or scale |
| ------------------- | ---------------------------------------------------------------------- | ----------------------- | ----------------------------------------------- | -------------------------------------------------------------- |
| `ad` | Axial Diffusivity (also called parallel diffusivity) | [Scalar](#scalar) | { `dki`, `dti`, `forecast`, `fwdti`, `wmti` } | \mu m<sup>2</sup>.ms<sup>-1</sup> <sup>[1](#diffusivity)</sup> |
| `ak` | Axial kurtosis | [Scalar](#scalar) | { `dki`, `wmti` } | Unitless |
| `afdtotal` | Total Apparent Fibre Density (AFD) \[[Calamante2015](#calamante2015)\] | [Scalar](#scalar) | { `csd` } | Unitless |
| `cl` | Tensor linearity \[[Westin1997](#westin1997)\] | [Scalar](#scalar) | { `dki`, `dti`, `fwdti`, `wmti` } | |
| `cp` | Tensor planarity \[[Westin1997](#westin1997)\] | [Scalar](#scalar) | { `dki`, `dti`, `fwdti`, `wmti` } | |
| `cs` | Tensor sphericity \[[Westin1997](#westin1997)\] | [Scalar](#scalar) | { `dki`, `dti`, `fwdti`, `wmti` } | |
| `evec` | Eigenvector(s) | [3-vectors](#3-vectors) | { `dki`, `dti`, `fwdti`, `wmti` } | \mu m<sup>2</sup>.ms<sup>-1</sup> <sup>[1](#diffusivity)</sup> |
| `fa` | Fractional Anisotropy \[[Basser1996](#basser1996)\] | [Scalar](#scalar) | { `dki`, `dti`, `forecast`, `fwdti`, `wmti` } | Proportion \[0.0-1.0\] |
| `fsum` | Sum of partial volume fractions of stick components | [Scalar](#scalar) | { `bs` } | Volume fraction \[0.0-1.0\] |
| `gfa` | Generalized Fractional Anisotropy \[[Tuch2004](#tuch2004)\] | [Scalar](#scalar) | { `csa`, `csd`, `forecast`, `mapmri`, `shore` } | Proportion \[0.0-1.0\] |
| `md` | Mean diffusivity (also called apparent diffusion coefficient, ADC) | [Scalar](#scalar) | { `dki`, `dti`, `forecast`, `fwdti`, `wmti` } | \mu m<sup>2</sup>.ms<sup>-1</sup> <sup>[1](#diffusivity)</sup> |
| `mk` | Mean kurtosis | [Scalar](#scalar) | { `dki`, `wmti` } | Unitless |
| `mode` | Mode of the tensor | [Scalar](#scalar) | { `dki`, `dti`, `fwdti`, `wmti` } | |
| `msd` | Mean-Squared Displacement | [Scalar](#scalar) | { `mapmri`, `shore` } | |
| `pdf` | Diffusion propagator | [3-vectors](#3-vectors) | | |
| `peak` | Direction(s) and amplitude(s) of ODF maximum (maxima) | [3-vectors](#3-vectors) | { `csa`, `csd`, `forecast`, `shore` } | Same units as ODF |
| `rd` | Radial Diffusivity (also called perpendicular diffusivity) | [Scalar](#scalar) | { `dki`, `dti`, `forecast`, `fwdti`, `wmti` } | \mu m<sup>2</sup>.ms<sup>-1</sup> <sup>[1](#diffusivity)</sup> |
| `rk` | Radial kurtosis | [Scalar](#scalar) | { `dki`, `wmti` } | Unitless |
| `rtap` | Return To Axis Probability | [Scalar](#scalar) | { `mapmri` } | Probability \[0.0-1.0\] |
| `rtop` | Return To Origin Probability | [Scalar](#scalar) | { `shore` } | Probability \[0.0-1.0\] |
| `rtpp` | Return To Plane Probability | [Scalar](#scalar) | { `mapmri` } | Probability \[0.0-1.0\] |
| `tort` | Tortuosity of extra-cellular space | [Scalar](#scalar) | { `dki` } | |
While not explicitly included in the table above, *any* [Scalar](#scalar)
extrinsic parameter can theoretically be combined with a separate source
of orientation information from the diffusion model in order to produce a
[directionally-encoded colours (DEC)](#directionally-encoded-colours),
[spherical coordinates](#spherical-coordinates) or
[3-vectors](#3-vectors) image.
## Demonstrative examples
@@ -451,7 +453,7 @@ information from the diffusion model in order to produce a
sub-01_dti.json
```
Dimensions of NIfTI image "`sub-01_dti.nii.gz`": *I*x*J*x*K*x6 ([parameter vectors])
Dimensions of NIfTI image "`sub-01_dti.nii.gz`": *I*x*J*x*K*x6 ([parameter vectors](#parameter-vectors))
Contents of JSON file:
@@ -482,9 +484,9 @@ information from the diffusion model in order to produce a
sub-01_csd.json
```
Dimensions of NIfTI image "`sub-01_desc-wm_csd.nii.gz`": *I*x*J*x*K*x45 ([spherical harmonics (SH)])
Dimensions of NIfTI image "`sub-01_desc-gm_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics (SH)])
Dimensions of NIfTI image "`sub-01_desc-csf_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics (SH)])
Dimensions of NIfTI image "`sub-01_desc-wm_csd.nii.gz`": *I*x*J*x*K*x45 ([spherical harmonics](#spherical-harmonics))
Dimensions of NIfTI image "`sub-01_desc-gm_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#spherical-harmonics))
Dimensions of NIfTI image "`sub-01_desc-csf_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#spherical-harmonics))
Contents of file "`sub-01_csd.json`" (common to all intrinsic model parameter images):
@@ -544,10 +546,10 @@ information from the diffusion model in order to produce a
sub-01_noddi.json
```
Dimensions of NIfTI image "`sub-01_parameter-icvf_noddi.nii.gz`": *I*x*J*x*K* ([scalar])
Dimensions of NIfTI image "`sub-01_parameter-isovf_noddi.nii.gz`": *I*x*J*x*K* ([scalar])
Dimensions of NIfTI image "`sub-01_parameter-od_noddi.nii.gz`": *I*x*J*x*K* ([scalar])
Dimensions of NIfTI image "`sub-01_parameter-direction_noddi.nii.gz`": *I*x*J*x*K*x3 ([3-vectors])
Dimensions of NIfTI image "`sub-01_parameter-icvf_noddi.nii.gz`": *I*x*J*x*K* ([scalar](#scalar))
Dimensions of NIfTI image "`sub-01_parameter-isovf_noddi.nii.gz`": *I*x*J*x*K* ([scalar](#scalar))
Dimensions of NIfTI image "`sub-01_parameter-od_noddi.nii.gz`": *I*x*J*x*K* ([scalar](#scalar))
Dimensions of NIfTI image "`sub-01_parameter-direction_noddi.nii.gz`": *I*x*J*x*K*x3 ([3-vectors](#3-vectors))
Contents of file "`sub-01_noddi.json`" (common to all intrinsic model parameter images):
@@ -586,11 +588,11 @@ information from the diffusion model in order to produce a
sub-01_bs.json
```
Dimensions of NIfTI image "`sub-01_desc-mean_parameter-bzero_bs.nii.gz`": *I*x*J*x*K* ([scalar])
Dimensions of NIfTI image "`sub-01_desc-mean_parameter-dmean_bs.nii.gz`": *I*x*J*x*K* ([scalar])
Dimensions of NIfTI image "`sub-01_desc-mean_parameter-dstd_bs.nii.gz`": *I*x*J*x*K* ([scalar])
Dimensions of NIfTI image "`sub-01_desc-mean_parameter-sticks_bs.nii.gz`": *I*x*J*x*K*x9 ([spherical coordinates], distance from origin encodes fibre volume fraction)
Dimensions of NIfTI image "`sub-01_desc-merged_parameter-sticks_bs.nii.gz`": *I*x*J*x*K*x9x50 ([spherical coordinates], distance from origin encodes fibre volume fraction; 50 bootstrap realisations)
Dimensions of NIfTI image "`sub-01_desc-mean_parameter-bzero_bs.nii.gz`": *I*x*J*x*K* ([scalar](#scalar))
Dimensions of NIfTI image "`sub-01_desc-mean_parameter-dmean_bs.nii.gz`": *I*x*J*x*K* ([scalar](#scalar))
Dimensions of NIfTI image "`sub-01_desc-mean_parameter-dstd_bs.nii.gz`": *I*x*J*x*K* ([scalar](#scalar))
Dimensions of NIfTI image "`sub-01_desc-mean_parameter-sticks_bs.nii.gz`": *I*x*J*x*K*x9 ([spherical coordinates](#spherical-coordinates), distance from origin encodes fibre volume fraction)
Dimensions of NIfTI image "`sub-01_desc-merged_parameter-sticks_bs.nii.gz`": *I*x*J*x*K*x9x50 ([spherical coordinates](#spherical-coordinates), distance from origin encodes fibre volume fraction; 50 bootstrap realisations)
Contents of JSON files "`sub-01_desc-mean_parameter-sticks_bs.json`"
and "`sub-01_desc-merged_parameter-sticks_bs.json`" (contents of two
@@ -668,7 +670,7 @@ should be approximately 3.0.
<a name="tournier2007">\[Tournier2007\]</a>: Tournier et al. 2007
<a name="tuch2004">\[Tuch2004\]</a>: Tuch 1994
<a name="tuch2004">\[Tuch2004\]</a>: Tuch 2004
<a name="wedeen2008">\[Wedeen2008\]</a>: Wedeen et al. 2008