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Merge branch 'bep-016' of github.com:arokem/bids-specification into bep-016
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‎src/derivatives/diffusion-derivatives.md‎

Lines changed: 37 additions & 21 deletions
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@@ -263,17 +263,21 @@ Some fields are relevant only to specific [orientation encoding types](#orientat
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- Where a field is *not* relevant for the corresponding image,
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that metadata field MUST NOT be specified.
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Auto-generated table:
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{{ MACROS___make_metadata_table(
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{
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"BootstrapAxis": ("OPTIONAL", "Applicable to any orientation encoding type"),
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"Description": ("OPTIONAL", "Applicable to any orientation encoding type"),
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"NonNegativity": ("OPTIONAL", "Applicable to all orientation encoding types except [spherical coordinates](#encoding-spherical) and [3-vectors](#encoding-3vector)"),
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"OrientationEncoding": ("REQUIRED", "Applicable to any orientation encoding type"),
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"ParameterURL": ("OPTIONAL", "Applicable to any orientation encoding type"),
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"ResponseFunction": ("OPTIONAL", "Applicable to [spherical harmonics](#encoding-sh)"),
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"BootstrapAxis": ("OPTIONAL", "Applicable to any orientation encoding type."),
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"Description": ("OPTIONAL", "Applicable to any orientation encoding type."),
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"NonNegativity": ("OPTIONAL", "Applicable to all orientation encoding types except [spherical coordinates](#encoding-spherical) and [3-vectors](#encoding-3vector)."),
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"OrientationEncoding": ("REQUIRED", "Applicable to any orientation encoding type."),
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"ParameterURL": ("OPTIONAL", "Applicable to any orientation encoding type."),
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"ResponseFunction": ("OPTIONAL", "Applicable to [spherical harmonics](#encoding-sh)."),
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}
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) }}
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Manual table:
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| **Key name** | Relevant [orientation encoding types](#orientation-encoding-types) | **Description** |
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| ------------------- | ------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| BootstrapAxis | Any | OPTIONAL. Integer. If multiple realizations of a given parameter are stored in a NIfTI image, this field nominates the image axis (indexed from zero) along which those multiple realizations are stored. |
@@ -285,8 +289,12 @@ Some fields are relevant only to specific [orientation encoding types](#orientat
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Dictionary `"OrientationEncoding"` has the following reserved keywords:
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Auto-generated table:
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{{ MACROS___make_subobject_table("metadata.OrientationEncoding") }}
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Manual table:
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| **Key name** | Relevant [orientation encoding types](#orientation-encoding-types) | **Description** |
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| ----------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| AmplitudesDirections | [Amplitudes](#encoding-amp) | REQUIRED for `"Type": "amplitudes"`; MUST NOT be specified otherwise. List of lists of floats. Data are either [spherical coordinates (directions only)](#encoding-spherical) or [3-vectors](#encoding-3vector) with unit norm. Defines the dense directional basis set on which samples of a spherical function within each voxel are provided. The length of the list must be equal to the number of volumes in the image. |
@@ -309,8 +317,12 @@ Field `"OrientationEncoding"["Reference"]` MUST contain one of the following val
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Dictionary `"ResponseFunction"` has the following reserved keywords:
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Auto-generated table:
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{{ MACROS___make_subobject_table("metadata.ResponseFunction") }}
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Manual table:
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| **Key name** | **LongName** | **Description** |
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| ------------ | ------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| coefficients | coefficients | REQUIRED. Either a list of floats, or a list of lists of floats, depending on the mathematical form of the response function and possibly the data to which it applies; see further below. |
@@ -468,10 +480,12 @@ Contents of JSON file "`sub-01_model-csd_param-wm_dwimap.json`":
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},
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"ParameterURL": "http://www.sciencedirect.com/science/article/pii/S1053811911012092",
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"ResponseFunction": {
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"Coefficients": [ [ 600.2 0.0 0.0 0.0 0.0 0.0 ],
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[ 296.3 -115.2 24.7 -4.4 -0.5 1.8 ],
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[ 199.8 -111.3 41.8 -10.2 2.1 -0.7 ],
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[ 158.3 -98.7 48.4 -17.1 4.5 -1.4 ] ],
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"Coefficients": [
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[600.2, 0.0, 0.0, 0.0, 0.0, 0.0],
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[296.3, -115.2, 24.7, -4.4, -0.5, 1.8],
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[199.8, -111.3, 41.8, -10.2, 2.1, -0.7],
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[158.3, -98.7, 48.4, -17.1, 4.5, -1.4]
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],
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"Type": "zsh"
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}
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}
@@ -495,10 +509,12 @@ Contents of JSON file "`sub-01_model-csd_param-gm_dwimap.json`":
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"Type": "sh",
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},
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"ResponseFunction": {
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"Coefficients": [ [ 1041.0 ],
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[ 436.6 ],
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[ 224.9 ],
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[ 128.8 ] ],
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"Coefficients": [
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[1041.0],
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[436.6],
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[224.9],
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[128.8]
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],
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"Type": "zsh"
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}
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}
@@ -523,10 +539,10 @@ Contents of JSON file "`sub-01_model-csd_param-csf_dwimap.json`":
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},
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"ResponseFunction": {
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"Coefficients": [
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[ 3544.90770181 ],
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[ 134.441453035 ],
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[ 32.0826839826 ],
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[ 29.3674604452 ]
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[3544.90770181],
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[134.441453035],
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[32.0826839826],
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[29.3674604452]
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],
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"Type": "zsh"
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}
@@ -993,8 +1009,8 @@ Notes:
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*N* = ((*l<sub>max</sub>*+1) x (*l<sub>max</sub>*+2)) / 2
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| ***l<sub>max</sub>*** | 0 | 2 | 4 | 6 | 8 | 10 | ... |
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| --------------------- |--:|--:|--: |--: |--: |--: | :--: |
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| ***l<sub>max</sub>*** | 0 | 2 | 4 | 6 | 8 | 10 | ... |
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| --------------------- | --:| --:| --: | --: | --: | --: | :--: |
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| ***N*** | 1 | 6 | 15 | 28 | 45 | 66 | ... |
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- Relationship between maximal degree of *zonal* spherical harmonic
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*N* = 1 + (*l<sub>max</sub>* / 2)
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| ***l<sub>max</sub>*** | 0 | 2 | 4 | 6 | 8 | 10 | ... |
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| --------------------- |--:|--:|--:|--:|--:|--: | :--: |
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| --------------------- | --: | --: | --: | --: | --: | --: | :--: |
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| ***N*** | 1 | 2 | 3 | 4 | 5 | 6 | ... |

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