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Move the desc- entity to the end of the file name.
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See bids-standard/bids-specification#1895
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@arokem
arokem committed Aug 20, 2024
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88 changes: 44 additions & 44 deletions src/derivatives/05-diffusion-derivatives.md
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Original file line number Diff line number Diff line change
Expand Up @@ -54,12 +54,12 @@ that warrant explicit mention due to their consequence in how they are represent
<pipeline_name>/
sub-<participant_label>/
dwi/
<source_keywords>[_space-<space>]_model-<label>[_desc-<desc>]_param-<label1>_dwimap.nii[.gz]
<source_keywords>[_space-<space>]_model-<label>[_desc-<desc>]_param-<label1>_dwimap.json
<source_keywords>[_space-<space>]_model-<label>[_desc-<desc>]_param-<label2>_dwimap.nii[.gz]
<source_keywords>[_space-<space>]_model-<label>[_desc-<desc>]_param-<label2>_dwimap.json
<source_keywords>[_space-<space>]_model-<label>[_desc-<desc>]_param-<label3>_dwimap.nii[.gz]
<source_keywords>[_space-<space>]_model-<label>[_desc-<desc>]_param-<label3>_dwimap.json
<source_keywords>[_space-<space>]_model-<label>_param-<label1>[_desc-<desc>]_dwimap.nii[.gz]
<source_keywords>[_space-<space>]_model-<label>_param-<label1>[_desc-<desc>]_dwimap.json
<source_keywords>[_space-<space>]_model-<label>_param-<label2>[_desc-<desc>]_dwimap.nii[.gz]
<source_keywords>[_space-<space>]_model-<label>_param-<label2>[_desc-<desc>]_dwimap.json
<source_keywords>[_space-<space>]_model-<label>_param-<label3>[_desc-<desc>]_dwimap.nii[.gz]
<source_keywords>[_space-<space>]_model-<label>_param-<label3>[_desc-<desc>]_dwimap.json
```

- Files "`<source_keywords>_model-<label>_param-<label*>_dwimap.nii[.gz]`"
Expand Down Expand Up @@ -572,41 +572,41 @@ A guide for using macros can be found at
"bedpostx_pipeline": {
"sub-01": {
"dwi": {
"sub-01_model-bs_desc-mean_param-s0_dwimap.nii.gz": "",
"sub-01_model-bs_desc-mean_param-s0_dwimap.json": "",
"sub-01_model-bs_desc-mean_param-polar_dwimap.nii.gz": "",
"sub-01_model-bs_desc-mean_param-polar_dwimap.json": "",
"sub-01_model-bs_desc-mean_param-vector_dwimap.nii.gz": "",
"sub-01_model-bs_desc-mean_param-vector_dwimap.json": "",
"sub-01_model-bs_desc-mean_param-vf_dwimap.nii.gz": "",
"sub-01_model-bs_desc-mean_param-vf_dwimap.json": "",
"sub-01_model-bs_desc-mean_param-vfsum_dwimap.nii.gz": "",
"sub-01_model-bs_desc-mean_param-vfsum_dwimap.json": "",
"sub-01_model-bs_desc-mean_param-diffusivity_dwimap.nii.gz": "",
"sub-01_model-bs_desc-mean_param-diffusivity_dwimap.json": "",
"sub-01_model-bs_desc-mean_param-dstd_dwimap.nii.gz": "",
"sub-01_model-bs_desc-mean_param-dstd_dwimap.json": "",
"sub-01_model-bs_desc-merged_param-polar_dwimap.nii.gz": "",
"sub-01_model-bs_desc-merged_param-polar_dwimap.json": "",
"sub-01_model-bs_desc-merged_param-vf_dwimap.nii.gz": "",
"sub-01_model-bs_desc-merged_param-vf_dwimap.json": "",
"sub-01_model-bs_param-s0_desc-mean_dwimap.nii.gz": "",
"sub-01_model-bs_param-s0_desc-mean_dwimap.json": "",
"sub-01_model-bs_param-polar_desc-mean_dwimap.nii.gz": "",
"sub-01_model-bs_param-polar_desc-mean_dwimap.json": "",
"sub-01_model-bs_param-vector_desc-mean_dwimap.nii.gz": "",
"sub-01_model-bs_param-vector_desc-mean_dwimap.json": "",
"sub-01_model-bs_param-vf_desc-mean_dwimap.nii.gz": "",
"sub-01_model-bs_param-vf_desc-mean_dwimap.json": "",
"sub-01_model-bs_param-vfsum_desc-mean_dwimap.nii.gz": "",
"sub-01_model-bs_param-vfsum_desc-mean_dwimap.json": "",
"sub-01_model-bs_param-diffusivity_desc-mean_dwimap.nii.gz": "",
"sub-01_model-bs_param-diffusivity_desc-mean_dwimap.json": "",
"sub-01_model-bs__param-dstd_desc-mean_dwimap.nii.gz": "",
"sub-01_model-bs__param-dstd_desc-mean_dwimap.json": "",
"sub-01_model-bs_param-polar_desc-merged_dwimap.nii.gz": "",
"sub-01_model-bs_param-polar_desc-merged_dwimap.json": "",
"sub-01_model-bs_param-vf_desc-merged_dwimap.nii.gz": "",
"sub-01_model-bs_param-vf_desc-merged_dwimap.json": "",
},
},
},
}
) }}

Dimensions of NIfTI image "`sub-01_model-bs_desc-mean_param-s0_dwimap.nii.gz`": *I*x*J*x*K* ([scalar](#encoding-scalar))
Dimensions of NIfTI image "`sub-01_model-bs_desc-mean_param-polar_dwimap.nii.gz`": *I*x*J*x*K*x(*2*x*N*) ([spherical coordinates](#encoding-spherical), orientations only; *N* orientations per voxel)
Dimensions of NIfTI image "`sub-01_model-bs_desc-mean_param-vector_dwimap.nii.gz`": *I*x*J*x*K*x(*3*x*N*) ([3-vectors](#encoding-3vectors), unit norm; *N* orientations per voxel)
Dimensions of NIfTI image "`sub-01_model-bs_desc-mean_param-vf_dwimap.nii.gz`": *I*x*J*x*K*x*N* ([scalar](#encoding-scalar); *N* values per voxel)
Dimensions of NIfTI image "`sub-01_model-bs_desc-mean_param-vfsum_dwimap.nii.gz`": *I*x*J*x*K* ([scalar](#encoding-scalar))
Dimensions of NIfTI image "`sub-01_model-bs_desc-mean_param-diffusivity_dwimap.nii.gz`": *I*x*J*x*K* ([scalar](#encoding-scalar))
Dimensions of NIfTI image "`sub-01_model-bs_desc-mean_param-dstd_dwimap.nii.gz`": *I*x*J*x*K* ([scalar](#encoding-scalar))
Dimensions of NIfTI image "`sub-01_model-bs_desc-merged_param-polar_dwimap.nii.gz`": *I*x*J*x*K*x(*2*x*N*)x*R* ([spherical coordinates](#encoding-spherical), orientations only; *N* orientations per voxel; *R* bootstrap realisations)
Dimensions of NIfTI image "`sub-01_model-bs_desc-merged_param-vf_dwimap.nii.gz`": *I*x*J*x*K*x*N*x*R* ([scalar](#encoding-scalar); *N* values per voxel; *R* bootstrap realisations)
Dimensions of NIfTI image "`sub-01_model-bs_param-s0_desc-mean_dwimap.nii.gz`": *I*x*J*x*K* ([scalar](#encoding-scalar))
Dimensions of NIfTI image "`sub-01_model-bs_param-polar_desc-mean_dwimap.nii.gz`": *I*x*J*x*K*x(*2*x*N*) ([spherical coordinates](#encoding-spherical), orientations only; *N* orientations per voxel)
Dimensions of NIfTI image "`sub-01_model-bs_param-vector_desc-mean_dwimap.nii.gz`": *I*x*J*x*K*x(*3*x*N*) ([3-vectors](#encoding-3vectors), unit norm; *N* orientations per voxel)
Dimensions of NIfTI image "`sub-01_model-bs_param-vf_desc-mean_dwimap.nii.gz`": *I*x*J*x*K*x*N* ([scalar](#encoding-scalar); *N* values per voxel)
Dimensions of NIfTI image "`sub-01_model-bs_param-vfsum_desc-mean_dwimap.nii.gz`": *I*x*J*x*K* ([scalar](#encoding-scalar))
Dimensions of NIfTI image "`sub-01_model-bs_param-diffusivity_desc-mean_dwimap.nii.gz`": *I*x*J*x*K* ([scalar](#encoding-scalar))
Dimensions of NIfTI image "`sub-01_model-bs_param-dstd_desc-mean_dwimap.nii.gz`": *I*x*J*x*K* ([scalar](#encoding-scalar))
Dimensions of NIfTI image "`sub-01_model-bs_param-polar_desc-merged_dwimap.nii.gz`": *I*x*J*x*K*x(*2*x*N*)x*R* ([spherical coordinates](#encoding-spherical), orientations only; *N* orientations per voxel; *R* bootstrap realisations)
Dimensions of NIfTI image "`sub-01_model-bs_param-vf_desc-merged_dwimap.nii.gz`": *I*x*J*x*K*x*N*x*R* ([scalar](#encoding-scalar); *N* values per voxel; *R* bootstrap realisations)

Contents of JSON file "`sub-01_model-bs_desc-mean_param-s0_dwimap.json`":
Contents of JSON file "`sub-01_model-bs_param-s0_desc-mean_dwimap.json`":

```JSON
{
Expand All @@ -627,7 +627,7 @@ Contents of JSON file "`sub-01_model-bs_desc-mean_param-s0_dwimap.json`":
}
```

Contents of JSON file "`sub-01_model-bs_desc-mean_param-polar_dwimap.json`":
Contents of JSON file "`sub-01_model-bs_param-polar_desc-mean_dwimap.json`":

```JSON
{
Expand All @@ -653,7 +653,7 @@ Contents of JSON file "`sub-01_model-bs_desc-mean_param-polar_dwimap.json`":
}
```

Contents of JSON file "`sub-01_model-bs_desc-mean_param-vector_dwimap.json`":
Contents of JSON file "`sub-01_model-bs_param-vector_desc-mean_dwimap.json`":

```JSON
{
Expand All @@ -679,7 +679,7 @@ Contents of JSON file "`sub-01_model-bs_desc-mean_param-vector_dwimap.json`":
}
```

Contents of JSON file "`sub-01_model-bs_desc-mean_param-vf_dwimap.json`":
Contents of JSON file "`sub-01_model-bs_param-vf_desc-mean_dwimap.json`":

```JSON
{
Expand All @@ -703,7 +703,7 @@ Contents of JSON file "`sub-01_model-bs_desc-mean_param-vf_dwimap.json`":
}
```

Contents of JSON file "`sub-01_model-bs_desc-mean_param-vfsum_dwimap.json`":
Contents of JSON file "`sub-01_model-bs_param-vfsum_desc-mean_dwimap.json`":

```JSON
{
Expand All @@ -724,7 +724,7 @@ Contents of JSON file "`sub-01_model-bs_desc-mean_param-vfsum_dwimap.json`":
}
```

Contents of JSON file "`sub-01_model-bs_desc-mean_param-diffusivity_dwimap.json`":
Contents of JSON file "`sub-01_model-bs_param-diffusivity_desc-mean_dwimap.json`":

```JSON
{
Expand All @@ -746,7 +746,7 @@ Contents of JSON file "`sub-01_model-bs_desc-mean_param-diffusivity_dwimap.json`
}
```

Contents of JSON file "`sub-01_model-bs_desc-mean_param-dstd_dwimap.json`":
Contents of JSON file "`sub-01_model-bs_param-dstd_desc-mean_dwimap.json`":

```JSON
{
Expand All @@ -767,7 +767,7 @@ Contents of JSON file "`sub-01_model-bs_desc-mean_param-dstd_dwimap.json`":
"Units": "TODO"
}

Contents of JSON file "`sub-01_model-bs_desc-merged_param-polar_dwimap.json`":
Contents of JSON file "`sub-01_model-bs_param-polar_desc-merged_dwimap.json`":

```JSON
{
Expand All @@ -793,7 +793,7 @@ Contents of JSON file "`sub-01_model-bs_desc-merged_param-polar_dwimap.json`":
}
}

Contents of JSON file "`sub-01_model-bs_desc-merged_param-vf_dwimap.json`":
Contents of JSON file "`sub-01_model-bs_param-vf_desc-merged_dwimap.json`":

```JSON
{
Expand Down Expand Up @@ -828,7 +828,7 @@ Notes:
- Care must be taken for images of greater than three dimensions
where additional dimensions do *not* encode anisotropy information:

- In image `"*_desc-mean*_param-vf_*"`,
- In image `"*_param-vf_desc-mean_dwimap.nii.gz"`,
the fourth image axis encodes scalar information across stick components.
Since this is *not* coefficients in some orientation encoding,
but the image possesses more than three axes,
Expand All @@ -838,7 +838,7 @@ Notes:
and therefore the fact that it encodes a scalar parameter
can be robustly inferred without reference to metadata information.

- In image `"sub-01_model-bs_desc-merged_param-vf_dwimap.json"`,
- In image `"sub-01_model-bs_param-vf_desc-merged_dwimap.json"`,
there are two extra image dimensions beyond the three spatial dimensions:
the fourth image axis encodes across the multiple stick components per voxel,
and the fifth axis encodes realisations across bootstraps.
Expand Down

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