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fix: force-push a rewrite addressing minimal changes
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oesteban committed Aug 13, 2019
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Showing 1 changed file with 55 additions and 5 deletions.
60 changes: 55 additions & 5 deletions src/05-derivatives/02-common-data-types.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ Template:
<pipeline_name>/
sub-<participant_label>/
anat|func|dwi/
<source_keywords>[_space-<space>][_desc-<label>]_<suffix>.<ext>
<source_keywords>[_space-<space>][_desc-<label>][_res-<index>][_den-<label>]_<suffix>.<ext>
```

Processing in this context means transformations of data that does not change
Expand All @@ -30,13 +30,22 @@ Note that even though `space` and `desc` are
optional at least one of them needs to be defined to avoid name conflict with
the raw file.

**Sampling**. When two or more instances of a given derivative are provided with resolution
(or surface sampling density) being the only difference between them, then the `res`
(for *resolution* of volumetric data) and/or `den` (for *density* of non-parametric surfaces)
SHOULD be used to avoid name conflicts.
Note that only CIFTI files combining both regularly gridded and surface sampled data
(and their downstream derivatives) are allowed to present both `res` and `den` keywords
simultaneously.

Examples:

```Text
pipeline1/
sub-001/
func/
sub-001_task-rest_run-1_space-MNI305_bold.nii.gz
sub-001_task-rest_run-1_space-MNI305_res-1_bold.nii.gz
sub-001_task-rest_run-1_space-MNI305_res-2_bold.nii.gz
sub-001_task-rest_run-1_space-MNI305_bold.json
```

Expand All @@ -62,9 +71,50 @@ makes them invalid (e.g., if a source 4D image is averaged to create a single
static volume, a SamplingFrequency property would no longer be relevant). In
addition, all processed files include the following metadata JSON fields:

| **Key name** | **Description** |
| ------------- | ----------------------------------------------------------------------------------------------- |
| SkullStripped | REQUIRED. Boolean. Whether the volume was skull stripped (non-brain voxels set to zero) or not. |
| **Key name** | **Description** |
| ------------- | ---------------------------------------------------------------------------------------------------------------------------- |
| SkullStripped | REQUIRED. Boolean. Whether the volume was skull stripped (non-brain voxels set to zero) or not. |
| Resolution | REQUIRED if `res` keyword present. Dictionary of Indexes to Strings. Specifies the interpretation of the resolution keyword. |
| Density | REQUIRED if `den` keyword present. Dictionary of Strings to Strings. Specifies the interpretation of the resolution keyword. |

Example JSON file corresponding to `pipeline1/sub-001/func/sub-001_task-rest_run-1_space-MNI305_bold.json` above:

```JSON
{
"SkullStripped": true,
"Resolution": {
"1": "MNI305 1mm isotropic resolution",
"2": "MNI305 2mm isotropic resolution"
}
}
```

Example of CIFTI files having both `res` and `den` keywords:

```Text
pipeline1/
sub-001/
func/
sub-001_task-rest_run-1_res-1_den-10k_bold.dtseries.nii
sub-001_task-rest_run-1_res-1_den-41k_bold.dtseries.nii
sub-001_task-rest_run-1_bold.dtseries.json
```

And the corresponding `sub-001_task-rest_run-1_bold.dtseries.json` file:

```JSON
{
"SkullStripped": true,
"Resolution": {
"1": "MNI152NLin6Asym 1.6mm isotropic"
},
"Density": {
"10k": "fsaverage5 (5th order icosahedron) - 10242 vertices per hemisphere",
"41k": "fsaverage6 (6th order icosahedron) - 40962 vertices per hemisphere"
}
}
```


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