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fix: avoid using an atlas name for a segmentation label
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As @CPernet mentioned, the spec was unclear because the example illustrating
``seg-`` was using an atlas name for the label.

I grepped the whole spec for ``seg-`` and only found ``seg-Desikan``.

This commit replaces that label, edits a bit the text around it and
updates the `seg-` entity definition in the schema to be more clear.

Even though its use with ``atlas-`` was already mentioned:

> For atlases, `seg-<label>` distinguish different realizations of a given
> segmentation or parcellation.
> For example, the [Yeo 2011 atlas](https://doi.org/10.1152/jn.00338.2011)
> is distributed within *FreeSurfer* with two different parcellations
> (*7 networks* and *17 networks*).

I have updated the entity's description to be more clear (hopefully).
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oesteban committed Oct 7, 2024
1 parent e5e27f1 commit 020918d
Showing 1 changed file with 6 additions and 4 deletions.
10 changes: 6 additions & 4 deletions src/derivatives/imaging.md
Original file line number Diff line number Diff line change
Expand Up @@ -293,9 +293,11 @@ In this case, the mask suffix MUST be used,
the [`label` entity](../appendices/entities.md#label)) SHOULD be used
to specify the masked structure
(see [Common image-derived labels](#common-image-derived-labels)),
and the [`seg` entity](../appendices/entities.md#segmentation) SHOULD be defined.
and the [`seg` entity](../appendices/entities.md#segmentation) specifying
what segmentation generated the mask SHOULD be defined.

For example:
For example, we can specify the gray-matter mask corresponding to the
results of a brain tissue segmentation algorithm as:

<!-- This block generates a file tree.
A guide for using macros can be found at
Expand All @@ -306,8 +308,8 @@ A guide for using macros can be found at
"pipeline": {
"sub-001": {
"anat": {
"sub-001_space-orig_seg-Desikan_label-GM_mask.nii.gz": "",
"sub-001_space-orig_seg-Desikan_label-GM_mask.json": "",
"sub-001_space-orig_seg-tissue_label-GM_mask.nii.gz": "",
"sub-001_space-orig_seg-tissue_label-GM_mask.json": "",
},
},
}
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