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enh: generalization of atlas metadata cc/ @jdkent
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@oesteban
oesteban committed Jun 17, 2024
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Expand Up @@ -227,6 +227,71 @@ MIAL67ThalamicNuclei-pipeline/
└─ sub-67_T1w.nii.gz
```

This folder structure can be generally applied when the atlas is derived into several
template spaces, for example:

```Text
MIAL67ThalamicNuclei-pipeline/
├─ atlas-MIAL67ThalamicNuclei_dseg.json
├─ atlas-MIAL67ThalamicNuclei_dseg.tsv
├─ label-ThalamicNuclei_dseg.json
├─ label-ThalamicNuclei_dseg.tsv
├─ tpl-MNI152NLin6Asym/
│ └─ anat/
│ ├─ tpl-MNI152NLin6Asym_atlas-MIAL67ThalamicNuclei_res-1_dseg.nii.gz
│ └─ tpl-MNI152NLin6Asym_atlas-MIAL67ThalamicNuclei_res-1_probseg.nii.gz
├─ tpl-MNI152NLin2009cAsym/
│ └─ anat/
│ ├─ tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_dseg.nii.gz
│ └─ tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_probseg.nii.gz
├─ sub-01
│ └─ anat/
│ ├─ sub-01_label-ThalamicNuclei_dseg.nii.gz
│ ├─ sub-01_space-MNI152NLin2009cAsym_T1w.nii.gz
│ └─ sub-01_T1w.nii.gz
┇
└─ sub-67
└─ anat/
├─ sub-67_label-ThalamicNuclei_dseg.nii.gz
├─ sub-67_space-MNI152NLin2009cAsym_T1w.nii.gz
└─ sub-67_T1w.nii.gz
```

In the case the pipeline generated atlas-based segmentations of the original subjects in
their native T1w space (for example, to compare with the original segmentation given by
`label-ThalamicNuclei`), the above example translates into:

```Text
MIAL67ThalamicNuclei-pipeline/
├─ atlas-MIAL67ThalamicNuclei_dseg.json
├─ atlas-MIAL67ThalamicNuclei_dseg.tsv
├─ label-ThalamicNuclei_dseg.json
├─ label-ThalamicNuclei_dseg.tsv
├─ tpl-MNI152NLin6Asym/
│ └─ anat/
│ ├─ tpl-MNI152NLin6Asym_atlas-MIAL67ThalamicNuclei_res-1_dseg.nii.gz
│ └─ tpl-MNI152NLin6Asym_atlas-MIAL67ThalamicNuclei_res-1_probseg.nii.gz
├─ tpl-MNI152NLin2009cAsym/
│ └─ anat/
│ ├─ tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_dseg.nii.gz
│ └─ tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_probseg.nii.gz
├─ sub-01
│ └─ anat/
│ ├─ sub-01_atlas-MIAL67ThalamicNuclei_dseg.nii.gz
│ ├─ sub-01_label-ThalamicNuclei_dseg.nii.gz
│ ├─ sub-01_space-MNI152NLin2009cAsym_T1w.nii.gz
│ └─ sub-01_T1w.nii.gz
┇
└─ sub-67
└─ anat/
├─ sub-67_atlas-MIAL67ThalamicNuclei_dseg.nii.gz
├─ sub-67_label-ThalamicNuclei_dseg.nii.gz
├─ sub-67_space-MNI152NLin2009cAsym_T1w.nii.gz
└─ sub-67_T1w.nii.gz
```

The next subsection describes this latter use-case in further depth.

## Filenames of derivatives with atlases in their provenance

Like for the [`space-` entity](../glossary.md#space-entities), outputs derived from atlases
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5 comments on commit f159e61

@PeerHerholz
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Thanks @oesteban! Just a quick question: would the transforms be derived in a different pipeline and indicated under "sources" in the json files?

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Good point -- I will address transforms ASAP. I agree it is a key aspect of this BEP, and should be reflected somewhere.

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The transforms between templates could be part of templateflow, right (I think there are already some)? There's also neuromaps, which has quite a few transforms ready to go. However, I'm not sure how this would then be linked to a given pipeline... For the template to subject space transforms: this could either re-use transforms computed during prior processing steps, e.g. fmriprep, or computed within the pipeline at hand. Sorry if I missed something obvious or if this is not aligned with your proposal. Thanks again for working on this!

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I think here we should encourage/signal the importance of providing subject-to-standard transforms for the subjects that were used in the atlas/template creation.

In other words, if we had a BIDS-derivatives dataset from MNI templates which preserved all the transformations of each subject to each of their different templates, it would be crazy awesome (e.g., to then build template-to-template transforms).

TemplateFlow is definitely interested in template-to-template transforms, but a BIDS derivatives dataset from which drawing them should have also the subject-to-template transforms in it.

Let me work this a bit further and I hope that will give you a full (and specific) answer - wdyt?

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+1 on all things you mentioned. Please let me know if I can be of any help!

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