From f159e61317c6a4ae2a318391b6c40d4b709df606 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Mon, 17 Jun 2024 09:57:39 +0200 Subject: [PATCH] enh: generalization of atlas metadata cc/ @jdkent --- src/derivatives/atlas.md | 65 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) diff --git a/src/derivatives/atlas.md b/src/derivatives/atlas.md index 477c8285a6..57d097387c 100644 --- a/src/derivatives/atlas.md +++ b/src/derivatives/atlas.md @@ -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