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Alternative proposal to BEP038 #1856

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4fa15e5
first iteration of the alternative proposal
oesteban Jun 12, 2024
0180e3b
STY: codespell
effigies Jun 12, 2024
bba4159
Replace links to the schema with links to the glossary
effigies Jun 12, 2024
f159e61
enh: generalization of atlas metadata cc/ @jdkent
oesteban Jun 17, 2024
9390602
enh: address some of @effigies' comments
oesteban Jun 17, 2024
3f8c210
enh: reference entities from glossary
oesteban Jun 17, 2024
927335c
fix: folder => directory
oesteban Jun 17, 2024
6a3dcc7
fix: resolving issues with/within entities
oesteban Jun 17, 2024
f7e906d
enh: add mention to transforms files cc/ @peerherholz
oesteban Jun 17, 2024
57160cd
fix: revise more glossary links
oesteban Jun 17, 2024
1db3fd4
enh: move all filetree examples to macros
oesteban Jun 17, 2024
48e77ae
enh: miscellaneous improvements (sort entries in examples, etc.)
oesteban Jun 17, 2024
d6cf6a4
enh: improve intro
oesteban Jun 18, 2024
8bfc7ac
enh: add datatype comment to make it recommended cc/ @effigies
oesteban Jun 18, 2024
f2be20a
enh: start drafting cohort
oesteban Jun 18, 2024
d15677a
enh: add multi-cohort example
oesteban Jun 18, 2024
b275ca3
fix: pacify pre-commit build
oesteban Jun 18, 2024
f9ff346
enh: add the PS13 example
oesteban Jun 18, 2024
f0e8e0e
test
jdkent Jun 21, 2024
b00bdf8
Update src/derivatives/atlas.md
jdkent Jun 21, 2024
abe37b4
Update src/derivatives/atlas.md
jdkent Jun 21, 2024
d812b08
incorporate meeting feedback in schema
jdkent Jun 21, 2024
3accb28
enh: add note about 'MNI Space' below template identifiers @CPernet
oesteban Oct 7, 2024
e5e27f1
enh: clarify the creation of BOTH a new template AND atlas
oesteban Oct 7, 2024
8ffda51
fix: avoid using an atlas name for a segmentation label
oesteban Oct 7, 2024
d62f0d9
enh: rework the text to clarify notions: atlas, template, space
oesteban Oct 7, 2024
161db11
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 7, 2024
44cb808
fix: addressing some inconsistencies about segmentations
oesteban Oct 11, 2024
c77df10
fix: add clarification about cohort
oesteban Oct 11, 2024
947f279
fix: replace ``_mimap`` with ``_pet``
oesteban Oct 11, 2024
a5111aa
fix: replace ``label-`` with ``seg-`` where applies
oesteban Oct 12, 2024
c05146c
enh: update schema according to this proposal
oesteban Oct 12, 2024
f221ad0
fix: folder -> directory (pacify pre-commit)
oesteban Oct 12, 2024
9ec94cd
fix: order of ``scale-`` in the schema
oesteban Oct 12, 2024
1a258b5
enh: refine atlas' definition in common principles
oesteban Oct 12, 2024
79f1ea9
enh: add "authoritative definition of spaces" to template
oesteban Oct 12, 2024
3f2bde5
enh: update schema to consider ``tpl-`` and ``cohort-``
oesteban Oct 12, 2024
95a85a1
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 12, 2024
0d7f965
enh(schema): add ``atlas`` to entities
oesteban Oct 12, 2024
a9fa24a
fix: delete photo from atlas' file rules
oesteban Oct 12, 2024
44c3ad8
Update src/schema/objects/columns.yaml
oesteban Oct 12, 2024
b66c3ee
fix: dereference twice schema files
oesteban Oct 14, 2024
c3b6f41
fix: add missing properties to atlas entity definition
oesteban Oct 14, 2024
891bcf0
FIX: update PET examples
mnoergaard Oct 23, 2024
ef1817b
Merge remote-tracking branch 'upstream/bep038' into bep038-review
effigies Nov 5, 2024
bc6b064
schema: Move templates out of rules.files
effigies Nov 5, 2024
226f134
test: Fix check to avoid overlap between common_principles and common
effigies Nov 5, 2024
ac745e6
schema: Update metaschema, fix errors caught by metaschema
effigies Nov 5, 2024
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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.
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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": "",
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"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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},
},
}
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