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[ENH] BEP030: Functional Near-Infrared Spectroscopy #802

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merged 110 commits into from
Oct 5, 2022
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Merged

[ENH] BEP030: Functional Near-Infrared Spectroscopy #802

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6b5b218
Add fNIRS
rob-luke May 22, 2021
c8712f6
Rename
rob-luke Feb 17, 2022
f25e11f
Review
rob-luke Feb 17, 2022
9ea41aa
Review
rob-luke Feb 17, 2022
ac458b5
Use macros
rob-luke Feb 17, 2022
ec0c9c3
Update metadata.yaml
rob-luke Mar 3, 2022
9d493ee
Update 11-functional-near-infrared-spectroscopy.md
rob-luke Mar 3, 2022
5aea159
Update columns.yaml
rob-luke Jun 12, 2022
b1e70ea
Update columns.yaml
rob-luke Jun 12, 2022
f3ef8c9
Update metadata.yaml
rob-luke Jun 12, 2022
b35cfe3
Use master schemacode
rob-luke Jun 12, 2022
11c7071
Revert "Use master schemacode"
rob-luke Jun 12, 2022
d109049
Merge branch 'master' into bep030
sappelhoff Jun 14, 2022
a6a7d41
SCHEMA: Update datatype rules to be named, have datatypes key
effigies Jun 14, 2022
5523bda
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Jun 20, 2022
1933ef5
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Jun 20, 2022
3954a71
Update src/schema/objects/columns.yaml
rob-luke Jun 20, 2022
a94b3c2
Update src/schema/objects/columns.yaml
rob-luke Jun 20, 2022
31c0f45
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Jun 20, 2022
9877469
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Jun 20, 2022
9a903f3
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Jun 20, 2022
dd91b62
Update src/schema/objects/columns.yaml
rob-luke Jun 20, 2022
a78574a
Update src/schema/objects/columns.yaml
rob-luke Jun 20, 2022
c64bc52
Update src/schema/objects/columns.yaml
rob-luke Jun 20, 2022
6190458
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Jun 20, 2022
0c160f9
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Jun 20, 2022
57f5209
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Jun 20, 2022
c8ec341
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Jun 20, 2022
16f3503
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Jun 20, 2022
948cd70
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Jun 20, 2022
fc881f4
Fix missing info in render
rob-luke Jun 20, 2022
8a37810
Fix missing rules for type in nirs
rob-luke Jun 20, 2022
2790e3f
Add acquisition
rob-luke Jun 20, 2022
6410775
Remove acquisition from photo
rob-luke Jun 22, 2022
e8a9d14
Merge remote-tracking branch 'upstream/master' into bep030
effigies Aug 19, 2022
c19e35b
add SPEC_ROOT prefix to links from schema to internal spec
sappelhoff Aug 25, 2022
57d4081
Merge branch 'master' into bep030
rwblair Aug 25, 2022
751273a
add sidecar and check rules for nirs
rwblair Aug 26, 2022
e5b79a3
Merge branch 'master' of github.com:bids-standard/bids-specification …
rwblair Aug 26, 2022
3623be5
misisng : in context.yaml
rwblair Aug 26, 2022
0bf2deb
yamllint fixes
rwblair Aug 26, 2022
66c021f
add level adendum for recommended descriptions
rwblair Aug 26, 2022
d571848
harmonize objects and rules
rwblair Aug 26, 2022
23e728d
we must appease the linting gods
rwblair Aug 26, 2022
35290d4
add missing display_name fields in objects. I am wildly inconsistent …
rwblair Aug 26, 2022
4e851de
change links to point at md not html in schema objects
rwblair Aug 26, 2022
6481c79
associations should be a suffix, can't nest them like I tried for nirs
rwblair Aug 26, 2022
3e6b52f
add coordsystem to associations, adjust rules accordingly
rwblair Aug 26, 2022
8a91620
Update src/schema/rules/datatypes/nirs.yaml
rwblair Aug 29, 2022
7143b0f
Update src/schema/rules/datatypes/nirs.yaml
rwblair Aug 29, 2022
947183a
Update src/schema/rules/sidecars/nirs.yaml
rwblair Aug 29, 2022
1dbc7ca
Update src/schema/rules/sidecars/nirs.yaml
rwblair Aug 29, 2022
ff347bf
Merge branch 'master' of github.com:bids-standard/bids-specification …
rwblair Aug 29, 2022
96478d5
Update src/schema/objects/metadata.yaml
rwblair Aug 29, 2022
28796af
Update src/schema/objects/metadata.yaml
rwblair Aug 29, 2022
3b28c22
detector__optoedes --> detector_type
rwblair Aug 29, 2022
172be76
SourceType format set to be just string
rwblair Aug 29, 2022
381828f
Add make_sidecar_table macros alongside old style tables to compare f…
rwblair Aug 29, 2022
ac75f5c
Merge branch 'bep030' of github.com:bids-standard/bids-specification …
rwblair Aug 29, 2022
9d4ba9c
correct mislabeled addendums
rwblair Aug 29, 2022
bcfe6ad
uncapitalize requirement level
rwblair Aug 29, 2022
9ebae61
add missing _ to make sidecar table macro, and fix spelling
rwblair Aug 29, 2022
be3daad
update coordsystem.json tables to use rules/sidecars/nirs entries.
rwblair Aug 29, 2022
031b9aa
fix typos in schema
sappelhoff Aug 30, 2022
3299fd9
Update src/schema/rules/checks/nirs.yaml
rwblair Aug 30, 2022
d2d4b80
Update src/schema/rules/checks/nirs.yaml
rwblair Aug 30, 2022
736a49e
Update src/schema/rules/checks/nirs.yaml
rwblair Aug 30, 2022
4e4c722
add nirs to common principles schema object
rwblair Aug 30, 2022
36202ca
no space in infra red even if for an acronym
rwblair Aug 30, 2022
638c11a
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Sep 1, 2022
991d7df
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Sep 1, 2022
ad74ef2
Implement cap description changes
rob-luke Sep 1, 2022
e678b15
Improvements to cap description fields
rob-luke Sep 1, 2022
cdbc04f
Move age details to modality agnostic page
rob-luke Sep 1, 2022
9b1ae4e
Update src/04-modality-specific-files/11-functional-near-infrared-spe…
rob-luke Sep 1, 2022
5aa31e0
Lint
rob-luke Sep 1, 2022
9abdb4d
Merge branch 'master' into bep030
sappelhoff Sep 1, 2022
4090a74
Update README.md
sappelhoff Sep 1, 2022
51d2b27
Merge branch 'master' into bep030
sappelhoff Sep 1, 2022
0cda6c6
Merge remote-tracking branch 'upstream/master' into bep030
effigies Sep 1, 2022
f9008e7
Make aux channel counts optional
rob-luke Sep 10, 2022
160bf12
Update metadata.yaml
rob-luke Sep 13, 2022
c110a93
apply small wording and typo fixes
sappelhoff Sep 27, 2022
07e28cb
Merge branch 'master' into bep030
sappelhoff Sep 27, 2022
024fbc4
add citation placeholder NIRS
sappelhoff Sep 27, 2022
66a04c2
Update src/schema/objects/metadata.yaml
sappelhoff Sep 27, 2022
5bbd39a
fix appendix links
sappelhoff Sep 27, 2022
69a2db3
Merge branch 'bep030' of https://github.com/bids-standard/bids-specif…
sappelhoff Sep 27, 2022
ca9550a
Update README.md
rob-luke Sep 29, 2022
f23adb7
Revert redundant NIRS age column suggestion
rob-luke Sep 29, 2022
d8238bb
Add link to coordinate system appendix
rob-luke Sep 29, 2022
4fdec60
Clarify relation between rows in channels.tsv and NIRSChannelCount
rob-luke Sep 29, 2022
3d957e3
Change NIRSCoordinateProcessingDescription example from none to n/a
rob-luke Sep 29, 2022
2481a59
Update src/schema/meta/context.yaml
rob-luke Sep 29, 2022
e93e10e
Try and fix path bug
rob-luke Sep 29, 2022
1bb288d
Still trying to fix appendix path bug
rob-luke Sep 29, 2022
6489d40
Still trying to get path working
rob-luke Sep 29, 2022
e7d652a
Path bug
rob-luke Sep 29, 2022
cda994f
Update src/schema/rules/checks/nirs.yaml
rob-luke Sep 29, 2022
cc35e17
Step one of adding IntendedFor
rob-luke Sep 29, 2022
435a8f6
Step two of adding IntendedFor
rob-luke Sep 29, 2022
3cb7e88
Step three of adding IntendedFor
rob-luke Sep 29, 2022
696d3b2
Revert naming change
rob-luke Sep 29, 2022
dcbfb9a
Move cap fields to recommended
rob-luke Sep 29, 2022
e600e69
update documentation regarding cap manufacturing. (#1285)
helenacockx Sep 29, 2022
f624497
Merge remote-tracking branch 'upstream/master' into bep030
effigies Sep 30, 2022
3ce06ae
SCHEMA: Sync table definitions, render from schema
effigies Sep 30, 2022
7e65f3a
SCHEMA: Update schema rules, including *ChannelCount checks
effigies Sep 30, 2022
501d3e8
Channels is recommended. Optodes is required if channels is present.
rob-luke Sep 30, 2022
fa5a56f
Variable naming changes suggested by tsalo
rob-luke Oct 3, 2022
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1 change: 1 addition & 0 deletions mkdocs.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@ nav:
- Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md
- Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md
- Microscopy: 04-modality-specific-files/10-microscopy.md
- Functional Near-Infrared Spectroscopy: 04-modality-specific-files/11-functional-near-infrared-spectroscopy.md
- Derivatives:
- BIDS Derivatives: 05-derivatives/01-introduction.md
- Common data types and metadata: 05-derivatives/02-common-data-types.md
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