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[FIX] Consistently refer to Neuromag/Elekta/MEGIN #1310

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merged 6 commits into from
Jun 6, 2024
Merged

[FIX] Consistently refer to Neuromag/Elekta/MEGIN #1310

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ed685a7
DRAFT: consistently refer to Neuromag/Elekta/MEGIN
sappelhoff Oct 3, 2022
3db93dc
Merge branch 'bids-standard:master' into meg/name
sappelhoff Jul 24, 2023
35894c9
Merge branch 'master' into meg/name
sappelhoff Nov 28, 2023
83789e9
add deprecation notices
sappelhoff Nov 28, 2023
8f21acb
add links to deprecation
sappelhoff Nov 28, 2023
3b12da1
Merge branch 'master' into meg/name
sappelhoff Jun 5, 2024
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5 changes: 3 additions & 2 deletions src/appendices/coordinate-systems.md
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Expand Up @@ -108,11 +108,12 @@ Restricted keywords for the `<CoordSysType>CoordinateSystem` field in the
`coordinatesystem.json` file for MEG datasets:

- `CTF`: ALS orientation and the origin between the ears
- `ElektaNeuromag`: RAS orientation and the origin between the ears
- `NeuromagElektaMEGIN`: RAS orientation and the origin between the ears
- `4DBti`: ALS orientation and the origin between the ears
- `KitYokogawa`: ALS orientation and the origin between the ears
- `ChietiItab`: RAS orientation and the origin between the ears
- Any keyword from the list of [Standard template identifiers](#standard-template-identifiers): RAS orientation and the origin at the center of the gradient coil for template NifTI images
- The use of `ElektaNeuromag` is [DEPRECATED][deprecated]. Dataset curators SHOULD use `NeuromagElektaMEGIN` instead.

In the case that MEG was recorded simultaneously with EEG,
the restricted keywords for
Expand Down Expand Up @@ -146,7 +147,7 @@ the restricted keywords for
can also be applied to EEG:

- `CTF`
- `ElektaNeuromag`
- `NeuromagElektaMEGIN`
- `4DBti`
- `KitYokogawa`
- `ChietiItab`
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10 changes: 9 additions & 1 deletion src/schema/objects/enums.yaml
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Expand Up @@ -20,7 +20,8 @@ _MEGCoordSys:
type: string
enum:
- $ref: objects.enums.CTF.value
- $ref: objects.enums.ElektaNeuromag.value
- $ref: objects.enums.ElektaNeuromag.value # deprecated
- $ref: objects.enums.NeuromagElektaMEGIN.value
- $ref: objects.enums.4DBti.value
- $ref: objects.enums.KitYokogawa.value
- $ref: objects.enums.ChietiItab.value
Expand Down Expand Up @@ -305,6 +306,13 @@ CTF:
ElektaNeuromag:
value: ElektaNeuromag
display_name: Elekta Neuromag
description: |
RAS orientation and the origin between the ears.
[DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
Dataset curators SHOULD use `NeuromagElektaMEGIN` instead.
Comment on lines +311 to +312
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If we're going to deprecate, then we should have checks to warn curators to normalize. It seems this shows up in 7 metadata fields:

$ git grep -B12 _MEGCoordSys | grep \ name:
src/schema/objects/metadata.yaml-  name: AnatomicalLandmarkCoordinateSystem
src/schema/objects/metadata.yaml-  name: DigitizedHeadPointsCoordinateSystem
src/schema/objects/metadata.yaml-  name: EEGCoordinateSystem
src/schema/objects/metadata.yaml-  name: FiducialsCoordinateSystem
src/schema/objects/metadata.yaml-  name: HeadCoilCoordinateSystem
src/schema/objects/metadata.yaml-  name: MEGCoordinateSystem
src/schema/objects/metadata.yaml-  name: NIRSCoordinateSystem

Could make a check in src/schema/rules/checks/deprecations.yaml:

AnatomicalLandmarkCoordinateSystemDeprecation:
  issue:
    code: ELEKTA_NEUROMAG_DEPRECATED
    message: |
        "ElektaNeuromag" as a coordinate system is deprecated.
        Use "NeuromagElektaMEGIN" instead.
    level: warning
  selectors:
    - sidecar.AnatomicalLandmarkCoordinateSystem
  checks:
    - sidecar.AnatomicalLandmarkCoordinateSystem != "ElektaNeuromag"

DigitizedHeadPointsCoordinateSystemDeprecation:
  $ref: rules.checks.deprecations.AnatomicalLandmarkCoordinateSystemDeprecation
  selectors:
    - sidecar.DigitizedHeadPointsCoordinateSystem
  checks:
    - sidecar.DigitizedHeadPointsCoordinateSystem != "ElektaNeuromag"

...

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Thanks for the suggestions @effigies I agree and have created a PR for this, using your code. Please feel free to adjust if that's not what you had in mind. #1848

NeuromagElektaMEGIN:
value: NeuromagElektaMEGIN
display_name: Neuromag Elekta MEGIN
description: |
RAS orientation and the origin between the ears.
4DBti:
Expand Down
5 changes: 4 additions & 1 deletion src/schema/rules/sidecars/meg.yaml
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Expand Up @@ -20,8 +20,11 @@ MEGHardware:
level: recommended
description_addendum: |
For MEG scanners, this must be one of:
`"CTF"`, `"Elekta/Neuromag"`, `"BTi/4D"`, `"KIT/Yokogawa"`,
`"CTF"`, `"Neuromag/Elekta/MEGIN"`, `"BTi/4D"`, `"KIT/Yokogawa"`,
`"ITAB"`, `"KRISS"`, `"Other"`.
The use of `"Elekta/Neuromag"` is
[DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
Dataset curators SHOULD use `"Neuromag/Elekta/MEGIN"` instead.
See the [MEG Systems Appendix](SPEC_ROOT/appendices/meg-systems.md) for
preferred names.
ManufacturersModelName:
Expand Down