From ed685a711218b8c42c80f939e85a1172ea46ef68 Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Mon, 3 Oct 2022 18:40:06 +0200 Subject: [PATCH 1/3] DRAFT: consistently refer to Neuromag/Elekta/MEGIN --- src/appendices/coordinate-systems.md | 2 +- src/schema/rules/sidecars/meg.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md index e48615eae7..76393b4b30 100644 --- a/src/appendices/coordinate-systems.md +++ b/src/appendices/coordinate-systems.md @@ -108,7 +108,7 @@ Restricted keywords for the `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 diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml index 41dae7a40f..a5f8fa796f 100644 --- a/src/schema/rules/sidecars/meg.yaml +++ b/src/schema/rules/sidecars/meg.yaml @@ -33,7 +33,7 @@ MEGRecommended: 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"`. See the [MEG Systems Appendix](SPEC_ROOT/appendices/meg-systems.md) for preferred names. From 83789e91231c2317083f94a5b951714c38dbd3ef Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Tue, 28 Nov 2023 11:27:13 +0100 Subject: [PATCH 2/3] add deprecation notices --- src/appendices/coordinate-systems.md | 3 ++- src/schema/objects/enums.yaml | 7 +++++++ src/schema/rules/sidecars/meg.yaml | 2 ++ 3 files changed, 11 insertions(+), 1 deletion(-) diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md index ce35c8ef6b..c3312a3e70 100644 --- a/src/appendices/coordinate-systems.md +++ b/src/appendices/coordinate-systems.md @@ -113,6 +113,7 @@ Restricted keywords for the `CoordinateSystem` field in the - `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 @@ -146,7 +147,7 @@ the restricted keywords for can also be applied to EEG: - `CTF` -- `ElektaNeuromag` +- `NeuromagElektaMEGIN` - `4DBti` - `KitYokogawa` - `ChietiItab` diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index f01d16cdc6..4fafd4ec28 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -21,6 +21,7 @@ _MEGCoordSys: enum: - $ref: objects.enums.CTF.value - $ref: objects.enums.ElektaNeuromag.value + - $ref: objects.enums.NeuromagElektaMEGIN.value - $ref: objects.enums.4DBti.value - $ref: objects.enums.KitYokogawa.value - $ref: objects.enums.ChietiItab.value @@ -305,6 +306,12 @@ CTF: ElektaNeuromag: value: ElektaNeuromag display_name: Elekta Neuromag + description: | + RAS orientation and the origin between the ears. + DEPRECATED. Dataset curators SHOULD use `NeuromagElektaMEGIN` instead. +NeuromagElektaMEGIN: + value: NeuromagElektaMEGIN + display_name: Neuromag Elekta MEGIN description: | RAS orientation and the origin between the ears. 4DBti: diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml index db3328725c..5277cf4c06 100644 --- a/src/schema/rules/sidecars/meg.yaml +++ b/src/schema/rules/sidecars/meg.yaml @@ -22,6 +22,8 @@ MEGHardware: For MEG scanners, this must be one of: `"CTF"`, `"Neuromag/Elekta/MEGIN"`, `"BTi/4D"`, `"KIT/Yokogawa"`, `"ITAB"`, `"KRISS"`, `"Other"`. + The use of `"Elekta/Neuromag"` is DEPRECATED. Dataset curators SHOULD + use `"Neuromag/Elekta/MEGIN"` instead. See the [MEG Systems Appendix](SPEC_ROOT/appendices/meg-systems.md) for preferred names. ManufacturersModelName: From 8f21acb782dc2c765de9e8412f106fa9bb79fa80 Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Tue, 28 Nov 2023 11:32:11 +0100 Subject: [PATCH 3/3] add links to deprecation --- src/schema/objects/enums.yaml | 5 +++-- src/schema/rules/sidecars/meg.yaml | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index 4fafd4ec28..2f63006460 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -20,7 +20,7 @@ _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 @@ -308,7 +308,8 @@ ElektaNeuromag: display_name: Elekta Neuromag description: | RAS orientation and the origin between the ears. - DEPRECATED. Dataset curators SHOULD use `NeuromagElektaMEGIN` instead. + [DEPRECATED](SPEC_ROOT/common-principles.md#definitions). + Dataset curators SHOULD use `NeuromagElektaMEGIN` instead. NeuromagElektaMEGIN: value: NeuromagElektaMEGIN display_name: Neuromag Elekta MEGIN diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml index 5277cf4c06..33d851f6af 100644 --- a/src/schema/rules/sidecars/meg.yaml +++ b/src/schema/rules/sidecars/meg.yaml @@ -22,8 +22,9 @@ MEGHardware: For MEG scanners, this must be one of: `"CTF"`, `"Neuromag/Elekta/MEGIN"`, `"BTi/4D"`, `"KIT/Yokogawa"`, `"ITAB"`, `"KRISS"`, `"Other"`. - The use of `"Elekta/Neuromag"` is DEPRECATED. Dataset curators SHOULD - use `"Neuromag/Elekta/MEGIN"` instead. + 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: