From e5f8f2a205dc1a9a306b053248de79b25fe19d60 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 23 Jan 2022 08:53:49 +0100 Subject: [PATCH 1/4] update definition acq_time for sessions.tsv --- src/03-modality-agnostic-files.md | 4 ++-- src/schema/objects/columns.yaml | 12 +----------- 2 files changed, 3 insertions(+), 13 deletions(-) diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md index 68bf8550cf..0de7ee068a 100644 --- a/src/03-modality-agnostic-files.md +++ b/src/03-modality-agnostic-files.md @@ -401,7 +401,7 @@ Such recordings MUST be documented with one row per file. {{ MACROS___make_columns_table( { "filename": ("REQUIRED", "There MUST be exactly one row for each file."), - "acq_time": "OPTIONAL", + "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point in each run was acquired. Furthermore, if this header is provided, the acquisition times of all files that to a recording MUST be identical.") } ) }} @@ -444,7 +444,7 @@ Column names in `sessions.tsv` files MUST be different from group level particip {{ MACROS___make_columns_table( { "session_id": ("REQUIRED", "There MUST be exactly one row for each session."), - "acq_time": "OPTIONAL", + "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point of the first run was acquired.") "pathology": "RECOMMENDED", } ) }} diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index ee658ffbbd..9e13fc4394 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -17,18 +17,8 @@ acq_time: Furthermore, if this header is provided, the acquisition times of all files that belong to a recording MUST be identical. - Datetime should be expressed as described in [Units](/02-common-principles.html#units). + Datetime format and their anonymization are described in [Units](/02-common-principles.html#units). - For anonymization purposes all dates within one subject should be shifted by a randomly - chosen (but consistent across all recordings) number of days. - This way relative timing would be preserved, but chances of identifying a person based - on the date and time of their scan would be decreased. - Dates that are shifted for anonymization purposes SHOULD be set to the year 1925 or earlier - to clearly distinguish them from unmodified data. - Note that some data formats do not support arbitrary recording dates. - For example, the [EDF](https://www.edfplus.info/) - data format can only contain recording dates after 1985. - Shifting dates is RECOMMENDED, but not required. type: string format: datetime age: From e767a83af5c5bb827123b5bfebfae0e68c151d63 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 23 Jan 2022 08:57:23 +0100 Subject: [PATCH 2/4] simplify acq_time definition from schema to make it common to scans and sessions TSVs --- src/schema/objects/columns.yaml | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 9e13fc4394..776a6334e6 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -12,13 +12,7 @@ abbreviation: type: string acq_time: name: acq_time - description: | - Acquisition time refers to when the first data point in each run was acquired. - Furthermore, if this header is provided, the acquisition times of all files that - belong to a recording MUST be identical. - - Datetime format and their anonymization are described in [Units](/02-common-principles.html#units). - + description: Datetime format and their anonymization are described in [Units](/02-common-principles.html#units). type: string format: datetime age: From ffcc6eef7003648ea0e18af1de582ebac9fb7ef2 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 23 Jan 2022 09:48:15 +0100 Subject: [PATCH 3/4] add missing coma --- src/03-modality-agnostic-files.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md index 0de7ee068a..d1cac29292 100644 --- a/src/03-modality-agnostic-files.md +++ b/src/03-modality-agnostic-files.md @@ -401,7 +401,7 @@ Such recordings MUST be documented with one row per file. {{ MACROS___make_columns_table( { "filename": ("REQUIRED", "There MUST be exactly one row for each file."), - "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point in each run was acquired. Furthermore, if this header is provided, the acquisition times of all files that to a recording MUST be identical.") + "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point in each run was acquired. Furthermore, if this header is provided, the acquisition times of all files that to a recording MUST be identical."), } ) }} @@ -444,7 +444,7 @@ Column names in `sessions.tsv` files MUST be different from group level particip {{ MACROS___make_columns_table( { "session_id": ("REQUIRED", "There MUST be exactly one row for each session."), - "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point of the first run was acquired.") + "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point of the first run was acquired."), "pathology": "RECOMMENDED", } ) }} From 03a5604afd9cb68db394ee07a97232991d051e93 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 3 Feb 2022 21:06:29 +0100 Subject: [PATCH 4/4] split acq time definition in 2 for session and scans TSV --- src/03-modality-agnostic-files.md | 4 ++-- src/schema/objects/columns.yaml | 15 +++++++++++++-- 2 files changed, 15 insertions(+), 4 deletions(-) diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md index d1cac29292..0de4fddd52 100644 --- a/src/03-modality-agnostic-files.md +++ b/src/03-modality-agnostic-files.md @@ -401,7 +401,7 @@ Such recordings MUST be documented with one row per file. {{ MACROS___make_columns_table( { "filename": ("REQUIRED", "There MUST be exactly one row for each file."), - "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point in each run was acquired. Furthermore, if this header is provided, the acquisition times of all files that to a recording MUST be identical."), + "acq_time__scans": ("OPTIONAL"), } ) }} @@ -444,7 +444,7 @@ Column names in `sessions.tsv` files MUST be different from group level particip {{ MACROS___make_columns_table( { "session_id": ("REQUIRED", "There MUST be exactly one row for each session."), - "acq_time": ("OPTIONAL", "Acquisition time refers to when the first data point of the first run was acquired."), + "acq_time__sessions": ("OPTIONAL"), "pathology": "RECOMMENDED", } ) }} diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 776a6334e6..316a2bd6af 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -10,9 +10,20 @@ abbreviation: description: | The unique label abbreviation type: string -acq_time: +acq_time__scans: name: acq_time - description: Datetime format and their anonymization are described in [Units](/02-common-principles.html#units). + description: | + Acquisition time refers to when the first data point in each run was acquired. + Furthermore, if this header is provided, the acquisition times of all files + from the same recording MUST be identical. + Datetime format and their anonymization are described in [Units](/02-common-principles.html#units). + type: string + format: datetime +acq_time__sessions: + name: acq_time + description: | + Acquisition time refers to when the first data point of the first run was acquired. + Datetime format and their anonymization are described in [Units](/02-common-principles.html#units). type: string format: datetime age: