From 64d0e8b70736331a56b36c51ffaba41c42bd1de1 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 14:59:59 +0100 Subject: [PATCH 1/4] try snippets --- includes/abbreviations.md | 15 +++++++++++++++ mkdocs.yml | 6 ++++++ 2 files changed, 21 insertions(+) create mode 100644 includes/abbreviations.md diff --git a/includes/abbreviations.md b/includes/abbreviations.md new file mode 100644 index 0000000000..d217147b94 --- /dev/null +++ b/includes/abbreviations.md @@ -0,0 +1,15 @@ + + + +*[ASL]: Arterial Spin Labeling +*[BEP]: BIDS Extension Proposal +*[BEPs]: BIDS Extension Proposals +*[BIDS]: Brain Imaging Data Structure +*[DOI]: Digital Object Identifiers +*[JSON]: JavaScript Object Notation +*[MRI]: Magnetic Resonance Imaging +*[NIRS]: Near-InfraRed Spectroscopy +*[PET]: Positron Imaging Tomography +*[TSV]: Tab Separated Values +*[URI]: Uniform Resource Identifier +*[URL]: Uniform Resource Locator diff --git a/mkdocs.yml b/mkdocs.yml index 08fd23ef68..05aa4487a3 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -107,6 +107,9 @@ markdown_extensions: - pymdownx.superfences - admonition - pymdownx.details + - pymdownx.snippets: + auto_append: + - includes/abbreviations.md plugins: - search - branchcustomization: @@ -153,3 +156,6 @@ plugins: "99-appendices/13-cross-modality-correspondence.md": "appendices/cross-modality-correspondence.md" docs_dir: "src" use_directory_urls: false + +watch: + - includes From a9293e2980ce77f4fd2a7a0dc2e97f601b25ebba Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 15:25:20 +0100 Subject: [PATCH 2/4] fix --- includes/abbreviations.md | 3 +-- mkdocs.yml | 2 ++ 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/includes/abbreviations.md b/includes/abbreviations.md index d217147b94..64ceee3050 100644 --- a/includes/abbreviations.md +++ b/includes/abbreviations.md @@ -1,5 +1,4 @@ - - + *[ASL]: Arterial Spin Labeling *[BEP]: BIDS Extension Proposal diff --git a/mkdocs.yml b/mkdocs.yml index 05aa4487a3..db7f48c150 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -102,6 +102,8 @@ extra: extra_javascript: - js/jquery-3.6.0.min.js markdown_extensions: + - abbr + - attr_list - toc: anchorlink: true - pymdownx.superfences From 8e0e50b4026cea39aaeaf48686593689af6c895d Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 12 Dec 2024 15:36:05 +0100 Subject: [PATCH 3/4] test --- includes/abbreviations.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/includes/abbreviations.md b/includes/abbreviations.md index 64ceee3050..f6881bdf8d 100644 --- a/includes/abbreviations.md +++ b/includes/abbreviations.md @@ -12,3 +12,5 @@ *[TSV]: Tab Separated Values *[URI]: Uniform Resource Identifier *[URL]: Uniform Resource Locator +*[subject]: A person or animal participating in the study. Used interchangeably with term **Participant**. +*[task]: A set of structured activities performed by the participant (see [glossary](https://bids-specification.readthedocs.io/en/latest/glossary.html#task-common_principles)) From 34d9a27ac5eec1df6694f45a2393486d2dffe03d Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 15 Dec 2024 14:21:26 +0100 Subject: [PATCH 4/4] add more links --- includes/abbreviations.md | 16 ++++++++++++++-- src/appendices/qmri.md | 6 +++--- src/appendices/schema.md | 2 +- 3 files changed, 18 insertions(+), 6 deletions(-) diff --git a/includes/abbreviations.md b/includes/abbreviations.md index f6881bdf8d..d51d68d011 100644 --- a/includes/abbreviations.md +++ b/includes/abbreviations.md @@ -5,12 +5,24 @@ *[BEPs]: BIDS Extension Proposals *[BIDS]: Brain Imaging Data Structure *[DOI]: Digital Object Identifiers +*[EEG]: Electroencephalography +*[iEEG]: Intracranial Electroencephalography *[JSON]: JavaScript Object Notation +*[MEG]: Magnetoencephalography *[MRI]: Magnetic Resonance Imaging *[NIRS]: Near-InfraRed Spectroscopy *[PET]: Positron Imaging Tomography *[TSV]: Tab Separated Values *[URI]: Uniform Resource Identifier *[URL]: Uniform Resource Locator -*[subject]: A person or animal participating in the study. Used interchangeably with term **Participant**. -*[task]: A set of structured activities performed by the participant (see [glossary](https://bids-specification.readthedocs.io/en/latest/glossary.html#task-common_principles)) + +*[dataset]: A set of neuroimaging and behavioral data acquired for a purpose of a particular study. A dataset consists of data acquired from one or more subjects, possibly from multiple sessions. +*[derivatives]: Derivatives are outputs of common processing pipelines, capturing data and meta-data sufficient for a researcher to understand and (critically) reuse those outputs in subsequent processing. +*[entity]: An "entity" is an attribute that can be associated with a file, contributing to the identification of that file as a component of its filename in the form of a hyphen-separated key-value pair. +*[event] Something that happens or may be perceived by a test subject as happening at a particular instant during the recording. +*[run]: An uninterrupted repetition of data acquisition that has the same acquisition parameters and task (however events can change from run to run due to different subject response or randomized nature of the stimuli). Run is a synonym of a data acquisition. +*[sample]: A sample pertaining to a subject such as tissue, primary cell or cell-free sample. +*[session]: A logical grouping of neuroimaging and behavioral data consistent across subjects. Session can (but doesn't have to) be synonymous to a visit in a longitudinal study. +*[subject]: A person or animal participating in the study. Used interchangeably with term Participant. +*[suffix]: An alphanumeric string that forms part of a filename, located after all entities and following a final `_`, right before the file extension. +*[task]: A set of structured activities performed by the participant. diff --git a/src/appendices/qmri.md b/src/appendices/qmri.md index d5367cfcdd..183e8504eb 100644 --- a/src/appendices/qmri.md +++ b/src/appendices/qmri.md @@ -219,7 +219,7 @@ in the [BIDS examples](https://bids-standard.github.io/bids-examples/#qmri). The table of required entities for qMRI file collections are provided in the [entity table](./entity-table.md). However, viability of a qMRI file collection is determined not only by the naming and organization of the input files, -but also by which metadata fields are provided in accompanying json files. +but also by which metadata fields are provided in accompanyingJSONfiles. ### Method-specific priority levels for qMRI file collections @@ -380,10 +380,10 @@ a proper interpretation of qMRI maps may critically depend on some metadata fiel For example, without the information of `MagneticFieldStrength`, white-matter T1 values in a `T1map` become elusive. - All the acquisition parameters that are constant across the files in a file collection are RECOMMENDED - to be added to the sidecar json of the qMRI maps. + to be added to the sidecarJSONof the qMRI maps. - Relevant acquisition parameters that vary across files in a qMRI file collection are RECOMMENDED - to be added to the sidecar json of the qMRI map **in array form**. + to be added to the sidecarJSONof the qMRI map **in array form**. - The JSON file accompanying a qMRI map which is obtained by using open-source software is RECOMMENDED to include additional metadata fields listed in the following table: diff --git a/src/appendices/schema.md b/src/appendices/schema.md index fc0855881d..dcd9a4ef20 100644 --- a/src/appendices/schema.md +++ b/src/appendices/schema.md @@ -10,7 +10,7 @@ to the BIDS standard. The BIDS schema is available in two machine readable formats: - as a set of [YAML](https://en.wikipedia.org/wiki/YAML) files in the [BIDS specification repository](https://github.com/bids-standard/bids-specification/tree/master/src/schema) -- as a [single dereferenced json file](https://bids-specification.readthedocs.io/en/stable/schema.json) +- as a [single dereferencedJSONfile](https://bids-specification.readthedocs.io/en/stable/schema.json) A didactic walkthrough of the schema can be found in the [BEP Guide](https://bids-extensions.readthedocs.io/en/latest/schema/), and a complete description is available in the [`bidsschematools` documentation](https://bidsschematools.readthedocs.io/en/latest/).