Merge branch 'master' into plus-sign-labels

Author: tsalo

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.31.0
+    rev: 0.31.1
     hooks:
       - id: check-dependabot
       - id: check-github-workflows
@@ -27,7 +27,7 @@ repos:
       - id: check-readthedocs
         files: readthedocs.yml
   - repo: https://github.com/psf/black
-    rev: 24.10.0
+    rev: 25.1.0
     hooks:
       - id: black
         files: ^tools/(?!schemacode)
@@ -37,7 +37,7 @@ repos:
         files: tools/schemacode
         args: ["--config", "tools/schemacode/pyproject.toml", "--verbose"]
   - repo: https://github.com/pyCQA/isort
-    rev: 5.13.2
+    rev: 6.0.0
     hooks:
       - id: isort
         files: ^tools/(?!schemacode)
@@ -69,7 +69,7 @@ repos:
       - id: pretty-format-toml
         args: [--autofix, --indent, '4', --no-sort]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]

README.md

@@ -20,7 +20,8 @@ In this repository, we develop the
 To organize your data in BIDS, all you need is neuro data, a computer, and the
 [BIDS specification](https://bids-specification.readthedocs.io/en/stable/).
 
-BIDS currently supports the following data modalities with more to come in the future:
+BIDS currently supports the following data modalities with
+[more to come in the future](https://bids.neuroimaging.io/get_involved.html#extending-the-bids-specification):
 
 - MRI
 - MEG

src/appendices/qmri.md

@@ -303,7 +303,7 @@ and a guide for using macros can be found at
 | -------------------- | ---------------------------------------------------------------------------------------------------- |
 | TB1DAM               | `FlipAngle`                                                                                          |
 | TB1EPI               | `EchoTime`, `FlipAngle`, `TotalReadoutTime`, `MixingTime`                                            |
-| TB1AFI               | `RepetitionTime`                                                                                     |
+| TB1AFI               | `RepetitionTimeExcitation`                                                                           |
 | TB1TFL               |                                                                                                      |
 | TB1RFM               |                                                                                                      |
 | TB1SRGE<sup>\*</sup> | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots` |

src/modality-agnostic-files.md

@@ -8,7 +8,7 @@ Templates:
 -   `README[.md|.rst|.txt]`
 -   `CITATION.cff`
 -   `CHANGES`
--   `LICENSE`
+-   `LICENSE[.md|.rst|.txt]`
 
 ### `dataset_description.json`
 

src/schema/README.md

@@ -399,6 +399,13 @@ These objects additionally have the field:
 | `type`   | The type (such as `string`, `integer`, `object`) of values the term describes                                                                                                                                   |
 | `format` | The format of the term (defined in `objects.formats`)                                                                                                                                                           |
 
+`objects.columns` additionally permit a `definition` field that may take any value permissible
+for the definition of a column in a JSON sidecar:
+
+| Field        | Description                                                                                                                                                                                                   |
+| ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `definition` | A JSON object that describes the column as in [Common principles - Tabular files][tabular files]. This is mutually exclusive with the `type` field, and is used for fields that have overridable definitions. |
+
 Value terms groups (`datatypes`, `suffixes`, `extensions`) define terms where a field
 can take on multiple values.
 For example, a file has one datatype, as compared to a collection of entities.
@@ -532,6 +539,7 @@ The convention can be summed up in the following rules:
     | `display_name` | Human-friendly name                                                 |
     | `description`  | Term definition                                                     |
     | `name`         | Name of column in TSV file (in `snake_case`)                        |
+    | `definition`   | JSON definition of a column, according to [Tabular files][]         |
     | `unit`         | Interpretation of numeric values                                    |
     | `type`         | Type of value                                                       |
     | `format`       | Permissible format of values, from definitions in `objects.formats` |
@@ -1052,3 +1060,5 @@ formalize the allowable directories, files, fields and values of the BIDS schema
 ensuring consistency across the entire schema directory. Validation of the schema is
 incorporated into the CI, so any changes that are inconsistent will be flagged before
 inclusion.
+
+[tabular files]: https://bids-specification.readthedocs.io/en/stable/common-principles.html#tabular-files

src/schema/objects/files.yaml

@@ -27,7 +27,10 @@ LICENSE:
     A `LICENSE` file MAY be provided in addition to the short specification of the
     used license in the `dataset_description.json` `"License"` field.
     The `"License"` field and `LICENSE` file MUST correspond.
-    The `LICENSE` file MUST be either in ASCII or UTF-8 encoding.
+    The `LICENSE` file MUST be either in ASCII or UTF-8 encoding and MAY have one of the extensions:
+    `.md` ([Markdown](https://www.markdownguide.org/)),
+    `.rst` ([reStructuredText](https://docutils.sourceforge.io/rst.html)),
+    or `.txt`.
 README:
   display_name: README
   file_type: regular

src/schema/objects/formats.yaml

@@ -78,9 +78,18 @@ datetime:
   display_name: Datetime
   description: |
     A datetime in the form `"YYYY-MM-DDThh:mm:ss[.000000][Z]"`,
-    where [.000000] is an optional subsecond resolution between 1 and 6 decimal points,
-    and [Z] is an optional, valid timezone code.
-  pattern: '[0-9]{4}-[0-9]{2}-[0-9]{2}T(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9](\.[0-9]{1,6})?([A-Z]{2,4})?'
+    where `[.000000]` is an optional subsecond resolution between 1 and 6 decimal points,
+    and `[Z]` is an optional literal character `Z` that indicates
+    Coordinated Universal Time (UTC).
+  pattern: "\
+    [0-9]{4}\
+    -(?:0[1-9]|1[0-2])\
+    -(?:0[1-9]|[12][0-9]|3[01])\
+    T(?:2[0-3]|[01][0-9])\
+    :[0-5][0-9]\
+    :(?:[0-5][0-9]|60)\
+    (?:\\.[0-9]{1,6})?\
+    Z?"
 file_relative:
   display_name: Path relative to the parent file
   description: |

src/schema/rules/files/common/core.yaml

@@ -21,7 +21,12 @@ CHANGES:
   path: CHANGES
 LICENSE:
   level: optional
-  path: LICENSE
+  stem: LICENSE
+  extensions:
+    - ''
+    - .md
+    - .rst
+    - .txt
 genetic_info:
   level: optional
   path: genetic_info.json

src/schema/rules/files/deriv/preprocessed_data.yaml

@@ -69,6 +69,54 @@ beh_noncontinuous_common:
     space: optional
     description: optional
 
+channels_channels_common:
+  $ref: rules.files.raw.channels.channels
+  entities:
+    $ref: rules.files.raw.channels.channels.entities
+    description: optional
+
+channels_channels__meg_common:
+  $ref: rules.files.raw.channels.channels__meg
+  entities:
+    $ref: rules.files.raw.channels.channels__meg.entities
+    description: optional
+
+channels_channels__motion_common:
+  $ref: rules.files.raw.channels.channels__motion
+  entities:
+    $ref: rules.files.raw.channels.channels__motion.entities
+    description: optional
+
+channels_coordsystem_common:
+  $ref: rules.files.raw.channels.coordsystem
+  entities:
+    $ref: rules.files.raw.channels.coordsystem.entities
+    description: optional
+
+channels_coordsystem__eeg_common:
+  $ref: rules.files.raw.channels.coordsystem__eeg
+  entities:
+    $ref: rules.files.raw.channels.coordsystem__eeg.entities
+    description: optional
+
+channels_electrodes_common:
+  $ref: rules.files.raw.channels.electrodes
+  entities:
+    $ref: rules.files.raw.channels.electrodes.entities
+    description: optional
+
+channels_electrodes__meg_common:
+  $ref: rules.files.raw.channels.electrodes__meg
+  entities:
+    $ref: rules.files.raw.channels.electrodes__meg.entities
+    description: optional
+
+channels_electrodes_optodes_common:
+  $ref: rules.files.raw.channels.optodes
+  entities:
+    $ref: rules.files.raw.channels.optodes.entities
+    description: optional
+
 dwi_dwi_common:
   $ref: rules.files.raw.dwi.dwi
   entities:
@@ -229,3 +277,9 @@ pet_blood_common:
     $ref: rules.files.raw.pet.blood.entities
     space: optional
     description: optional
+
+task_events_common:
+  $ref: rules.files.raw.task.events
+  entities:
+    $ref: rules.files.raw.task.events.entities
+    description: optional

src/schema/rules/sidecars/qmri.yaml

@@ -0,0 +1,104 @@
+---
+# Anatomical qMRI sequences
+VariableFlipAngleMetadata:
+  selectors:
+    - suffix == "VFA"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+    PulseSequenceType: required
+    RepetitionTimeExcitation: required
+
+InversionRecoveryT1Metadata:
+  selectors:
+    - suffix == "IRT1"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    InversionTime: required
+
+MP2RAGEMetadata:
+  selectors:
+    - suffix == "MP2RAGE"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+    InversionTime: required
+    RepetitionTimeExcitation: required
+    RepetitionTimePreparation: required
+    NumberShots: required
+    MagneticFieldStrength: required
+
+MESpinEchoMetadata:
+  selectors:
+    - suffix == "MESE"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    EchoTime: required
+
+MEGradientEchoMetadata:
+  selectors:
+    - suffix == "MEGRE"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    EchoTime: required
+
+MTRatioMetadata:
+  selectors:
+    - suffix == "MTR"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    MTState: required
+
+MTSaturationMetadata:
+  selectors:
+    - suffix == "MTS"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+    MTState: required
+    RepetitionTimeExcitation: required
+
+MultiParametricMappingMetadata:
+  selectors:
+    - suffix == "MPM"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+    MTState: required
+    RepetitionTimeExcitation: required
+
+# Field mapping qMRI sequences
+TB1DAMMetadata:
+  selectors:
+    - suffix == "TB1DAM"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+
+TB1EPIMetadata:
+  selectors:
+    - suffix == "TB1EPI"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    EchoTime: required
+    FlipAngle: required
+    TotalReadoutTime: required
+    MixingTime: required
+
+TB1AFIMetadata:
+  selectors:
+    - suffix == "TB1AFI"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    RepetitionTimeExcitation: required
+
+TB1SRGEMetadata:
+  selectors:
+    - suffix == "TB1SRGE"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+    InversionTime: required
+    RepetitionTimeExcitation: required
+    RepetitionTimePreparation: required
+    NumberShots: required