Objects¶
The Objects portion of the schema contains the following collection of schema files:
text
src/schema/objects
├── columns.yaml
├── common_principles.yaml
├── datatypes.yaml
├── entities.yaml
├── extensions.yaml
├── files.yaml
├── formats.yaml
├── metadata.yaml
├── modalities.yaml
└── suffixes.yaml
Objects contain selectors, issues and error messages to raise during validation, descriptors, messages, and units. Every property needed describe a an entity in BIDS contained within an object's contents. We'll take a closer look below at a few specific objects to better introduce the structure that they represent and take on.
BIDS terms¶
objects.common_principles: Terms, such as "data acquisition" or "datatype", used throughout BIDS
data acquisition
yaml
data_acquisition:
display_name: Data acquisition
description: |
A continuous uninterrupted block of time during which a brain scanning instrument was acquiring data according to
particular scanning sequence/protocol.
data type
yaml
data_type:
display_name: Data type
description: |
A functional group of different types of data.
Data files are contained in a directory named for the data type.
In raw datasets, the data type directory is nested inside subject and (optionally) session directories.
BIDS defines the following data types:
1. `func` (task based and resting state functional MRI)
2. `dwi` (diffusion weighted imaging)
3. `fmap` (field inhomogeneity mapping data such as field maps)
4. `anat` (structural imaging such as T1, T2, PD, and so on)
5. `perf` (perfusion)
6. `meg` (magnetoencephalography)
7. `eeg` (electroencephalography)
8. `ieeg` (intracranial electroencephalography)
9. `beh` (behavioral)
10. `pet` (positron emission tomography)
11. `micr` (microscopy)
12. `nirs` (near infrared spectroscopy)
Name/value terms¶
objects.entities: Entities (sub-01)
Subject
yaml
subject:
name: sub
display_name: Subject
description: |
A person or animal participating in the study.
type: string
format: label
objects.metadata: Sidecar fields ("PhaseEncodingDirection": "j")
PhaseEncodingDirection
yaml
PhaseEncodingDirection:
name: PhaseEncodingDirection
display_name: Phase Encoding Direction
description: |
The letters `i`, `j`, `k` correspond to the first, second and third axis of
the data in the NIFTI file.
The polarity of the phase encoding is assumed to go from zero index to
maximum index unless `-` sign is present
(then the order is reversed - starting from the highest index instead of
zero).
`PhaseEncodingDirection` is defined as the direction along which phase is was
modulated which may result in visible distortions.
Note that this is not the same as the DICOM term
`InPlanePhaseEncodingDirection` which can have `ROW` or `COL` values.
type: string
enum:
- i
- j
- k
- i-
- j-
- k-
objects.columns: TSV columns ("participant_id", ["sub-01", "sub-02", …])
partcipant_id
yaml
participant_id:
name: participant_id
display_name: Participant ID
description: |
A participant identifier of the form `sub-<label>`,
matching a participant entity found in the dataset.
type: string
pattern: ^sub-[0-9a-zA-Z]+$
Value terms¶
objects.datatypes (func)
func
yaml
func:
value: func
display_name: Task-Based Magnetic Resonance Imaging
description: |
Task (including resting state) imaging data
objects.suffixes (bold)
object.suffixes.bold
yaml
bold:
value: bold
display_name: Blood-Oxygen-Level Dependent image
description: |
Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)
objects.extensions (.nii.gz)
Formats¶
objects.formats: Types of values objects referenced in the schema can take (label, index, boolean)
boolean
yaml
boolean:
display_name: Boolean
description: |
A boolean.
Must be either "true" or "false".
pattern: '(true|false)'
Files¶
objects.files: One-off files, not constructed from path components, like README
README
yaml
README:
display_name: README
file_type: regular
description: |
A REQUIRED text file, `README`, SHOULD describe the dataset in more detail.
The `README` 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`.
A BIDS dataset MUST NOT contain more than one `README` file (with or without extension)
at its root directory.
BIDS does not make any recommendations with regards to the
[Markdown flavor](https://www.markdownguide.org/extended-syntax/#lightweight-markup-languages)
and does not validate the syntax of Markdown and reStructuredText.
The `README` file SHOULD be structured such that its contents can be easily understood
even if the used format is not rendered.
A guideline for creating a good `README` file can be found in the
[bids-starter-kit](https://github.com/bids-standard/bids-starter-kit/blob/master/templates/README).