Rules¶
rules.files¶
rules.files: Filename construction rules
rules.files.common: Top-level (dataset_description.json) and tables (participants.tsv)
dataset_description
yaml
dataset_description:
level: required
path: dataset_description.json
participants
yaml
participants:
level: optional
stem: participants
extensions:
- .tsv
- .json
rules.files.raw: Data files defined in "BIDS-Raw"
rules.files.raw.anat.nonparametric
yaml
nonparametric:
suffixes:
- T1w
- T2w
- PDw
- T2starw
- FLAIR
- inplaneT1
- inplaneT2
- PDT2
- angio
- T2star # deprecated
- FLASH # deprecated
- PD # deprecated
extensions:
- .nii.gz
- .nii
- .json
datatypes:
- anat
entities:
subject: required
session: optional
task: optional
acquisition: optional
ceagent: optional
reconstruction: optional
run: optional
part: optional
rules.files.deriv: Data files defined in "BIDS-Derivatives"
rules.files.raw.beh.noncontinuous:
beh_noncontinous
```yaml
Non-continuous data¶
noncontinuous: suffixes: - beh extensions: - .tsv - .json datatypes: - beh entities: subject: required session: optional task: required acquisition: optional run: optional ```
rules.sidecars¶
rules.sidecars: Sidecar construction rules
rules.sidecars.anat.MRIAnatomyCommonMetadataFields
MRIAnatomyCommonMetadataFields
yaml
MRIAnatomyCommonMetadataFields:
selectors:
- modality == "mri"
- datatype == "anat"
fields:
ContrastBolusIngredient: optional
RepetitionTimeExcitation: optional
RepetitionTimePreparation: optional
rules.tabular_data¶
rules.tabular_data: TSV construction rules
`rules.tablular_data.task.TaskEvents
TaskEvents
yaml
TaskEvents:
selectors:
- '"task" in entities'
- suffix == "events"
columns:
onset: required
duration: required
trial_type: optional
...
additional_columns: allowed
initial_columns:
- 'onset'
- 'duration'
rules.checks¶
rules.checks: Dataset consistency rules, relies heavily on an expression language
If all selectors are true, the rule applies to a file; if any check fails, the issue is raised.
`rules.checks.dwi.DWIVolumeCount
DWIVolumeCount
yaml
DWIVolumeCount:
issue:
code: VOLUME_COUNT_MISMATCH
message: |
The number of volumes in this scan does not match the number
of volumes in the corresponding .bvec and .bval files.
level: error
selectors:
- suffix == "dwi"
- '"bval" in associations'
- '"bvec" in associations'
checks:
- associations.bval.n_cols == nifti_header.dim[4]
- associations.bvec.n_cols == nifti_header.dim[4]
One-off rules¶
-
rules.entities: Global order of entities -
rules.dataset_metadata: Contents of dataset_description.json and genetic_info.json, constructed similarly to rules.sidecars -
rules.modalities: Grouping of data types by "modality" (somewhat ill-defined) -
rules.common_principles: Order of BIDS terms listed in "Common principles" section -
rules.errors: Error messages found in the validator that cannot be schematized (e.g., NIFTI_HEADER_UNREADABLE), intended to promote consistency across tooling